Harmonized Cancer Datasets
English
United States, Chicago
the Genomic Data Commons
数据描述
High-quality datasets spanning cases from cancer genomic studies such as The Cancer Genomic Atlas (TCGA), Human Cancer Models Initiative (HCMI), Foundation Medicine Inc. (FMI), and Clinical Proteomic Tumor Analysis Consortium (CPTAC).
portal.gdc.cancer.gov
IP: 192.170.230.249
加载中...
相关论文
628TPX2 expression as a negative predictor of gemcitabine efficacy in pancreatic cancer
Guenther Michael•Surendran Sai Agash•Haas Michael•Heinemann Volker•von Bergwelt-Baildon Michael等 9 人
British Journal Of Cancer
2023
•2023/5/4
•00 p.1-8
Targeting protein for Xenopus kinesin-like protein 2 (TPX2) overexpression in human tumours is associated with increased malignancy. Its effect on gemcitabine resistance in pancreatic ductal adenocarcinoma (PDAC) has not been studied yet. The prognostic impact of TPX2 expression was examined in the ...
Pancreatic cancerPredictive markersTumour biomarkers
10.1038/S41416-023-02295-X
ISSN:0007-0920
Prediction of tumor origin in cancers of unknown primary origin with cytology-based deep learning
Fei Tian•Dong Liu•Na Wei•Qianqian Fu•Lin Sun等 27 人
Nature Medicine
2024
•2024/4/16
•00 p.1-11
Cancer of unknown primary (CUP) site poses diagnostic challenges due to its elusive nature. Many cases of CUP manifest as pleural and peritoneal serous effusions. Leveraging cytological images from 57,220 cases at four tertiary hospitals, we developed a deep-learning method for tumor origin differen...
Cancer of unknown primaryCancer screeningMetastasis
10.1038/S41591-024-02915-W
ISSN:1078-8956
Pan-cancer proteogenomic investigations identify post-transcriptional kinase targets
Elmas Abdulkadir•Tharakan Serena•Jaladanki Suraj•Galsky Matthew D.•Liu Tao等 6 人
Communications Biology
2021
•2021/9/22
•Vol.4 No.1 p.1-13
Identifying genomic alterations of cancer proteins has guided the development of targeted therapies, but proteomic analyses are required to validate and reveal new treatment opportunities. Herein, we develop a new algorithm, OPPTI, to discover overexpressed kinase proteins across 10 cancer types usi...
Cancer genomicsProteome informatics
10.1038/S42003-021-02636-7
ISSN:2399-3642
De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution
Liao Jie•Qian Jingyang•Fang Yin•Chen Zhuo•Zhuang Xiang等 20 人
Nature Communications
2022
•2022/10/30
•Vol.13 No.1 p.1-19
Uncovering the tissue molecular architecture at single-cell resolution could help better understand organisms’ biological and pathological processes. However, bulk RNA-seq can only measure gene expression in cell mixtures, without revealing the transcriptional heterogeneity and spatial patterns of s...
Computational modelsMachine learningRNA sequencingTranscriptomics
10.1038/S41467-022-34271-Z
ISSN:2041-1723
Validation of MSIntuit as an AI-based pre-screening tool for MSI detection from colorectal cancer histology slides
Charlie Saillard•Rémy Dubois•Oussama Tchita•Nicolas Loiseau•Thierry Garcia等 19 人
Nature Communications
2023
•2023/11/6
•Vol.14 No.1 p.1-11
Mismatch Repair Deficiency (dMMR)/Microsatellite Instability (MSI) is a key biomarker in colorectal cancer (CRC). Universal screening of CRC patients for MSI status is now recommended, but contributes to increased workload for pathologists and delayed therapeutic decisions. Deep learning has the pot...
Colorectal cancerPredictive markers
10.1038/S41467-023-42453-6
ISSN:2041-1723
Nociceptive neurons promote gastric tumour progression via a CGRP–RAMP1 axis
Xiaofei Zhi•Feijing Wu•Jin Qian•Yosuke Ochiai•Guodong Lian等 17 人
Nature
2025
•2025/2/19
•00 p.1-9
Cancer cells have been shown to exploit neurons to modulate their survival and growth, including through the establishment of neural circuits within the central nervous system1–3. Here we report a distinct pattern of cancer–nerve interactions between the peripheral nervous system and gastric cancer....
CancerGastric cancer
10.1038/S41586-025-08591-1
ISSN:0028-0836
Deep learning to assess microsatellite instability directly from histopathological whole slide images in endometrial cancer
Ching-Wei Wang•Hikam Muzakky•Nabila Puspita Firdi•Tzu-Chien Liu•Po-Jen Lai等 8 人
Npj Digital Medicine
2024
•2024/5/29
•Vol.7 No.1 p.1-13
Molecular classification, particularly microsatellite instability-high (MSI-H), has gained attention for immunotherapy in endometrial cancer (EC). MSI-H is associated with DNA mismatch repair defects and is a crucial treatment predictor. The NCCN guidelines recommend pembrolizumab and nivolumab for ...
Endometrial cancerImmunotherapyMachine learningMicrosatellite instability
10.1038/S41746-024-01131-7
ISSN:2398-6352
Aggresome formation promotes ASK1/JNK signaling activation and stemness maintenance in ovarian cancer
Yurou Chen•Yulong Qiang•Jiachen Fan•Qian Zheng•Leilei Yan等 16 人
Nature Communications
2024
•2024/2/13
•Vol.15 No.1 p.1-18
Aggresomes are the product of misfolded protein aggregation, and the presence of aggresomes has been correlated with poor prognosis in cancer patients. However, the exact role of aggresomes in tumorigenesis and cancer progression remains largely unknown. Herein, the multiomics screening reveal that ...
Cancer stem cellsCell signallingMechanisms of diseaseOvarian cancer
10.1038/S41467-024-45698-X
ISSN:2041-1723
Interpretable niche-based cell‒cell communication inference using multi-view graph neural networks
Juntian Qi•Zhengchao Luo•Chuan-Yun Li•Jinzhuo Wang•Wanqiu Ding
Nature Computational Science
2025
•2025/5/27
•00 p.1-12
Cell‒cell communication (CCC) is a fundamental biological process for the harmonious functioning of biological systems. Increasing evidence indicates that cells of the same type or cluster may exhibit different interaction patterns under varying niches, yet most prevailing methods perform CCC infere...
Computational modelsGene regulationTranscriptomics
10.1038/S43588-025-00809-6
ISSN:2662-8457
Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy
Marjan M. Naeini•Felicity Newell•Lauren G. Aoude•Vanessa F. Bonazzi•Kalpana Patel等 40 人
Nature Communications
2023
•2023/5/31
•Vol.14 No.1 p.1-17
Oesophageal adenocarcinoma is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigate whole genome, transcriptomic and methylation data from 115 oesophageal adenocarcinoma patients mostly from the DOCTOR phase II clinical trial (Australian...
BioinformaticsCancer epigeneticsCancer genomicsOesophageal cancerTumour immunology
10.1038/S41467-023-38891-X
ISSN:2041-1723
Efficient diagnosis of IDH-mutant gliomas: 1p/19qNET assesses 1p/19q codeletion status using weakly-supervised learning
Gi Jeong Kim•Tonghyun Lee•Sangjeong Ahn•Youngjung Uh•Se Hoon Kim
Npj Precision Oncology
2023
•2023/9/16
•Vol.7 No.1 p.1-9
Accurate identification of molecular alterations in gliomas is crucial for their diagnosis and treatment. Although, fluorescence in situ hybridization (FISH) allows for the observation of diverse and heterogeneous alterations, it is inherently time-consuming and challenging due to the limitations of...
CNS cancerMathematics and computingPathology
10.1038/S41698-023-00450-4
ISSN:2397-768X
Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer
Busso-Lopes Ariane F.•Neves Leandro X.•Câmara Guilherme A.•Granato Daniela C.•Pretti Marco Antônio M.等 33 人
Nature Communications
2022
•2022/11/7
•Vol.13 No.1 p.1-24
The poor prognosis of head and neck cancer (HNC) is associated with metastasis within the lymph nodes (LNs). Herein, the proteome of 140 multisite samples from a 59-HNC patient cohort, including primary and matched LN-negative or -positive tissues, saliva, and blood cells, reveals insights into the ...
Head and neck cancerMetastasisPrognostic markersProteomicsTumour biomarkers
10.1038/S41467-022-34407-1
ISSN:2041-1723
Lymphoid-specific helicase in epigenetics, DNA repair and cancer
Chen Xiangyu•Li Yamei•Rubio Karla•Deng Bi•Li Yuyi等 11 人
British Journal Of Cancer
2021
•2021/9/7
•00 p.1-9
Lymphoid-specific helicase (LSH) is a member of the SNF2 helicase family of chromatin-remodelling proteins. Dysfunctions or mutations in LSH causes an autosomal recessive disease known as immunodeficiency-centromeric instability-facial anomaly (ICF) syndrome. Interestingly, LSH participates in vario...
Oncogenes
10.1038/S41416-021-01543-2
ISSN:0007-0920
Alterations in PD-L1 succinylation shape anti-tumor immune responses in melanoma
Long Liang•Xinwei Kuang•Yi He•Lin Zhu•Poyee Lau等 22 人
Nature Genetics
2025
•2025/3/11
•Vol.57 No.3 p.680-693
Tumors undergo metabolic reprogramming to meet the energetic, synthetic and redox demands essential for malignancy, often characterized by increased glycolysis and lactate production. However, the role of mitochondrial metabolism in tumor immunity remains unclear. The present study integrates spatia...
ImmunotherapyMelanomaTumour immunology
10.1038/S41588-025-02077-6
ISSN:1061-4036
The CINSARC signature predicts the clinical outcome in patients with Luminal B breast cancer
Anthony Goncalves•Pascal Finetti•Daniel Birnbaum•François Bertucci
Npj Breast Cancer
2021
•2021/5/5
•Vol.7 No.1 p.1-9
CINSARC, a multigene expression signature originally developed in sarcomas, was shown to have prognostic impact in various cancers. We tested the prognostic value for disease-free survival (DFS) of CINSARC in a series of 6035 early-stage invasive primary breast cancers. CINSARC had independent progn...
Breast cancerPrognostic markers
10.1038/S41523-021-00256-2
ISSN:2374-4677
KDM4 orchestrates epigenomic remodeling of senescent cells and potentiates the senescence-associated secretory phenotype
Boyi Zhang•Qilai Long•Shanshan Wu•Qixia Xu•Shuling Song等 18 人
Nature Aging
2021
•2021/5/13
•Vol.1 No.5 p.454-472
Cellular senescence restrains the expansion of neoplastic cells through several layers of regulation. We report that the histone H3-specific demethylase KDM4 is expressed as human stromal cells undergo senescence. In clinical oncology, upregulated KDM4 and diminished H3K9/H3K36 methylation correlate...
AgeingCancerSenescence
10.1038/S43587-021-00063-1
ISSN:2662-8465
Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots
Pégah Jalili•Danae Bowen•Adam Langenbucher•Shinho Park•Kevin Aguirre等 10 人
Nature Communications
2020
•2020/6/12
•Vol.11 No.1 p.1-13
APOBEC3A is a cytidine deaminase driving mutagenesis, DNA replication stress and DNA damage in cancer cells. While the APOBEC3A-induced vulnerability of cancers offers an opportunity for therapy, APOBEC3A protein and mRNA are difficult to quantify in tumors due to their low abundance. Here, we descr...
BiochemistryBiological techniquesBiotechnologyCancerComputational biology and bioinformatics
10.1038/S41467-020-16802-8
ISSN:2041-1723
AI-based pathology predicts origins for cancers of unknown primary
Ming Y. Lu•Tiffany Y. Chen•Drew F. K. Williamson•Melissa Zhao•Maha Shady等 7 人
Nature
2021
•2021/5/5
•Vol.594 No.7861 p.106-110
Cancer of unknown primary (CUP) origin is an enigmatic group of diagnoses in which the primary anatomical site of tumour origin cannot be determined1,2. This poses a considerable challenge, as modern therapeutics are predominantly specific to the primary tumour3. Recent research has focused on using...
Cancer of unknown primaryComputational scienceImage processingMachine learningPathology
10.1038/S41586-021-03512-4
ISSN:0028-0836
Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures
Khoa A. Tran•Venkateswar Addala•Rebecca L. Johnston•David Lovell•Andrew Bradley等 15 人
Nature Communications
2023
•2023/9/16
•Vol.14 No.1 p.1-17
Cells within the tumour microenvironment (TME) can impact tumour development and influence treatment response. Computational approaches have been developed to deconvolve the TME from bulk RNA-seq. Using scRNA-seq profiling from breast tumours we simulate thousands of bulk mixtures, representing tumo...
Breast cancerCancer microenvironmentComputational modelsSoftwareTumour heterogeneity
10.1038/S41467-023-41385-5
ISSN:2041-1723
CD137L promotes immune surveillance in melanoma via HLTF regulation
Long Liang•Lin Zhu•Xin Li•Wenbin Zhou•Yanbin Zhang等 13 人
Nature Communications
2025
•2025/9/26
•Vol.16 No.1 p.1-16
Immune checkpoint blockers (ICBs) have demonstrated substantial efficacy across various malignancies, yet the benefits of ICBs are limited to a subset of patients. Therefore, it is essential to identify novel therapeutic targets. By integrating multi-omics data from cohorts of patients with melanoma...
Cancer immunotherapyTumour immunology
10.1038/S41467-025-63338-W
ISSN:2041-1723
NRAV promotes HCC stemness via the m6A-regulated let-7c-5p/LIN28B axis
Yuhang Chen•Suoyi Dai•Liping Zhuang•Wenxun Cai•Hao Chen等 9 人
Cancer Gene Therapy
2025
•2025/12/12
•00 p.1-15
Long non-coding RNAs (lncRNAs) plays critical roles in hepatocellular carcinoma (HCC), but their post-transcriptional regulation via N6-methyladenosine (m6A) remains poorly understood. Here, we identify NRAV as an m6A-modified lncRNA that promotes HCC stemness through a defined molecular axis. Integ...
Cancer stem cellsCell biology
10.1038/S41417-025-00995-5
ISSN:0929-1903
ROCK1 mechano-signaling dependency of human malignancies driven by TEAD/YAP activation
Esposito Davide•Pant Ila•Shen Yao•Qiao Rui F.•Yang Xiaobao等 9 人
Nature Communications
2022
•2022/2/4
•Vol.13 No.1 p.1-14
Rho family mechano-signaling through the actin cytoskeleton positively regulates physiological TEAD/YAP transcription, while the evolutionarily conserved Hippo tumor suppressor pathway antagonizes this transcription through YAP cytoplasmic localization/degradation. The mechanisms responsible for onc...
OncogenesTargeted therapies
10.1038/S41467-022-28319-3
ISSN:2041-1723
A pathology foundation model for cancer diagnosis and prognosis prediction
Xiyue Wang•Junhan Zhao•Eliana Marostica•Wei Yuan•Jietian Jin等 29 人
Nature
2024
•2024/9/4
•00 p.1-9
Histopathology image evaluation is indispensable for cancer diagnoses and subtype classification. Standard artificial intelligence methods for histopathology image analyses have focused on optimizing specialized models for each diagnostic task1,2. Although such methods have achieved some success, th...
CancerComputational modelsImage processingMachine learningPredictive medicine
10.1038/S41586-024-07894-Z
ISSN:0028-0836
Alternate RNA decoding results in stable and abundant proteins in mammals
Shira Tsour•Rainer Machné•Andrew Leduc•Simon Widmer•Eunice Koo等 8 人
Nature
2026
•2026/6/24
•00 p.1-10
Amino acid substitutions may substantially alter protein stability and function1,2. However, the contribution of substitutions that arise from alternate translation (deviations from the genetic code) is unknown. Here to address this issue, we analysed deep proteomic, transcriptomic and genomic data ...
Cell biologyProteome informaticsProteomicsTranslation
10.1038/S41586-026-10678-2
ISSN:0028-0836
Knowledge-guided adaptation of pathology foundation models effectively improves cross-domain generalization and demographic fairness
Yanyan Huang•Weiqin Zhao•Zhengyu Zhang•Yihang Chen•Yu Fu等 10 人
Nature Communications
2025
•2025/12/12
0Foundation models in computational pathology suffer from site-specific and demographic biases, which compromise their generalizability and fairness. We introduce FLEX, a framework that employs a task-specific information bottleneck, guided by visual and textual domain knowledge, to disentangle robus...
Cancer imagingComputer scienceMachine learningMedical imagingPathology
10.1038/S41467-025-66300-Y
ISSN:2041-1723
A subset of lung cancer cases shows robust signs of homologous recombination deficiency associated genomic mutational signatures
Miklos Diossy•Zsofia Sztupinszki•Judit Borcsok•Marcin Krzystanek•Viktoria Tisza等 14 人
Npj Precision Oncology
2021
•2021/6/18
•Vol.5 No.1 p.1-8
PARP inhibitors are approved for the treatment of solid tumor types that frequently harbor alterations in the key homologous recombination (HR) genes, BRCA1/2. Other tumor types, such as lung cancer, may also be HR deficient, but the frequency of such cases is less well characterized. Specific DNA a...
Non-small-cell lung cancer
10.1038/S41698-021-00199-8
ISSN:2397-768X
Mutational signature-based identification of DNA repair deficient gastroesophageal adenocarcinomas for therapeutic targeting
Aurel Prosz•Pranshu Sahgal•Brandon M. Huffman•Zsofia Sztupinszki•Clare X. Morris等 23 人
Npj Precision Oncology
2024
•2024/4/8
•Vol.8 No.1 p.1-14
Homologous recombination (HR) and nucleotide excision repair (NER) are the two most frequently disabled DNA repair pathways in cancer. HR-deficient breast, ovarian, pancreatic and prostate cancers respond well to platinum chemotherapy and PARP inhibitors. However, the frequency of HR deficiency in g...
Cancer genomicsHigh-throughput screening
10.1038/S41698-024-00561-6
ISSN:2397-768X
A network analysis to identify mediators of germline-driven differences in breast cancer prognosis
Maria Escala-Garcia•Jean Abraham•Irene L. Andrulis•Hoda Anton-Culver•Volker Arndt等 145 人
Nature Communications
2020
•2020/1/16
•Vol.11 No.1 p.1-14
Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based...
Breast cancerComputational biology and bioinformaticsGenome-wide association studies
10.1038/S41467-019-14100-6
ISSN:2041-1723
The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1
Han Han•Nakaoka Hiroki J.•Hofmann Line•Zhou Jeff Jiajing•Yu Clinton等 18 人
Nature Cell Biology
2022
•2022/1/13
•00 p.1-14
Heavy metals are both integral parts of cells and environmental toxicants, and their deregulation is associated with severe cellular dysfunction and various diseases. Here we show that the Hippo pathway plays a critical role in regulating heavy metal homeostasis. Hippo signalling deficiency promotes...
Cell signallingHIPPO signallingTranscription
10.1038/S41556-021-00813-8
ISSN:1465-7392
Deep learning-based classification of mesothelioma improves prediction of patient outcome
Pierre Courtiol•Charles Maussion•Matahi Moarii•Elodie Pronier•Samuel Pilcer等 17 人
Nature Medicine
2019
•2019/10/7
•Vol.25 No.10 p.1519-1525
Malignant mesothelioma (MM) is an aggressive cancer primarily diagnosed on the basis of histological criteria1. The 2015 World Health Organization classification subdivides mesothelioma tumors into three histological types: epithelioid, biphasic and sarcomatoid MM. MM is a highly complex and heterog...
Cancer imagingMachine learningMesothelioma
10.1038/S41591-019-0583-3
ISSN:1078-8956
Large-scale single-cell analysis and in silico perturbation reveal dynamic evolution of HCC: from initiation to therapeutic targeting
Peng Xia•Si Shuang•Daosen Fu•Luyao Liu•Dongliang Yang等 12 人
Npj Precision Oncology
2026
•2026/1/30
•Vol.10 No.1 p.1000
The extensive intratumoral and microenvironmental heterogeneity of hepatocellular carcinoma (HCC) remains a major therapeutic barrier. Integrating single-cell transcriptomics samples spanning normal liver, primary tumors, portal vein tumor thrombus (PVTT), and metastatic lymph nodes (MLN) with spati...
BiomarkersCancerCancer microenvironmentCancer therapyComputational biology and bioinformaticsMetastasis
10.1038/S41698-026-01307-2
ISSN:2397-768X
RNF208, an estrogen-inducible E3 ligase, targets soluble Vimentin to suppress metastasis in triple-negative breast cancers
Kyoungwha Pang•Jinah Park•Sung Gwe Ahn•Jihee Lee•Yuna Park等 14 人
Nature Communications
2019
•2019/12/20
•Vol.10 No.1 p.1-13
The development of triple-negative breast cancer (TNBC) negatively impacts both quality of life and survival in a high percentage of patients. Here, we show that RING finger protein 208 (RNF208) decreases the stability of soluble Vimentin protein through a polyubiquitin-mediated proteasomal degradat...
Breast cancerCell invasion
10.1038/S41467-019-13852-5
ISSN:2041-1723
Thermophoretic glycan profiling of extracellular vesicles for triple-negative breast cancer management
Yike Li•Shaohua Zhang•Chao Liu•Jinqi Deng•Fei Tian等 12 人
Nature Communications
2024
•2024/3/14
•Vol.15 No.1 p.1-15
Triple-negative breast cancer (TNBC) is a highly metastatic and heterogeneous type of breast cancer with poor outcomes. Precise, non-invasive methods for diagnosis, monitoring and prognosis of TNBC are particularly challenging due to a paucity of TNBC biomarkers. Glycans on extracellular vesicles (E...
BiochemistryBiomarkers
10.1038/S41467-024-46557-5
ISSN:2041-1723
Deep learning for endometrial cancer subtyping and predicting tumor mutational burden from histopathological slides
Ching-Wei Wang•Nabila Puspita Firdi•Yu-Ching Lee•Tzu-Chiao Chu•Hikam Muzakky等 8 人
Npj Precision Oncology
2024
•2024/12/21
•Vol.8 No.1 p.1-18
Endometrial cancer (EC) diagnosis traditionally relies on tumor morphology and nuclear grade, but personalized therapy demands a deeper understanding of tumor mutational burden (TMB), i.e., a key biomarker for immune checkpoint inhibition and immunotherapy response. Traditional TMB prediction method...
Cancer immunotherapyEndometrial cancerPrognostic markersTumour biomarkers
10.1038/S41698-024-00766-9
ISSN:2397-768X
Very low mutation burden is a feature of inflamed recurrent glioblastomas responsive to cancer immunotherapy
Matthias Gromeier•Michael C. Brown•Gao Zhang•Xiang Lin•Yeqing Chen等 28 人
Nature Communications
2021
•2021/1/13
•Vol.12 No.1 p.1-7
Several immunotherapy clinical trials in recurrent glioblastoma have reported long-term survival benefits in 10–20% of patients. Here we perform genomic analysis of tumor tissue from recurrent WHO grade IV glioblastoma patients acquired prior to immunotherapy intervention. We report that very low tu...
Cancer immunotherapyCNS cancerImmunoediting
10.1038/S41467-020-20469-6
ISSN:2041-1723
Discovering anticancer drug target combinations via network-informed signaling-based approach
Bengi Ruken Yavuz•Hyunbum Jang•Ruth Nussinov
Communications Medicine
2025
•2025/10/17
•Vol.5 No.1 p.1-17
Oncologists deciding on cancer treatments must make difficult decisions as to which prescription and implementation strategies would best suit each patient. Much is still unknown about combinations of prescription drugs as there are many to choose from. At the outset, the oncologist reckons with at ...
Computational biology and bioinformaticsSystems biology
10.1038/S43856-025-01150-9
ISSN:2730-664X
Deep immunophenotyping reveals clinically distinct cellular states and ecosystems in large-scale colorectal cancer
Si Li•Tao Pan•Gang Xu•Yueying Gao•Ya Zhang等 11 人
Communications Biology
2023
•2023/7/27
•Vol.6 No.1 p.1-12
Determining the diverse cell types in the tumor microenvironment (TME) and their organization into cellular communities, is critical for understanding the biological heterogeneity and therapy of cancer. Here, we deeply immunophenotype the colorectal cancer (CRC) by integrative analysis of large-scal...
Computational biology and bioinformaticsData integrationTumour immunology
10.1038/S42003-023-05117-1
ISSN:2399-3642
TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data
Guorui Zhang•Chao Song•Mingxue Yin•Liyuan Liu•Yuexin Zhang等 9 人
Nature Communications
2025
•2025/4/16
•Vol.16 No.1 p.1-20
It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of diseases. The use of large-scale multi-omics epigenomic data enables the representation...
Computational modelsGene regulatory networksSoftware
10.1038/S41467-025-58921-0
ISSN:2041-1723
UbiDash: A UPS proteomic atlas for tissue-aware degrader design
Tania J. González-Robles•Paul Sastourné•Marisa Triola•Maha Khan•Áron Bartha等 11 人
Cell Death & Differentiation
2026
•2026/7/10
•00 p.1-10
Targeted protein degradation repurposes endogenous E3 ubiquitin ligases to eliminate disease-driving proteins, yet the ligase toolkit deployed clinically remains narrow and largely tissue-agnostic. To support rational expansion of this toolkit, we built a harmonized pan-tissue proteomic atlas of the...
CancerCancer geneticsProteomicsSmall molecules
10.1038/S41418-026-01791-W
ISSN:1350-9047
A dendritic cell vaccine for both vaccination and neoantigen-reactive T cell preparation for cancer immunotherapy in mice
Qing Li•Hao Zeng•Ting Liu•Peipei Wang•Rui Zhang等 15 人
Nature Communications
2024
•2024/11/29
•Vol.15 No.1 p.1-24
Adoptive cell transfer (ACT) using neoantigen-specific T cells is an effective immunotherapeutic strategy. However, the difficult isolation of neoantigen-specific T cells limits the clinical application of ACT. Here, we propose a method to prepare neoantigen-reactive T cells (NRT) for ACT following ...
Cell vaccinesNon-small-cell lung cancerT cellsTumour immunology
10.1038/S41467-024-54650-Y
ISSN:2041-1723
Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors
Jiang Biaobin•Mu Quanhua•Qiu Fufang•Li Xuefeng•Xu Weiqi等 9 人
Nature Communications
2021
•2021/11/18
•Vol.12 No.1 p.1-15
Metastatic cancer is associated with poor patient prognosis but its spatiotemporal behavior remains unpredictable at early stage. Here we develop MetaNet, a computational framework that integrates clinical and sequencing data from 32,176 primary and metastatic cancer cases, to assess metastatic risk...
Data integrationGene regulatory networksMachine learning
10.1038/S41467-021-27017-W
ISSN:2041-1723
A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
Yingying Zhang•Alden K. Leung•Jin Joo Kang•Yu Sun•Guanxi Wu等 14 人
Nature Communications
2025
•2025/1/24
•Vol.16 No.1 p.1-18
A major goal of cancer biology is to understand the mechanisms driven by somatically acquired mutations. Two distinct methodologies—one analyzing mutation clustering within protein sequences and 3D structures, the other leveraging protein-protein interaction network topology—offer complementary stre...
Cancer genomicsComputational modelsComputer modellingProtein–protein interaction networks
10.1038/S41467-024-54176-3
ISSN:2041-1723
Aligning knowledge concepts to whole slide images for precise histopathology image analysis
Weiqin Zhao•Ziyu Guo•Yinshuang Fan•Yuming Jiang•Maximus C. F. Yeung等 6 人
Npj Digital Medicine
2024
•2024/12/30
•Vol.7 No.1 p.1-12
Due to the large size and lack of fine-grained annotation, Whole Slide Images (WSIs) analysis is commonly approached as a Multiple Instance Learning (MIL) problem. However, previous studies only learn from training data, posing a stark contrast to how human clinicians teach each other and reason abo...
Biomedical engineeringComputational modelsMachine learning
10.1038/S41746-024-01411-2
ISSN:2398-6352
A foundation model for generalizable cancer diagnosis and survival prediction from histopathological images
Zhaochang Yang•Ting Wei•Ying Liang•Xin Yuan•RuiTian Gao等 9 人
Nature Communications
2025
•2025/3/10
•Vol.16 No.1 p.1-16
Computational pathology, utilizing whole slide images (WSIs) for pathological diagnosis, has advanced the development of intelligent healthcare. However, the scarcity of annotated data and histological differences hinder the general application of existing methods. Extensive histopathological data a...
Cancer imagingComputational modelsMachine learningSoftware
10.1038/S41467-025-57587-Y
ISSN:2041-1723
Adversarial attacks and adversarial robustness in computational pathology
Ghaffari Laleh Narmin•Truhn Daniel•Veldhuizen Gregory Patrick•Han Tianyu•van Treeck Marko等 11 人
Nature Communications
2022
•2022/9/29
•Vol.13 No.1 p.1-10
Artificial Intelligence (AI) can support diagnostic workflows in oncology by aiding diagnosis and providing biomarkers directly from routine pathology slides. However, AI applications are vulnerable to adversarial attacks. Hence, it is essential to quantify and mitigate this risk before widespread c...
Cancer imagingComputational scienceDiagnostic markersImage processingMachine learning
10.1038/S41467-022-33266-0
ISSN:2041-1723
Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer
Katharina von Loga•Andrew Woolston•Marco Punta•Louise J. Barber•Beatrice Griffiths等 15 人
Nature Communications
2020
•2020/1/16
•Vol.11 No.1 p.1-14
Mismatch repair deficient (dMMR) gastro-oesophageal adenocarcinomas (GOAs) show better outcomes than their MMR-proficient counterparts and high immunotherapy sensitivity. The hypermutator-phenotype of dMMR tumours theoretically enables high evolvability but their evolution has not been investigated....
CancerCancer geneticsCancer genomicsGastrointestinal cancerTumour heterogeneity
10.1038/S41467-019-13915-7
ISSN:2041-1723
Crosstalk of cell death pathways unveils an autophagy-related gene AOC3 as a critical prognostic marker in colorectal cancer
Hui Xu•Haiyang Cui•Siyuan Weng•Yuyuan Zhang•Libo Wang等 8 人
Communications Biology
2024
•2024/3/9
•Vol.7 No.1 p.1-12
The intricate crosstalk of various cell death forms was recently implicated in cancers, laying a foundation for exploring the association between cell death and cancers. Recent evidence has demonstrated that biological networks outperform snapshot gene expression profiles at discovering promising bi...
Classification and taxonomyColorectal cancerTumour heterogeneity
10.1038/S42003-024-05980-6
ISSN:2399-3642
From whole-slide image to biomarker prediction: end-to-end weakly supervised deep learning in computational pathology
Omar S. M. El Nahhas•Marko van Treeck•Georg Wölflein•Michaela Unger•Marta Ligero等 12 人
Nature Protocols
2024
•2024/9/16
•00 p.1-24
Hematoxylin- and eosin-stained whole-slide images (WSIs) are the foundation of diagnosis of cancer. In recent years, development of deep learning-based methods in computational pathology has enabled the prediction of biomarkers directly from WSIs. However, accurately linking tissue phenotype to biom...
BioinformaticsCancer imagingImage processing
10.1038/S41596-024-01047-2
ISSN:1754-2189
Demographic bias in misdiagnosis by computational pathology models
Anurag Vaidya•Richard J. Chen•Drew F. K. Williamson•Andrew H. Song•Guillaume Jaume等 13 人
Nature Medicine
2024
•2024/4/19
•Vol.30 No.4 p.1174-1190
Despite increasing numbers of regulatory approvals, deep learning-based computational pathology systems often overlook the impact of demographic factors on performance, potentially leading to biases. This concern is all the more important as computational pathology has leveraged large public dataset...
DiagnosisHealth policyMachine learningPathology
10.1038/S41591-024-02885-Z
ISSN:1078-8956
Integration of clinical features and deep learning on pathology for the prediction of breast cancer recurrence assays and risk of recurrence
Howard Frederick M.•Dolezal James•Kochanny Sara•Khramtsova Galina•Vickery Jasmine等 13 人
Npj Breast Cancer
2023
•2023/4/14
•Vol.9 No.1 p.1-6
Gene expression-based recurrence assays are strongly recommended to guide the use of chemotherapy in hormone receptor-positive, HER2-negative breast cancer, but such testing is expensive, can contribute to delays in care, and may not be available in low-resource settings. Here, we describe the train...
Breast cancerPrognostic markersTranslational research
10.1038/S41523-023-00530-5
ISSN:2374-4677
Clinical response to nivolumab in an INI1-deficient pediatric chordoma correlates with immunogenic recognition of brachyury
Williamson Laura M.•Rive Craig M.•Di Francesco Daniela•Titmuss Emma•Chun Hye-Jung E.等 25 人
Npj Precision Oncology
2021
•2021/12/20
•Vol.5 No.1 p.1-12
Poorly differentiated chordoma (PDC) is a recently recognized subtype of chordoma characterized by expression of the embryonic transcription factor, brachyury, and loss of INI1. PDC primarily affects children and is associated with a poor prognosis and limited treatment options. Here we describe the...
Molecular medicinePaediatric cancerPredictive markersSarcoma
10.1038/S41698-021-00238-4
ISSN:2397-768X
DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations
Bo Wen•Chenwei Wang•Kai Li•Ping Han•Matthew V. Holt等 11 人
Nature Methods
2025
•2025/8/26
•00 p.1-11
Post-translational modifications (PTMs) are critical regulators of protein function, and their disruption is a key mechanism by which missense variants contribute to disease. Accurate PTM site prediction using deep learning can help identify PTM-altering variants, but progress has been limited by th...
GenomicsMachine learningPost-translational modificationsProteome informaticsProteomics
10.1038/S41592-025-02797-X
ISSN:1548-7091
A multi-classifier system integrated by clinico-histology-genomic analysis for predicting recurrence of papillary renal cell carcinoma
Kang-Bo Huang•Cheng-Peng Gui•Yun-Ze Xu•Xue-Song Li•Hong-Wei Zhao等 41 人
Nature Communications
2024
•2024/7/23
•Vol.15 No.1 p.1-12
Integrating genomics and histology for cancer prognosis demonstrates promise. Here, we develop a multi-classifier system integrating a lncRNA-based classifier, a deep learning whole-slide-image-based classifier, and a clinicopathological classifier to accurately predict post-surgery localized (stage...
Computational biology and bioinformaticsGenetic markersPrognostic markersRenal cell carcinoma
10.1038/S41467-024-50369-Y
ISSN:2041-1723
Inflammatory bone marrow signaling in pediatric acute myeloid leukemia distinguishes patients with poor outcomes
Bolouri Hamid•Ries Rhonda E.•Wiedeman Alice E.•Hylkema Tiffany•Scheiding Sheila等 11 人
Nature Communications
2022
•2022/11/23
•Vol.13 No.1 p.1-12
High levels of the inflammatory cytokine IL-6 in the bone marrow are associated with poor outcomes in pediatric acute myeloid leukemia (pAML), but its etiology remains unknown. Using RNA-seq data from pre-treatment bone marrows of 1489 children with pAML, we show that > 20% of patients have concu...
Acute myeloid leukaemiaTumour immunology
10.1038/S41467-022-34965-4
ISSN:2041-1723
IL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer
E. Koncina•M. Nurmik•V. I. Pozdeev•C. Gilson•M. Tsenkova等 28 人
Nature Communications
2023
•2023/7/17
•Vol.14 No.1 p.1-17
Fibroblasts have a considerable functional and molecular heterogeneity and can play various roles in the tumor microenvironment. Here we identify a pro-tumorigenic IL1R1+, IL-1-high-signaling subtype of fibroblasts, using multiple colorectal cancer (CRC) patient single cell sequencing datasets. This...
Cancer microenvironmentGastrointestinal cancerTumour immunology
10.1038/S41467-023-39953-W
ISSN:2041-1723
GLUD1 supports ovarian cancer progression by counteracting anoikis via ARAF/MEK/ERK signaling
Huolun Feng•Yanzhen Chen•Geyan Wu•Zhentao Zhang•Hongkun Lai等 12 人
Npj Precision Oncology
2026
•2026/3/5
•Vol.10 No.1 p.1510
Peritoneal dissemination is the major cause of mortality in epithelial ovarian cancer (EOC) and requires tumor cells to survive in a detached state by evading anoikis. However, the molecular mechanisms supporting anchorage-independent survival remain poorly defined. Here, we identify glutamate dehyd...
CancerOncology
10.1038/S41698-026-01349-6
ISSN:2397-768X
Targeting MCM10 disrupts cancer stemness and counteracts sorafenib resistance in hepatocellular carcinoma
Ziyun Zhang•Lu Liang•Yi Li•Ye Fan•Yao Liu等 10 人
Cancer Gene Therapy
2025
•2025/8/1
•Vol.32 No.10 p.1076-1089
Hepatocellular carcinoma (HCC) is the most prevalent primary malignant tumor, with sorafenib as the main treatment for advanced cases. However, the development of resistance to sorafenib, often driven by cancer stemness, significantly limits its therapeutic efficacy. Minichromosome maintenance compl...
Cancer stem cellsOncogenes
10.1038/S41417-025-00946-0
ISSN:0929-1903
Overcoming therapeutic resistance in oncolytic herpes virotherapy by targeting IGF2BP3-induced NETosis in malignant glioma
Weiwei Dai•Ruotong Tian•Liubing Yu•Shasha Bian•Yuling Chen等 15 人
Nature Communications
2024
•2024/1/2
•Vol.15 No.1 p.1-19
Oncolytic virotherapy holds promise for cancer treatment, but the factors determining its oncolytic activity remain unclear. Neutrophil extracellular traps (NETs) are associated with cancer progression, yet their formation mechanism and role in oncolytic virotherapy remain elusive. In this study, we...
Cancer immunotherapyCNS cancerHerpes virus
10.1038/S41467-023-44576-2
ISSN:2041-1723
FAP+ fibroblasts orchestrate tumor microenvironment remodeling in renal cell carcinoma with tumor thrombus
Jiacheng Ma•Yan Huang•Jie Chen•Yang Li•Rongyan Yao等 16 人
Nature Communications
2025
•2025/10/23
•Vol.16 No.1 p.1-24
Tumor thrombus (TT) worsens prognosis and complicates surgery in renal cell carcinoma (RCC), yet its formation mechanisms remain unclear. Here, we perform integrative single-cell and spatial transcriptomic analyses on 71 tissues and 48 sections from RCC patients with or without TT. The cellular and ...
Cancer microenvironmentData integrationData miningMetastasisRenal cell carcinoma
10.1038/S41467-025-64447-2
ISSN:2041-1723
Uniform genomic data analysis in the NCI Genomic Data Commons
Zhenyu Zhang•Kyle Hernandez•Jeremiah Savage•Shenglai Li•Dan Miller等 10 人
Nature Communications
2021
•2021/2/22
•Vol.12 No.1 p.1-11
The goal of the National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The...
BioinformaticsCancer genomics
10.1038/S41467-021-21254-9
ISSN:2041-1723
Molecular and functional landscape of malignant serous effusions for precision oncology
Rebekka Wegmann•Lorenz Bankel•Yasmin Festl•Kate Lau•Sohyon Lee等 17 人
Nature Communications
2024
•2024/10/2
•Vol.15 No.1 p.1-21
Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells from patient biopsies. Here, we comprehensively characterize a pan-cancer cohort of 150 malignant serous effusion (MSE) samples at the cellular, molecular, and functional lev...
Cancer therapyData integrationPhenotypic screeningSingle-cell imaging
10.1038/S41467-024-52694-8
ISSN:2041-1723
The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling
Cui Huanhuan•Yi Hongyang•Bao Hongyu•Tan Ying•Tian Chi等 18 人
Nature Communications
2022
•2022/8/9
•Vol.13 No.1 p.1-16
DPF3, a component of the SWI/SNF chromatin remodeling complex, has been associated with clear cell renal cell carcinoma (ccRCC) in a genome-wide association study. However, the functional role of DPF3 in ccRCC development and progression remains unknown. In this study, we demonstrate that DPF3a, the...
EpigeneticsMetastasisTranscription
10.1038/S41467-022-32472-0
ISSN:2041-1723
A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study
Hui Chen•Zeyang Wang•Lihai Gong•Qixuan Wang•Wenyan Chen等 17 人
Nature Communications
2024
•2024/2/26
•Vol.15 No.1 p.1-16
Alternative polyadenylation plays an important role in cancer initiation and progression; however, current transcriptome-wide association studies mostly ignore alternative polyadenylation when identifying putative cancer susceptibility genes. Here, we perform a pan-cancer 3′ untranslated region alte...
Cancer geneticsData miningNon-coding RNAs
10.1038/S41467-024-46064-7
ISSN:2041-1723
SIMD: Synergistic integration mutualistic platform based on single-cell and proteotranscriptomics for drug repositioning
Soo Youn Lee•Min Young Song•Yu-Rim Lee•Jeung Hee An
Npj Breast Cancer
2025
•2025/12/24
0This study aimed to introduce a synergistic integration platform based on single-cell and proteotranscriptomics for drug repositioning (SIMD) to repurpose breast cancer drug candidates by considering the bidirectional nature of molecular dynamics in protein transcriptomics and tumor heterogeneity at...
CancerDrug discoveryOncology
10.1038/S41523-025-00869-X
ISSN:2374-4677
Integrative bioinformatics analysis and experimental validation identify CHEK1 as an unfavorable prognostic biomarker related to immunosuppressive phenotypes in soft tissue sarcomas
Chao Rong•Yun Liu•Fang Xiang•Xin Zhao•Jinjin Zhang等 16 人
Npj Precision Oncology
2025
•2025/8/1
•Vol.9 No.1 p.1-14
Soft tissue sarcomas (STS), including rhabdomyosarcoma (RMS), exhibit significant heterogeneity and limited responsiveness to immune checkpoint blockade (ICB). Unsupervised tumor immune phenotype based on multi-omics expression profiling of STS has been less studied. To reveal the tumor immune pheno...
BiomarkersCancerHealth careMedical researchMolecular medicineOncology
10.1038/S41698-025-01064-8
ISSN:2397-768X
EFA6B regulates a stop signal for collective invasion in breast cancer
Racha Fayad•Monserrat Vázquez Rojas•Mariagrazia Partisani•Pascal Finetti•Shiraz Dib等 14 人
Nature Communications
2021
•2021/4/13
•Vol.12 No.1 p.1-17
Cancer is initiated by somatic mutations in oncogenes or tumor suppressor genes. However, additional alterations provide selective advantages to the tumor cells to resist treatment and develop metastases. Their identification is of paramount importance. Reduced expression of EFA6B (Exchange Factor f...
Breast cancerRHO signalling
10.1038/S41467-021-22522-4
ISSN:2041-1723
Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication
Chaitali Chakraborty•Itzel Nissen•Craig A. Vincent•Anna-Carin Hägglund•Andreas Hörnblad等 6 人
Nature Communications
2023
•2023/10/13
•Vol.14 No.1 p.1-18
Chromatin organization controls transcription by modulating 3D-interactions between enhancers and promoters in the nucleus. Alterations in epigenetic states and 3D-chromatin organization result in gene expression changes contributing to cancer. Here, we map the promoter-enhancer interactome and regu...
Cancer genomicsCNS cancerGene regulationGene regulatory networks
10.1038/S41467-023-41919-X
ISSN:2041-1723
An integrated bioinformatic investigation of mitochondrial solute carrier family 25 (SLC25) in colon cancer followed by preliminary validation of member 5 (SLC25A5) in tumorigenesis
Chen Yan-Jie•Hong Wei-Feng•Liu Meng-Ling•Guo Xi•Yu Yi-Yi等 8 人
Cell Death & Disease
2022
•2022/3/14
•Vol.13 No.3 p.1-16
Solute carrier family 25 (SLC25) encodes transport proteins at the inner mitochondrial membrane and functions as carriers for metabolites. Although SLC25 genetic variants correlate with human metabolic diseases, their roles in colon cancer remain unknown. Cases of colon cancer were retrieved from Th...
Cancer metabolismColon cancerMetabolomicsOncogenesTumour biomarkers
10.1038/S41419-022-04692-1
ISSN:2041-4889
SNP-mediated lncRNA-ENTPD3-AS1 upregulation suppresses renal cell carcinoma via miR-155/HIF-1α signaling
Jiangyi Wang•Yun Zou•Bowen Du•Wenzhi Li•Guopeng Yu等 13 人
Cell Death & Disease
2021
•2021/7/3
•Vol.12 No.7 p.1-9
Over the last decade, more than 10 independent SNPs have been discovered to be associated with the risk of renal cell carcinoma among different populations. However, the biological functions of them remain poorly understood. In this study, we performed eQTL analysis, ChIP-PCR, luciferase reporter as...
Cancer epigeneticsRenal cell carcinoma
10.1038/S41419-021-03958-4
ISSN:2041-4889
Pigment epithelium-derived factor promotes peritoneal dissemination of ovarian cancer through induction of immunosuppressive macrophages
Ueno Sayaka•Sudo Tamotsu•Saya Hideyuki•Sugihara Eiji
Communications Biology
2022
•2022/9/2
•Vol.5 No.1 p.1-16
Peritoneal dissemination of ovarian cancer (OC) correlates with poor prognosis, but the mechanisms underlying the escape of OC cells from the intraperitoneal immune system have remained unknown. We here identify pigment epithelium–derived factor (PEDF) as a promoting factor of OC dissemination, whic...
Cancer microenvironmentOvarian cancerTumour biomarkers
10.1038/S42003-022-03837-4
ISSN:2399-3642
BAP1 is a haploinsufficient tumor suppressor linking chronic pancreatitis to pancreatic cancer in mice
Stephanie Perkail•Jaclyn Andricovich•Yan Kai•Alexandros Tzatsos
Nature Communications
2020
•2020/6/15
•Vol.11 No.1 p.1-17
Chronic pancreatitis represents a risk factor for the development of pancreatic cancer. We find that heterozygous loss of histone H2A lysine 119 deubiquitinase BAP1 (BRCA1 Associated Protein-1) associates with a history of chronic pancreatitis and occurs in 25% of pancreatic ductal adenocarcinomas a...
CancerGenetics
10.1038/S41467-020-16589-8
ISSN:2041-1723
Transcriptional activation of PHKG2 by TP53 promotes ferroptosis through nuclear export of NRF2 in head and neck squamous cell carcinoma
Yalian Yu•Meng Luan•Jian Zang•Le Luo•Tianyi Wang等 8 人
Cell Death & Disease
2025
•2025/8/30
•Vol.16 No.1 p.1-14
Head and neck squamous cell carcinoma (HNSCC) is a common malignancy with a poor prognosis despite multiple available treatments. Ferroptosis, an iron-dependent form of regulated cell death characterized by lipid peroxidation, has recently emerged as a promising strategy for cancer therapy, particul...
Head and neck cancerOncogenes
10.1038/S41419-025-07985-3
ISSN:2041-4889
Targeting PLK1 potentiates the antitumor efficacy of EGFR-TKIs through inhibiting the JAK1/STAT3 pathway
Cheng Li•Shangxuan Shi•Long Li•Yafang Wang•Mingyue Yao等 8 人
Cell Death & Disease
2026
•2026/1/15
•Vol.17 No.1 p.410
Despite the rapid development of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in recent decades, resistance remains a significant challenge in managing advanced non-small cell lung cancer (NSCLC). Elucidating the mechanisms underlying EGFR-TKI resistance and developing nov...
Cancer therapeutic resistanceTumour biomarkers
10.1038/S41419-025-08220-9
ISSN:2041-4889
MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas
Barbara Oldrini•Nuria Vaquero-Siguero•Quanhua Mu•Paula Kroon•Ying Zhang等 19 人
Nature Communications
2020
•2020/8/4
•Vol.11 No.1 p.1-10
Temozolomide (TMZ) is an oral alkylating agent used for the treatment of glioblastoma and is now becoming a chemotherapeutic option in patients diagnosed with high-risk low-grade gliomas. The O-6-methylguanine-DNA methyltransferase (MGMT) is responsible for the direct repair of the main TMZ-induced ...
Cancer genomicsCancer therapyCNS cancer
10.1038/S41467-020-17717-0
ISSN:2041-1723
Non-viral precision T cell receptor replacement for personalized cell therapy
Foy Susan P.•Jacoby Kyle•Bota Daniela A.•Hunter Theresa•Pan Zheng等 54 人
Nature
2022
•2022/11/10
•00 p.1-10
T cell receptors (TCRs) enable T cells to specifically recognize mutations in cancer cells1–3. Here we developed a clinical-grade approach based on CRISPR–Cas9 non-viral precision genome-editing to simultaneously knockout the two endogenous TCR genes TRAC (which encodes TCRα) and TRBC (which encodes...
CancerImmunology
10.1038/S41586-022-05531-1
ISSN:0028-0836
Targeting ACE2-BRD4 crosstalk in colorectal cancer and the deregulation of DNA repair and apoptosis
Zhang Shilan•Kapoor Sabeeta•Tripathi Chakrapani•Perez Jorge Tovar•Mohan Nivedhitha等 9 人
Npj Precision Oncology
2023
•2023/2/18
•Vol.7 No.1 p.1-7
ACE2 overexpression in colorectal cancer patients might increase susceptibility to SARS-CoV-2 infection. We report that knockdown, forced overexpression, and pharmacologic inhibition in human colon cancer cells targeted ACE2-BRD4 crosstalk to mediate marked changes in DNA damage/repair and apoptosis...
Colon cancerMolecular medicine
10.1038/S41698-023-00361-4
ISSN:2397-768X
Liver tumour immune microenvironment subtypes and neutrophil heterogeneity
Xue Ruidong•Zhang Qiming•Cao Qi•Kong Ruirui•Xiang Xiao等 15 人
Nature
2022
•2022/11/9
•Vol.612 No.7938 p.141-147
The heterogeneity of the tumour immune microenvironment (TIME), organized by various immune and stromal cells, is a major contributing factor of tumour metastasis, relapse and drug resistance1–3, but how different TIME subtypes are connected to the clinical relevance in liver cancer remains unclear....
Cancer microenvironmentLiver cancerTumour immunology
10.1038/S41586-022-05400-X
ISSN:0028-0836
Characterization of immune microenvironment in patients with HPV-positive and negative head and neck cancer
Zhongqiu Wang•Qingxin Wang•Yuxuan Tao•Jingru Chen•Zhiyong Yuan等 6 人
Scientific Data
2023
•2023/10/12
•Vol.10 No.1 p.1-10
Human papillomavirus (HPV) status strongly predicts positive clinical outcomes in patients with head and neck squamous cell cancer (HNSCC); however, the potential reasons have not been fully elucidated. Here, we characterized the immune context in HPV+ and HPV− HNSCC by integrating scRNA-seq and bul...
Cancer microenvironmentHead and neck cancer
10.1038/S41597-023-02611-3
ISSN:2052-4463
Breaking NGF–TrkA immunosuppression in melanoma sensitizes immunotherapy for durable memory T cell protection
Tao Yin•Guoping Wang•Liuyang Wang•Poorva Mudgal•Ergang Wang等 22 人
Nature Immunology
2024
•2024/1/9
•00 p.1-14
Melanoma cells, deriving from neuroectodermal melanocytes, may exploit the nervous system’s immune privilege for growth. Here we show that nerve growth factor (NGF) has both melanoma cell intrinsic and extrinsic immunosuppressive functions. Autocrine NGF engages tropomyosin receptor kinase A (TrkA) ...
Cancer immunotherapyImmune evasionImmunological memoryImmunosurveillance
10.1038/S41590-023-01723-7
ISSN:1529-2908
Methionine-driven YTHDF1 expression facilitates bladder cancer progression by attenuating RIG-I-modulated immune responses and enhancing the eIF5B-PD-L1 axis
Anze Yu•Liangmin Fu•Lanyu Jing•Yinghan Wang•Zifang Ma等 16 人
Cell Death & Differentiation
2024
•2024/12/13
•00 p.1-16
The impact of amino acids on tumor immunotherapy is gradually being uncovered. In this study, we screened various essential and non-essential amino acids and found that methionine enhances mRNA methylation and reduced the activation of Type I interferon pathway in bladder cancer. Through RNA sequenc...
Cell death and immune responseTumour biomarkers
10.1038/S41418-024-01434-Y
ISSN:1350-9047
Non-canonical MLL1 activity regulates centromeric phase separation and genome stability
Liang Sha•Zi Yang•Sojin An•Wentao Yang•Sungmin Kim等 13 人
Nature Cell Biology
2023
•2023/11/9
•Vol.25 No.11 p.1637-1649
Epigenetic dysregulation is a prominent feature in cancer, as exemplified by frequent mutations in chromatin regulators, including the MLL/KMT2 family of histone methyltransferases. Although MLL1/KMT2A activity on H3K4 methylation is well documented, their non-canonical activities remain mostly unex...
CentromeresGenomic instabilityHepatocellular carcinomaMitosis
10.1038/S41556-023-01270-1
ISSN:1465-7392
RAN-S100A10-EGFR axis facilitates papillary thyroid cancer metastasis by PI3K/AKT signaling
Wenbin Song•Zhaoyi Liu•Cangchang Shi•Guixin Wang•Long He等 16 人
Cell Death & Disease
2026
•2026/4/16
0Background: The incidence of thyroid cancer has been increasing in recent years, with papillary thyroid carcinoma (PTC) accounting for the majority of cases. Accumulating studies have demonstrated that S100A10 acts as an oncogene in the progression of various malignancies. However, the function and ...
OncogenesisThyroid cancerThyroid diseases
10.1038/S41419-026-08649-6
ISSN:2041-4889
Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix
Kay Emily J.•Paterson Karla•Riera-Domingo Carla•Sumpton David•Däbritz J. Henry M.等 29 人
Nature Metabolism
2022
•2022/6/27
•Vol.4 No.6 p.693-710
Elevated production of collagen-rich extracellular matrix is a hallmark of cancer-associated fibroblasts (CAFs) and a central driver of cancer aggressiveness. Here we find that proline, a highly abundant amino acid in collagen proteins, is newly synthesized from glutamine in CAFs to make tumour coll...
Cancer metabolismCancer microenvironmentMetabolism
10.1038/S42255-022-00582-0
ISSN:2522-5812
Non-invasive early detection of cancer four years before conventional diagnosis using a blood test
Xingdong Chen•Jeffrey Gole•Athurva Gore•Qiye He•Ming Lu等 32 人
Nature Communications
2020
•2020/7/21
•Vol.11 No.1 p.1-10
Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long...
EpigenomicsNext-generation sequencingTumour biomarkers
10.1038/S41467-020-17316-Z
ISSN:2041-1723
A deep learning model to predict RNA-Seq expression of tumours from whole slide images
Benoît Schmauch•Alberto Romagnoni•Elodie Pronier•Charlie Saillard•Pascale Maillé等 14 人
Nature Communications
2020
•2020/8/3
•Vol.11 No.1 p.1-15
Deep learning methods for digital pathology analysis are an effective way to address multiple clinical questions, from diagnosis to prediction of treatment outcomes. These methods have also been used to predict gene mutations from pathology images, but no comprehensive evaluation of their potential ...
CancerMachine learning
10.1038/S41467-020-17678-4
ISSN:2041-1723
KK-LC-1 as a therapeutic target to eliminate ALDH+ stem cells in triple negative breast cancer
Bu Jiawen•Zhang Yixiao•Wu Sijin•Li Haonan•Sun Lisha等 15 人
Nature Communications
2023
•2023/5/5
•Vol.14 No.1 p.1-18
Failure to achieve complete elimination of triple negative breast cancer (TNBC) stem cells after adjuvant therapy is associated with poor outcomes. Aldehyde dehydrogenase 1 (ALDH1) is a marker of breast cancer stem cells (BCSCs), and its enzymatic activity regulates tumor stemness. Identifying upstr...
Breast cancerCancer stem cellsDrug discovery
10.1038/S41467-023-38097-1
ISSN:2041-1723
Targeting FSP1 to induce ferroptosis in chromophobe renal cell carcinoma
Samer Salem•Tiegang Han•Michel Alchoueiry•Nadine Mahmoud•Wafaa Bzeih等 13 人
Oncogene
2025
•2025/9/6
•00 p.1-12
There are no proven therapies for metastatic or unresectable Chromophobe Renal Cell Carcinoma (ChRCC). ChRCC is characterized by high glutathione levels and hypersensitivity to ferroptosis, an iron-dependent form of cell death characterized by peroxidation of polyunsaturated fatty acids. The underly...
Cancer therapyRenal cell carcinoma
10.1038/S41388-025-03562-2
ISSN:0950-9232
A spatially resolved human glioblastoma atlas reveals distinct cellular and molecular patterns of anatomical niches
Pranali Sonpatki•Hyun Jung Park•Yao Lulu Xing•Kyung Yeon Han•Brett A. Schroeder等 25 人
Nature Communications
2026
•2026/2/20
•Vol.17 No.1 p.29510
Glioblastoma is an aggressive brain cancer with limited treatment options and poor patient survival, driven in part by cellular diversity within tumors. While individual cell types have been catalogued, how malignant, vascular, and immune cells are spatially organized inside human tumors remains inc...
Cancer microenvironmentCNS cancerTranscriptomics
10.1038/S41467-026-69716-2
ISSN:2041-1723
H&E-based MSI/MMR testing with AI in colorectal cancer: a multi-centred blinded evaluation
Cher Bass•Foivos Ntelemis•Julian Schmidt•Steffen Wolf•André Geraldes等 28 人
Npj Digital Medicine
2025
•2025/12/15
0Mismatch repair (MMR) deficiency occurs in 10–20% of colorectal cancer (CRC) cases, leading to microsatellite instability (MSI). Although MSI/MMR testing is critical for CRC management, high costs and long turnaround times limit testing rates and clinical utility, highlighting the need for more acce...
BiomarkersCancerComputational biology and bioinformaticsGastroenterologyOncology
10.1038/S41746-025-02218-5
ISSN:2398-6352
The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer
Evan D. Paul•Barbora Huraiová•Natália Valková•Natalia Matyasovska•Daniela Gábrišová等 28 人
Nature Communications
2025
•2025/1/2
•Vol.16 No.1 p.1-22
Current assays fail to address breast cancer’s complex biology and accurately predict treatment response. On a retrospective cohort of 1082 female breast tissues, we develop and validate mFISHseq, which integrates multiplexed RNA fluorescent in situ hybridization with RNA-sequencing, guided by laser...
Breast cancerFluorescence in situ hybridizationRNA sequencingTumour biomarkers
10.1038/S41467-024-55583-2
ISSN:2041-1723
Targeted inhibition of the methyltransferase SETD8 synergizes with the Wee1 inhibitor adavosertib in restraining glioblastoma growth
Rosa Della Monica•Michela Buonaiuto•Mariella Cuomo•Cristina Pagano•Federica Trio等 23 人
Cell Death & Disease
2023
•2023/9/27
•Vol.14 No.9 p.1-13
Despite intense research efforts, glioblastoma remains an incurable brain tumor with a dismal median survival time of 15 months. Thus, identifying new therapeutic targets is an urgent need. Here, we show that the lysine methyltransferase SETD8 is overexpressed in 50% of high-grade gliomas. The small...
CheckpointsTargeted therapies
10.1038/S41419-023-06167-3
ISSN:2041-4889
A coregulatory influence map of glioblastoma heterogeneity and plasticity
Chloé Bernhard•Konstantinos Geles•Geoffrey Pawlak•Wajdi Dhifli•Aurélien Dispot等 16 人
Npj Precision Oncology
2025
•2025/4/15
•Vol.9 No.1 p.1-18
We present GBM-cRegMap, an online resource providing a comprehensive coregulatory influence network perspective on glioblastoma (GBM) heterogeneity and plasticity. Using representation learning algorithms, we derived two components of this resource: GBM-CoRegNet, a highly specific coregulatory netwo...
CNS cancerComputational biology and bioinformaticsSystems biologyTumour heterogeneity
10.1038/S41698-025-00890-0
ISSN:2397-768X
ELAVL2 loss promotes aggressive mesenchymal transition in glioblastoma
Yona Kim•Ji Hyeon You•Yeonjoo Ryu•Gyuri Park•Urim Lee等 11 人
Npj Precision Oncology
2024
•2024/3/28
•Vol.8 No.1 p.1-16
Glioblastoma (GBM), the most lethal primary brain cancer, exhibits intratumoral heterogeneity and molecular plasticity, posing challenges for effective treatment. Despite this, the regulatory mechanisms underlying such plasticity, particularly mesenchymal (MES) transition, remain poorly understood. ...
CNS cancerPrognostic markers
10.1038/S41698-024-00566-1
ISSN:2397-768X
Annotation and cluster analysis of long noncoding RNA linked to male sex and estrogen in cancers
Shouping Liu•Weiwei Lai•Ying Shi•Na Liu•Lianlian Ouyang等 14 人
Npj Precision Oncology
2020
•2020/3/3
•Vol.4 No.1 p.1-13
The sex difference in cancer occurrence is a consistent finding in cancer epidemiology. Several solid tumors, including lung cancer, colorectal cancer, hepatic carcinoma, and renal carcinoma, are generally more common in males. Although sexual dimorphism is attributed to hormonal or behavioral diffe...
Cancer genomicsComputational biology and bioinformatics
10.1038/S41698-020-0110-5
ISSN:2397-768X
GZMKhigh CD8+ T effector memory cells are associated with CD15high neutrophil abundance in non-metastatic colorectal tumors and predict poor clinical outcome
Tiberti Silvia•Catozzi Carlotta•Croci Ottavio•Ballerini Mattia•Cagnina Danilo等 28 人
Nature Communications
2022
•2022/11/8
•Vol.13 No.1 p.1-20
CD8+ T cells are a major prognostic determinant in solid tumors, including colorectal cancer (CRC). However, understanding how the interplay between different immune cells impacts on clinical outcome is still in its infancy. Here, we describe that the interaction of tumor infiltrating neutrophils ex...
Colorectal cancerTumour immunology
10.1038/S41467-022-34467-3
ISSN:2041-1723
Spatiotemporal analysis of glioma heterogeneity reveals COL1A1 as an actionable target to disrupt tumor progression
Comba Andrea•Faisal Syed M.•Dunn Patrick J.•Argento Anna E.•Hollon Todd C.等 18 人
Nature Communications
2022
•2022/6/24
•Vol.13 No.1 p.1-23
Intra-tumoral heterogeneity is a hallmark of glioblastoma that challenges treatment efficacy. However, the mechanisms that set up tumor heterogeneity and tumor cell migration remain poorly understood. Herein, we present a comprehensive spatiotemporal study that aligns distinctive intra-tumoral histo...
Cancer imagingCancer microenvironmentCNS cancerTumour biomarkersTumour heterogeneity
10.1038/S41467-022-31340-1
ISSN:2041-1723
Reply to ‘Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data’
Marc J. Williams•Benjamin Werner•Timon Heide•Chris P. Barnes•Trevor A. Graham等 6 人
Nature Genetics
2018
•2018/9/24
•Vol.50 No.12 p.1628-1630
CancerData processingGenome informatics
10.1038/S41588-018-0210-0
ISSN:1061-4036
Systemic IFN-I combined with topical TLR7/8 agonists promotes distant tumor suppression by c-Jun-dependent IL-12 expression in dendritic cells
Martina Sanlorenzo•Philipp Novoszel•Igor Vujic•Tommaso Gastaldi•Martina Hammer等 14 人
Nature Cancer
2025
•2025/1/23
•Vol.6 No.1 p.175-193
Dendritic cell (DC) activation by pattern recognition receptors like Toll-like-receptors (TLRs) is crucial for cancer immunotherapies. Here, we demonstrate the effectiveness of the TLR7/8 agonist imiquimod (IMQ) in treating both local tumors and distant metastases. Administered orally, IMQ activates...
CancerCancer immunotherapyMelanomaToll-like receptors
10.1038/S43018-024-00889-9
ISSN:2662-1347
Machine learning-driven glycolytic subtyping and exosome-based PKM splicing modulation overcome drug resistance in hyper-glycolytic myeloid leukemia
Fangmin Zhong•Song Chen•Fangyi Yao•Jing Liu•Jing Zhang等 14 人
Npj Digital Medicine
2025
•2025/12/1
0This study comprehensively investigates the role of glycolysis in acute myeloid leukemia (AML) pathogenesis. Elevated glycolysis correlated significantly with poor prognosis. Bioinformatics identified HIF1A and MIF as key regulators and revealed two robust molecular subtypes: a high-glycolysis subty...
CancerCell biologyOncology
10.1038/S41746-025-02185-X
ISSN:2398-6352
Pan-cancer, multi-omic correlates of survival transcending tumor lineage across 11,019 patients reveal targets and pathways
Yiqun Zhang•Fengju Chen•Chad J. Creighton
Npj Precision Oncology
2025
•2025/7/5
•Vol.9 No.1 p.1-19
Molecular correlates of cancer patient overall survival (OS) can provide new insights. Here, we systematically cataloged pan-cancer, multi-omic correlates of OS transcending tumor lineage across 11,019 patients, involving multiple cancer types while correcting for cancer-type-intrinsic OS difference...
Cancer genomicsComputational biology and bioinformatics
10.1038/S41698-025-01029-X
ISSN:2397-768X
Neutral ceramidase regulates breast cancer progression by metabolic programming of TREM2-associated macrophages
Rui Sun•Chao Lei•Zhishan Xu•Xuemei Gu•Liu Huang等 14 人
Nature Communications
2024
•2024/2/1
•Vol.15 No.1 p.1-20
The tumor microenvironment is reprogrammed by cancer cells and participates in all stages of tumor progression. Neutral ceramidase is a key regulator of ceramide, the central intermediate in sphingolipid metabolism. The contribution of neutral ceramidase to the reprogramming of the tumor microenviro...
Breast cancerCancer microenvironmentTumour immunology
10.1038/S41467-024-45084-7
ISSN:2041-1723
Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of esophageal cancer
Piyali Ganguli•Celia C. Basanta•Amelia Acha-Sagredo•Hrvoje Misetic•Maria Armero等 18 人
Nature Cancer
2025
•2025/1/3
•00 p.1-17
CDKN2A is a tumor suppressor located in chromosome 9p21 and frequently lost in Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC). How CDKN2A and other 9p21 gene co-deletions affect EAC evolution remains understudied. We explored the effects of 9p21 loss in EACs and cancer progressor and n...
CancerCancer genomicsOesophageal cancerTumour-suppressor proteins
10.1038/S43018-024-00876-0
ISSN:2662-1347
Evolutionary dynamics of neoantigens in growing tumors
Eszter Lakatos•Marc J. Williams•Ryan O. Schenck•William C. H. Cross•Jacob Househam等 13 人
Nature Genetics
2020
•2020/9/14
•Vol.52 No.10 p.1057-1066
Cancers accumulate mutations that lead to neoantigens, novel peptides that elicit an immune response, and consequently undergo evolutionary selection. Here we establish how negative selection shapes the clonality of neoantigens in a growing cancer by constructing a mathematical model of neoantigen e...
CancerComputational scienceGenetics research
10.1038/S41588-020-0687-1
ISSN:1061-4036
Genomic and immune landscape Of metastatic pheochromocytoma and paraganglioma
Calsina Bruna•Piñeiro-Yáñez Elena•Martínez-Montes Ángel M.•Caleiras Eduardo•Fernández-Sanromán Ángel等 53 人
Nature Communications
2023
•2023/2/28
•Vol.14 No.1 p.1-20
The mechanisms triggering metastasis in pheochromocytoma/paraganglioma are unknown, hindering therapeutic options for patients with metastatic tumors (mPPGL). Herein we show by genomic profiling of a large cohort of mPPGLs that high mutational load, microsatellite instability and somatic copy-number...
Adrenal gland diseasesCancer genomicsNeuroendocrine cancerPrognostic markers
10.1038/S41467-023-36769-6
ISSN:2041-1723
Meta single-cell atlas and xQTL post-GWAS analysis revealed the pathogenic features of thyroid cancer for target therapy: A multi-omics study
Cong Zhang•Yu Wang•Biao Xie
Cancer Gene Therapy
2025
•2025/11/17
•00 p.1-16
Thyroid cancer (TC) is an endocrine malignancy characterized by metabolic abnormalities, with its incidence continually on the rise. Understanding the pathogenesis of this cancer would help develop better diagnostic and therapeutic methods. We aimed to integrate single-cell transcriptomics, bulk tra...
BiomarkersCancer geneticsCancer genomics
10.1038/S41417-025-00988-4
ISSN:0929-1903
An interpretable deep learning model for predicting endometrial cancer molecular subtypes from H&E-stained slides
Qinhao Guo•Haoyu Cui•Yangyang Zhang•Shaoxian Tang•Weicheng Yan等 18 人
Npj Precision Oncology
2026
•2026/1/21
•Vol.10 No.1 p.710
The molecular subtype of endometrial cancer is important for predicting prognosis and treatment effectiveness. This study aimed to develop an interpretable deep learning model based on H&E-stained whole slide images (WSIs) to predict the molecular subtype of endometrial cancer. Data from the Fud...
Computational biology and bioinformaticsOncology
10.1038/S41698-026-01280-W
ISSN:2397-768X
Fast and scalable search of whole-slide images via self-supervised deep learning
Chen Chengkuan•Lu Ming Y.•Williamson Drew F. K.•Chen Tiffany Y.•Schaumberg Andrew J.等 6 人
Nature Biomedical Engineering
2022
•2022/10/10
•Vol.6 No.12 p.1420-1434
The adoption of digital pathology has enabled the curation of large repositories of gigapixel whole-slide images (WSIs). Computationally identifying WSIs with similar morphologic features within large repositories without requiring supervised training can have significant applications. However, the ...
BioinformaticsBiomedical engineeringMedical imagingPathology
10.1038/S41551-022-00929-8
ISSN:2157-846X
Epigenomic diagnosis and prognosis of Acute Myeloid Leukemia
Francisco Marchi•Vivek M. Shastri•Richard J. Marrero•Nam H. K. Nguyen•Antonella Öttl等 29 人
Nature Communications
2025
•2025/7/29
•Vol.16 No.1 p.1-19
Despite the critical role of DNA methylation, clinical implementations harnessing its promise have not been described in acute myeloid leukemia. Utilizing DNA methylation from 3314 leukemia patient samples across 11 harmonized cohorts, we describe the Acute Leukemia Methylome Atlas, which includes r...
Haematological cancerPaediatric cancer
10.1038/S41467-025-62005-4
ISSN:2041-1723
Targetable leukaemia dependency on noncanonical PI3Kγ signalling
Qingyu Luo•Evangeline G. Raulston•Miguel A. Prado•Xiaowei Wu•Kira Gritsman等 16 人
Nature
2024
•2024/5/8
•00 p.1-8
Phosphoinositide-3-kinase-γ (PI3Kγ) is implicated as a target to repolarize tumour-associated macrophages and promote antitumour immune responses in solid cancers1–4. However, cancer cell-intrinsic roles of PI3Kγ are unclear. Here, by integrating unbiased genome-wide CRISPR interference screening wi...
Acute myeloid leukaemiaOncogenes
10.1038/S41586-024-07410-3
ISSN:0028-0836
Data-efficient and weakly supervised computational pathology on whole-slide images
Ming Y. Lu•Drew F. K. Williamson•Tiffany Y. Chen•Richard J. Chen•Matteo Barbieri等 6 人
Nature Biomedical Engineering
2021
•2021/3/1
•00 p.1-16
Deep-learning methods for computational pathology require either manual annotation of gigapixel whole-slide images (WSIs) or large datasets of WSIs with slide-level labels and typically suffer from poor domain adaptation and interpretability. Here we report an interpretable weakly supervised deep-le...
Image processingMachine learningPathology
10.1038/S41551-020-00682-W
ISSN:2157-846X
Escape from nonsense-mediated decay associates with anti-tumor immunogenicity
Kevin Litchfield•James L. Reading•Emilia L. Lim•Hang Xu•Po Liu等 20 人
Nature Communications
2020
•2020/7/30
•Vol.11 No.1 p.1-11
Frameshift insertion/deletions (fs-indels) are an infrequent but highly immunogenic mutation subtype. Although fs-indels are degraded through the nonsense-mediated decay (NMD) pathway, we hypothesise that some fs-indels escape degradation and elicit anti-tumor immune responses. Using allele-specific...
Cancer genomicsImmunoeditingSkin cancerTumour immunology
10.1038/S41467-020-17526-5
ISSN:2041-1723
Cancer drug sensitivity prediction from routine histology images
Muhammad Dawood•Quoc Dang Vu•Lawrence S. Young•Kim Branson•Louise Jones等 7 人
Npj Precision Oncology
2024
•2024/1/6
•Vol.8 No.1 p.1-13
Drug sensitivity prediction models can aid in personalising cancer therapy, biomarker discovery, and drug design. Such models require survival data from randomised controlled trials which can be time consuming and expensive. In this proof-of-concept study, we demonstrate for the first time that deep...
Breast cancer
10.1038/S41698-023-00491-9
ISSN:2397-768X
Adaptive compression framework for giga-pixel whole slide images
Jonghyun Lee•Lina Takemaru•D. M. Bappy•Ye Sul Jeong•Won-Ki Jeong等 9 人
Nature Communications
2025
•2025/12/3
0Digital pathology generates gigapixel whole-slide images that require extensive storage, limiting scalability and increasing costs. Traditional compression methods apply uniform ratios, disregarding variations in diagnostic importance across regions. Here we show Adaptive compression for gigapixel w...
Computational modelsImage processingMedical imaging
10.1038/S41467-025-66889-0
ISSN:2041-1723
HOXC11 drives lung adenocarcinoma progression through transcriptional regulation of SPHK1
Peng Xin•Liu Xiaoli•Hu Wanshan•Zhou Yanling•Ouyang Lianlian等 14 人
Cell Death & Disease
2023
•2023/2/23
•Vol.14 No.2 p.1-13
Lung adenocarcinoma (LUAD) is a fatal threat to human health, while the mechanism remains unclear, and the therapy brings limited therapeutic effects. Transcription factor Homeobox C11 (HOXC11) was previously proved to be related to hind limbs and metanephric development during the embryonic phase, ...
Non-small-cell lung cancerPrognostic markers
10.1038/S41419-023-05673-8
ISSN:2041-4889
Estimating the predictive power of silent mutations on cancer classification and prognosis
Gutman Tal•Goren Guy•Efroni Omri•Tuller Tamir
Npj Genomic Medicine
2021
•2021/8/12
•Vol.6 No.1 p.1-15
In recent years it has been shown that silent mutations, in and out of the coding region, can affect gene expression and may be related to tumorigenesis and cancer cell fitness. However, the predictive ability of these mutations for cancer type diagnosis and prognosis has not been evaluated yet. In ...
Gene expressionGenome informaticsPredictive markersSystems biology
10.1038/S41525-021-00229-1
ISSN:2056-7944
Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women
Babatunde Adedokun•Zhaohui Du•Guimin Gao•Thomas U. Ahearn•Kathryn L. Lunetta等 60 人
Nature Communications
2021
•2021/7/7
•Vol.12 No.1 p.1-8
Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases a...
Breast cancerCancer epidemiology
10.1038/S41467-021-24327-X
ISSN:2041-1723
CDK13 drives clear cell renal carcinoma through METTL16-mediated m6A modification of ACLY mRNA
Jinsuo Chen•Huan Liu•Yong Zhang•Junfei Gu•Xiaoli Wu等 13 人
Experimental & Molecular Medicine
2026
•2026/2/12
•Vol.58 No.2 p.472-486
Cyclin-dependent kinase 13 (CDK13) has emerged as a critical regulator of oncogenic metabolism, but its role in rewiring lipid metabolism in clear cell renal cell carcinoma (ccRCC) remains undefined. Here we identify CDK13 as a master orchestrator of lipid dysregulation in ccRCC, demonstrating that ...
Cancer metabolismPhosphorylationRenal cell carcinomaRNA modification
10.1038/S12276-025-01634-7
ISSN:2092-6413
Deep learning generates synthetic cancer histology for explainability and education
James M. Dolezal•Rachelle Wolk•Hanna M. Hieromnimon•Frederick M. Howard•Andrew Srisuwananukorn等 23 人
Npj Precision Oncology
2023
•2023/5/29
•Vol.7 No.1 p.1-13
Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make their predictions remains a significant challenge, but explai...
CancerMathematics and computing
10.1038/S41698-023-00399-4
ISSN:2397-768X
Three-dimensional genome landscape of primary human cancers
Kathryn E. Yost•Yanding Zhao•King L. Hung•Kaiyuan Zhu•Duo Xu等 25 人
Nature Genetics
2025
•2025/5/12
•Vol.57 No.5 p.1189-1200
Genome conformation underlies transcriptional regulation by distal enhancers, and genomic rearrangements in cancer can alter critical regulatory interactions. Here we profiled the three-dimensional genome architecture and enhancer connectome of 69 tumor samples spanning 15 primary human cancer types...
CancerEpigenomicsGene regulation
10.1038/S41588-025-02188-0
ISSN:1061-4036
Identification of relevant genetic alterations in cancer using topological data analysis
Raúl Rabadán•Yamina Mohamedi•Udi Rubin•Tim Chu•Adam N. Alghalith等 11 人
Nature Communications
2020
•2020/7/30
•Vol.11 No.1 p.1-10
Large-scale cancer genomic studies enable the systematic identification of mutations that lead to the genesis and progression of tumors, uncovering the underlying molecular mechanisms and potential therapies. While some such mutations are recurrently found in many tumors, many others exist solely wi...
Cancer genomicsComputational biology and bioinformatics
10.1038/S41467-020-17659-7
ISSN:2041-1723
Generalizable AI predicts immunotherapy outcomes across cancers and treatments
Wanxiang Shen•Intae Moon•Thinh H. Nguyen•Michelle M. Li•Yepeng Huang等 8 人
Nature Medicine
2026
•2026/7/3
•00 p.1-13
Immune checkpoint inhibitors (ICIs) are a standard treatment across cancers, yet most patients do not respond, and existing biomarkers generalize poorly across tumor types and therapies. Here we present COMPASS, a pan-cancer foundation model that predicts immunotherapy response from bulk tumor trans...
BiomarkersDrug developmentMachine learning
10.1038/S41591-026-04502-7
ISSN:1078-8956
Histone lactylation increases CXCL1 expression for neutrophil infiltration and immune escape in pancreatic cancer
Peng Zhang•Jinrong Ma•Yi Wan•Chenxi Li•Lijuan Liu等 21 人
Nature Communications
2026
•2026/2/9
•Vol.17 No.1 p.25260
Aerobic glycolysis and lactate have been shown to modulate tumor microenvironment (TME) and disease progression. Lactate-mediated histone lysine lactylation (Kla) is a newly recognized epigenetic modification whose biological function remains poorly understood. Here, through integrated bioinformatic...
Cancer microenvironmentPancreatic cancer
10.1038/S41467-026-69311-5
ISSN:2041-1723
HDAC6 facilitates LUAD progression by inducing EMT and enhancing macrophage polarization towards the M2 phenotype
Yantao Jiang•Ju Zhang•Junjie Yu•Wei Luo•Qingwu Du等 11 人
Npj Precision Oncology
2025
•2025/5/22
•Vol.9 No.1 p.1-21
Histone deacetylase 6 (HDAC6) plays a critical role in lung adenocarcinoma (LUAD) prognosis and the tumor immune microenvironment (TIME). This study, utilizing public datasets and experimental validation, revealed that HDAC6 is upregulated in LUAD, correlating with poor survival outcomes and an immu...
Lung cancerTumour biomarkers
10.1038/S41698-025-00949-Y
ISSN:2397-768X
Tumour–brain crosstalk restrains cancer immunity via a sensory–sympathetic axis
Haohan K. Wei•Chuyue D. Yu•Bo Hu•Xing Zeng•Hiroshi Ichise等 11 人
Nature
2026
•2026/2/4
•Vol.650 No.8103 p.1007-1016
Body–brain communication has emerged as a key regulator of tissue homeostasis1–5. Solid tumours are innervated by different branches of the peripheral nervous system and increased tumour innervation is associated with poor cancer outcomes6–8. However, it remains unclear how the brain senses and resp...
Cancer microenvironmentNeuroimmunology
10.1038/S41586-025-10028-8
ISSN:0028-0836
GrandQC: A comprehensive solution to quality control problem in digital pathology
Zhilong Weng•Alexander Seper•Alexey Pryalukhin•Fabian Mairinger•Claudia Wickenhauser等 23 人
Nature Communications
2024
•2024/12/16
•Vol.15 No.1 p.1-12
Histological slides contain numerous artifacts that can significantly deteriorate the performance of image analysis algorithms. Here we develop the GrandQC tool for tissue and multi-class artifact segmentation. GrandQC allows for high-precision tissue segmentation (Dice score 0.957) and segmentation...
Computer scienceMedical imagingPathology
10.1038/S41467-024-54769-Y
ISSN:2041-1723
YTHDF1/RNF7/p27 axis promotes prostate cancer progression
Yulin Shi•Baiyang Liu•Yong Zhang•Sen Zhao•Li Zuo等 12 人
Cell Death & Disease
2025
•2025/4/18
•Vol.16 No.1 p.1-12
Prostate cancer (PCa) is a prevalent malignant tumor of the urinary system and remains the most common cancer among males. In this study, we showed that YTHDF1, one of the reader proteins involved in the N6-methyladenosine (m6A) modification signaling pathway, is highly expressed in PCa cancerous ti...
OncogenesisTumour biomarkers
10.1038/S41419-025-07648-3
ISSN:2041-4889
A machine learning approach for multimodal data fusion for survival prediction in cancer patients
Nikolaos Nikolaou•Domingo Salazar•Harish RaviPrakash•Miguel Gonçalves•Rob Mulla等 8 人
Npj Precision Oncology
2025
•2025/5/6
•Vol.9 No.1 p.1-14
Technological advancements of the past decade have transformed cancer research, improving patient survival predictions through genotyping and multimodal data analysis. However, there is no comprehensive machine-learning pipeline for comparing methods to enhance these predictions. To address this, a ...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41698-025-00917-6
ISSN:2397-768X
Machine learning-based integration develops an immune-derived lncRNA signature for improving outcomes in colorectal cancer
Liu Zaoqu•Liu Long•Weng Siyuan•Guo Chunguang•Dang Qin等 11 人
Nature Communications
2022
•2022/2/10
•Vol.13 No.1 p.1-14
Long noncoding RNAs (lncRNAs) are recently implicated in modifying immunology in colorectal cancer (CRC). Nevertheless, the clinical significance of immune-related lncRNAs remains largely unexplored. In this study, we develope a machine learning-based integrative procedure for constructing a consens...
CancerComputational biology and bioinformaticsDrug discoveryImmunologyMolecular biology
10.1038/S41467-022-28421-6
ISSN:2041-1723
Tumour-targeted interleukin-12 and entinostat combination therapy improves cancer survival by reprogramming the tumour immune cell landscape
Hicks Kristin C.•Chariou Paul L.•Ozawa Yohei•Minnar Christine M.•Knudson Karin M.等 10 人
Nature Communications
2021
•2021/8/26
•Vol.12 No.1 p.1-18
Poorly inflamed carcinomas do not respond well to immune checkpoint blockade. Converting the tumour microenvironment into a functionally inflamed immune hub would extend the clinical benefit of immune therapy to a larger proportion of cancer patients. Here we show, by using comprehensive single-cell...
Cancer microenvironmentImmunoeditingImmunotherapyTumour vaccines
10.1038/S41467-021-25393-X
ISSN:2041-1723
An RFC4/Notch1 signaling feedback loop promotes NSCLC metastasis and stemness
Lei Liu•Tianyu Tao•Shihua Liu•Xia Yang•Xuwei Chen等 28 人
Nature Communications
2021
•2021/5/11
•Vol.12 No.1 p.1-16
Notch signaling represents a key mechanism mediating cancer metastasis and stemness. To understand how Notch signaling is overactivated to couple tumor metastasis and self-renewal in NSCLC cells, we performed the current study and showed that RFC4, a DNA replication factor amplified in more than 40%...
MetastasisNon-small-cell lung cancer
10.1038/S41467-021-22971-X
ISSN:2041-1723
Deep learning for dual detection of microsatellite instability and POLE mutations in colorectal cancer histopathology
Marco Gustav•Nic Gabriel Reitsam•Zunamys I. Carrero•Chiara M. L. Loeffler•Marko van Treeck等 18 人
Npj Precision Oncology
2024
•2024/5/23
•Vol.8 No.1 p.1-11
In the spectrum of colorectal tumors, microsatellite-stable (MSS) tumors with DNA polymerase ε (POLE) mutations exhibit a hypermutated profile, holding the potential to respond to immunotherapy similarly to their microsatellite-instable (MSI) counterparts. Yet, due to their rarity and the associated...
Diagnostic markersMathematics and computingPathologyTumour biomarkers
10.1038/S41698-024-00592-Z
ISSN:2397-768X
The DNA methylation landscape of primary triple-negative breast cancer
Mattias Aine•Deborah F. Nacer•Elsa Arbajian•Srinivas Veerla•Anna Karlsson等 11 人
Nature Communications
2025
•2025/3/28
•Vol.16 No.1 p.1-23
Triple-negative breast cancer (TNBC) is a clinically challenging and molecularly heterogenous breast cancer subgroup. Here, we investigate the DNA methylation landscape of TNBC. By analyzing tumor methylome profiles and accounting for the genomic context of CpG methylation, we divide TNBC into two e...
Breast cancerCancer epigeneticsCancer genomicsCancer metabolismCancer microenvironment
10.1038/S41467-025-58158-X
ISSN:2041-1723
PRET is a few-shot system for pan-cancer recognition without example training
Yi Li•Ziyu Ning•Tianqi Xiang•Qixiang Zhang•Zhihao Lin等 20 人
Nature Cancer
2026
•2026/4/3
•00 p.1-15
Pathological examination stands as the cornerstone in cancer diagnosis, impacting millions worldwide annually. With the shortage of pathologists globally, artificial intelligence (AI) has emerged rapidly to automate the diagnostics process. However, conventional AI models require substantial labeled...
CancerImage processingMachine learning
10.1038/S43018-026-01141-2
ISSN:2662-1347
Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology
Dylan Domenico•Gunes Gundem•Max F. Levine•Juan Esteban Arango-Ossa•Pauline Robbe等 23 人
Nature Communications
2025
•2025/11/27
•Vol.16 No.1 p.106490
The adoption of whole genome sequencing (WGS) in clinical oncology is challenged by low data quality and increased artifacts in standard-of-care formalin-fixed paraffin-embedded (FFPE) samples. Analysis of 56 fresh frozen (FF) and FFPE matched pairs demonstrates that FFPE processing results in a med...
Cancer genomicsData processingPersonalized medicineSoftware
10.1038/S41467-025-65654-7
ISSN:2041-1723
A comprehensive overview of genomic imprinting in breast and its deregulation in cancer
Tine Goovaerts•Sandra Steyaert•Chari A. Vandenbussche•Jeroen Galle•Olivier Thas等 7 人
Nature Communications
2018
•2018/10/8
•Vol.9 No.1 p.1-14
Genomic imprinting plays an important role in growth and development. Loss of imprinting (LOI) has been found in cancer, yet systematic studies are impeded by data-analytical challenges. We developed a methodology to detect monoallelically expressed loci without requiring genotyping data, and applie...
Breast cancerCancer genomicsGenetics research
10.1038/S41467-018-06566-7
ISSN:2041-1723
Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk
Yaohua Yang•Yaxin Chen•Shuai Xu•Xingyi Guo•Guochong Jia等 23 人
Nature Communications
2024
•2024/7/18
•Vol.15 No.1 p.1-13
The relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these mo...
Cancer epidemiologyDNA methylationPredictive markers
10.1038/S41467-024-50404-Y
ISSN:2041-1723
Nutrient-delivery and metabolism reactivation therapy for melanoma
Yang Chen•Chaochao Wang•Yelin Wu•Ya Wang•Yun Meng等 16 人
Nature Nanotechnology
2024
•2024/6/11
•00 p.1-10
To fulfil the demands of rapid proliferation, tumour cells undergo significant metabolic alterations. Suppression of hyperactivated metabolism has been proven to counteract tumour growth. However, whether the reactivation of downregulated metabolic pathways has therapeutic effects remains unexplored...
BiomaterialsMaterials science
10.1038/S41565-024-01690-6
ISSN:1748-3387
HPV status impacts oncobacteria abundance and prognostic relevance in head and neck squamous cell carcinoma
Travis D. Kerr•Natalie L. Silver•Radhika Duggal•Jin Dai•Hannah Simmons等 10 人
Oncogene
2025
•2025/6/10
•00 p.1-7
The intratumoral microbiome is emerging as an intrinsic microenvironment feature of some cancers, most notably those along the digestive tract. Opportunistic pathogenic bacteria, such as Fusobacterium nucleatum, can enrich within certain tumors, ultimately leading to alterations in the tumor microen...
Cancer microenvironmentHead and neck cancerPrognostic markers
10.1038/S41388-025-03463-4
ISSN:0950-9232
Stage IV colon cancer patients without DENND2D expression benefit more from neoadjuvant chemotherapy
Ma Wen-juan•Chen Yukun•Peng Jian-hong•Tang Chaoming•Zhang Ling等 14 人
Cell Death & Disease
2022
•2022/5/6
•Vol.13 No.5 p.1-12
According to the EPOC study, chemotherapy could improve 5-year disease-free survival of stage IV colon cancer patients by 8.1%. However, more molecular biomarkers are required to identify patients who need neoadjuvant chemotherapy. DENND2D expression was evaluated by immunohistochemistry in 181 stag...
Colon cancerTumour biomarkers
10.1038/S41419-022-04885-8
ISSN:2041-4889
Semaphorin 3C (Sema3C) reshapes stromal microenvironment to promote hepatocellular carcinoma progression
Hao Peng•Meng Yang•Kun Feng•Qingpeng Lv•Yewei Zhang
Signal Transduction And Targeted Therapy
2024
•2024/7/3
•Vol.9 No.1 p.1-20
More than 90% of hepatocellular carcinoma (HCC) cases develop in the presence of fibrosis or cirrhosis, making the tumor microenvironment (TME) of HCC distinctive due to the intricate interplay between cancer-associated fibroblasts (CAFs) and cancer stem cells (CSCs), which collectively regulate HCC...
Cancer microenvironmentCancer stem cells
10.1038/S41392-024-01887-0
ISSN:2059-3635
TCP1 promotes the progression of malignant tumours by stabilizing c-Myc through the AKT/GSK-3β and ERK signalling pathways
Hekun Liu•Linying Chen•Yuwen Chen•Yiyi Jin•Xiance Chen等 15 人
Communications Biology
2025
•2025/4/4
•Vol.8 No.1 p.1-13
The chaperonin tailless complex polypeptide 1 (TCP1) is a key subunit of chaperonin containing TCP1 (CCT) that regulates the folding and stability of proteins during cancer progression. Here, the prognostic significance of TCP1 was explored mainly in patients with hepatocellular carcinoma (HCC) and ...
Cancer geneticsCancer genomics
10.1038/S42003-025-07867-6
ISSN:2399-3642
Mutational signatures are markers of drug sensitivity of cancer cells
Levatić Jurica•Salvadores Marina•Fuster-Tormo Francisco•Supek Fran
Nature Communications
2022
•2022/5/25
•Vol.13 No.1 p.1-19
Genomic analyses have revealed mutational footprints associated with DNA maintenance gone awry, or with mutagen exposures. Because cancer therapeutics often target DNA synthesis or repair, we asked if mutational signatures make useful markers of drug sensitivity. We detect mutational signatures in c...
Cancer genomicsData miningDrug screeningPharmacogenomicsTargeted therapies
10.1038/S41467-022-30582-3
ISSN:2041-1723
LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation
Yixiao Zhu•Chengmei Huang•Chao Zhang•Yi Zhou•Enen Zhao等 10 人
Nature Communications
2023
•2023/12/8
•Vol.14 No.1 p.1-19
Gastric cancer (GC) is a heterogeneous disease, threatening millions of lives worldwide, yet the functional roles of long non-coding RNAs (lncRNAs) in different GC subtypes remain poorly characterized. Microsatellite stable (MSS)/epithelial-mesenchymal transition (EMT) GC is the most aggressive subt...
Gastric cancerLong non-coding RNAsmiRNAs
10.1038/S41467-023-43974-W
ISSN:2041-1723
STING-induced regulatory B cells compromise NK function in cancer immunity
Li Sirui•Mirlekar Bhalchandra•Johnson Brandon M.•Brickey W. June•Wrobel John A.等 16 人
Nature
2022
•2022/10/5
•Vol.610 No.7931 p.373-380
An immunosuppressive tumour microenvironment is a major obstacle in the control of pancreatic and other solid cancers1–3. Agonists of the stimulator of interferon genes (STING) protein trigger inflammatory innate immune responses to potentially overcome tumour immunosuppression4. Although these agon...
ImmunotherapyTumour immunology
10.1038/S41586-022-05254-3
ISSN:0028-0836
SMAD4 Limits PARP1 dependent DNA Repair to Render Pancreatic Cancer Cells Sensitive to Radiotherapy
Yang Wang•Tianyu Yu•Zhangting Zhao•Xiaobing Li•Yiran Song等 10 人
Cell Death & Disease
2024
•2024/11/11
•Vol.15 No.11 p.1-11
Dysregulation of SMAD4 (i.e. somatic mutation) is strongly associated with poor pancreatic ductal adenocarcinoma (PDAC) prognosis, yet the molecular mechanisms remain underlying this relationship obscure. Previously, we discovered that SMAD4 mutation renders pancreatic cancer resistant to radiothera...
Cancer therapeutic resistanceRadiotherapy
10.1038/S41419-024-07210-7
ISSN:2041-4889
Androgen-targeted hsa_circ_0085121 encodes a novel protein and improves the development of prostate cancer through facilitating the activity of PI3K/Akt/mTOR pathway and enhancing AR-V7 alternative splicing
Jianfeng Li•Hui Qiu•Qingzhuo Dong•Hongyuan Yu•Chiyuan Piao等 8 人
Cell Death & Disease
2024
•2024/11/20
•Vol.15 No.11 p.1-20
Prostate cancer (PCa) is the most prevalent type of cancer and the second leading cause of mortality in males, with a marked increase in incidence observed across the globe. In the present study, whole-transcriptome analysis was conducted to identify differentially expressed circular RNAs (DE-circRN...
Prostate cancerTranscriptomics
10.1038/S41419-024-07246-9
ISSN:2041-4889
A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas
Rui Jiang•Xiaoxu Yin•Pengshuai Yang•Lingchao Cheng•Juan Hu等 16 人
Nature Machine Intelligence
2024
•2024/7/18
•00 p.1-16
The complex diagnostic criteria for gliomas pose great challenges for making accurate diagnoses with computational pathology methods. There are no in-depth analyses of the accuracy, reliability and auxiliary capability of present approaches from a clinical perspective. Previous studies have overlook...
Cancer screeningMachine learningPathology
10.1038/S42256-024-00868-W
ISSN:2522-5839
Single-cell landscape of undifferentiated pleomorphic sarcoma
Yifei Lu•Deqian Chen•Bingnan Wang•Wenjun Chai•Mingxia Yan等 13 人
Oncogene
2024
•2024/3/8
•00 p.1-16
Undifferentiated pleomorphic sarcoma (UPS) is a highly aggressive malignant soft tissue tumor with a poor prognosis; however, the identity and heterogeneity of tumor populations remain elusive. Here, eight major cell clusters were identified through the RNA sequencing of 79,569 individual cells of U...
Prognostic markersSarcomaSequencing
10.1038/S41388-024-03001-8
ISSN:0950-9232
Swarm learning for decentralized artificial intelligence in cancer histopathology
Saldanha Oliver Lester•Quirke Philip•West Nicholas P.•James Jacqueline A.•Loughrey Maurice B.等 27 人
Nature Medicine
2022
•2022/4/25
•00 p.1-8
Artificial intelligence (AI) can predict the presence of molecular alterations directly from routine histopathology slides. However, training robust AI systems requires large datasets for which data collection faces practical, ethical and legal obstacles. These obstacles could be overcome with swarm...
Biomedical engineeringCancer imagingImage processingMachine learningPredictive markers
10.1038/S41591-022-01768-5
ISSN:1078-8956
ITGB6 modulates resistance to anti-CD276 therapy in head and neck cancer by promoting PF4+ macrophage infiltration
Caihua Zhang•Kang Li•Hongzhang Zhu•Maosheng Cheng•Shuang Chen等 8 人
Nature Communications
2024
•2024/8/16
•Vol.15 No.1 p.1-23
Enoblituzumab, an immunotherapeutic agent targeting CD276, shows both safety and efficacy in activating T cells and oligodendrocyte-like cells against various cancers. Preclinical studies and mouse models suggest that therapies targeting CD276 may outperform PD1/PD-L1 blockade. However, data from mo...
Cancer immunotherapyHead and neck cancerImmunosuppression
10.1038/S41467-024-51096-0
ISSN:2041-1723
Comprehensive characterization of protein–protein interactions perturbed by disease mutations
Feixiong Cheng•Junfei Zhao•Yang Wang•Weiqiang Lu•Zehui Liu等 24 人
Nature Genetics
2021
•2021/2/8
•Vol.53 No.3 p.342-353
Technological and computational advances in genomics and interactomics have made it possible to identify how disease mutations perturb protein–protein interaction (PPI) networks within human cells. Here, we show that disease-associated germline variants are significantly enriched in sequences encodi...
Computational biology and bioinformaticsGeneticsStructural biologySystems biology
10.1038/S41588-020-00774-Y
ISSN:1061-4036
Integrative multi-omics and machine learning framework identifies PRDX4 as a redox-EMT regulator and predictive marker in bone-metastatic breast cancer
Xiao Zhou•Longgui Xie•Jianhui Liu•Geyi Liao•Huawei Yang
Npj Precision Oncology
2026
•2026/1/22
•Vol.10 No.1 p.430
Bone metastasis is a major cause of morbidity and mortality in breast cancer, yet effective prognostic models and targeted therapies remain limited. Here, a machine learning (ML)-driven multi-omics framework integrating epithelial–mesenchymal transition (EMT) and nucleotide metabolism (NM) signature...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41698-025-01240-W
ISSN:2397-768X
NAALADL1 modulates cellular resistance to Tumor Treating Fields in colorectal cancer
Zhaoran Su•Menglan Liu•Mathias Krohn•Jasmin Ostermann•Sandra Schwarz等 10 人
Npj Precision Oncology
2026
•2026/5/26
•Vol.10 No.1 p.1910
Colorectal cancer (CRC), the third most common malignancy worldwide, remains difficult to treat in advanced stages. Tumor Treating Fields (TTFields) are a non-invasive therapy that disrupts mitosis via intermediate frequency alternating electric fields, already clinically approved and widely impleme...
CancerCell biologyComputational biology and bioinformaticsOncology
10.1038/S41698-026-01492-0
ISSN:2397-768X
Leveraging multi-modal foundation models for analysing spatial multi-omic and histopathology data
Tianyu Liu•Tinglin Huang•Tong Ding•Hao Wu•Peter Humphrey等 12 人
Nature Biomedical Engineering
2026
•2026/2/5
•00 p.1-18
Recent advances in pathology foundation models, pre-trained on large-scale histopathology images, have greatly advanced disease-focused applications. At the same time, spatial multi-omic technologies now measure gene and protein expression with high spatial resolution, offering valuable insights int...
Computational modelsMachine learning
10.1038/S41551-025-01602-6
ISSN:2157-846X
Loss of long-range co-expression is a common feature in cancer
Diana García-Cortés•Enrique Hernández-Lemus•Jesús Espinal-Enríquez
Npj Systems Biology And Applications
2026
•2026/4/4
0Cancer cells display common features and enabling characteristics collectively known as the Hallmarks of Cancer, which occur alongside alterations in the regulatory mechanisms controlling gene transcription. Gene co-expression networks (GCNs) provide a framework to identify correlated gene sets that...
BiomarkersCancerComputational biology and bioinformaticsGeneticsOncology
10.1038/S41540-026-00706-2
ISSN:2056-7189
Parkin inhibits proliferation and migration of bladder cancer via ubiquitinating Catalase
Renjie Zhang•Wenyu Jiang•Gang Wang•Yi Zhang•Wei Liu等 15 人
Communications Biology
2024
•2024/2/29
•Vol.7 No.1 p.1-16
PRKN is a key gene involved in mitophagy in Parkinson’s disease. However, recent studies have demonstrated that it also plays a role in the development and metastasis of several types of cancers, both in a mitophagy-dependent and mitophagy-independent manner. Despite this, the potential effects and ...
Bladder cancerTumour-suppressor proteinsUbiquitylation
10.1038/S42003-024-05935-X
ISSN:2399-3642
Synergistic immunotherapy of glioblastoma by dual targeting of IL-6 and CD40
Fan Yang•Zhenqiang He•Hao Duan•Duo Zhang•Juehui Li等 18 人
Nature Communications
2021
•2021/6/8
•Vol.12 No.1 p.1-15
Immunologically-cold tumors including glioblastoma (GBM) are refractory to checkpoint blockade therapy, largely due to extensive infiltration of immunosuppressive macrophages (Mϕs). Consistent with a pro-tumor role of IL-6 in alternative Mϕs polarization, we here show that targeting IL-6 by genetic ...
Cancer immunotherapyCNS cancer
10.1038/S41467-021-23832-3
ISSN:2041-1723
Down-regulated m6A reader FTO destabilizes PHF1 that triggers enhanced stemness capacity and tumor progression in lung adenocarcinoma
Ning Jinfeng•Wang Fengjiao•Bu Jianlong•Zhu Kaibin•Liu Wei
Cell Death Discovery
2022
•2022/8/9
•Vol.8 No.1 p.1-13
Aberrant epigenetic drivers or suppressors contribute to LUAD progression and drug resistance, including KRAS, PTEN, Keap1. Human Plant Homeodomain (PHD) finger protein 1 (PHF1) coordinates with H3K36me3 to increase nucleosomal DNA accessibility. Previous studies revealed that PHF1 is markedly upreg...
Chromatin remodellingNon-small-cell lung cancer
10.1038/S41420-022-01125-Y
ISSN:2058-7716
GPR182 limits antitumor immunity via chemokine scavenging in mouse melanoma models
Torphy Robert J.•Sun Yi•Lin Ronggui•Caffrey-Carr Alayna•Fujiwara Yuki等 12 人
Nature Communications
2022
•2022/1/10
•Vol.13 No.1 p.1-16
For many solid tumors, immune checkpoint blockade therapy has become first line treatment, yet a large proportion of patients with immunologically cold tumors do not benefit due to the paucity of tumor infiltrating lymphocytes. Here we show that the orphan G Protein-Coupled Receptor 182 (GPR182) con...
Cell signallingChemokinesImmunosuppressionTumour immunology
10.1038/S41467-021-27658-X
ISSN:2041-1723
Multi-modal clustering reveals event-free patient subgroup in colorectal cancer survival
Nikita Janakarajan•Guillaume Larghero•María Rodríguez Martínez
Npj Systems Biology And Applications
2025
•2025/8/2
•Vol.11 No.1 p.1-7
Colorectal cancer (CRC) benefits from a multi-omics-based stratification in the context of survival. Our TCGA-based study employs targeted feature selection and unsupervised clustering to stratify patients based on disease-specific survival, identifying an event-free subgroup undetectable with unimo...
CancerComputational biology and bioinformatics
10.1038/S41540-025-00557-3
ISSN:2056-7189
Integration of radiomics, deep learning, transcriptomics, and metabolomics reveals prognostic risk stratification and underlying biological mechanisms in colorectal cancer
Zhiheng Li•Rongzhi Cai•Yangyang Qin•Xiaoqing Liao•Enqi Wang等 9 人
Npj Precision Oncology
2026
•2026/3/6
0Colorectal cancer (CRC) is the third most common malignancy and the second leading cause of cancer-related death worldwide, yet current prognostic stratification is hindered by tumor heterogeneity. Here, we developed a deep learning radiomics model (DLRM), optimized through systematic evaluation of ...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41698-026-01331-2
ISSN:2397-768X
Carcinogenesis promotion in oral squamous cell carcinoma: KDM4A complex-mediated gene transcriptional suppression by LEF1
Yiming Hou•Wenqian Yu•Gaoyi Wu•Zhaoling Wang•Shuai Leng等 8 人
Cell Death & Disease
2023
•2023/8/8
•Vol.14 No.8 p.1-13
Oral squamous cell carcinoma (OSCC) is the most prevalent cancer of the mouth, characterised by rapid progression and poor prognosis. Hence, an urgent need exists for the development of predictive targets for early diagnosis, prognosis determination, and clinical therapy. Dysregulation of lymphoid e...
EpigeneticsOncogenesOral cancer
10.1038/S41419-023-06024-3
ISSN:2041-4889
TRIP13, identified as a hub gene of tumor progression, is the target of microRNA-4693-5p and a potential therapeutic target for colorectal cancer
Chen Yan•Chen Danqi•Qin Ying•Qiu Cheng•Zhou Yaoyao等 9 人
Cell Death Discovery
2022
•2022/1/24
•Vol.8 No.1 p.1-10
Colorectal cancer (CRC) is one of the digestive tract malignancies whose early symptoms are not obvious. This study aimed to identify novel targets for CRC therapy, especially early-stage CRC, by reanalyzing the publicly available GEO and TCGA databases. Thyroid hormone receptor interactor 13 (TRIP1...
OncogenesTumour biomarkers
10.1038/S41420-022-00824-W
ISSN:2058-7716
A visual-language foundation model for computational pathology
Ming Y. Lu•Bowen Chen•Drew F. K. Williamson•Richard J. Chen•Ivy Liang等 13 人
Nature Medicine
2024
•2024/3/19
•Vol.30 No.3 p.863-874
The accelerated adoption of digital pathology and advances in deep learning have enabled the development of robust models for various pathology tasks across a diverse array of diseases and patient cohorts. However, model training is often difficult due to label scarcity in the medical domain, and a ...
Machine learningMedical researchPathology
10.1038/S41591-024-02856-4
ISSN:1078-8956
Macrophage-derived CCL23 upregulates expression of T-cell exhaustion markers in ovarian cancer
Kamat Kalika•Krishnan Venkatesh•Dorigo Oliver
British Journal Of Cancer
2022
•2022/6/24
•00 p.1-8
Macrophages are an important component of the tumour immune microenvironment (TME) and can promote tumour growth and metastasis. Macrophage-secreted chemokine-ligand-23 (CCL23) induces ovarian cancer cell migration via chemokine-receptor 1 (CCR1). However, the effect of CCL23 on other immune cells i...
ChemokinesOvarian cancer
10.1038/S41416-022-01887-3
ISSN:0007-0920
Ligand-receptor interactions combined with histopathology for improved prognostic modeling in HPV-negative head and neck squamous cell carcinoma
Bohai Feng•Di Zhao•Zheng Zhang•Ru Jia•Patrick J. Schuler等 6 人
Npj Precision Oncology
2025
•2025/2/28
•Vol.9 No.1 p.1-17
Head and neck squamous cell carcinoma (HNSC) is a prevalent malignancy, with HPV-negative tumors exhibiting aggressive behavior and poor prognosis. Understanding the intricate interactions within the tumor microenvironment (TME) is crucial for improving prognostic models and identifying therapeutic ...
Computational biology and bioinformaticsHead and neck cancer
10.1038/S41698-025-00844-6
ISSN:2397-768X
Machine learning-based MRI radiomics predict IL18 expression and overall survival of low-grade glioma patients
Zhe Zhang•Yao Xiao•Jun Liu•Feng Xiao•Jie Zeng等 8 人
Npj Precision Oncology
2025
•2025/6/19
•Vol.9 No.1 p.1-13
Interleukin-18 has broad immune regulatory functions. Genomic data and enhanced Magnetic Resonance Imaging data related to LGG patients were downloaded from The Cancer Genome Atlas and Cancer Imaging Archive, and the constructed model was externally validated using hospital MRI enhanced images and c...
CNS cancerTumour biomarkers
10.1038/S41698-025-00966-X
ISSN:2397-768X
Mapping convergent regulators of melanoma drug resistance by PerturbFate
Zihan Xu•Ziyu Lu•Aileen Ugurbil•Abdulraouf Abdulraouf•Andrew Liao等 8 人
Nature
2026
•2026/4/15
•00 p.1-11
High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes. However, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here we present PerturbFate, a high-throughput, ...
Gene expression profilingMelanomaTranscriptomics
10.1038/S41586-026-10367-0
ISSN:0028-0836
Single-cell transcriptome profiling of the stepwise progression of head and neck cancer
Choi Ji-Hye•Lee Bok-Soon•Jang Jeon Yeob•Lee Yun Sang•Kim Hyo Jeong等 9 人
Nature Communications
2023
•2023/2/24
•Vol.14 No.1 p.1-13
Head and neck squamous cell carcinoma (HNSCC) undergoes stepwise progression from normal tissues to precancerous leukoplakia, primary HNSCC, and metastasized tumors. To delineate the heterogeneity of tumor cells and their interactions during the progression of HNSCC, we employ single-cell RNA-seq pr...
Cancer genomicsHead and neck cancerMolecular medicineRNA sequencingTumour heterogeneity
10.1038/S41467-023-36691-X
ISSN:2041-1723
TXN inhibitor impedes radioresistance of colorectal cancer cells with decreased ALDH1L2 expression via TXN/NF-κB signaling pathway
Yu Lu•Guo Qiqing•Luo Ziqian•Wang Yongjia•Weng Jiawen等 13 人
British Journal Of Cancer
2022
•2022/5/21
•00 p.1-12
Colorectal cancer (CRC) is prevalent worldwide and is often challenged by treatment failure and recurrence due to resistance to radiotherapy. Here, we aimed to identify the elusive underlying molecular mechanisms of radioresistance in CRC. Weighted gene co-expression network analysis was used to ide...
Colorectal cancerRadiotherapy
10.1038/S41416-022-01835-1
ISSN:0007-0920
USP5 regulates ferroptosis in colorectal cancer by targeting the YBX3/SLC7A11 axis through lysosomal degradation
Haowen Qiu•Yi Liu•Haimeng Zhou•Lingjuan Hu•Wei Qi等 17 人
Cell Death & Disease
2025
•2025/11/10
•Vol.16 No.1 p.8220
Colorectal cancer (CRC) is the third most common cancer worldwide and a significant public health threat. Ferroptosis, an iron-dependent form of regulated cell death, has emerged as a promising therapeutic target in CRC treatment. Despite its significant clinical potential, the precise regulatory me...
Cell deathOncogenes
10.1038/S41419-025-08146-2
ISSN:2041-4889
EZH2-induced lysine K362 methylation enhances TMPRSS2-ERG oncogenic activity in prostate cancer
Marita Zoma•Laura Curti•Dheeraj Shinde•Domenico Albino•Abhishek Mitra等 18 人
Nature Communications
2021
•2021/7/6
•Vol.12 No.1 p.1-19
The TMPRSS2-ERG gene fusion is the most frequent alteration observed in human prostate cancer. However, its role in disease progression is still unclear. In this study, we uncover an important mechanism promoting ERG oncogenic activity. We show that ERG is methylated by Enhancer of zest homolog 2 (E...
EpigeneticsOncologyProstate cancer
10.1038/S41467-021-24380-6
ISSN:2041-1723
Automated cell annotation and classification on histopathology for spatial biomarker discovery
Zhe Li•Seyed Hossein Mirjahanmardi•Rasoul Sali•Feyisope Eweje•Matthew Gopaulchan等 10 人
Nature Communications
2025
•2025/7/7
•Vol.16 No.1 p.1-15
Histopathology with hematoxylin and eosin (H&E) staining is routinely employed for clinical diagnoses. Single-cell analysis of histopathology provides a powerful tool for understanding the intricate cellular interactions underlying disease progression and therapeutic response. However, existing ...
Cancer microenvironmentComputational modelsGastrointestinal cancerPredictive markersPrognostic markers
10.1038/S41467-025-61349-1
ISSN:2041-1723
Predicting and affecting response to cancer therapy based on pathway-level biomarkers
Rotem Ben-Hamo•Adi Jacob Berger•Nancy Gavert•Mendy Miller•Guy Pines等 13 人
Nature Communications
2020
•2020/7/3
•Vol.11 No.1 p.1-16
Identifying robust, patient-specific, and predictive biomarkers presents a major obstacle in precision oncology. To optimize patient-specific therapeutic strategies, here we couple pathway knowledge with large-scale drug sensitivity, RNAi, and CRISPR-Cas9 screening data from 460 cell lines. Pathway ...
Cancer therapeutic resistanceCellular signalling networks
10.1038/S41467-020-17090-Y
ISSN:2041-1723
Deep learning-enabled breast cancer hormonal receptor status determination from base-level H&E stains
Nikhil Naik•Ali Madani•Andre Esteva•Nitish Shirish Keskar•Michael F. Press等 8 人
Nature Communications
2020
•2020/11/16
•Vol.11 No.1 p.1-8
For newly diagnosed breast cancer, estrogen receptor status (ERS) is a key molecular marker used for prognosis and treatment decisions. During clinical management, ERS is determined by pathologists from immunohistochemistry (IHC) staining of biopsied tissue for the targeted receptor, which highlight...
Breast cancerMachine learning
10.1038/S41467-020-19334-3
ISSN:2041-1723
N 6 -methyladenosine-dependent pri-miR-17-92 maturation suppresses PTEN/TMEM127 and promotes sensitivity to everolimus in gastric cancer
Yiting Sun•Song Li•Wenbin Yu•Zeyi Zhao•Jing Gao等 10 人
Cell Death & Disease
2020
•2020/10/9
•Vol.11 No.10 p.1-16
N6-methyladenosine (m6A) is the most common epigenetic RNA modification with essential roles in cancer progression. However, roles of m6A and its regulator METTL3 on non-coding RNA in gastric cancer are unknown. In this study, we found elevated levels of m6A and METTL3 in gastric cancer. Increased M...
Gastric cancerGenetics research
10.1038/S41419-020-03049-W
ISSN:2041-4889
A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer
Wu Yin•Biswas Dhruva•Usaite Ieva•Angelova Mihaela•Boeing Stefan等 20 人
Nature Cancer
2022
•2022/5/30
•00 p.1-14
Murine tissues harbor signature γδ T cell compartments with profound yet differential impacts on carcinogenesis. Conversely, human tissue-resident γδ cells are less well defined. In the present study, we show that human lung tissues harbor a resident Vδ1 γδ T cell population. Moreover, we demonstrat...
CancerGammadelta T cellsNon-small-cell lung cancerTumour immunology
10.1038/S43018-022-00376-Z
ISSN:2662-1347
Exploiting common patterns in diverse cancer types via multi-task learning
Bo-Run Wu•Sofia Ormazabal Arriagada•Te-Cheng Hsu•Tsung-Wei Lin•Che Lin
Npj Precision Oncology
2024
•2024/10/29
•Vol.8 No.1 p.1-13
Cancer prognosis requires precision to identify high-risk patients and improve survival outcomes. Conventional methods struggle with the complexity of genetic biomarkers and diverse medical data. Our study uses deep learning to distil high-dimensional medical data into low-dimensional feature vector...
Cancer screeningPrognosisPrognostic markers
10.1038/S41698-024-00700-Z
ISSN:2397-768X
Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas
Grayson A. Herrgott•James M. Snyder•Ruicong She•Tathiane M. Malta•Thais S. Sabedot等 35 人
Nature Communications
2023
•2023/9/13
•Vol.14 No.1 p.1-19
Recurrence of meningiomas is unpredictable by current invasive methods based on surgically removed specimens. Identification of patients likely to recur using noninvasive approaches could inform treatment strategy, whether intervention or monitoring. In this study, we analyze the DNA methylation lev...
CNS cancerDiagnostic markersPredictive markersPrognostic markers
10.1038/S41467-023-41434-Z
ISSN:2041-1723
Androgen receptor variant shows heterogeneous expression in prostate cancer according to differentiation stage
Ada Gjyrezi•Giuseppe Galletti•Jiaren Zhang•Daniel Worroll•Michael Sigouros等 16 人
Communications Biology
2021
•2021/6/24
•Vol.4 No.1 p.1-9
Quantitation of androgen receptor variant (AR-V) expression in circulating tumor cells (CTCs) from patients with metastatic castration-resistant prostate cancer (mCRPC) has great potential for treatment customization. However, the absence of a uniform CTC isolation platform and consensus on an analy...
Prostate cancer
10.1038/S42003-021-02321-9
ISSN:2399-3642
An artificial intelligence-based model for prediction of clonal hematopoiesis variants in cell-free DNA samples
Gustavo Arango-Argoty•Marzieh Haghighi•Gerald J. Sun•Elizabeth Y. Choe•Aleksandra Markovets等 8 人
Npj Precision Oncology
2025
•2025/5/20
•Vol.9 No.1 p.1-8
Circulating tumor DNA is a critical biomarker in cancer diagnostics, but its accurate interpretation requires careful consideration of clonal hematopoiesis (CH), which can contribute to variants in cell-free DNA and potentially obscure true tumor-derived signals. Accurate detection of somatic varian...
BiomarkersCancerComputational biology and bioinformatics
10.1038/S41698-025-00921-W
ISSN:2397-768X
LncRNA RP11-19E11 is an E2F1 target required for proliferation and survival of basal breast cancer
A. Giro-Perafita•L. Luo•A. Khodadadi-Jamayran•M. Thompson•B. Akgol Oksuz等 9 人
Npj Breast Cancer
2020
•2020/1/6
•Vol.6 No.1 p.1-14
Long non-coding RNAs (lncRNAs) play key roles in the regulation of breast cancer initiation and progression. LncRNAs are differentially expressed in breast cancer subtypes. Basal-like breast cancers are generally poorly differentiated tumors, are enriched in embryonic stem cell signatures, lack expr...
Breast cancerNon-coding RNAsPredictive markersTumour heterogeneity
10.1038/S41523-019-0144-4
ISSN:2374-4677
Solid tumour-induced systemic immunosuppression involves dichotomous myeloid–B cell interactions
Xiaoxin Hao•Yichao Shen•Jun Liu•Angela Alexander•Ling Wu等 19 人
Nature Cell Biology
2024
•2024/9/12
•00 p.1-13
Solid tumours induce systemic immunosuppression that involves myeloid and T cells. B cell-related mechanisms remain relatively understudied. Here we discover two distinct patterns of tumour-induced B cell abnormality (TiBA; TiBA-1 and TiBA-2), both associated with abnormal myelopoiesis in the bone m...
B cellsBreast cancerImmune evasion
10.1038/S41556-024-01508-6
ISSN:1465-7392
Histopathology-based protein multiplex generation using deep learning
Sonali Andani•Boqi Chen•Joanna Ficek-Pascual•Simon Heinke•Ruben Casanova等 10 人
Nature Machine Intelligence
2025
•2025/8/4
•00 p.1-16
Multiplexed protein imaging offers valuable insights into interactions between tumours and their surrounding tumour microenvironment, but its widespread use is limited by cost, time and tissue availability. Here we present HistoPlexer, a deep learning framework that generates spatially resolved prot...
Computational modelsMachine learningMelanoma
10.1038/S42256-025-01074-Y
ISSN:2522-5839
Epigenetic determinants of an immune-evasive phenotype in HER2-low triple-negative breast cancer
Andrés F. Bedoya-López•Sookyung Ahn•Miquel Ensenyat-Mendez•Javier I. J. Orozco•Sandra Iñiguez-Muñoz等 14 人
Npj Precision Oncology
2025
•2025/8/16
•Vol.9 No.1 p.1-12
Identifying molecular drivers in triple-negative breast cancer (TNBC) is crucial. While HER2-low expression predicts response to novel antibody-drug conjugates, its biological influence on TNBC biology is unknown. We performed a comprehensive multi-omics analysis, integrating genomic, epigenomic, tr...
CancerMolecular biologyOncology
10.1038/S41698-025-01023-3
ISSN:2397-768X
Complex rearrangements fuel ER+ and HER2+ breast tumours
Kathleen E. Houlahan•Lise Mangiante•Cristina Sotomayor-Vivas•Alvina Adimoelja•Seongyeol Park等 10 人
Nature
2025
•2025/1/8
•00 p.1-9
Breast cancer is a highly heterogeneous disease whose prognosis and treatment as defined by the expression of three receptors—oestrogen receptor (ER), progesterone receptor and human epidermal growth factor receptor 2 (HER2; encoded by ERBB2)—is insufficient to capture the full spectrum of clinical ...
Breast cancerCancer genomicsTumour heterogeneity
10.1038/S41586-024-08377-X
ISSN:0028-0836
A multimodal knowledge-enhanced whole-slide pathology foundation model
Yingxue Xu•Yihui Wang•Fengtao Zhou•Jiabo Ma•Cheng Jin等 19 人
Nature Communications
2025
•2025/12/12
0Computational pathology has advanced through foundation models, yet faces challenges in multimodal integration and capturing whole-slide context. Current approaches typically utilize either vision-only or image-caption data, overlooking distinct insights from pathology reports and gene expression pr...
Biomedical engineeringComputational modelsComputational scienceMachine learningMedical research
10.1038/S41467-025-66220-X
ISSN:2041-1723
A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance
Juan M. Arriaga•Sukanya Panja•Mohammed Alshalalfa•Junfei Zhao•Min Zou等 26 人
Nature Cancer
2020
•2020/10/19
•Vol.1 No.11 p.1082-1096
Understanding the intricacies of lethal prostate cancer poses specific challenges due to difficulties in accurate modeling of metastasis in vivo. Here we show that NPKEYFP mice (for Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+) develop prostate cancer with a high penetrance of...
CancerCancer modelsMetastasisProstate cancer
10.1038/S43018-020-00125-0
ISSN:2662-1347
CD160 dictates anti-PD-1 immunotherapy resistance by regulating CD8+ T cell exhaustion in colorectal cancer
Tongsen Zheng•Chujie Ding•Shihui Lai•Yang Gao•Cheng Lyu等 22 人
Nature Cell Biology
2025
•2025/9/9
•Vol.27 No.9 p.1555-1571
The colon exhibits higher propensity for tumour development than ileum. However, the role of immune microenvironment differences in driving this disparity remains unclear. Here, by comparing paired ileum and colon samples from patients with colorectal cancer (CRC) and healthy donors, we identified i...
Cancer immunotherapyCancer therapeutic resistanceColorectal cancerT cells
10.1038/S41556-025-01753-3
ISSN:1465-7392
The clinical implication and translational research of OSCC differentiation
Qianhui Shang•Yuchen Jiang•Zixin Wan•Jiakuan Peng•Ziang Xu等 13 人
British Journal Of Cancer
2024
•2024/1/5
•00 p.1-11
The clinical value and molecular characteristics of tumor differentiation in oral squamous cell carcinoma (OSCC) remain unclear. There is a lack of a related molecular classification prediction system based on pathological images for precision medicine. Integration of epidemiology, genomics, experim...
Cancer epidemiologyFunctional clusteringMachine learning
10.1038/S41416-023-02566-7
ISSN:0007-0920
Multi-omics analysis identifies an M-MDSC-like immunosuppressive phenotype in lineage-switched AML with KMT2A rearrangement
Takashi Mikami•Itaru Kato•Akira Nishimura•Minenori Eguchi-Ishimae•Tatsuya Kamitori等 25 人
Nature Communications
2025
•2025/8/26
•Vol.16 No.1 p.1-15
Lineage switching (LS) is the conversion of cancer cell lineage during the course of a disease. LS in leukemia cell lineage facilitates cancer cells escaping targeting strategy like CD19 targeted immunotherapy. However, the genetic and biological mechanisms underlying immune evasion by LS leukemia c...
CancerImmunosuppressionTumour heterogeneity
10.1038/S41467-025-63271-Y
ISSN:2041-1723
Androgen receptor and MYC equilibration centralizes on developmental super-enhancer
Guo Haiyang•Wu Yiming•Nouri Mannan•Spisak Sandor•Russo Joshua W.等 16 人
Nature Communications
2021
•2021/12/15
•Vol.12 No.1 p.1-18
Androgen receptor (AR) in prostate cancer (PCa) can drive transcriptional repression of multiple genes including MYC, and supraphysiological androgen is effective in some patients. Here, we show that this repression is independent of AR chromatin binding and driven by coactivator redistribution, and...
Gene regulationProstateTranscriptional regulatory elements
10.1038/S41467-021-27077-Y
ISSN:2041-1723
Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse
Taavitsainen S.•Engedal N.•Cao S.•Handle F.•Erickson A.等 33 人
Nature Communications
2021
•2021/9/6
•Vol.12 No.1 p.1-16
Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalu...
Data integrationProstate cancer
10.1038/S41467-021-25624-1
ISSN:2041-1723
THY1+ cancer stem cells drive metastasis through a pseudohypoxic state shaped by neutrophil-derived mitochondria
Wen-Hua Wan•Pei-Lin Li•Wen-Jie Cao•Zheng-Xi Li•Yu-Qi Xin等 13 人
Nature Cell Biology
2026
•2026/2/12
•Vol.28 No.3 p.596-607
Whether a distinct subset of cancer stem cells (CSCs) is exclusively responsible for metastasis and how this process occurs remain unresolved. Through multi-omics, pan-cancer analysis and multiple tumour-bearing models, we identify THY1⁺ CSCs as the key drivers of metastasis and uncover a previously...
Cancer microenvironmentCancer stem cellsMetastasisTumour immunology
10.1038/S41556-026-01876-1
ISSN:1465-7392
Somatic mutation distribution across tumour cohorts provides a signal for positive selection in cancer
Boström Martin•Larsson Erik
Nature Communications
2022
•2022/11/17
•Vol.13 No.1 p.1-9
Cancer gene discovery is reliant on distinguishing driver mutations from a multitude of passenger mutations in tumour genomes. While driver genes may be revealed based on excess mutation recurrence or clustering, there is a need for orthogonal principles. Here, we take advantage of the fact that non...
CancerCancer genomicsComputational biology and bioinformaticsGenome evolutionMutation
10.1038/S41467-022-34746-Z
ISSN:2041-1723
Risk subtyping and prognostic assessment of prostate cancer based on consensus genes
Meng Jialin•Guan Yu•Wang Bijun•Chen Lei•Chen Junyi等 7 人
Communications Biology
2022
•2022/3/15
•Vol.5 No.1 p.1-13
Prostate cancer (PCa) is the most frequent malignancy in male urogenital system around worldwide. We performed molecular subtyping and prognostic assessment based on consensus genes in patients with PCa. Five cohorts containing 1,046 PCa patients with RNA expression profiles and recorded clinical fo...
ProstateUrological cancer
10.1038/S42003-022-03164-8
ISSN:2399-3642
Impact of HMGA1 on tumorigenesis, prognosis and immune microenvironment in HNSCC: a multi-omics study
Ziang Xu•Moxu Wang•Jilin Cai•Tianxiao Wang•Nan Ni等 12 人
Npj Precision Oncology
2025
•2025/8/2
•Vol.9 No.1 p.1-15
HMGA1 plays an important role in a variety of biological processes. However, it is still unclear what role HMGA1 plays in HNSCC. By integrating multi-omics data from public and private cohorts, we conducted a comprehensive analysis. The results showed that HMGA1 expression was significantly higher i...
Cancer epidemiologyCancer preventionHead and neck cancerOncogenesTumour biomarkers
10.1038/S41698-025-01068-4
ISSN:2397-768X
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution
Zhu Tianyu•Liu Jacklyn•Beck Stephan•Pan Sun•Capper David等 9 人
Nature Methods
2022
•2022/3/11
•Vol.19 No.3 p.296-306
Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet c...
Computational biology and bioinformaticsEpigenomics
10.1038/S41592-022-01412-7
ISSN:1548-7091
Mitotic tethering enables inheritance of shattered micronuclear chromosomes
Prasad Trivedi•Christopher D. Steele•Franco K. C. Au•Ludmil B. Alexandrov•Don W. Cleveland
Nature
2023
•2023/6/14
•00 p.1-8
Chromothripsis, the shattering and imperfect reassembly of one (or a few) chromosome(s)1, is an ubiquitous2 mutational process generating localized and complex chromosomal rearrangements that drive genome evolution in cancer. Chromothripsis can be initiated by mis-segregation errors in mitosis3,4 or...
Cancer genomicsCell divisionChromosomes
10.1038/S41586-023-06216-Z
ISSN:0028-0836
Genomic characterization of the HER2-enriched intrinsic molecular subtype in primary ER-positive HER2-negative breast cancer
Lennart Hohmann•Kristin Sigurjonsdottir•Ana Bosch Campos•Deborah F. Nacer•Srinivas Veerla等 17 人
Nature Communications
2025
•2025/3/5
•Vol.16 No.1 p.1-17
ER-positive/HER2-negative (ERpHER2n) breast cancer classified as PAM50 HER2-enriched (ERpHER2n-HER2E) represents a small high-risk patient subgroup. In this study, we investigate genomic, transcriptomic, and clinical features of ERpHER2n-HER2E breast tumors using two primary ERpHER2n cohorts compris...
Breast cancerCancer geneticsPrognostic markers
10.1038/S41467-025-57419-Z
ISSN:2041-1723
Customized transformer for lymph node metastasis prediction from lung adenocarcinoma histology in a multicentric study
Huibo Zhang•Tao Wang•Junwei Feng•Jie Wu•Junju He等 8 人
Npj Precision Oncology
2025
•2025/12/2
0Reliable lymph node metastasis (LNM) assessment underpins staging and treatment decisions in lung adenocarcinoma (LUAD), yet approximately 10% of patients remain pNx due to sampling limitations. Existing LNM prediction methods mainly rely on imaging or molecular data, while the potential of histopat...
CancerComputational biology and bioinformaticsOncology
10.1038/S41698-025-01199-8
ISSN:2397-768X
The NUCKS1-SKP2-p21/p27 axis controls S phase entry
Hume Samuel•Grou Claudia P.•Lascaux Pauline•D’Angiolella Vincenzo•Legrand Arnaud J.等 7 人
Nature Communications
2021
•2021/11/29
•Vol.12 No.1 p.1-14
Efficient entry into S phase of the cell cycle is necessary for embryonic development and tissue homoeostasis. However, unscheduled S phase entry triggers DNA damage and promotes oncogenesis, underlining the requirement for strict control. Here, we identify the NUCKS1-SKP2-p21/p27 axis as a checkpoi...
BiochemistryCell-cycle exitCheckpointsGene expression analysisUbiquitin ligases
10.1038/S41467-021-27124-8
ISSN:2041-1723
Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants
Xiang Shu•Jirong Long•Qiuyin Cai•Sun-Seog Kweon•Ji-Yeob Choi等 62 人
Nature Communications
2020
•2020/3/5
•Vol.11 No.1 p.1-9
Known risk variants explain only a small proportion of breast cancer heritability, particularly in Asian women. To search for additional genetic susceptibility loci for breast cancer, here we perform a meta-analysis of data from genome-wide association studies (GWAS) conducted in Asians (24,206 case...
Breast cancerCancer genomics
10.1038/S41467-020-15046-W
ISSN:2041-1723
Targeting the C/EBPβ-PRAME-EZH2 complex modulates the Netrin-4/AKT axis to inhibit renal cancer tumorigenesis and metastasis
Li-Zhen Zhang•Zheng-Kun Zhang•Liang-Min Fu•Enyi Zhu•Chan Huang等 13 人
Cell Death & Differentiation
2026
•2026/2/12
•00 p.1-18
Cancer-testis antigens are considered clinically attractive targets for cancer treatment, but their functions and mechanisms are not well elucidated. Here, based on comprehensive bioinformatics analyses, we identify PRAME, a nuclear cancer-testis antigen, as a potential regulator of metastasis in cl...
Drug developmentEpigeneticsOncogenesPrognostic markers
10.1038/S41418-026-01683-Z
ISSN:1350-9047
A deep learning-based multiscale integration of spatial omics with tumor morphology
Benoît Schmauch•Loïc Herpin•Antoine Olivier•Thomas Duboudin•Rémy Dubois等 17 人
Nature Communications
2025
•2025/11/27
0Spatial Transcriptomics (spTx) offers unprecedented insights into the spatial arrangement of the tumor microenvironment, tumor initiation/progression and identification of new therapeutic target candidates. However, spTx remains unlikely to be routinely used in the near future. Hematoxylin and eosin...
Cancer genomicsMachine learning
10.1038/S41467-025-66691-Y
ISSN:2041-1723
Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation
Han Jin•Cheng Zhang•Martin Zwahlen•Kalle von Feilitzen•Max Karlsson等 14 人
Nature Communications
2023
•2023/9/5
•Vol.14 No.1 p.1-15
Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-à-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding g...
Cancer modelsProtein databasesRNA sequencing
10.1038/S41467-023-41132-W
ISSN:2041-1723
Metabolic enzyme LDHA activates Rac1 GTPase as a noncanonical mechanism to promote cancer
Liu Juan•Zhang Cen•Zhang Tianliang•Chang Chun-Yuan•Wang Jianming等 10 人
Nature Metabolism
2022
•2022/12/19
•Vol.4 No.12 p.1830-1846
The glycolytic enzyme lactate dehydrogenase A (LDHA) is frequently overexpressed in cancer, which promotes glycolysis and cancer. The oncogenic effect of LDHA has been attributed to its glycolytic enzyme activity. Here we report an unexpected noncanonical oncogenic mechanism of LDHA; LDHA activates ...
Cancer metabolismMetabolismMolecular biologyMolecular medicine
10.1038/S42255-022-00708-4
ISSN:2522-5812
FBXL2 counteracts Grp94 to destabilize EGFR and inhibit EGFR-driven NSCLC growth
Niu Mengmeng•Xu Jing•Liu Yang•Li Yuhuang•He Tao等 30 人
Nature Communications
2021
•2021/10/11
•Vol.12 No.1 p.1-15
Abnormal activation of epidermal growth factor receptor (EGFR) drives non-small cell lung cancer (NSCLC) development. EGFR mutations-mediated resistance to tyrosine-kinase inhibitors (TKIs) is a major hurdle for NSCLC treatment. Here, we show that F-box protein FBXL2 targets EGFR and EGFR TKI-resist...
Growth factor signallingNon-small-cell lung cancerUbiquitylation
10.1038/S41467-021-26222-X
ISSN:2041-1723
Histopathologic image–based deep learning classifier for predicting platinum-based treatment responses in high-grade serous ovarian cancer
Byungsoo Ahn•Damin Moon•Hyun-Soo Kim•Chung Lee•Nam Hoon Cho等 26 人
Nature Communications
2024
•2024/5/18
•Vol.15 No.1 p.1-13
Platinum-based chemotherapy is the cornerstone treatment for female high-grade serous ovarian carcinoma (HGSOC), but choosing an appropriate treatment for patients hinges on their responsiveness to it. Currently, no available biomarkers can promptly predict responses to platinum-based treatment. The...
Cancer imagingOvarian cancerPredictive markers
10.1038/S41467-024-48667-6
ISSN:2041-1723
LMNB2-mediated high PD-L1 transcription triggers the immune escape of hepatocellular carcinoma
Yuxuan Li•Jie Zhu•Fengguang Zhai•Yidong Ge•Ziqing Zhan等 18 人
Cell Death Discovery
2025
•2025/6/7
•Vol.11 No.1 p.1-16
While immune checkpoint inhibitors targeting programmed cell death-ligand 1 (PD-L1) demonstrate clinical efficacy in hepatocellular carcinoma (HCC), tumor cells frequently evade immune surveillance through PD-L1 overexpression, a phenomenon whose regulatory mechanisms remain poorly understood. Throu...
Immune evasionPost-translational modifications
10.1038/S41420-025-02540-7
ISSN:2058-7716
Genomic and transcriptomic dynamics in the stepwise progression of lung adenocarcinoma
Fangqiu Fu•Jun Shang•Yueren Yan•He Jiang•Han Han等 24 人
Cell Research
2025
•2025/12/4
•00 p.1-19
Lung adenocarcinoma (LUAD) progresses from pre-invasive to invasive stages, as well as from ground-glass opacities (GGOs) to solid nodules. However, the dynamic genomic and transcriptomic changes underlying LUAD progression are incompletely understood. Here, we performed whole-genome and transcripto...
Cancer genomicsNon-small-cell lung cancer
10.1038/S41422-025-01200-W
ISSN:1748-7838
Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer
Meng Liu•Maria O. Hernandez•Darko Castven•Hsin-Pei Lee•Wenqi Wu等 10 人
Nature Communications
2026
•2026/2/21
•Vol.17 No.1 p.19860
Spatial cellular context is crucial in shaping intratumor heterogeneity. However, understanding how each tumor establishes its unique spatial landscape and what factors drive the landscape for tumor fitness remains significantly challenging. Here, we analyze over 2 million cells from 50 tumor biospe...
Liver cancerTumour heterogeneity
10.1038/S41467-026-69797-Z
ISSN:2041-1723
Microbial metabolite drives ageing-related clonal haematopoiesis via ALPK1
Puneet Agarwal•Avery Sampson•Kathleen Hueneman•Kwangmin Choi•Niels Asger Jakobsen等 16 人
Nature
2025
•2025/4/23
•00 p.1-11
Clonal haematopoiesis of indeterminate potential (CHIP) involves the gradual expansion of mutant pre-leukaemic haematopoietic cells, which increases with age and confers a risk for multiple diseases, including leukaemia and immune-related conditions1. Although the absolute risk of leukaemic transfor...
Cell signallingHaematological diseases
10.1038/S41586-025-08938-8
ISSN:0028-0836
ALAN is a computational approach that interprets genomic findings in the context of tumor ecosystems
Bergom Hannah E.•Shabaneh Ashraf•Day Abderrahman•Ali Atef•Boytim Ella等 18 人
Communications Biology
2023
•2023/4/14
•Vol.6 No.1 p.1-12
Gene behavior is governed by activity of other genes in an ecosystem as well as context-specific cues including cell type, microenvironment, and prior exposure to therapy. Here, we developed the Algorithm for Linking Activity Networks (ALAN) to compare gene behavior purely based on patient -omic dat...
Cancer genomicsSoftware
10.1038/S42003-023-04795-1
ISSN:2399-3642
Kinic index: an artificial intelligence-driven predictive model and multitarget drug discovery framework for hepatocellular carcinoma patients
Jinglin Zhou•Yuhan Jiang•Miao Yu•Mengyuan Wang•Yixiao Li等 8 人
Npj Precision Oncology
2026
•2026/2/14
•Vol.10 No.1 p.1320
Hepatocellular carcinoma (HCC) remains a major global health challenge due to its molecular heterogeneity, late diagnosis, and limited therapeutic options. Recent studies have identified isonicotinylation (Kinic), a novel lysine acylation, as a regulatory modification influencing carcinogenic protei...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41698-026-01324-1
ISSN:2397-768X
Role of the miR-301a/Fra-2/GLIPR1 axis in lung cancer cisplatin resistance
Rampioni Vinciguerra Gian Luca•Capece Marina•Distefano Rosario•Nigita Giovanni•Vecchione Andrea等 7 人
Signal Transduction And Targeted Therapy
2023
•2023/1/27
•Vol.8 No.1 p.1-4
Lung cancer
10.1038/S41392-022-01228-Z
ISSN:2059-3635
Development of a breast cancer invasion score to predict tumor aggressiveness and prognosis via PI3K/AKT/mTOR pathway analysis
Xiujuan Li•Ya Zhang•Jianping Gong•Wenjia Liu•Hanchen Zhao等 9 人
Cell Death Discovery
2025
•2025/4/9
•Vol.11 No.1 p.1-16
Invasiveness is a key indicator of tumor malignancy and is often linked to poor prognosis in breast cancer (BC). To explore the diverse characteristics of invasive cells, single-cell RNA sequencing (scRNA-seq) data from three ductal carcinoma stages were analyzed, classifying samples into invasion a...
Breast cancerPrognostic markers
10.1038/S41420-025-02422-Y
ISSN:2058-7716
Annotation-efficient deep learning for breast cancer whole-slide image classification using tumour infiltrating lymphocytes and slide-level labels
Rashindrie Perera•Peter Savas•Damith Senanayake•Roberto Salgado•Heikki Joensuu等 9 人
Communications Engineering
2024
•2024/7/25
•Vol.3 No.1 p.1-11
Tumour-Infiltrating Lymphocytes (TILs) are pivotal in the immune response against cancer cells. Existing deep learning methods for TIL analysis in whole-slide images (WSIs) demand extensive patch-level annotations, often requiring labour-intensive specialist input. To address this, we propose a fram...
CancerImage processing
10.1038/S44172-024-00246-9
ISSN:2731-3395
Implementing trust in non-small cell lung cancer diagnosis with a conformalized uncertainty-aware AI framework
Xiaoge Zhang•Tao Wang•Chao Yan•Fedaa Najdawi•Kai Zhou等 9 人
Nature Biomedical Engineering
2026
•2026/6/23
•00 p.1-18
Ensuring trustworthiness is fundamental in cancer diagnostics, where a misdiagnosis can have dire consequences. Current pathology AI models lack systematic solutions to address trustworthiness concerns arising from model limitations and data discrepancies between model deployment and development env...
Machine learningNon-small-cell lung cancerPathology
10.1038/S41551-026-01694-8
ISSN:2157-846X
Single-cell and spatial RNA sequencing identify divergent microenvironments and progression signatures in early- versus late-onset prostate cancer
Yifei Cheng•Bingxin Liu•Junyi Xin•Xiaobin Wu•Wenchao Li等 12 人
Nature Aging
2025
•2025/4/10
•00 p.1-20
The clinical and pathological outcomes differ between early-onset (diagnosed in men ≤55 years of age) and late-onset prostate cancer, potentially attributed to the changes in hormone levels and immune activities associated with aging. Exploring the heterogeneity therein holds potential for developin...
AgeingBioinformaticsCancerEpithelial–mesenchymal transitionTranscriptomics
10.1038/S43587-025-00842-0
ISSN:2662-8465
An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression
Shen Ting•Ni Ting•Chen Jiaxuan•Chen Haitao•Ma Xiaopin等 23 人
Nature Communications
2022
•2022/3/9
•Vol.13 No.1 p.1-15
Most cancer causal variants are found in gene regulatory elements, e.g., enhancers. However, enhancer variants predisposing to hepatocellular carcinoma (HCC) remain unreported. Here we conduct a genome-wide survey of HCC-susceptible enhancer variants through a three-stage association study in 11,958...
EpigeneticsGenome-wide association studiesHepatocellular carcinoma
10.1038/S41467-022-28861-0
ISSN:2041-1723
Multi-omics characterization of autophagy-related molecular features for therapeutic targeting of autophagy
Luo Mei•Ye Lin•Chang Ruimin•Ye Youqiong•Zhang Zhao等 17 人
Nature Communications
2022
•2022/10/26
•Vol.13 No.1 p.1-17
Autophagy is a major contributor to anti-cancer therapy resistance. Many efforts have been made to understand and overcome autophagy-mediated therapy resistance, but these efforts have been unsuccessful in clinical applications. In this study, we establish an autophagy signature to estimate tumor au...
AutophagyCancer genomicsCancer therapeutic resistanceData mining
10.1038/S41467-022-33946-X
ISSN:2041-1723
Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers
Marina Salvadores•Fran Supek
Nature Cancer
2024
•2024/1/10
•00 p.1-17
Mutations in human cells exhibit increased burden in heterochromatic, late DNA replication time (RT) chromosomal domains, with variation in mutation rates between tissues mirroring variation in heterochromatin and RT. We observed that regional mutation risk further varies between individual tumors i...
Cancer genomicsChromatin remodellingEpigenomicsMutationTumour-suppressor proteins
10.1038/S43018-023-00707-8
ISSN:2662-1347
MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer
Trine B. Mattesen•Mads H. Rasmussen•Juan Sandoval•Halit Ongen•Sigrid S. Árnadóttir等 14 人
Nature Communications
2020
•2020/4/24
•Vol.11 No.1 p.1-15
Transcriptional characterization and classification has potential to resolve the inter-tumor heterogeneity of colorectal cancer and improve patient management. Yet, robust transcriptional profiling is difficult using formalin-fixed, paraffin-embedded (FFPE) samples, which complicates testing in clin...
Classification and taxonomyColorectal cancerPrognostic markers
10.1038/S41467-020-16000-6
ISSN:2041-1723
Multi-omics prediction of immune-related adverse events during checkpoint immunotherapy
Ying Jing•Jin Liu•Youqiong Ye•Lei Pan•Hui Deng等 13 人
Nature Communications
2020
•2020/10/2
•Vol.11 No.1 p.1-7
Immune-related adverse events (irAEs), caused by anti-PD-1/PD-L1 antibodies, can lead to fulminant and even fatal consequences and thus require early detection and aggressive management. However, a comprehensive approach to identify biomarkers of irAE is lacking. Here, we utilize a strategy that com...
Cancer genomicsComputational biology and bioinformaticsImmunotherapyPredictive markers
10.1038/S41467-020-18742-9
ISSN:2041-1723
Mitochondrial RNA modifications shape metabolic plasticity in metastasis
Delaunay Sylvain•Pascual Gloria•Feng Bohai•Klann Kevin•Behm Mikaela等 14 人
Nature
2022
•2022/6/29
•Vol.607 No.7919 p.593-603
Aggressive and metastatic cancers show enhanced metabolic plasticity1, but the precise underlying mechanisms of this remain unclear. Here we show how two NOP2/Sun RNA methyltransferase 3 (NSUN3)-dependent RNA modifications—5-methylcytosine (m5C) and its derivative 5-formylcytosine (f5C) (refs.2–4)—d...
Mechanisms of diseaseOral cancer
10.1038/S41586-022-04898-5
ISSN:0028-0836
Causal network inference based on cross-validation predictability
Yuelei Zhang•Qingcui Li•Jiachen Wang•Xiao Chang•Luonan Chen等 6 人
Communications Physics
2025
•2025/4/18
•Vol.8 No.1 p.1-15
Identifying causal relations or causal networks among molecules/genes, rather than just their correlations, is of great importance but challenging in biology and medical field, which is essential for unraveling molecular mechanisms of disease progression and developing effective therapies for diseas...
Computational biophysicsComputational scienceInformation theory and computation
10.1038/S42005-025-02091-4
ISSN:2399-3650
Depletion of slow-cycling PDGFRα+ADAM12+ mesenchymal cells promotes antitumor immunity by restricting macrophage efferocytosis
Selene E. Di Carlo•Jerome Raffenne•Hugo Varet•Anais Ode•David Cabrerizo Granados等 10 人
Nature Immunology
2023
•2023/10/5
•00 p.1-12
The capacity to survive and thrive in conditions of limited resources and high inflammation is a major driver of tumor malignancy. Here we identified slow-cycling ADAM12+PDGFRα+ mesenchymal stromal cells (MSCs) induced at the tumor margins in mouse models of melanoma, pancreatic cancer and prostate ...
CancerTumour immunology
10.1038/S41590-023-01642-7
ISSN:1529-2908
Single-cell and spatial genomic landscape of non-small cell lung cancer brain metastases
Somnath Tagore•Lindsay Caprio•Amit Dipak Amin•Kresimir Bestak•Karan Luthria等 50 人
Nature Medicine
2025
•2025/2/27
•00 p.1-13
Brain metastases frequently develop in patients with non-small cell lung cancer (NSCLC) and are a common cause of cancer-related deaths, yet our understanding of the underlying human biology is limited. Here we performed multimodal single-nucleus RNA and T cell receptor, single-cell spatial and whol...
Cancer genomicsMetastasis
10.1038/S41591-025-03530-Z
ISSN:1078-8956
Artificial intelligence links CT images to pathologic features and survival outcomes of renal masses
Ying Xiong•Linpeng Yao•Jinglai Lin•Jiaxi Yao•Qi Bai等 19 人
Nature Communications
2025
•2025/2/7
•Vol.16 No.1 p.1-14
Treatment decisions for an incidental renal mass are mostly made with pathologic uncertainty. Improving the diagnosis of benign renal masses and distinguishing aggressive cancers from indolent ones is key to better treatment selection. We analyze 13261 pre-operative computed computed tomography (CT)...
Cancer imagingDiagnostic markersMachine learningRenal cell carcinoma
10.1038/S41467-025-56784-Z
ISSN:2041-1723
A disease model resource reveals core principles of tissue-specific cancer evolution
Sebastian Mueller•Niklas de Andrade Krätzig•Markus Tschurtschenthaler•Miguel G. Silva•Chiara Thordsen等 66 人
Nature
2026
•2026/2/25
•00 p.1-12
Oncogenes such as KRAS display marked tissue specificity in their oncogenic potential, genetic interactions and phenotypic effects, but the underlying determinants remain largely unresolved1–5. Here, to address these questions, we developed the Mouse Cancer Cell line Atlas, a broad-utility resource ...
Cancer geneticsCancer modelsOncogenes
10.1038/S41586-026-10187-2
ISSN:0028-0836
γδ T cells are effectors of immunotherapy in cancers with HLA class I defects
de Vries Natasja L.•van de Haar Joris•Veninga Vivien•Chalabi Myriam•Ijsselsteijn Marieke E.等 21 人
Nature
2023
•2023/1/11
•Vol.613 No.7945 p.743-750
DNA mismatch repair-deficient (MMR-d) cancers present an abundance of neoantigens that is thought to explain their exceptional responsiveness to immune checkpoint blockade (ICB)1,2. Here, in contrast to other cancer types3–5, we observed that 20 out of 21 (95%) MMR-d cancers with genomic inactivatio...
Antigen processing and presentationCancer immunotherapyColon cancerGammadelta T cellsTumour immunology
10.1038/S41586-022-05593-1
ISSN:0028-0836
Germline variants associated with leukocyte genes predict tumor recurrence in breast cancer patients
Jean-Sébastien Milanese•Chabane Tibiche•Jinfeng Zou•Zhigang Meng•Andre Nantel等 8 人
Npj Precision Oncology
2019
•2019/11/1
•Vol.3 No.1 p.1-9
Germline variants such as BRCA1/2 play an important role in tumorigenesis and clinical outcomes of cancer patients. However, only a small fraction (i.e., 5–10%) of inherited variants has been associated with clinical outcomes (e.g., BRCA1/2, APC, TP53, PTEN and so on). The challenge remains in using...
Cancer geneticsCancer modelsComputational biology and bioinformaticsPredictive markers
10.1038/S41698-019-0100-7
ISSN:2397-768X
The GPR171 pathway suppresses T cell activation and limits antitumor immunity
Fujiwara Yuki•Torphy Robert J.•Sun Yi•Miller Emily N.•Ho Felix等 11 人
Nature Communications
2021
•2021/10/6
•Vol.12 No.1 p.1-14
The recently identified G-protein-coupled receptor GPR171 and its ligand BigLEN are thought to regulate food uptake and anxiety. Though GPR171 is commonly used as a T cell signature gene in transcriptomic studies, its potential role in T cell immunity has not been explored. Here we show that GPR171 ...
Extracellular signalling moleculesLymphocyte activationT cellsTumour immunology
10.1038/S41467-021-26135-9
ISSN:2041-1723
Impact of a deep learning assistant on the histopathologic classification of liver cancer
Amirhossein Kiani•Bora Uyumazturk•Pranav Rajpurkar•Alex Wang•Rebecca Gao等 21 人
Npj Digital Medicine
2020
•2020/2/26
•Vol.3 No.1 p.1-8
Artificial intelligence (AI) algorithms continue to rival human performance on a variety of clinical tasks, while their actual impact on human diagnosticians, when incorporated into clinical workflows, remains relatively unexplored. In this study, we developed a deep learning-based assistant to help...
Liver cancerMachine learningPathology
10.1038/S41746-020-0232-8
ISSN:2398-6352
Single-cell transcriptomic analysis highlights origin and pathological process of human endometrioid endometrial carcinoma
Ren Xiaojun•Liang Jianqing•Zhang Yiming•Jiang Ning•Xu Yuhui等 9 人
Nature Communications
2022
•2022/10/22
•Vol.13 No.1 p.1-15
Endometrial cancers are complex ecosystems composed of cells with distinct phenotypes, genotypes, and epigenetic states. Current models do not adequately reflect oncogenic origin and pathological progression in patients. Here we use single-cell RNA sequencing to profile cells from normal endometrium...
Cancer genomicsCancer microenvironmentEndometrial cancerTumour heterogeneity
10.1038/S41467-022-33982-7
ISSN:2041-1723
WNT inhibitor SP5-mediated SERPING1 suppresses lung adenocarcinoma progression via TSC2/mTOR pathway
Yefeng Shen•Xiaofeng Dong•Xujia Li•Zhiyuan Shi•Tingting Shao等 7 人
Cell Death & Disease
2025
•2025/2/17
•Vol.16 No.1 p.1-15
The long-term outlook for patients grappling with lung cancer (LC) remains bleak, with lung adenocarcinoma (LUAD) emerging as the most predominant histological subtype. Our Mendelian randomization (MR) investigation spotlighted that heightened levels of the circulating protein serpin peptidase inhib...
Non-small-cell lung cancerTumour-suppressor proteins
10.1038/S41419-025-07440-3
ISSN:2041-4889
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
Becker Winston R.•Nevins Stephanie A.•Chen Derek C.•Chiu Roxanne•Horning Aaron M.等 18 人
Nature Genetics
2022
•2022/6/20
•00 p.1-11
To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single-cell chromatin accessibility profiles and single-cell transcriptomes from 1,000 to 10,000 cells per sample for 48 polyps, 27...
CancerEpigeneticsFunctional genomicsGastrointestinal cancerGene regulation
10.1038/S41588-022-01088-X
ISSN:1061-4036
Inflammation promotes resistance to immune checkpoint inhibitors in high microsatellite instability colorectal cancer
Sui Qiaoqi•Zhang Xi•Chen Chao•Tang Jinghua•Yu Jiehai等 22 人
Nature Communications
2022
•2022/11/28
•Vol.13 No.1 p.1-11
Inflammation is a common medical complication in colorectal cancer (CRC) patients, which plays significant roles in tumor progression and immunosuppression. However, the influence of inflammatory conditions on the tumor response to immune checkpoint inhibitors (ICI) is incompletely understood. Here ...
Colorectal cancerImmunotherapyInflammationTumour immunology
10.1038/S41467-022-35096-6
ISSN:2041-1723
The impact of site-specific digital histology signatures on deep learning model accuracy and bias
Frederick M. Howard•James Dolezal•Sara Kochanny•Jefree Schulte•Heather Chen等 13 人
Nature Communications
2021
•2021/7/20
•Vol.12 No.1 p.1-13
The Cancer Genome Atlas (TCGA) is one of the largest biorepositories of digital histology. Deep learning (DL) models have been trained on TCGA to predict numerous features directly from histology, including survival, gene expression patterns, and driver mutations. However, we demonstrate that these ...
Cancer imagingDiagnostic markers
10.1038/S41467-021-24698-1
ISSN:2041-1723
Targeting brain lesions of non-small cell lung cancer by enhancing CCL2-mediated CAR-T cell migration
Li Hongxia•Harrison Emily B.•Li Huizhong•Hirabayashi Koichi•Chen Jing等 13 人
Nature Communications
2022
•2022/4/20
•Vol.13 No.1 p.1-12
Metastatic non-small cell lung cancer (NSCLC) remains largely incurable and the prognosis is extremely poor once it spreads to the brain. In particular, in patients with brain metastases, the blood brain barrier (BBB) remains a significant obstacle for the biodistribution of antitumor drugs and immu...
Cancer immunotherapyImmunotherapyTumour immunology
10.1038/S41467-022-29647-0
ISSN:2041-1723
Inactivation of LATS1/2 drives luminal-basal plasticity to initiate basal-like mammary carcinomas
Kern Joseph G.•Tilston-Lunel Andrew M.•Federico Anthony•Ning Boting•Mueller Amy等 13 人
Nature Communications
2022
•2022/11/28
•Vol.13 No.1 p.1-13
Basal-like breast cancers, an aggressive breast cancer subtype that has poor treatment options, are thought to arise from luminal mammary epithelial cells that undergo basal plasticity through poorly understood mechanisms. Using genetic mouse models and ex vivo primary organoid cultures, we show tha...
Breast cancerMammary stem cellsTumour-suppressor proteins
10.1038/S41467-022-34864-8
ISSN:2041-1723
IdentifiHR predicts homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression
Ashley L. Weir•Samuel C. Lee•Mengbo Li•Ahwan Pandey•Chin Wee Tan等 8 人
Communications Medicine
2026
•2026/1/14
•Vol.6 No.1 p.1190
Approximately half of all high-grade serous ovarian carcinomas (HGSCs) have a therapeutically targetable defect in homologous recombination (HR) DNA repair. While there are genomic and transcriptomic methods, developed for other cancers, to identify HR deficient (HRD) samples, there are no gene expr...
Cancer genomicsComputational biology and bioinformaticsOvarian cancer
10.1038/S43856-026-01387-Y
ISSN:2730-664X
CloneSig can jointly infer intra-tumor heterogeneity and mutational signature activity in bulk tumor sequencing data
Abécassis Judith•Reyal Fabien•Vert Jean-Philippe
Nature Communications
2021
•2021/9/9
•Vol.12 No.1 p.1-16
Systematic DNA sequencing of cancer samples has highlighted the importance of two aspects of cancer genomics: intra-tumor heterogeneity (ITH) and mutational processes. These two aspects may not always be independent, as different mutational processes could be involved in different stages or regions ...
Cancer genomicsMachine learningTumour heterogeneity
10.1038/S41467-021-24992-Y
ISSN:2041-1723
Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets
Xiaoguang Xu•Chachrit Khunsriraksakul•James M. Eales•Sebastien Rubin•David Scannali等 38 人
Nature Communications
2024
•2024/3/19
•Vol.15 No.1 p.1-29
Genetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identifie...
Gene expressionGene regulationGenome-wide association studies
10.1038/S41467-024-46132-Y
ISSN:2041-1723
ADAMTS16 drives epithelial-mesenchymal transition and metastasis through a feedback loop upon TGF-β1 activation in lung adenocarcinoma
Lingyan Xiao•Qian Li•Shuaijun Chen•Yongbiao Huang•Li Ma等 12 人
Cell Death & Disease
2024
•2024/11/17
•Vol.15 No.11 p.1-14
Lung adenocarcinoma (LUAD) is the major subtype of lung cancer. The poor prognosis of LUAD patients is attributed primarily to metastasis. ADAMTS16 is a crucial member of the ADAMTS family and is involved in tumor progression. However, its role and regulatory mechanism in LUAD remain unexplored. In ...
CancerCell biology
10.1038/S41419-024-07226-Z
ISSN:2041-4889
Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma
Julien Calderaro•Narmin Ghaffari Laleh•Qinghe Zeng•Pascale Maille•Loetitia Favre等 85 人
Nature Communications
2023
•2023/12/14
•Vol.14 No.1 p.1-10
Primary liver cancer arises either from hepatocytic or biliary lineage cells, giving rise to hepatocellular carcinoma (HCC) or intrahepatic cholangiocarcinoma (ICCA). Combined hepatocellular- cholangiocarcinomas (cHCC-CCA) exhibit equivocal or mixed features of both, causing diagnostic uncertainty a...
Biomedical engineeringLiver cancerMachine learningPathologyTumour heterogeneity
10.1038/S41467-023-43749-3
ISSN:2041-1723
Activated MAFB in ovarian cancer promotes cytoskeletal remodeling and immune microenvironment suppression by interfering with m6A modifications through WTAP competition
Qinke Li•Siying Zhang•Min Wang•Qiang Yi•Hang Xu等 7 人
Oncogene
2025
•2025/8/12
•00 p.1-17
The tumor microenvironment (TME) coordinates cancer progression through complex transcriptional networks, but the molecular mechanisms controlling immune evasion in ovarian cancer remain elusive. Here, by integrating immune dysfunction characteristics across multiple clinical cohorts and single-cell...
Cancer microenvironmentOncogenesOvarian cancer
10.1038/S41388-025-03522-W
ISSN:0950-9232
YAP/TAZ drives cell proliferation and tumour growth via a polyamine–eIF5A hypusination–LSD1 axis
Li Hongde•Wu Bo-Kuan•Kanchwala Mohammed•Cai Jing•Wang Li等 8 人
Nature Cell Biology
2022
•2022/2/17
•00 p.1-11
Metabolic reprogramming is central to oncogene-induced tumorigenesis by providing the necessary building blocks and energy sources, but how oncogenic signalling controls metabolites that play regulatory roles in driving cell proliferation and tumour growth is less understood. Here we show that oncog...
CancerCancer epigeneticsCancer metabolismCell signalling
10.1038/S41556-022-00848-5
ISSN:1465-7392
The m6A reader IGF2BP3 promotes acute myeloid leukemia progression by enhancing RCC2 stability
Zhang Nan•Shen Yan•Li Huan•Chen Ying•Zhang Ping等 7 人
Experimental & Molecular Medicine
2022
•2022/2/25
•Vol.54 No.2 p.194-205
N6-methyladenosine (m6A) is the most abundant posttranscriptional modification of mRNA in eukaryotes. Recent evidence suggests that dysregulated m6A-associated proteins and m6A modifications play a pivotal role in the initiation and progression of diseases such as cancer. Here, we identified that IG...
EpigeneticsMyeloma
10.1038/S12276-022-00735-X
ISSN:1226-3613
Emerging significance and therapeutic targets of ferroptosis: a potential avenue for human kidney diseases
Jinghan Li•Sujuan Zheng•Yumei Fan•Ke Tan
Cell Death & Disease
2023
•2023/9/22
•Vol.14 No.9 p.1-21
Kidney diseases remain one of the leading causes of human death and have placed a heavy burden on the medical system. Regulated cell death contributes to the pathology of a plethora of renal diseases. Recently, with in-depth studies into kidney diseases and cell death, a new iron-dependent cell deat...
Cell deathKidney diseasesNatural products
10.1038/S41419-023-06144-W
ISSN:2041-4889
Cuproptosis-associated PDHA1 promotes sarcoma progression and immunotherapy responsiveness via the E2F1–PD-L1 axis: a multi-omics and clinical validation study
Haotian Qin•Tiantian Qi•Nan Yao•Weibei Sheng•Jinhao Deng等 11 人
Npj Precision Oncology
2026
•2026/3/6
0Sarcomas are aggressive, immunologically cold tumors with limited benefit from immune-checkpoint blockade (ICB). Through integrated multi-omics, functional, and clinical analyses, we identify pyruvate dehydrogenase alpha 1 (PDHA1)—a cuproptosis-linked metabolic gene—as a driver of sarcoma progressio...
BiomarkersBone cancerCancerCancer microenvironmentCancer therapyComputational biology and bioinformatics+3
10.1038/S41698-026-01298-0
ISSN:2397-768X
Metabolic targeting of cancer associated fibroblasts overcomes T-cell exclusion and chemoresistance in soft-tissue sarcomas
Marina T. Broz•Emily Y. Ko•Kristin Ishaya•Jinfen Xiao•Marco De Simone等 14 人
Nature Communications
2024
•2024/3/20
•Vol.15 No.1 p.1-18
T cell-based immunotherapies have exhibited promising outcomes in tumor control; however, their efficacy is limited in immune-excluded tumors. Cancer-associated fibroblasts (CAFs) play a pivotal role in shaping the tumor microenvironment and modulating immune infiltration. Despite the identification...
Cancer microenvironmentSarcomaTumour immunology
10.1038/S41467-024-46504-4
ISSN:2041-1723
A deep learning model and human-machine fusion for prediction of EBV-associated gastric cancer from histopathology
Zheng Xueyi•Wang Ruixuan•Zhang Xinke•Sun Yan•Zhang Haohuan等 23 人
Nature Communications
2022
•2022/5/19
•Vol.13 No.1 p.1-12
Epstein–Barr virus-associated gastric cancer (EBVaGC) shows a robust response to immune checkpoint inhibitors. Therefore, a cost-efficient and accessible tool is needed for discriminating EBV status in patients with gastric cancer. Here we introduce a deep convolutional neural network called EBVNet ...
Gastric cancerMachine learningTumour virus infections
10.1038/S41467-022-30459-5
ISSN:2041-1723
Clinical utility of receptor status prediction in breast cancer and misdiagnosis identification using deep learning on hematoxylin and eosin-stained slides
Gil Shamai•Ran Schley•Alexandra Cretu•Tal Neoran•Edmond Sabo等 12 人
Communications Medicine
2024
•2024/12/20
•Vol.4 No.1 p.1-16
Molecular profiling of estrogen receptor (ER), progesterone receptor (PR), and ERBB2 (also known as Her2) is essential for breast cancer diagnosis and treatment planning. Nevertheless, current methods rely on the qualitative interpretation of immunohistochemistry and fluorescence in situ hybridizati...
Breast cancerComputational biology and bioinformaticsDiagnostic markers
10.1038/S43856-024-00695-5
ISSN:2730-664X
Targeting ALDH16A1 mediated thioredoxin lysosomal degradation to enhance ferroptosis susceptibility in SMARCA4-deficient NSCLC
Guoshu Bi•Jiaqi Liang•Yunyi Bian•Guangyao Shan•Shencheng Ren等 12 人
Nature Communications
2025
•2025/9/2
•Vol.16 No.1 p.1-20
Ferroptosis, an iron-dependent form of cell death, holds promise for cancer therapy. However, the intricate link between ferroptosis and oncogenic mutations remains unclear. Here we show that SMARCA4, a well-established tumour suppressor whose deficiency is associated with poor prognosis and resista...
Cancer therapeutic resistanceCell deathNon-small-cell lung cancer
10.1038/S41467-025-63687-6
ISSN:2041-1723
Identification of a novel prognostic ADME-related signature associated with tumor immunity for aiding therapy in head and neck squamous cell carcinoma
Liu Zhifeng•Tian Yuxi•Zhang Xin•Wang Juncheng•Yang Jing
Cancer Gene Therapy
2022
•2022/11/15
•00 p.1-12
The genes that control drug absorption, distribution, metabolism, and excretion (ADME) are also involved in carcinogenesis, cancer progression, and chemoresistance. However, no studies have systematically investigated the clinical significance and underlying functions of ADME genes in head and neck ...
BiomarkersHead and neck cancer
10.1038/S41417-022-00557-Z
ISSN:0929-1903
USP43 stabilizes c-Myc to promote glycolysis and metastasis in bladder cancer
Mingxing Li•Jingtian Yu•Lingao Ju•Yejinpeng Wang•Wan Jin等 14 人
Cell Death & Disease
2024
•2024/1/13
•Vol.15 No.1 p.1-15
A hallmark of tumor cells, including bladder cancer (BLCA) cells, is metabolic reprogramming toward aerobic glycolysis (Warburg effect). The classical oncogene MYC, which is crucial in regulating glycolysis, is amplified and activated in BLCA. However, direct targeting of the c-Myc oncoprotein, whic...
Bladder cancerOncogenesUbiquitylation
10.1038/S41419-024-06446-7
ISSN:2041-4889
Multi-omics analyses reveal interactions between GREM1+ fibroblasts and SPP1+ macrophages in gastric cancer
Lupeng Qiu•Xiao Zhao•Sheng Yao•Yang Fei•Yixin Gong等 8 人
Npj Precision Oncology
2025
•2025/6/5
•Vol.9 No.1 p.1-13
Gastric cancer (GC) is among the most lethal human malignancies with limited treatment options. Cell-cell interactions within the tumor microenvironment (TME) can promote tumor growth, yet their therapeutic value has not been fully explored. Here, bulk RNA-seq, single-cell RNA sequencing (scRNA-seq)...
Cancer microenvironmentGastric cancer
10.1038/S41698-025-00967-W
ISSN:2397-768X
Mutant p53 gains oncogenic functions through a chromosomal instability-induced cytosolic DNA response
Mei Zhao•Tianxiao Wang•Frederico O. Gleber-Netto•Zhen Chen•Daniel J. McGrail等 22 人
Nature Communications
2024
•2024/1/2
•Vol.15 No.1 p.1-18
Inactivating TP53 mutations leads to a loss of function of p53, but can also often result in oncogenic gain-of-function (GOF) of mutant p53 (mutp53) proteins which promotes tumor development and progression. The GOF activities of TP53 mutations are well documented, but the mechanisms involved remain...
DNA damage and repairTumour-suppressor proteins
10.1038/S41467-023-44239-2
ISSN:2041-1723
Implications of different cell death patterns for prognosis and immunity in lung adenocarcinoma
Yang Zhou•Weitong Gao•Yu Xu•Jiale Wang•Xueying Wang等 10 人
Npj Precision Oncology
2023
•2023/11/15
•Vol.7 No.1 p.1-17
In recent years, lung adenocarcinoma (LUAD) has become a focus of attention due to its low response to treatment, poor prognosis, and lack of reliable indicators to predict the progression or therapeutic effect of LUAD. Different cell death patterns play a crucial role in tumor development and are p...
ImmunosurveillanceNon-small-cell lung cancer
10.1038/S41698-023-00456-Y
ISSN:2397-768X
KPNA2 silencing sensitizes triple-negative breast cancer to chemotherapy by promoting multipolar division and suppressing DNA damage repair
Yufan Cai•Junxian Du•Haiyu Wang•Lei Shen•Zujing Xu等 15 人
Oncogene
2025
•2025/9/18
•00 p.1-17
Breast cancer is one of the most common malignancies among women. Triple-negative breast cancer (TNBC) is a distinct subtype of breast cancer characterized by the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Consequently, patient...
Breast cancerChemotherapy
10.1038/S41388-025-03503-Z
ISSN:0950-9232
Pan-cancer analysis reveals cooperativity of both strands of microRNA that regulate tumorigenesis and patient survival
Ramkrishna Mitra•Clare M. Adams•Wei Jiang•Evan Greenawalt•Christine M. Eischen
Nature Communications
2020
•2020/2/20
•Vol.11 No.1 p.1-15
Recently, both 5p and 3p miRNA strands are being recognized as functional instead of only one, leaving many miRNA strands uninvestigated. To determine whether both miRNA strands, which have different mRNA-targeting sequences, cooperate to regulate pathways/functions across cancer types, we evaluate ...
CancerComputational biology and bioinformaticsData integrationFunctional clusteringGene regulatory networks
10.1038/S41467-020-14713-2
ISSN:2041-1723
LGI3 promotes the progression of TFE3-rearranged renal cell carcinoma through GEMIN6/AURKB axis
Junxiao Liu•Huayi Feng•Zhuang Xiong•Shouqing Cao•Tianwei Cai等 10 人
Oncogene
2025
•2025/8/23
•00 p.1-12
Transcription factor binding to IGHM enhancer 3-rearranged renal cell carcinoma (TFE3-RCC) is characterized by its aggressive nature, limited treatment options, and poor prognosis. However, the downstream targets of TFE3 fusion protein responsible for its tumorigenesis and progression remain unclear...
OncogenesRenal cell carcinoma
10.1038/S41388-025-03553-3
ISSN:0950-9232
pathCHEMO, a generalizable computational framework uncovers molecular pathways of chemoresistance in lung adenocarcinoma
Nusrat J. Epsi•Sukanya Panja•Sharon R. Pine•Antonina Mitrofanova
Communications Biology
2019
•2019/9/6
•Vol.2 No.1 p.1-13
Despite recent advances in discovering a wide array of novel chemotherapy agents, identification of patients with poor and favorable chemotherapy response prior to treatment administration remains a major challenge in clinical oncology. To tackle this challenge, we present a generalizable genome-wid...
Computational modelsLung cancerPredictive medicine
10.1038/S42003-019-0572-6
ISSN:2399-3642
Proteogenomics of diffuse gliomas reveal molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms
Wang Yunzhi•Luo Rongkui•Zhang Xuan•Xiang Hang•Yang Bing等 21 人
Nature Communications
2023
•2023/1/31
•Vol.14 No.1 p.1-32
Diffuse gliomas are devastating brain tumors. Here, we perform a proteogenomic profiling of 213 retrospectively collected glioma tumors. Proteogenomic analysis reveals the downstream biological events leading by EGFR-, IDH1-, TP53-mutations. The comparative analysis illustrates the distinctive featu...
CNS cancerProteomics
10.1038/S41467-023-36005-1
ISSN:2041-1723
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer
Zhu Han•Weizhi Zhang•Wanshan Ning•Chenwei Wang•Wankun Deng等 14 人
Nature Communications
2021
•2021/5/31
•Vol.12 No.1 p.1-18
Autophagy can selectively target protein aggregates, pathogens, and dysfunctional organelles for the lysosomal degradation. Aberrant regulation of autophagy promotes tumorigenesis, while it is far less clear whether and how tumor-specific alterations result in autophagic aberrance. To form a link be...
Cancer metabolismData miningMacroautophagy
10.1038/S41467-021-23539-5
ISSN:2041-1723
Model systems and unique biological features of high and low-grade colorectal cancer (CRC) revealed by xenografting 84 human CRC cell lines
Ian Y. Luk•Jennifer K. Mooi•Dmitri Mouradov•Tao Tan•Cameron M. Scott等 26 人
Communications Biology
2025
•2025/6/5
•Vol.8 No.1 p.1-13
Colorectal cancers (CRCs) present across a range of differentiation grades, which impact patient outcome and management; however, the molecular features and drivers of differentiation status are not fully understood. To address this, 84 commonly used human CRC cell lines were grown as xenografts in ...
CancerCell biology
10.1038/S42003-025-08251-0
ISSN:2399-3642
FSP1 confers ferroptosis resistance in KEAP1 mutant non-small cell lung carcinoma in NRF2-dependent and -independent manner
Jong Woo Kim•Min-Ju Kim•Tae-Hee Han•Ji-Yoon Lee•Sangok Kim等 15 人
Cell Death & Disease
2023
•2023/8/26
•Vol.14 No.8 p.1-11
Ferroptosis, a type of cell death induced by lipid peroxidation, has emerged as a novel anti-cancer strategy. Cancer cells frequently acquire resistance to ferroptosis. However, the underlying mechanisms are poorly understood. To address this issue, we conducted a thorough investigation of the genom...
Cell deathNon-small-cell lung cancer
10.1038/S41419-023-06070-X
ISSN:2041-4889
An end-to-end multifunctional AI platform for intraoperative diagnosis
Xueyi Zheng•Ke Zheng•Yongqin Wen•Jiajia Meng•Xinke Zhang等 19 人
Npj Digital Medicine
2025
•2025/7/20
•Vol.8 No.1 p.1-12
Intraoperative frozen section diagnosis provides essential, real-time histological insights to guide surgical decisions. However, the quality of these time-sensitive sections is often suboptimal, posing significant diagnostic challenges for pathologists. To address these limitations, we utilized ove...
DiagnosisMachine learning
10.1038/S41746-025-01808-7
ISSN:2398-6352
Feature-interactive Siamese graph encoder-based image analysis to predict STAS from histopathology images in lung cancer
Liangrui Pan•Qingchun Liang•Wenwu Zeng•Yijun Peng•Zhenyu Zhao等 9 人
Npj Precision Oncology
2024
•2024/12/20
•Vol.8 No.1 p.1-12
Spread through air spaces (STAS) is a distinct invasion pattern in lung cancer, crucial for prognosis assessment and guiding surgical decisions. Histopathology is the gold standard for STAS detection, yet traditional methods are subjective, time-consuming, and prone to misdiagnosis, limiting large-s...
Predictive markersSurgical oncology
10.1038/S41698-024-00771-Y
ISSN:2397-768X
TET2-mediated tumor cGAS triggers endothelial STING activation to regulate vasculature remodeling and anti-tumor immunity in liver cancer
Hongwei Lv•Qianni Zong•Cian Chen•Guishuai Lv•Wei Xiang等 15 人
Nature Communications
2024
•2024/1/4
•Vol.15 No.1 p.1-21
Induction of tumor vascular normalization is a crucial measure to enhance immunotherapy efficacy. cGAS-STING pathway is vital for anti-tumor immunity, but its role in tumor vasculature is unclear. Herein, using preclinical liver cancer models in Cgas/Sting-deficient male mice, we report that the int...
Cancer immunotherapyHepatocellular carcinomaTumour angiogenesis
10.1038/S41467-023-43743-9
ISSN:2041-1723
Clonal dynamics and Stereo-seq resolve origin and phenotypic plasticity of adenosquamous carcinoma
Ruiying Zhao•Yunhua Xu•Yedan Chen•Jiajun Zhang•Fei Teng等 17 人
Npj Precision Oncology
2023
•2023/8/26
•Vol.7 No.1 p.1-14
The genomic origin and development of the biphasic lung adenosquamous carcinoma (ASC) remain inconclusive. Here, we derived potential evolutionary trajectory of ASC through whole-exome sequencing, Stereo-seq, and patient-derived xenografts. We showed that EGFR and MET activating mutations were the m...
Cancer genomicsNon-small-cell lung cancer
10.1038/S41698-023-00430-8
ISSN:2397-768X
Real-world benchmarking and validation of foundation model transformers for endometrial cancer subtyping from histopathology
Vincent M. Wagner•Casey M. Cosgrove•Stephanie J. Chen•Daniel T. Griffin•Megan I. Samuelson等 7 人
Npj Precision Oncology
2026
•2026/4/4
0We benchmarked histopathology foundation encoders paired with attention-based multiple instance learning (MIL) against convolutional neural networks (CNNs) to assess their robustness for endometrial cancer molecular classification (MMR-deficient, p53 aberrant, POLE pathogenic mutation, and no specif...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41698-026-01402-4
ISSN:2397-768X
An agentic framework for autonomous scientific discovery in cancer pathology
Florian Trost•Bide Zhang•Ines Aring•Marcus Bauer•Lennert Glamann等 26 人
Nature Medicine
2026
•2026/4/29
•00 p.1-13
Artificial intelligence has advanced cancer pathology, but many systems still depend on hand-crafted features, are hard to explain and rely on fragmented workflows. We introduce SPARK (System of Pathology Agents for Research and Knowledge), a foundational agentic artificial intelligence approach tha...
BiomarkersCancerEvolution
10.1038/S41591-026-04357-Y
ISSN:1078-8956
Functional synapses between neurons and small cell lung cancer
Vignesh Sakthivelu•Anna Schmitt•Franka Odenthal•Kristiano Ndoci•Marian Touet等 75 人
Nature
2025
•2025/9/10
•00 p.1-11
Small cell lung cancer (SCLC) is a highly aggressive type of lung cancer, characterized by rapid proliferation, early metastatic spread, frequent early relapse and a high mortality rate1–3. Recent evidence has suggested that innervation has an important role in the development and progression o...
Cancer genomicsCancer microenvironmentNeuroscienceSmall-cell lung cancerTargeted therapies
10.1038/S41586-025-09434-9
ISSN:0028-0836
CG>TG mutation frequency as negative predictor of homologous recombination deficiency in ovarian and breast cancer
Eva Romanovsky•Michael Menzel•Klaus Kluck•Susanne Beck•Markus Ball等 9 人
Communications Biology
2025
•2025/7/29
•Vol.8 No.1 p.1-13
Homologous recombination deficiency (HRD) is a predictive biomarker for PARP inhibition and platinum-based chemotherapy. While copy number alteration-based scores such as HRDsum = LST + TAI + LOH are included in therapy approvals, single base substitutions (SBS) are underinvestigated as predictors o...
Homologous recombinationOvarian cancerPredictive medicine
10.1038/S42003-025-08529-3
ISSN:2399-3642
TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis
Tulstrup Morten•Soerensen Mette•Hansen Jakob Werner•Gillberg Linn•Needhamsen Maria等 10 人
Nature Communications
2021
•2021/10/18
•Vol.12 No.1 p.1-10
Mutations in the epigenetic modifier TET2 are frequent in myeloid malignancies and clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS). Here, we investigate associations between TET2 mutations and DNA methylation in whole blood in 305 elder...
Acute myeloid leukaemiaCancer geneticsEpigenomicsHaematological diseasesRisk factors
10.1038/S41467-021-26093-2
ISSN:2041-1723
Mature tertiary lymphoid structures evoke intra-tumoral T and B cell responses via progenitor exhausted CD4+ T cells in head and neck cancer
Hao Li•Meng-Jie Zhang•Boxin Zhang•Wen-Ping Lin•Shu-Jin Li等 12 人
Nature Communications
2025
•2025/5/7
•Vol.16 No.1 p.1-20
Tumor tertiary lymphoid structures (TLS), especially mature TLS (mTLS), have been associated with better prognosis and improved responses to immune checkpoint blockade (ICB), but the underlying mechanisms remain incompletely understood. Here, by performing single-cell RNA, antigen receptor sequencin...
Cancer genomicsCancer microenvironmentHead and neck cancer
10.1038/S41467-025-59341-W
ISSN:2041-1723
Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction
David V. Conti•Burcu F. Darst•Lilit C. Moss•Edward J. Saunders•Xin Sheng等 231 人
Nature Genetics
2021
•2021/1/4
•Vol.53 No.1 p.65-75
Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independ...
EpidemiologyGenome-wide association studiesPersonalized medicineProstate cancer
10.1038/S41588-020-00748-0
ISSN:1061-4036
A platform for oncogenomic reporting and interpretation
Reisle Caralyn•Williamson Laura M.•Pleasance Erin•Davies Anna•Pellegrini Brayden等 33 人
Nature Communications
2022
•2022/2/9
•Vol.13 No.1 p.1-11
Manual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire...
Cancer geneticsCancer genomicsComputational platforms and environmentsData integrationGenetics research
10.1038/S41467-022-28348-Y
ISSN:2041-1723
Checkpoint kinase 1/2 inhibition potentiates anti-tumoral immune response and sensitizes gliomas to immune checkpoint blockade
Dmello Crismita•Zhao Junfei•Chen Li•Gould Andrew•Castro Brandyn等 27 人
Nature Communications
2023
•2023/3/22
•Vol.14 No.1 p.1-18
Whereas the contribution of tumor microenvironment to the profound immune suppression of glioblastoma (GBM) is clear, tumor-cell intrinsic mechanisms that regulate resistance to CD8 T cell mediated killing are less understood. Kinases are potentially druggable targets that drive tumor progression an...
Cancer therapyCNS cancerTumour immunology
10.1038/S41467-023-36878-2
ISSN:2041-1723
SLC1A5 enhances malignant phenotypes through modulating ferroptosis status and immune microenvironment in glioma
Han Liying•Zhou Jinpeng•Li Leiyang•Wu Xun•Shi Yingwu等 20 人
Cell Death & Disease
2022
•2022/12/24
•Vol.13 No.12 p.1-14
Glioma is the most common type of primary malignant tumor in the central nervous system with limited treatment satisfaction. Finding new therapeutic targets has remained a major challenge. Ferroptosis is a novel and distinct type of programmed cell death, playing a regulatory role in the progression...
Cell deathCNS cancerPrognostic markers
10.1038/S41419-022-05526-W
ISSN:2041-4889
Pan-cancer proteogenomic interrogation of the ubiquitin-proteasome system
Tania J. González-Robles•Maha Khan•Paul Sastourné•Marisa Triola•Hua Zhou等 13 人
Cell Death & Differentiation
2026
•2026/7/19
•00 p.1-13
Somatic mutations rewire the ubiquitin–proteasome system (UPS) to support tumor growth, but the proteome-wide consequences of cancer-driver alterations on UPS composition remain incompletely understood. Using harmonized proteogenomic data from up to 11 CPTAC cohorts, we performed an integrated pan-c...
Cancer genomicsCancer modelsPrognostic markersProtein–protein interaction networksUbiquitin ligases
10.1038/S41418-026-01787-6
ISSN:1350-9047
A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients
Zingone Adriana•Sinha Sanju•Ante Michael•Nguyen Cu•Daujotyte Dalia等 14 人
Nature Communications
2021
•2021/9/23
•Vol.12 No.1 p.1-12
Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)—regulation of mRNA 3′UTR length by alternating poly(A) site usage—is a key PTM mechanism whose com...
Lung cancerTranscriptomics
10.1038/S41467-021-25763-5
ISSN:2041-1723
Farnesoid X receptor promotes non-small cell lung cancer metastasis by activating Jak2/STAT3 signaling via transactivation of IL-6ST and IL-6 genes
Xiuye Jin•Bin Shang•Junren Wang•Jian Sun•Jing Li等 10 人
Cell Death & Disease
2024
•2024/2/15
•Vol.15 No.2 p.1-14
Metastasis accounts for the majority of cases of cancer recurrence and death in patients with advanced non-small cell lung cancer (NSCLC). Farnesoid X Receptor (FXR) is a bile acid nuclear receptor that was recently found to be upregulated in NSCLC tissues. However, whether and how FXR regulates NSC...
MetastasisNon-small-cell lung cancer
10.1038/S41419-024-06495-Y
ISSN:2041-4889
TFAP2A potentiates lung adenocarcinoma metastasis by a novel miR-16 family/TFAP2A/PSG9/TGF-β signaling pathway
Yanlu Xiong•Yangbo Feng•Jinbo Zhao•Jie Lei•Tianyun Qiao等 10 人
Cell Death & Disease
2021
•2021/4/6
•Vol.12 No.4 p.1-13
Transcription factor AP-2α (TFAP2A) was previously regarded as a critical regulator during embryonic development, and its mediation in carcinogenesis has received intensive attention recently. However, its role in lung adenocarcinoma (LUAD) has not been fully elucidated. Here, we tried to investigat...
MetastasisNon-small-cell lung cancer
10.1038/S41419-021-03606-X
ISSN:2041-4889
CPT2 inhibition enhances selective autophagy and proliferation in colorectal cancer via GPAT4-dependent glycerophospholipid biosynthesis
Kuo Li•Hongyan Wang•Chan Li•Mingming Xiao•Yuan Luo等 15 人
Communications Biology
2025
•2025/10/17
•Vol.8 No.1 p.1-15
Metabolic reprogramming is one of the hallmark events in colorectal cancer. Tumor cells adapt to microenvironmental changes by regulating energy and biomaterial metabolism. This study identifys abnormal lipid accumulation and significant downregulation of fatty acid metabolism in colorectal cancer. ...
Cancer metabolismColorectal cancer
10.1038/S42003-025-08877-0
ISSN:2399-3642
Exome sequencing of affected duos and trios uncovers PRUNE2 as a novel prostate cancer predisposition gene
Cardoso Marta•Maia Sofia•Brandão Andreia•Sahasrabudhe Ruta•Lott Paul等 9 人
British Journal Of Cancer
2022
•2022/12/23
•Vol.128 No.6 p.1077-1085
Prostate cancer (PrCa) is one of the most hereditable human cancers, however, only a small fraction of patients has been shown to carry deleterious variants in known cancer predisposition genes. Whole-exome sequencing was performed in multiple affected members of 45 PrCa families to select the best ...
Cancer genetics
10.1038/S41416-022-02125-6
ISSN:0007-0920
Integrated multidimensional bioinformatics analysis of the molecular mechanisms of ulcerative colitis-associated colorectal cancer and MMP1 as a potential therapeutic target
Xiaopeng Yu•Yutian Tang•Junjie Niu•Jinyang Hu
Cancer Gene Therapy
2025
•2025/7/18
•00 p.1-12
This study aimed to investigate the molecular mechanisms underlying ulcerative colitis (UC)-associated colorectal cancer (CRC) development and identify potential therapeutic targets through integrated multi-omics analysis. Mendelian randomization (MR) analysis, combined with bioinformatics approache...
Cancer immunotherapyGastrointestinal cancer
10.1038/S41417-025-00917-5
ISSN:0929-1903
CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data
Akdes Serin Harmanci•Arif O. Harmanci•Xiaobo Zhou
Nature Communications
2020
•2020/1/3
•Vol.11 No.1 p.1-16
RNA sequencing experiments generate large amounts of information about expression levels of genes. Although they are mainly used for quantifying expression levels, they contain much more biologically important information such as copy number variants (CNVs). Here, we present CaSpER, a signal process...
Computational biology and bioinformaticsGenetics researchRNA sequencingStructural variation
10.1038/S41467-019-13779-X
ISSN:2041-1723
Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect
Gongwang Yu•Yao Liu•Zizhang Li•Shuyun Deng•Zhuoxing Wu等 10 人
Nature Communications
2023
•2023/9/20
•Vol.14 No.1 p.1-18
The transcriptional intermediates of RNAs fold into secondary structures with multiple regulatory roles, yet the details of such cotranscriptional RNA folding are largely unresolved in eukaryotes. Here, we present eSPET-seq (Structural Probing of Elongating Transcripts in eukaryotes), a method to as...
EvolutionMutationRNA foldingTranscription
10.1038/S41467-023-41550-W
ISSN:2041-1723
Confounding factors and biases abound when predicting molecular biomarkers from histological images
Muhammad Dawood•Kim Branson•Sabine Tejpar•Nasir Rajpoot•Fayyaz ul Amir Afsar Minhas
Nature Biomedical Engineering
2026
•2026/3/2
•00 p.1-15
Deep learning models that infer clinically relevant biomarker status from tissue images are being explored as rapid and low-cost alternatives to molecular testing. Here we show, through statistical analysis across multiple cancer types, datasets and modelling approaches, that the datasets used to tr...
Cancer screeningMachine learning
10.1038/S41551-026-01616-8
ISSN:2157-846X
Strength of immune selection in tumors varies with sex and age
Andrea Castro•Rachel Marty Pyke•Xinlian Zhang•Wesley Kurt Thompson•Chi-Ping Day等 8 人
Nature Communications
2020
•2020/8/17
•Vol.11 No.1 p.1-9
Individual MHC genotype constrains the mutational landscape during tumorigenesis. Immune checkpoint inhibition reactivates immunity against tumors that escaped immune surveillance in approximately 30% of cases. Recent studies demonstrated poorer response rates in female and younger patients. Althoug...
Cancer genomicsTumour immunology
10.1038/S41467-020-17981-0
ISSN:2041-1723
Classification and mutation prediction based on histopathology H&E images in liver cancer using deep learning
Mingyu Chen•Bin Zhang•Win Topatana•Jiasheng Cao•Hepan Zhu等 9 人
Npj Precision Oncology
2020
•2020/6/8
•Vol.4 No.1 p.1-7
Hepatocellular carcinoma (HCC) is the most common subtype of liver cancer, and assessing its histopathological grade requires visual inspection by an experienced pathologist. In this study, the histopathological H&E images from the Genomic Data Commons Databases were used to train a neural network (...
Cancer imagingCancer modelsHepatocellular carcinoma
10.1038/S41698-020-0120-3
ISSN:2397-768X
RNF2 ablation reprograms the tumor-immune microenvironment and stimulates durable NK and CD4+ T-cell-dependent antitumor immunity
Zhang Zhuo•Luo Lin•Xing Chuan•Chen Yu•Xu Peng等 17 人
Nature Cancer
2021
•2021/10/22
•Vol.2 No.10 p.1018-1038
Expanding the utility of immune-based cancer treatments is a clinical challenge due to tumor-intrinsic factors that suppress the immune response. Here we report the identification of tumoral ring finger protein 2 (RNF2), the core subunit of polycomb repressor complex 1, as a negative regulator of an...
Breast cancerCancerTumour immunology
10.1038/S43018-021-00263-Z
ISSN:2662-1347
CHEK2 knockout is a therapeutic target for TP53-mutated hepatocellular carcinoma
Yuyan Chen•Zhengyi Zhu•Xingyu Wu•Hui Li•Wenxian Guan等 6 人
Cell Death Discovery
2024
•2024/1/19
•Vol.10 No.1 p.1-12
Currently, there is still a lack of novel and effective drug targets to improve the prognosis of hepatocellular carcinoma (HCC). Additionally, the role of CHEK2 in HCC has not been reported yet. The eQTLgen database and two HCC Genome-Wide Association Study (GWAS) datasets (ieu-b-4953, ICD10 C22.0) ...
Hepatocellular carcinomaTarget validation
10.1038/S41420-023-01777-4
ISSN:2058-7716
ADAR1 is required for acute myeloid leukemia cell survival by modulating post-transcriptional Wnt signaling through impairing miRNA biogenesis
Zhongrui Shi•Jiaxing Li•Jiayu Ding•Yiwen Zhang•Wenjian Min等 16 人
Leukemia
2024
•2024/12/19
•00 p.1-15
Recent extensive studies on the genomic and molecular profiles of acute myeloid leukemia (AML) have expanded the treatment options, including, a range of compounds represented by fms-like tyrosine kinase 3 and isocitrate dehydrogenase 1/2 inhibitors. However, despite this progress, further treatment...
Cell signallingOncogenes
10.1038/S41375-024-02500-7
ISSN:0887-6924
CENPF (+) cancer cells promote malignant progression of early-stage TP53 mutant lung adenocarcinoma
Yanlu Xiong•Jie Lei•Miaomiao Wen•Yongfu Ma•Jinbo Zhao等 19 人
Oncogenesis
2025
•2025/3/5
•Vol.14 No.1 p.1-15
The prevention and precise treatment of early-stage lung adenocarcinoma (LUAD) characterized by small nodules (stage IA) remains a significant challenge for clinicians, which is due largely to the limited understanding of the oncogenic mechanisms spanning from preneoplasia to invasive adenocarcinoma...
Non-small-cell lung cancerOncogenes
10.1038/S41389-025-00546-5
ISSN:2157-9024
Charting cell-type-specific positive genetic interaction at single-cell resolution for lung adenocarcinoma
Bo Chen•Mingyue Liu•Qi Dong•Chen Lv•Kaidong Liu等 11 人
Npj Precision Oncology
2026
•2026/2/18
•Vol.10 No.1 p.1370
Genetic interactions (GIs) drive carcinogenesis and treatment resistance via non-additive phenotypic effects between genes. Traditional bulk-based methods fail to capture cell-type-specific interactions in heterogeneous tumors like lung adenocarcinoma (LUAD), limiting precision oncology. Resolving c...
Cancer genomicsComputational biology and bioinformaticsTumour biomarkers
10.1038/S41698-026-01328-X
ISSN:2397-768X
Proteomic analysis reveals key differences between squamous cell carcinomas and adenocarcinomas across multiple tissues
Song Qi•Yang Ye•Jiang Dongxian•Qin Zhaoyu•Xu Chen等 25 人
Nature Communications
2022
•2022/7/18
•Vol.13 No.1 p.1-20
Squamous cell carcinoma (SCC) and adenocarcinoma (AC) are two main histological subtypes of solid cancer; however, SCCs are derived from different organs with similar morphologies, and it is challenging to distinguish the origin of metastatic SCCs. Here we report a deep proteomic analysis of 333 SCC...
Cancer microenvironmentProteomicsSquamous cell carcinomaTumour biomarkersTumour virus infections
10.1038/S41467-022-31719-0
ISSN:2041-1723
Truncated FGFR2 is a clinically actionable oncogene in multiple cancers
Zingg Daniel•Bhin Jinhyuk•Yemelyanenko Julia•Kas Sjors M.•Rolfs Frank等 48 人
Nature
2022
•2022/8/10
•Vol.608 No.7923 p.609-617
Somatic hotspot mutations and structural amplifications and fusions that affect fibroblast growth factor receptor 2 (encoded by FGFR2) occur in multiple types of cancer1. However, clinical responses to FGFR inhibitors have remained variable1–9, emphasizing the need to better understand which FGFR2 a...
Breast cancerCancer modelsGrowth factor signallingOncogenes
10.1038/S41586-022-05066-5
ISSN:0028-0836
A-to-I edited SNHG3 promotes non-small cell lung cancer metastasis by promoting fatty acid oxidation and resisting ferroptosis
Shizhen Chen•Amei Zhuo•Renyu Tang•Siming Su•Binbin Wen等 13 人
Communications Biology
2025
•2025/9/2
•Vol.8 No.1 p.1-16
Adenosine-to-inosine (A-to-I) RNA editing is a critical post-transcriptional modification that enhances tumor genome diversity and contributes to cancer progression. In non-small cell lung cancer (NSCLC), while specific A-to-I editing events have been identified, their functional mechanisms and clin...
Cancer epigeneticsPrognostic markers
10.1038/S42003-025-08776-4
ISSN:2399-3642
Multiscale imaging on proton pump-driven acidity for assessing tumor progression and metastasis
Silue Zeng•Jingqin Chen•Yaguang Ren•Jianyou Gu•Junfeng Zhang等 16 人
Nature Communications
2026
•2026/1/16
•Vol.17 No.1 p.17850
An acidic tumor microenvironment (TME), a hallmark of cancer progression, promotes tumor growth, invasion, and metastasis. Detecting and targeting tumor acidity have emerged as key frontiers in early cancer diagnosis and treatment. However, current approaches lack sensitive and specific methods to v...
Cancer imagingCancer metabolism
10.1038/S41467-026-68491-4
ISSN:2041-1723
Cytosolic pH regulates proliferation and tumour growth by promoting expression of cyclin D1
Lisa Maria Koch•Eivind Salmorin Birkeland•Stefania Battaglioni•Xiao Helle•Mayura Meerang等 11 人
Nature Metabolism
2020
•2020/10/19
•Vol.2 No.11 p.1212-1222
Enhanced growth and proliferation of cancer cells are accompanied by profound changes in cellular metabolism. These metabolic changes are also common under physiological conditions, and include increased glucose fermentation accompanied by elevated cytosolic pH (pHc)1,2. However, how these changes c...
Cancer metabolismCell-cycle exitMesotheliomaMetabolismMetabolomics
10.1038/S42255-020-00297-0
ISSN:2522-5812
Regression-based Deep-Learning predicts molecular biomarkers from pathology slides
Omar S. M. El Nahhas•Chiara M. L. Loeffler•Zunamys I. Carrero•Marko van Treeck•Fiona R. Kolbinger等 17 人
Nature Communications
2024
•2024/2/10
•Vol.15 No.1 p.1-13
Deep Learning (DL) can predict biomarkers from cancer histopathology. Several clinically approved applications use this technology. Most approaches, however, predict categorical labels, whereas biomarkers are often continuous measurements. We hypothesize that regression-based DL outperforms cla...
Cancer imagingImage processingMachine learningPrognostic markersTumour biomarkers
10.1038/S41467-024-45589-1
ISSN:2041-1723
Visual barcodes for clonal-multiplexing of live microscopy-based assays
Kaufman Tom•Nitzan Erez•Firestein Nir•Ginzberg Miriam Bracha•Iyengar Seshu等 13 人
Nature Communications
2022
•2022/5/18
•Vol.13 No.1 p.1-17
While multiplexing samples using DNA barcoding revolutionized the pace of biomedical discovery, multiplexing of live imaging-based applications has been limited by the number of fluorescent proteins that can be deconvoluted using common microscopy equipment. To address this limitation, we develop vi...
CancerRegulatory networksStress signalling
10.1038/S41467-022-30008-0
ISSN:2041-1723
Chromothripsis drives the evolution of gene amplification in cancer
Ofer Shoshani•Simon F. Brunner•Rona Yaeger•Peter Ly•Yael Nechemia-Arbely等 15 人
Nature
2020
•2020/12/23
•Vol.591 No.7848 p.137-141
Focal chromosomal amplification contributes to the initiation of cancer by mediating overexpression of oncogenes1–3, and to the development of cancer therapy resistance by increasing the expression of genes whose action diminishes the efficacy of anti-cancer drugs. Here we used whole-genome sequenci...
Cancer genomicsCancer therapeutic resistanceChromosomesMechanisms of diseaseOncogenes
10.1038/S41586-020-03064-Z
ISSN:0028-0836
Bio-interpretable ensemble learning model for invasive pulmonary adenocarcinoma grade using CT and histopathology images
Zhihe Yang•Fan Li•Qijia Han•Zhu Ai•Minyi Wu等 13 人
Npj Precision Oncology
2025
•2025/12/18
0The significant heterogeneity and complex morphology of invasive pulmonary adenocarcinoma (IPA) make grading challenging for pathologists. However, thorough investigations into radiopathomics features extracted from computed tomography (CT) and whole slide images (WSIs) for IPA grading and their bio...
Cancer genomicsCancer imagingCancer modelsComputational biology and bioinformaticsNon-small-cell lung cancerTumour biomarkers+1
10.1038/S41698-025-01239-3
ISSN:2397-768X
Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing
Jiao Cao•Zhong Zheng•Di Sun•Xin Chen•Rui Cheng等 11 人
Nature Biotechnology
2024
•2024/1/16
•00 p.1-12
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high resolution. Decoder-seq combines dendrimeric nan...
Gene expression analysisRNA sequencing
10.1038/S41587-023-02086-Y
ISSN:1087-0156
Polymerase theta expression is correlated with proliferative capacity but not with DNA repair deficiency status in solid tumors
Zsofia Sztupinszki•Regina Fiam•Orsolya Pipek•Miklos Diossy•Judit Börcsök等 8 人
Npj Precision Oncology
2025
•2025/6/20
•Vol.9 No.1 p.1-7
Polymerase theta (POLθ) inhibitors were developed to overcome resistance to PARP inhibitor treatment in homologous recombination (HR) deficient cancer. Biomarkers identifying PARP inhibitor-resistant cancer cases that specifically rely on POLθ activity for cancer cell survival will help to identify ...
Cancer genomicsGynaecological cancerPredictive markersTranslational researchTumour biomarkers
10.1038/S41698-025-01000-W
ISSN:2397-768X
A spatially localized DNA linear classifier for cancer diagnosis
Linlin Yang•Qian Tang•Mingzhi Zhang•Yuan Tian•Xiaoxing Chen等 10 人
Nature Communications
2024
•2024/5/29
•Vol.15 No.1 p.1-11
Molecular computing is an emerging paradigm that plays an essential role in data storage, bio-computation, and clinical diagnosis with the future trends of more efficient computing scheme, higher modularity with scaled-up circuity and stronger tolerance of corrupted inputs in a complex environment. ...
Bioanalytical chemistryBiosynthesisDNA computingDNA sequencingNanobiotechnology
10.1038/S41467-024-48869-Y
ISSN:2041-1723
Differential whole-genome doubling and homologous recombination deficiencies across breast cancer subtypes from the Taiwanese population
Wu Chia-Hsin•Hsieh Chia-Shan•Chang Yo-Cheng•Huang Chi-Cheng•Yeh Hsien-Tang等 15 人
Communications Biology
2021
•2021/9/9
•Vol.4 No.1 p.1-12
Whole-genome doubling (WGD) is an early macro-evolutionary event in tumorigenesis, involving the doubling of an entire chromosome complement. However, its impact on breast cancer subtypes remains unclear. Here, we performed a comprehensive and quantitative analysis of WGD and its influence on breast...
Breast cancerCancer geneticsCancer genomics
10.1038/S42003-021-02597-X
ISSN:2399-3642
NgR1 is an NK cell inhibitory receptor that destabilizes the immunological synapse
Oh Se-Chan•Kim Seong-Eun•Jang In-Hwan•Kim Seok-Min•Lee Soo Yun等 12 人
Nature Immunology
2023
•2023/1/9
•Vol.24 No.3 p.463-473
The formation of an immunological synapse (IS) is essential for natural killer (NK) cells to eliminate target cells. Despite an advanced understanding of the characteristics of the IS and its formation processes, the mechanisms that regulate its stability via the cytoskeleton are unclear. Here, we s...
NK cellsTumour immunology
10.1038/S41590-022-01394-W
ISSN:1529-2908
TM9SF1 drives the lipophagic flux via AMPK-ULK1 signaling to sustain metabolic fitness in HER2-positive breast cancer
Xiaofen Li•Xiaoqin Yu•Kaiyan Huang•Xin Yu•Shiping Luo等 7 人
Cell Death & Disease
2025
•2025/10/24
•Vol.16 No.1 p.1-13
Therapeutic resistance and recurrence in human epidermal growth factor receptor 2-positive breast cancer (HER2 + BC) remain critical challenges that portend poor patient outcomes. Dysregulated autophagy and lipid metabolism contribute to tumor progression, yet the crosstalk between these pathways is...
AutophagyBreast cancerPrognostic markers
10.1038/S41419-025-08093-Y
ISSN:2041-4889
Pan-cancer image-based detection of clinically actionable genetic alterations
Jakob Nikolas Kather•Lara R. Heij•Heike I. Grabsch•Chiara Loeffler•Amelie Echle等 28 人
Nature Cancer
2020
•2020/7/27
•Vol.1 No.8 p.789-799
Molecular alterations in cancer can cause phenotypic changes in tumor cells and their microenvironment. Routine histopathology tissue slides, which are ubiquitously available, can reflect such morphological changes. Here, we show that deep learning can consistently infer a wide range of genetic muta...
CancerCancer genomicsComputer sciencePredictive markers
10.1038/S43018-020-0087-6
ISSN:2662-1347
Tumor diversity and the trade-off between universal cancer tasks
Jean Hausser•Pablo Szekely•Noam Bar•Anat Zimmer•Hila Sheftel等 7 人
Nature Communications
2019
•2019/11/28
•Vol.10 No.1 p.1-13
Recent advances have enabled powerful methods to sort tumors into prognosis and treatment groups. We are still missing, however, a general theoretical framework to understand the vast diversity of tumor gene expression and mutations. Here we present a framework based on multi-task evolution theory, ...
CancerSystems biology
10.1038/S41467-019-13195-1
ISSN:2041-1723
The USP11/Nrf2 positive feedback loop promotes colorectal cancer progression by inhibiting mitochondrial apoptosis
Yuanyuan Lu•Wanhui wei•Mengting Li•Danyang Chen•Wenjie Li等 9 人
Cell Death & Disease
2024
•2024/12/1
•Vol.15 No.12 p.1-12
Abnormal antioxidant capacity of cancer is closely related to tumor malignancy. Modulation of oxidative stress status is a novel anticancer therapeutic target. Nrf2 is a key regulator of various antioxidant enzymes, but the mechanism of its deubiquitination remains largely unclear. This study unveil...
Colorectal cancerGastrointestinal diseases
10.1038/S41419-024-07188-2
ISSN:2041-4889
The clinical and molecular landscape of breast cancer in women of African and South Asian ancestry
Graeme J. Thorn•Emanuela Gadaleta•Abu Z. M. Dayem Ullah•Lewis G. E. James•Maryam Abdollahyan等 8 人
Nature Communications
2025
•2025/5/20
•Vol.16 No.1 p.1-20
Addressing existing racial disparity in breast cancer is crucial to ensure equitable benefit across diverse communities. We evaluate the molecular and clinical effects of genetic ancestry in African and South Asian women compared to European using a combined cohort of 7136 breast cancer patients. We...
Breast cancerCancer geneticsCancer genomicsComputational biology and bioinformatics
10.1038/S41467-025-59144-Z
ISSN:2041-1723
Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy
Sung Pil Hong•Thalia E. Chan•Ylenia Lombardo•Giacomo Corleone•Nicole Rotmensz等 12 人
Nature Communications
2019
•2019/9/2
•Vol.10 No.1 p.1-14
Resistant tumours are thought to arise from the action of Darwinian selection on genetically heterogenous cancer cell populations. However, simple clonal selection is inadequate to describe the late relapses often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting ...
Breast cancerCancer therapeutic resistanceComputational modelsMechanisms of disease
10.1038/S41467-019-11721-9
ISSN:2041-1723
Digital profiling of gene expression from histology images with linearized attention
Marija Pizurica•Yuanning Zheng•Francisco Carrillo-Perez•Humaira Noor•Wei Yao等 9 人
Nature Communications
2024
•2024/11/14
•Vol.15 No.1 p.1-14
Cancer is a heterogeneous disease requiring costly genetic profiling for better understanding and management. Recent advances in deep learning have enabled cost-effective predictions of genetic alterations from whole slide images (WSIs). While transformers have driven significant progress in non-med...
Cancer genomicsCancer imagingMachine learningTranscriptomicsTumour heterogeneity
10.1038/S41467-024-54182-5
ISSN:2041-1723
Distinct resistance mechanisms arise to allosteric vs. ATP-competitive AKT inhibitors
Savill Kristin M. Zimmerman•Lee Brian B.•Oeh Jason•Lin Jie•Lin Eva等 22 人
Nature Communications
2022
•2022/4/19
•Vol.13 No.1 p.1-17
The AKT kinases have emerged as promising therapeutic targets in oncology and both allosteric and ATP-competitive AKT inhibitors have entered clinical investigation. However, long-term efficacy of such inhibitors will likely be challenged by the development of resistance. We have established prostat...
Cancer therapyKinasesProstate cancerTarget identificationTarget validation
10.1038/S41467-022-29655-0
ISSN:2041-1723
Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes
Ting Fu•Kofi Amoah•Tracey W. Chan•Jae Hoon Bahn•Jae-Hyung Lee等 9 人
Nature Communications
2024
•2024/4/18
•Vol.15 No.1 p.1-20
Understanding the function of rare non-coding variants represents a significant challenge. Using MapUTR, a screening method, we studied the function of rare 3′ UTR variants affecting mRNA abundance post-transcriptionally. Among 17,301 rare gnomAD variants, an average of 24.5% were functional, with 7...
Gene expression profilingGene regulation
10.1038/S41467-024-46795-7
ISSN:2041-1723
Pan-cancer multi-omic integration of Trop2 reveals biological determinants and translational implications for ADC therapy
Giulia Notini•Barbara Galbardi•Giulia Viale•Matteo M. Naldini•Carlo Bosi等 22 人
Npj Precision Oncology
2026
•2026/6/15
•Vol.10 No.1 p.2180
Trop2–directed antibody-drug conjugates (ADCs) show activity across epithelial cancers, yet determinants of target expression in tumors and normal tissues remain poorly defined. We integrated bulk and single-cell transcriptomic profiles from over 20,000 samples across TCGA, GTEx and public atlases t...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41698-026-01523-W
ISSN:2397-768X
Learning to predict RNA sequence expressions from whole slide images with applications for search and classification
Alsaafin Areej•Safarpoor Amir•Sikaroudi Milad•Hipp Jason D.•Tizhoosh H. R.
Communications Biology
2023
•2023/3/22
•Vol.6 No.1 p.1-9
Deep learning methods are widely applied in digital pathology to address clinical challenges such as prognosis and diagnosis. As one of the most recent applications, deep models have also been used to extract molecular features from whole slide images. Although molecular tests carry rich information...
Cancer imagingSoftware
10.1038/S42003-023-04583-X
ISSN:2399-3642
Towards a general-purpose foundation model for computational pathology
Richard J. Chen•Tong Ding•Ming Y. Lu•Drew F. K. Williamson•Guillaume Jaume等 20 人
Nature Medicine
2024
•2024/3/19
•Vol.30 No.3 p.850-862
Quantitative evaluation of tissue images is crucial for computational pathology (CPath) tasks, requiring the objective characterization of histopathological entities from whole-slide images (WSIs). The high resolution of WSIs and the variability of morphological features present significant challeng...
Biomedical engineeringMachine learningPathology
10.1038/S41591-024-02857-3
ISSN:1078-8956
The EHMT2-MBLAC2 axis suppresses ribosomal DNA transcription in response to nucleolar DNA damage
Chenyue Wang•Qiutian Lu•Lianbao Cao•Simeng Zeng•Zihan Gao等 9 人
Cell Death & Disease
2026
•2026/3/18
•Vol.17 No.1 p.3200
The induction of DNA double-strand breaks (DSBs) within actively transcribed ribosomal DNA (rDNA) arrays triggers transcriptional suppression and drives nucleolar reorganization, including the formation of nucleolar caps that facilitate the engagement of DSBs with canonical DSB signaling and repair ...
DNA damage and repairMolecular biology
10.1038/S41419-026-08616-1
ISSN:2041-4889
TRIM24 is critical for the cellular response to DNA double-strand breaks through regulating the recruitment of MRN complex
Wang Ya•Yao Yuanbing•Wei Qunhui•Long Shichao•Chen Yuqiao等 13 人
Oncogene
2022
•2022/12/22
•Vol.42 No.8 p.586-600
The MRE11-RAD50-NBS1 (MRN) complex plays a crucial role in DNA double-strand breaks (DSBs) sensing and initiation of signaling cascades. However, the precise mechanisms by which the recruitment of MRN complex is regulated has yet to be elucidated. Here, we identified TRIpartite motif-containing prot...
Cell deathOncogenes
10.1038/S41388-022-02580-8
ISSN:0950-9232
Tumour vasculature at single-cell resolution
Xu Pan•Xin Li•Liang Dong•Teng Liu•Min Zhang等 16 人
Nature
2024
•2024/7/10
•Vol.632 No.8024 p.429-436
Tumours can obtain nutrients and oxygen required to progress and metastasize through the blood supply1. Inducing angiogenesis involves the sprouting of established vessel beds and their maturation into an organized network2,3. Here we generate a comprehensive atlas of tumour vasculature at single-ce...
Cancer microenvironmentTumour angiogenesis
10.1038/S41586-024-07698-1
ISSN:0028-0836
Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer
Y. A. Jakubek•K. Chang•S. Sivakumar•Y. Yu•M. R. Giordano等 10 人
Nature Biotechnology
2019
•2019/11/4
•Vol.38 No.1 p.90-96
Mosaicism, the presence of subpopulations of cells bearing somatic mutations, is associated with disease and aging and has been detected in diverse tissues, including apparently normal cells adjacent to tumors. To analyze mosaicism on a large scale, we surveyed haplotype-specific somatic copy number...
Cancer genomicsHaplotypes
10.1038/S41587-019-0297-6
ISSN:1087-0156
A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer
Kaivalya Walavalkar•Bharath Saravanan•Anurag Kumar Singh•Ranveer Singh Jayani•Ashwin Nair等 14 人
Nature Communications
2020
•2020/7/17
•Vol.11 No.1 p.1-14
Genetic variation at the 8q24 locus is linked with the greater susceptibility to prostate cancer in men of African ancestry. One such African ancestry specific rare variant, rs72725854 (A>G/T) (~6% allele frequency) has been associated with a ~2-fold increase in prostate cancer risk. However, the fu...
Cancer epigeneticsChromatin structureFunctional genomics
10.1038/S41467-020-17325-Y
ISSN:2041-1723
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries
Sean A. Misek•Aaron Fultineer•Jeremie Kalfon•Javad Noorbakhsh•Isabella Boyle等 17 人
Nature Communications
2024
•2024/6/7
•Vol.15 No.1 p.1-11
Reducing disparities is vital for equitable access to precision treatments in cancer. Socioenvironmental factors are a major driver of disparities, but differences in genetic variation likely also contribute. The impact of genetic ancestry on prioritization of cancer targets in drug discovery pipeli...
Cancer genomicsCancer modelsCRISPR-Cas9 genome editing
10.1038/S41467-024-48957-Z
ISSN:2041-1723
Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants
Anqi Wang•Jiayi Shen•Alex A. Rodriguez•Edward J. Saunders•Fei Chen等 291 人
Nature Genetics
2023
•2023/11/9
•00 p.1-10
The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls...
Genetics researchGenome-wide association studiesPreventive medicineProstate cancer
10.1038/S41588-023-01534-4
ISSN:1061-4036
Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy
Maxime W. Lafarge•Enric Domingo•Korsuk Sirinukunwattana•Ruby Wood•Leslie Samuel等 20 人
Npj Precision Oncology
2024
•2024/4/9
•Vol.8 No.1 p.1-11
The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (W...
Translational researchTumour biomarkers
10.1038/S41698-024-00580-3
ISSN:2397-768X
Noninvasive prediction of occult pT3a upstaging in localized ccRCC with radiogenomic insights and prognostic relevance
Shichao Li•Chuhuai Wang•Feng Li•Mengmeng Gao•Kangwen He等 13 人
Npj Precision Oncology
2026
•2026/2/3
•Vol.10 No.1 p.1040
Occult pathological T3a (pT3a) upstaging in cT1b–T2a clear cell renal cell carcinoma (ccRCC) correlated with poor prognosis and necessitated modifications in surgical planning. However, predicting it preoperatively remains challenging. In this multicenter study involving 1661 patients across five in...
BiomarkersCancerComputational biology and bioinformaticsOncologyUrology
10.1038/S41698-026-01315-2
ISSN:2397-768X
Integrating multimodal cancer data using deep latent variable path modelling
Alex Ing•Alvaro Andrades•Marco Raffaele Cosenza•Jan O. Korbel
Nature Machine Intelligence
2025
•2025/7/22
•Vol.7 No.7 p.1053-1075
Cancers are commonly characterized by a complex pathology encompassing genetic, microscopic and macroscopic features, which can be probed individually using imaging and omics technologies. Integrating these data to obtain a full understanding of pathology remains challenging. We introduce a method c...
Breast cancerComputer scienceData integrationMachine learning
10.1038/S42256-025-01052-4
ISSN:2522-5839
Deep learning inference of cell type-specific gene expression from breast tumor histopathology
Andrew T. Wang•Saugato Rahman Dhruba•Emma M. Campagnolo•Keluo Yao•Peng Jiang等 9 人
Npj Precision Oncology
2026
•2026/4/16
0Cell type-specific gene expression from single-cell RNA sequencing (RNA-seq) is valuable for breast cancer precision oncology but available cohorts are still limited due to its high cost. Deconvolution methods infer cell type-specific expression from bulk RNA-seq at a lower cost, yet expenses and pr...
Breast cancerCancer microenvironment
10.1038/S41698-026-01419-9
ISSN:2397-768X
Generation of synthetic whole-slide image tiles of tumours from RNA-sequencing data via cascaded diffusion models
Francisco Carrillo-Perez•Marija Pizurica•Yuanning Zheng•Tarak Nath Nandi•Ravi Madduri等 7 人
Nature Biomedical Engineering
2024
•2024/3/21
•00 p.1-13
Training machine-learning models with synthetically generated data can alleviate the problem of data scarcity when acquiring diverse and sufficiently large datasets is costly and challenging. Here we show that cascaded diffusion models can be used to synthesize realistic whole-slide image tiles from...
Cancer imagingComputational modelsMachine learning
10.1038/S41551-024-01193-8
ISSN:2157-846X
Inhibition of SF3B1 improves the immune microenvironment through pyroptosis and synergizes with αPDL1 in ovarian cancer
Shourong Wang•Yao Liu•Huimin Xiao•Zhongshao Chen•Xiaohang Yang等 14 人
Cell Death & Disease
2023
•2023/11/27
•Vol.14 No.11 p.1-14
Ovarian cancer is resistant to immune checkpoint blockade (ICB) treatment. Combination of targeted therapy and immunotherapy is a promising strategy for ovarian cancer treatment benefit from an improved immune microenvironment. In this study, Clinical Proteomic Tumor Analysis Consortium (CPTAC) and ...
Cancer microenvironmentImmunotherapyOvarian cancer
10.1038/S41419-023-06301-1
ISSN:2041-4889
KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage
Zheqi Li•Guillermo Peluffo•Laura E. Stevens•Xintao Qiu•Marco Seehawer等 38 人
Nature Genetics
2025
•2025/6/2
•00 p.1-15
Basal breast cancer is a subtype with a poor prognosis in need of more effective therapeutic approaches. Here we describe a unique role for the KDM4C histone lysine demethylase in KDM4C-amplified basal breast cancers, where KDM4C inhibition reshapes chromatin and transcriptomic landscapes without su...
Breast cancerEpigenetics
10.1038/S41588-025-02197-Z
ISSN:1061-4036
Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes
Erin Pleasance•Emma Titmuss•Laura Williamson•Harwood Kwan•Luka Culibrk等 71 人
Nature Cancer
2020
•2020/4/13
•Vol.1 No.4 p.452-468
Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging ...
Cancer genomicsCancer therapy
10.1038/S43018-020-0050-6
ISSN:2662-1347
INPP5A phosphatase is a synthetic lethal target in GNAQ and GNA11-mutant melanomas
Ahmed M. O. Elbatsh•Ali Amin-Mansour•Anne Haberkorn•Claudia Textor•Nicolas Ebel等 22 人
Nature Cancer
2024
•2024/1/17
•00 p.1-19
Activating mutations in GNAQ/GNA11 occur in over 90% of uveal melanomas (UMs), the most lethal melanoma subtype; however, targeting these oncogenes has proven challenging and inhibiting their downstream effectors show limited clinical efficacy. Here, we performed genome-scale CRISPR screens along wi...
CancerCancer geneticsEye cancer
10.1038/S43018-023-00710-Z
ISSN:2662-1347
Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Bilal Unal•Omer Faruk Kuzu•Yang Jin•Daniel Osorio•Wanja Kildal等 14 人
Nature Communications
2024
•2024/10/15
•Vol.15 No.1 p.1-21
Unfolded protein response (UPR) is a central stress response pathway that is hijacked by tumor cells for their survival. Here, we find that IRE1α signaling, one of the canonical UPR arms, is increased in prostate cancer (PCa) patient tumors. Genetic or small molecule inhibition of IRE1α in syngeneic...
Cancer microenvironmentProstate cancerStress signalling
10.1038/S41467-024-53039-1
ISSN:2041-1723
Unraveling mutagenic processes influencing the tumor mutational patterns of individuals with constitutional mismatch repair deficiency
Dilys D. Weijers•Snežana Hinić•Emma Kroeze•Mark AJ Gorris•Gerty Schreibelt等 20 人
Nature Communications
2025
•2025/5/14
•Vol.16 No.1 p.1-13
Constitutional mismatch repair deficiency (CMMRD), caused by bi-allelic germline variants in mismatch repair (MMR) genes, is associated with high cancer incidence early in life. A better understanding of mutational processes driving sequential CMMRD tumors can advance optimal treatment. Here, we des...
Cancer geneticsCancer genomicsPaediatric cancerTumour heterogeneity
10.1038/S41467-025-59775-2
ISSN:2041-1723
Targeting BCL9/BCL9L enhances antigen presentation by promoting conventional type 1 dendritic cell (cDC1) activation and tumor infiltration
Fenglian He•Zhongen Wu•Chenglong Liu•Yuanyuan Zhu•Yan Zhou等 10 人
Signal Transduction And Targeted Therapy
2024
•2024/5/29
•Vol.9 No.1 p.1-15
Conventional type 1 dendritic cells (cDC1) are the essential antigen-presenting DC subset in antitumor immunity. Suppressing B-cell lymphoma 9 and B-cell lymphoma 9-like (BCL9/BCL9L) inhibits tumor growth and boosts immune responses against cancer. However, whether oncogenic BCL9/BCL9L impairs antig...
Cancer microenvironmentTumour immunology
10.1038/S41392-024-01838-9
ISSN:2059-3635
Exosomal miR-1304-3p promotes breast cancer progression in African Americans by activating cancer-associated adipocytes
Zhao Dan•Wu Kerui•Sharma Sambad•Xing Fei•Wu Shih-Ying等 11 人
Nature Communications
2022
•2022/12/14
•Vol.13 No.1 p.1-15
Breast cancer displays disparities in mortality between African Americans and Caucasian Americans. However, the exact molecular mechanisms remain elusive. Here, we identify miR-1304-3p as the most upregulated microRNA in African American patients. Importantly, its expression significantly correlates...
Breast cancerCancer geneticsCancer microenvironment
10.1038/S41467-022-35305-2
ISSN:2041-1723
The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma
Xiaoxi Pan•Khalid AbdulJabbar•Jose Coelho-Lima•Anca-Ioana Grapa•Hanyun Zhang等 19 人
Nature Cancer
2024
•2024/1/10
•00 p.1-17
The introduction of the International Association for the Study of Lung Cancer grading system has furthered interest in histopathological grading for risk stratification in lung adenocarcinoma. Complex morphology and high intratumoral heterogeneity present challenges to pathologists, prompting the d...
Image processingMachine learningNon-small-cell lung cancer
10.1038/S43018-023-00694-W
ISSN:2662-1347
Inactivation of the Hippo tumor suppressor pathway promotes melanoma
Vittoria Marc A.•Kingston Nathan•Kotynkova Kristyna•Xia Eric•Hong Rui等 15 人
Nature Communications
2022
•2022/6/29
•Vol.13 No.1 p.1-17
Melanoma is commonly driven by activating mutations in the MAP kinase BRAF; however, oncogenic BRAF alone is insufficient to promote melanomagenesis. Instead, its expression induces a transient proliferative burst that ultimately ceases with the development of benign nevi comprised of growth-arreste...
Cell divisionGrowth factor signallingMelanomaOncogenes
10.1038/S41467-022-31399-W
ISSN:2041-1723
Mitochondrial clonal mosaicism encodes a biphasic molecular clock of aging
Zhenguo Wang•Zhe Li•Hongyu Liu•Chenghua Yang•Xin Li
Nature Aging
2025
•2025/5/27
•00 p.1-15
Mitochondria rapidly accumulate mutations throughout a lifetime, potentially acting as a molecular clock for aging and disease. We profiled mitochondrial RNA across 47 human tissues from 838 individuals, revealing rapid development of clonal mosaicism with two distinct tissue-specific aging signatur...
BiomarkersGenetics
10.1038/S43587-025-00890-6
ISSN:2662-8465
A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes
Yueyuan Zheng•Guowei Huang•Tiago C. Silva•Qian Yang•Yan-Yi Jiang等 8 人
Nature Communications
2021
•2021/4/30
•Vol.12 No.1 p.1-16
CpG Island promoter genes make up more than half of human genes, and a subset regulated by Polycomb-Repressive Complex 2 (PRC2+-CGI) become DNA hypermethylated and silenced in cancer. Here, we perform a systematic analysis of CGI genes across TCGA cancer types, finding that PRC2+-CGI genes are frequ...
Cancer genomicsEpigenomics
10.1038/S41467-021-22720-0
ISSN:2041-1723
The genotypes and phenotypes of missense mutations in the proline domain of the p53 protein
Hoyos David•Greenbaum Benjamin•Levine Arnold J.
Cell Death & Differentiation
2022
•2022/4/5
•00 p.1-8
The p53 protein is structurally and functionally divided into five domains. The proline-rich domain is localized at amino acids 55–100. 319 missense mutations were identified solely in the proline domain from human cancers. Six hotspot mutations were identified at amino acids 72, 73, 82, 84, 89, and...
Cancer geneticsTumour-suppressor proteins
10.1038/S41418-022-00980-7
ISSN:1350-9047
Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology
Chu Tinyi•Wang Zhong•Pe’er Dana•Danko Charles G.
Nature Cancer
2022
•2022/4/25
•Vol.3 No.4 p.505-517
Inferring single-cell compositions and their contributions to global gene expression changes from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we develop Bayesian cell proportion reconstruction inferred using statistical marginalization (BayesPrism), a Bayesian metho...
CancerCancer genomicsStatistical methods
10.1038/S43018-022-00356-3
ISSN:2662-1347
Inhibition of MBTPS1 enhances antitumor immunity and potentiates anti-PD-1 immunotherapy
Yi-Yu Wang•Jin-Fei Lin•Wen-Wei Wu•Zhe Fu•Fen Cao等 14 人
Nature Communications
2025
•2025/4/30
•Vol.16 No.1 p.1-21
Despite advances in cancer immunotherapy, colorectal cancer patients exhibit limited therapeutic responses. Therefore, the exploration of strategies combining immunotherapy with adjuvant approaches to enhance adaptive immune responses is in demand. Here, we perform a customized in vivo CRISPR-Cas9 s...
Cancer epigeneticsCancer immunotherapyCancer microenvironmentCancer therapy
10.1038/S41467-025-59193-4
ISSN:2041-1723
Personalized risk stratification in colorectal cancer via PIANOS system
Du Cai•Haoning Qi•Qiuxia Yang•Huayu Li•Chenghang Li等 11 人
Nature Communications
2025
•2025/7/16
•Vol.16 No.1 p.1-18
Current prognostic biomarkers for colorectal cancer (CRC) lack stability and generalizability across different cohorts and platforms, challenging precise patient stratification. Here, we introduce a Platform Independent and Normalization Free Single-sample Classifier (PIANOS), designed to refine tre...
Cancer genomicsColorectal cancerPrognostic markersStatistical methods
10.1038/S41467-025-61713-1
ISSN:2041-1723
SPOP/NOLC1/B4GALT1 signaling axis enhances paclitaxel resistance in endometrial cancer by inducing O-dysglycosylation
Fengguang Zhai•Yuxuan Li•Jingfei Zheng•Chunhong Yan•Shuyan Wang等 17 人
Oncogene
2025
•2025/3/17
•00 p.1-15
The effective treatment of paclitaxel-resistant patients remains a major challenge. We found that nucleolar and coiled body phosphoprotein 1 (NOLC1) was highly expressed in the paclitaxel-resistant endometrial cancer (ECa) cells and pathological tissue of ECa patients, which could promote the occurr...
Cancer therapeutic resistanceDiagnostic markers
10.1038/S41388-025-03347-7
ISSN:0950-9232
A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology
Julian Petersen•Lukas Englmaier•Artem V. Artemov•Irina Poverennaya•Ruba Mahmoud等 45 人
Nature Communications
2023
•2023/5/29
•Vol.14 No.1 p.1-22
In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through th...
Evolutionary geneticsGenetic modelsKidney
10.1038/S41467-023-38663-7
ISSN:2041-1723
Multi-omics clustering analysis carries out the molecular-specific subtypes of thyroid carcinoma: implicating for the precise treatment strategies
Zhenglin Wang•Qijun Han•Xianyu Hu•Xu Wang•Rui Sun等 7 人
Genes & Immunity
2025
•2025/3/4
•00 p.1-14
Thyroid cancer (TC) is the most prevalent endocrine malignancy worldwide. This study aimed to explore the molecular subtypes and improve the selection of targeted therapies. We used multi-omics data from 539 patients with DNA methylation, gene mutations, mRNA, lncRNA, and miRNA expressions. This stu...
Cancer geneticsGenetic markers
10.1038/S41435-025-00322-W
ISSN:1476-5470
Alternative ANKHD1 transcript promotes proliferation and inhibits migration in uterine corpus endometrial carcinoma
Sun Wenhuizi•Huang Runzhi•Li Zhenyu•Zhu Yaru•Bai Yan等 13 人
Npj Genomic Medicine
2022
•2022/9/29
•Vol.7 No.1 p.1-12
Alternative splicing (AS) is common in gene expression, and abnormal splicing often results in several cancers. Overall survival-associated splicing events (OS-SEs) have been used to predict prognosis in cancer. The aim of this study was to investigate the presence and function of OS-SEs in uterine ...
Endometrial cancerGene regulationGene regulatory networksMetastasis
10.1038/S41525-022-00321-0
ISSN:2056-7944
Targeting SNRNP200-induced splicing dysregulation offers an immunotherapy opportunity for glycolytic triple-negative breast cancer
Wenxiao Yang•Luo Hong•Linwei Guo•Yunjin Wang•Xiangchen Han等 13 人
Cell Discovery
2024
•2024/9/17
•Vol.10 No.1 p.1-19
Metabolic dysregulation is prominent in triple-negative breast cancer (TNBC), yet therapeutic strategies targeting cancer metabolism are limited. Here, utilizing multiomics data from our TNBC cohort (n = 465), we demonstrated widespread splicing deregulation and increased spliceosome abundance in th...
Breast cancerCancer metabolismCancer microenvironmentTumour immunology
10.1038/S41421-024-00715-7
ISSN:2056-5968
Bone morphogenetic protein 7 promotes resistance to immunotherapy
Maria Angelica Cortez•Fatemeh Masrorpour•Cristina Ivan•Jie Zhang•Ahmed I. Younes等 18 人
Nature Communications
2020
•2020/9/24
•Vol.11 No.1 p.1-14
Immunotherapies revolutionized cancer treatment by harnessing the immune system to target cancer cells. However, most patients are resistant to immunotherapies and the mechanisms underlying this resistant is still poorly understood. Here, we report that overexpression of BMP7, a member of the TGFB s...
Cancer immunotherapyCancer therapeutic resistance
10.1038/S41467-020-18617-Z
ISSN:2041-1723
Increased ONECUT2 induced by Helicobacter pylori promotes gastric cancer cell stemness via an AKT-related pathway
Mi Lin•Ru-Hong Tu•Sheng-Ze Wu•Qing Zhong•Kai Weng等 15 人
Cell Death & Disease
2024
•2024/7/12
•Vol.15 No.7 p.1-13
Helicobacter pylori (HP) infection initiates and promotes gastric carcinogenesis. ONECUT2 shows promise for tumor diagnosis, prognosis, and treatment. This study explored ONECUT2’s role and the specific mechanism underlying HP infection-associated gastric carcinogenesis to suggest a basis for target...
Cancer stem cellsGastric cancer
10.1038/S41419-024-06885-2
ISSN:2041-4889
T-bet+CD8+ T cells govern anti-PD-1 responses in microsatellite-stable gastric cancers
Shiying Tang•Xiaofang Che•Jinyan Wang•Ce Li•Xin He等 14 人
Nature Communications
2025
•2025/4/25
•Vol.16 No.1 p.1-17
More than 90% of advanced gastric cancers (GC) are microsatellite-stable (MSS). Compared to the high response rate of immune checkpoint inhibitors (ICI) in microsatellite-instability-high (MSI-H) GCs, only 10% of unstratified MSS GCs respond to ICIs. In this study, we apply semi-supervised learning ...
Cancer microenvironmentCytotoxic T cellsGastrointestinal cancerImmunotherapy
10.1038/S41467-025-58958-1
ISSN:2041-1723
Predicting the tumor microenvironment composition and immunotherapy response in non-small cell lung cancer from digital histopathology images
Sushant Patkar•Alex Chen•Alina Basnet•Amber Bixby•Rahul Rajendran等 17 人
Npj Precision Oncology
2024
•2024/12/19
•Vol.8 No.1 p.1-15
Immune checkpoint inhibitors (ICI) have become integral to treatment of non-small cell lung cancer (NSCLC). However, reliable biomarkers predictive of immunotherapy efficacy are limited. Here, we introduce HistoTME, a novel weakly supervised deep learning approach to infer the tumor microenvironment...
Cancer imagingCancer microenvironmentNon-small-cell lung cancerTumour biomarkers
10.1038/S41698-024-00765-W
ISSN:2397-768X
Self-supervised attention-based deep learning for pan-cancer mutation prediction from histopathology
Saldanha Oliver Lester•Loeffler Chiara M. L.•Niehues Jan Moritz•van Treeck Marko•Seraphin Tobias P.等 11 人
Npj Precision Oncology
2023
•2023/3/28
•Vol.7 No.1 p.1-5
The histopathological phenotype of tumors reflects the underlying genetic makeup. Deep learning can predict genetic alterations from pathology slides, but it is unclear how well these predictions generalize to external datasets. We performed a systematic study on Deep-Learning-based prediction of ge...
Computational biology and bioinformaticsDiagnostic markersMathematics and computing
10.1038/S41698-023-00365-0
ISSN:2397-768X
SMMILe enables accurate spatial quantification in digital pathology using multiple-instance learning
Zeyu Gao•Anyu Mao•Yuxing Dong•Hannah Clayton•Jialun Wu等 11 人
Nature Cancer
2025
•2025/11/19
•00 p.1-17
Spatial quantification is a critical step in most computational pathology tasks, from guiding pathologists to areas of clinical interest to discovering tissue phenotypes behind novel biomarkers. To circumvent the need for manual annotations, modern computational pathology methods have favored multip...
CancerCancer imagingComputational biology and bioinformaticsTumour biomarkersTumour heterogeneity
10.1038/S43018-025-01060-8
ISSN:2662-1347
Nuclear import of PTPN18 inhibits breast cancer metastasis mediated by MVP and importin β2
Wang Tao•Ba Xinlei•Zhang Xiaonan•Zhang Na•Wang Guowen等 11 人
Cell Death & Disease
2022
•2022/8/18
•Vol.13 No.8 p.1-10
Distant metastasis is the primary cause of breast cancer-associated death. The existing information, such as the precise molecular mechanisms and effective therapeutic strategies targeting metastasis, is insufficient to combat breast cancer. This study demonstrates that the protein tyrosine phosphat...
Breast cancerEpithelial–mesenchymal transition
10.1038/S41419-022-05167-Z
ISSN:2041-4889
MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment
Yi Zhang•Guanjue Xiang•Alva Yijia Jiang•Allen Lynch•Zexian Zeng等 15 人
Nature Communications
2023
•2023/5/6
•Vol.14 No.1 p.1-12
Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states in the non-cancerous cells in tumors. The integration of multiple scRNA-seq datasets across tumors can indicate common cell types and states in the tumor microenvironment (TME). We develop a ...
Cancer microenvironmentClassification and taxonomyData integrationSoftwareTumour immunology
10.1038/S41467-023-38333-8
ISSN:2041-1723
Sox2 protein stability is enhanced by BRafV600E and Pten deletion in adult neural stem/progenitor cells
Eugenia Guida•Ambra Colopi•Valeriana Cesarini•Marco Pieraccioli•Luca Mignini等 13 人
Npj Precision Oncology
2026
•2026/4/20
0BRAF mutations are oncogenic drivers present in about 7% of human cancers, with the V600E substitution being the most frequent. In the nervous system, BRAFV600E has been identified in both low- and high-grade gliomas (LGG and HGG) and in tumors of the peripheral nervous system. To investigate the me...
CancerCell biologyMolecular biologyNeuroscienceOncology
10.1038/S41698-026-01439-5
ISSN:2397-768X
MHC II immunogenicity shapes the neoepitope landscape in human tumors
Kim Jeong Yeon•Cha Hongui•Kim Kyeonghui•Sung Changhwan•An Jinhyeon等 15 人
Nature Genetics
2023
•2023/1/9
•Vol.55 No.2 p.221-231
Despite advances in predicting physical peptide-major histocompatibility complex I (pMHC I) binding, it remains challenging to identify functionally immunogenic neoepitopes, especially for MHC II. By using the results of >36,000 immunogenicity assay, we developed a method to identify pMHC whose s...
Genome informaticsGenomicsImmunogeneticsTumour immunology
10.1038/S41588-022-01273-Y
ISSN:1061-4036
PD-L1 and ICOSL discriminate human Secretory and Helper dendritic cells in cancer, allergy and autoimmunity
Hoffmann Caroline•Noel Floriane•Grandclaudon Maximilien•Massenet-Regad Lucile•Michea Paula等 20 人
Nature Communications
2022
•2022/4/13
•Vol.13 No.1 p.1-20
Dendritic cells (DC) are traditionally classified according to their ontogeny and their ability to induce T cell response to antigens, however, the phenotypic and functional state of these cells in cancer does not necessarily align to the conventional categories. Here we show, by using 16 different ...
AutoimmunityCancer microenvironmentDendritic cellsGene regulation in immune cells
10.1038/S41467-022-29516-W
ISSN:2041-1723
Epigenetic regulation of HOXA2 expression affects tumor progression and predicts breast cancer patient survival
Fatima Domenica Elisa De Palma•Jonathan G. Pol•Vincent Carbonnier•Sarah Adriana Scuderi•Deborah Mannino等 24 人
Cell Death & Differentiation
2025
•2025/1/20
•00 p.1-15
Accumulating evidence suggests that genetic and epigenetic biomarkers hold potential for enhancing the early detection and monitoring of breast cancer (BC). Epigenetic alterations of the Homeobox A2 (HOXA2) gene have recently garnered significant attention in the clinical management of various malig...
Diagnostic markersTumour biomarkers
10.1038/S41418-024-01430-2
ISSN:1350-9047
Immuno-subtyping of breast cancer reveals distinct myeloid cell profiles and immunotherapy resistance mechanisms
Ik Sun Kim•Yang Gao•Thomas Welte•Hai Wang•Jun Liu等 29 人
Nature Cell Biology
2019
•2019/8/26
•Vol.21 No.9 p.1113-1126
Cancer-induced immune responses affect tumour progression and therapeutic response. In multiple murine models and clinical datasets, we identified large variations of neutrophils and macrophages that define ‘immune subtypes’ of triple-negative breast cancer (TNBC), including neutrophil-enriched (NES...
Breast cancerCancerCancer microenvironmentTumour immunology
10.1038/S41556-019-0373-7
ISSN:1465-7392
Silent mutations reveal therapeutic vulnerability in RAS Q61 cancers
Kobayashi Yoshihisa•Chhoeu Chhayheng•Li Jiaqi•Price Kristin S.•Kiedrowski Lesli A.等 12 人
Nature
2022
•2022/3/2
•Vol.603 No.7900 p.335-342
RAS family members are the most frequently mutated oncogenes in human cancers. Although KRAS(G12C)-specific inhibitors show clinical activity in patients with cancer1–3, there are no direct inhibitors of NRAS, HRAS or non-G12C KRAS variants. Here we uncover the requirement of the silent KRASG60G mut...
Cancer geneticsRNA splicingTargeted therapies
10.1038/S41586-022-04451-4
ISSN:0028-0836
Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12
Wang Zixiang•Wang Shourong•Qin Junchao•Zhang Xiyu•Lu Gang等 12 人
Nature Communications
2022
•2022/10/21
•Vol.13 No.1 p.1-18
Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a challenge to identify the cancer-specific splicing variants. Here we demonstrate that spliceosome component BUD31 is increased in ovarian cancer, and its higher expression pre...
RNARNA splicing
10.1038/S41467-022-34042-W
ISSN:2041-1723
Network models of primary melanoma microenvironments identify key melanoma regulators underlying prognosis
Won-Min Song•Praveen Agrawal•Richard Von Itter•Barbara Fontanals-Cirera•Minghui Wang等 9 人
Nature Communications
2021
•2021/2/22
•Vol.12 No.1 p.1-14
Melanoma is the most lethal skin malignancy, driven by genetic and epigenetic alterations in the complex tumour microenvironment. While large-scale molecular profiling of melanoma has identified molecular signatures associated with melanoma progression, comprehensive systems-level modeling remains e...
CancerCD4-positive T cellsComputational biology and bioinformaticsGeneticsImmune evasion
10.1038/S41467-021-21457-0
ISSN:2041-1723
Pan-cancer analyses suggest kindlin-associated global mechanochemical alterations
Debojyoti Chowdhury•Ayush Mistry•Debashruti Maity•Riti Bhatia•Shreyansh Priyadarshi等 8 人
Communications Biology
2024
•2024/3/28
•Vol.7 No.1 p.1-16
Kindlins serve as mechanosensitive adapters, transducing extracellular mechanical cues to intracellular biochemical signals and thus, their perturbations potentially lead to cancer progressions. Despite the kindlin involvement in tumor development, understanding their genetic and mechanochemical cha...
Cancer genomicsCellular signalling networksData processing
10.1038/S42003-024-06044-5
ISSN:2399-3642
Cytoplasmic TRIM24 promotes colorectal cancer cell proliferation by activating Wnt/β-catenin signaling
Ya Wang•Yuanbing Yao•Zehong Liu•Shichao Long•Feng Yi等 12 人
Nature Communications
2025
•2025/9/29
•Vol.16 No.1 p.1-15
Aberrant activation of Wnt/β-catenin signaling is proposed as a major molecular mechanism underlying the occurrence and progression of colorectal cancer (CRC). However, the precise mechanisms controlling the accumulation of β-catenin protein in CRC cells remain incompletely understood. Here, we show...
Colon cancerOncogenes
10.1038/S41467-025-63685-8
ISSN:2041-1723
Long non-coding RNA MIR200CHG promotes breast cancer proliferation, invasion, and drug resistance by interacting with and stabilizing YB-1
Li Tang•Da Wei•Xinyu Xu•Xuelian Mao•Dongping Mo等 8 人
Npj Breast Cancer
2021
•2021/7/16
•Vol.7 No.1 p.1-12
Long non-coding RNAs (lncRNA) have been identified as key regulators of tumorigenesis and development. We aim to explore the biological functions and molecular mechanisms of lncRNA MIR200CHG in breast cancer. We found that MIR200CHG is highly expressed in breast cancer tissues and is related to the ...
Breast cancer
10.1038/S41523-021-00293-X
ISSN:2374-4677
Enhancer decommissioning by MLL4 ablation elicits dsRNA-interferon signaling and GSDMD-mediated pyroptosis to potentiate anti-tumor immunity
Ning Hanhan•Huang Shan•Lei Yang•Zhi Renyong•Yan Han等 14 人
Nature Communications
2022
•2022/11/2
•Vol.13 No.1 p.1-20
Enhancer deregulation is a well-established pro-tumorigenic mechanism but whether it plays a regulatory role in tumor immunity is largely unknown. Here, we demonstrate that tumor cell ablation of mixed-lineage leukemia 3 and 4 (MLL3 and MLL4, also known as KMT2C and KMT2D, respectively), two enhance...
Histone post-translational modificationsTranscriptional regulatory elementsTumour immunology
10.1038/S41467-022-34253-1
ISSN:2041-1723
Tumor suppressor mediated ubiquitylation of hnRNPK is a barrier to oncogenic translation
Mucha Bartosz•Qie Shuo•Bajpai Sagar•Tarallo Vincenzo•Diehl J. Nathaniel等 24 人
Nature Communications
2022
•2022/11/3
•Vol.13 No.1 p.1-18
Heterogeneous Nuclear Ribonucleoprotein K (hnRNPK) is a multifunctional RNA binding protein (RBP) localized in the nucleus and the cytoplasm. Abnormal cytoplasmic enrichment observed in solid tumors often correlates with poor clinical outcome. The mechanism of cytoplasmic redistribution and ensuing ...
Mechanisms of diseaseMetastasisTranslation
10.1038/S41467-022-34402-6
ISSN:2041-1723
Timing of whole genome duplication is associated with tumor-specific MHC-II depletion in serous ovarian cancer
Nikki L. Burdett•Madelynne O. Willis•Ahwan Pandey•Laura Twomey•Sara Alaei等 7 人
Nature Communications
2024
•2024/7/18
•Vol.15 No.1 p.1-13
Whole genome duplication is frequently observed in cancer, and its prevalence in our prior analysis of end-stage, homologous recombination deficient high grade serous ovarian cancer (almost 80% of samples) supports the notion that whole genome duplication provides a fitness advantage under the selec...
Cancer genomicsOvarian cancerTumour immunology
10.1038/S41467-024-50137-Y
ISSN:2041-1723
Histopathology images predict multi-omics aberrations and prognoses in colorectal cancer patients
Tsai Pei-Chen•Lee Tsung-Hua•Kuo Kun-Chi•Su Fang-Yi•Lee Tsung-Lu Michael等 21 人
Nature Communications
2023
•2023/4/13
•Vol.14 No.1 p.1-13
Histopathologic assessment is indispensable for diagnosing colorectal cancer (CRC). However, manual evaluation of the diseased tissues under the microscope cannot reliably inform patient prognosis or genomic variations crucial for treatment selections. To address these challenges, we develop the Mul...
Cancer imagingColorectal cancerDiagnostic markersMachine learningPrognostic markers
10.1038/S41467-023-37179-4
ISSN:2041-1723
Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes
Hyeon Do Young•Nam Dowoon•Han Youngmin•Kim Duk Ki•Kim Gibeom等 36 人
Nature Cancer
2022
•2022/12/22
•Vol.4 No.2 p.290-307
We report a proteogenomic analysis of pancreatic ductal adenocarcinoma (PDAC). Mutation–phosphorylation correlations identified signaling pathways associated with somatic mutations in significantly mutated genes. Messenger RNA–protein abundance correlations revealed potential prognostic biomarkers c...
CancerCancer genomicsPancreatic cancerProteomics
10.1038/S43018-022-00479-7
ISSN:2662-1347
Large-vocabulary forensic pathological analyses via prototypical cross-modal contrastive learning
Chen Shen•Chunfeng Lian•Wanqing Zhang•Fan Wang•Jianhua Zhang等 14 人
Nature Communications
2025
•2025/7/23
•Vol.16 No.1 p.1-20
Forensic pathology plays a vital role in determining the cause and manner of death through macroscopic and microscopic post-mortem examinations. However, the field faces challenges such as variability in outcomes, labor-intensive processes, and a shortage of skilled professionals. This paper introdu...
Computational modelsDiagnosisMachine learningMedical imaging
10.1038/S41467-025-62060-X
ISSN:2041-1723
Soft multiclass feature augmented deep learning to predict tumor origins using cytology or histology whole slide images
Ching-Wei Wang•Po-Jen Lai•Tzu-Chiao Chu•Tzu-Kang Wu•Chih-Hsuan Liang等 6 人
Npj Digital Medicine
2026
•2026/4/13
0Tailoring cancer treatment to the primary tumor site is essential for optimal outcomes, yet identifying the source of metastasis remains a significant clinical challenge. The primary tumor location influences not only the choice of treatment but also its delivery method, potential side effects and o...
CancerComputational biology and bioinformaticsOncology
10.1038/S41746-026-02604-7
ISSN:2398-6352
Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer
Chatila Walid K.•Kim Jin K.•Walch Henry•Marco Michael R.•Chen Chin-Tung等 37 人
Nature Medicine
2022
•2022/8/15
•00 p.1-10
The incidence of rectal cancer is increasing in patients younger than 50 years. Locally advanced rectal cancer is still treated with neoadjuvant radiation, chemotherapy and surgery, but recent evidence suggests that patients with a complete response can avoid surgery permanently. To define correlate...
Cancer genomicsRectal cancerTranslational researchTumour biomarkers
10.1038/S41591-022-01930-Z
ISSN:1078-8956
Primary tumors release ITGBL1-rich extracellular vesicles to promote distal metastatic tumor growth through fibroblast-niche formation
Qing Ji•Lihong Zhou•Hua Sui•Liu Yang•Xinnan Wu等 20 人
Nature Communications
2020
•2020/3/5
•Vol.11 No.1 p.1-18
Tumor metastasis is a hallmark of cancer. Metastatic cancer cells often reside in distal tissues and organs in their dormant state. Mechanisms underlying the pre-metastatic niche formation are poorly understood. Here we show that in a colorectal cancer (CRC) model, primary tumors release integrin be...
CancerGastrointestinal diseasesPrognostic markersTranslational research
10.1038/S41467-020-14869-X
ISSN:2041-1723
Meta-encoder: a unified integration framework for multiple pathological foundation models in cancer detection
Ruitian Gao•Zhaochang Yang•Xin Yuan•Yifan Wang•Yujia Xia等 11 人
Nature Communications
2026
•2026/4/15
0The emergence of diverse pathological foundation models has empowered computational pathology tasks within the field of oncology, including tumor subtyping, cancer prognosis, biomarker prediction, gene expression prediction, and so on. However, variations in model architecture and data sources hinde...
Computational modelsData integrationImage processingMachine learning
10.1038/S41467-026-71558-X
ISSN:2041-1723
Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing
Nicolas Lynn•Tamir Tuller
Npj Systems Biology And Applications
2024
•2024/3/7
•Vol.10 No.1 p.1-15
Cancer research has long relied on non-silent mutations. Yet, it has become overwhelmingly clear that silent mutations can affect gene expression and cancer cell fitness. One fundamental mechanism that apparently silent mutations can severely disrupt is alternative splicing. Here we introduce Oncosp...
Computational biology and bioinformaticsGeneticsMolecular medicine
10.1038/S41540-024-00351-7
ISSN:2056-7189
Glycolytic heterogeneity drives metabolic-targeted therapy in pancreatic ductal adenocarcinoma
Ugo Chianese•Chiara Papulino•Gerardo Saggese•Ahmad Ali•Marianna Ciotola等 19 人
Signal Transduction And Targeted Therapy
2026
•2026/1/20
•Vol.11 No.1 p.250
Pancreatic ductal adenocarcinoma is traditionally characterized as a glycolytic tumor. However, the extent and clinical relevance of its metabolic heterogeneity remain poorly understood. In this study, we investigated whether glycolytic activity follows a consistent expression pattern across pancrea...
Cancer metabolismCancer therapyMolecular biology
10.1038/S41392-025-02546-8
ISSN:2059-3635
Broad misappropriation of developmental splicing profile by cancer in multiple organs
Singh Arashdeep•Rajeevan Arati•Gopalan Vishaka•Agrawal Piyush•Day Chi-Ping等 6 人
Nature Communications
2022
•2022/12/12
•Vol.13 No.1 p.1-18
Oncogenesis mimics key aspects of embryonic development. However, the underlying mechanisms are incompletely understood. Here, we demonstrate that the splicing events specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. Such events are associated with ...
CancerDevelopmental biologyGene regulatory networksMembrane traffickingRNA
10.1038/S41467-022-35322-1
ISSN:2041-1723
An EGFR co-amplified lncRNA HELDR promotes glioblastoma malignancy through KAT7-driven gene programs
Xiaozhou Yu•Xiao Song•Richard A. Schäfer•Qingshu Meng•Deanna Tiek等 12 人
Nature Cell Biology
2026
•2026/3/27
•00 p.1-14
EGFR amplification frequently occurs within extrachromosomal DNAs (ecDNAs) and is the most prevalent mutation in glioblastoma (GBM). However, targeting EGFR for GBM treatments has been unsuccessful. Here we show a long non-coding RNA (lncRNA) that is co-amplified with EGFR, which we name hidden EGFR...
CNS cancerLong non-coding RNAsTargeted therapies
10.1038/S41556-026-01924-W
ISSN:1465-7392
Titration of RAS alters senescent state and influences tumour initiation
Adelyne S. L. Chan•Haoran Zhu•Masako Narita•Liam D. Cassidy•Andrew R. J. Young等 14 人
Nature
2024
•2024/8/7
•00 p.1-8
Oncogenic RAS-induced senescence (OIS) is an autonomous tumour suppressor mechanism associated with premalignancy1,2. Achieving this phenotype typically requires a high level of oncogenic stress, yet the phenotype provoked by lower oncogenic dosage remains unclear. Here we develop oncogenic RAS dose...
SenescenceTumour heterogeneity
10.1038/S41586-024-07797-Z
ISSN:0028-0836
Target receptor identification and subsequent treatment of resected brain tumors with encapsulated and engineered allogeneic stem cells
Bhere Deepak•Choi Sung Hugh•van de Donk Pim•Hope David•Gortzak Kiki等 33 人
Nature Communications
2022
•2022/5/19
•Vol.13 No.1 p.1-16
Cellular therapies offer a promising therapeutic strategy for the highly malignant brain tumor, glioblastoma (GBM). However, their clinical translation is limited by the lack of effective target identification and stringent testing in pre-clinical models that replicate standard treatment in GBM...
Cancer therapyCNS cancer
10.1038/S41467-022-30558-3
ISSN:2041-1723
Deep learning for malignancy and tumor origin prediction using cytology or histopathology whole slide images
Ching-Wei Wang•Tzu-Chiao Chu•Tzu-Kang Wu•Yu-Pang Chung•Sin-Si Lin等 6 人
Npj Digital Medicine
2026
•2026/1/24
•Vol.9 No.1 p.1750
Pleural and ascitic cytology is essential for diagnosing metastatic cancer and predicting tumor origin, yet microscopic observation alone often leads to low accuracy and observer variability. Although deep learning shows great potential in pathology, its use in pleural and ascitic cytology remains l...
CancerCancer of unknown primaryCancer screeningDiagnostic markersMachine learningSoftware
10.1038/S41746-026-02359-1
ISSN:2398-6352
A ZEB1/p53 signaling axis in stromal fibroblasts promotes mammary epithelial tumours
Rong Fu•Chen-Feng Han•Ting Ni•Lei Di•Li-Juan Liu等 18 人
Nature Communications
2019
•2019/7/19
•Vol.10 No.1 p.1-18
Accumulating evidence indicates that the zinc-finger transcription factor ZEB1 is predominantly expressed in the stroma of several tumours. However, the role of stromal ZEB1 in tumour progression remains unexplored. In this study, while interrogating human databases, we uncover a remarkable decrease...
Breast cancerCancer microenvironment
10.1038/S41467-019-11278-7
ISSN:2041-1723
Transposable elements-mediated recruitment of KDM1A epigenetically silences HNF4A expression to promote hepatocellular carcinoma
Tiantian Jing•Dianhui Wei•Xiaoli Xu•Chengsi Wu•Lili Yuan等 9 人
Nature Communications
2024
•2024/7/4
•Vol.15 No.1 p.1-21
Transposable elements (TEs) contribute to gene expression regulation by acting as cis-regulatory elements that attract transcription factors and epigenetic regulators. This research aims to explore the functional and clinical implications of transposable element-related molecular events in hepatocel...
Gene silencingHepatocellular carcinomaOncogenes
10.1038/S41467-024-49926-2
ISSN:2041-1723
Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq
Jessica J. Simon•Douglas M. Fowler•Dustin J. Maly
Nature Methods
2024
•2024/10/21
•00 p.1-13
Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding...
Cell signallingProteomic analysisRNA
10.1038/S41592-024-02456-7
ISSN:1548-7091
Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings
Zequn Lu•Can Chen•Heng Zhang•Bin Li•Yizhuo Liu等 37 人
Nature Cancer
2025
•2025/8/25
•00 p.1-23
Genetic variants associated with colorectal cancer (CRC) are primarily noncoding and reside in cis-regulatory elements (CREs), yet their underlying mechanisms remain elusive. Here we established a dynamic epigenetic atlas using multiomics data from 533 colorectal tissues spanning normal to advanced ...
CancerCancer genomicsColorectal cancerGenome-wide association studies
10.1038/S43018-025-01031-Z
ISSN:2662-1347
N6-methyladenosine-modified ALDH9A1 modulates lipid accumulation and tumor progression in clear cell renal cell carcinoma through the NPM1/IQGAP2/AKT signaling pathway
Diaoyi Tan•Daojia Miao•Chuanyi Zhao•Jian Shi•Qingyang Lv等 9 人
Cell Death & Disease
2024
•2024/7/22
•Vol.15 No.7 p.1-22
Aldehyde dehydrogenases superfamily (ALDHs), which are ubiquitously present in various organisms with diverse subcellular localizations, play a crucial role in regulating malignant tumor progression; Nevertheless, their involvement in clear cell renal cell carcinoma (ccRCC) has not been elucidated. ...
Fatty acidsLipid signallingRenal cell carcinoma
10.1038/S41419-024-06896-Z
ISSN:2041-4889
Dual modulation of cytotoxic and checkpoint receptors tunes the efficacy of adoptive Delta One T cell therapy against colorectal cancer
Rafael Blanco-Domínguez•Leandro Barros•Mariana Carreira•Manon van der Ploeg•Carolina Condeço等 13 人
Nature Cancer
2025
•2025/4/16
•00 p.1-17
Colorectal cancer (CRC) remains a challenge for current immunotherapies. Vδ1+ γδ T cells offer a promising alternative because of their HLA-I-independent cytotoxicity and natural tissue tropism. We developed Delta One T (DOT) cells, a Vδ1+ γδ T cell-based adoptive cell therapy clinically explored fo...
CancerColorectal cancerImmunotherapyTumour immunology
10.1038/S43018-025-00948-9
ISSN:2662-1347
Cytogenetic signatures favoring metastatic organotropism in colorectal cancer
Mariola Monika Golas•Bastian Gunawan•Angelika Gutenberg•Bernhard C. Danner•Jan S. Gerdes等 9 人
Nature Communications
2025
•2025/4/5
•Vol.16 No.1 p.1-19
Colorectal carcinoma (CRC) exhibits metastatic organotropism, primarily targeting liver, lung, and rarely the brain. Here, we study chromosomal imbalances (CIs) in cohorts of primary CRCs and metastases. Brain metastases show the highest burden of CIs, including aneuploidies and focal CIs, with enri...
Cancer geneticsCancer genomicsColorectal cancerGenomic instability
10.1038/S41467-025-58413-1
ISSN:2041-1723
The lactate receptor HCAR1 drives the recruitment of immunosuppressive PMN-MDSCs in colorectal cancer
Jiacheng He•Xiaolei Chai•Qiansen Zhang•Yang Wang•Yijie Wang等 38 人
Nature Immunology
2025
•2025/2/4
•Vol.26 No.3 p.391-403
Most patients with colorectal cancer do not achieve durable clinical benefits from immunotherapy, underscoring the existence of alternative immunosuppressive mechanisms. Here we found that activation of the lactate receptor HCAR1 signaling pathway induced the expression of chemokines CCL2 and CCL7 i...
Cancer therapy
10.1038/S41590-024-02068-5
ISSN:1529-2908
GINS2 regulates temozolomide chemosensitivity via the EGR1/ECT2 axis in gliomas
Hua He•Lu Liang•Shiyao Jiang•Yueying Liu•Jingjing Huang等 9 人
Cell Death & Disease
2024
•2024/3/11
•Vol.15 No.3 p.1-16
Temozolomide (TMZ), a DNA alkylating agent, has become the primary treatment for glioma, the most common malignancy of the central nervous system. Although TMZ-containing regimens produce significant clinical response rates, some patients inevitably suffer from inferior treatment outcomes or disease...
CNS cancerTumour biomarkers
10.1038/S41419-024-06586-W
ISSN:2041-4889
AI-enabled virtual spatial proteomics from histopathology for interpretable biomarker discovery in lung cancer
Zhe Li•Yuchen Li•Jinxi Xiang•Xiyue Wang•Sen Yang等 20 人
Nature Medicine
2026
•2026/1/5
•Vol.32 No.1 p.231-244
Spatial proteomics enables high-resolution mapping of protein expression and can transform our understanding of biology and disease. However, major challenges remain for clinical translation, including cost, complexity and scalability. Here we present H&E to protein expression (HEX), an AI model...
Cancer immunotherapyNon-small-cell lung cancerPrognostic markers
10.1038/S41591-025-04060-4
ISSN:1078-8956
Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer
Jakob Nikolas Kather•Alexander T. Pearson•Niels Halama•Dirk Jäger•Jeremias Krause等 17 人
Nature Medicine
2019
•2019/6/3
•Vol.25 No.7 p.1054-1056
Microsatellite instability determines whether patients with gastrointestinal cancer respond exceptionally well to immunotherapy. However, in clinical practice, not every patient is tested for MSI, because this requires additional genetic or immunohistochemical tests. Here we show that deep residual ...
Cancer imagingColorectal cancerGastric cancerImage processingPredictive markers
10.1038/S41591-019-0462-Y
ISSN:1078-8956
HESpotEx: a dual-stream deep learning framework for spot-level gene expression prediction from histological images
Wang Yin•Qin Peng•Fanyi Meng•You Wan•Weilong Zhang等 6 人
Nature Computational Science
2026
•2026/5/15
•00 p.1-14
Whole-slide histopathological images (WSIs) constitute a fundamental approach in disease diagnosis and prognosis. Recently emerging spatial transcriptomics (ST) methods can reveal the spatial gene expression landscape behind the histopathological images, but with much higher cost. Here, therefore, w...
BioinformaticsComputational biology and bioinformatics
10.1038/S43588-026-00992-0
ISSN:2662-8457
Dual therapeutic targeting of MYC and JUNB transcriptional programs for enhanced anti-myeloma activity
Judith Lind•Osman Aksoy•Michaela Prchal-Murphy•Fengjuan Fan•Mariateresa Fulciniti等 13 人
Blood Cancer Journal
2024
•2024/8/19
•Vol.14 No.1 p.1-12
Deregulation of transcription factors (TFs) leading to uncontrolled proliferation of tumor cells within the microenvironment represents a hallmark of cancer. However, the biological and clinical impact of transcriptional interference, particularly in multiple myeloma (MM) cells, remains poorly under...
Haematological cancerPathogenesis
10.1038/S41408-024-01117-4
ISSN:2044-5385
Predictive models for the occurrence and lymph node metastasis of papillary thyroid carcinoma with regional risk heterogeneity
Zhigang Zhang•Hongyu Liu•Zheng Zhao•Guoyu Tan•Yang Zhao等 6 人
Npj Digital Medicine
2026
•2026/4/18
0Papillary thyroid carcinoma (PTC) is the most common thyroid malignancy, and cervical lymph node metastasis significantly impacts patient prognosis. This study aimed to develop interpretable artificial intelligence models based on transcriptomics to predict PTC occurrence and cervical lymph node met...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41746-026-02649-8
ISSN:2398-6352
AI allows pre-screening of FGFR3 mutational status using routine histology slides of muscle-invasive bladder cancer
Pierre-Antoine Bannier•Charlie Saillard•Philipp Mann•Maxime Touzot•Charles Maussion等 15 人
Nature Communications
2024
•2024/12/30
•Vol.15 No.1 p.1-11
Pathogenic activating mutations in the fibroblast growth factor receptor 3 (FGFR3) drive disease maintenance and progression in urothelial cancer. 10–15% of muscle-invasive and metastatic urothelial cancer (MIBC/mUC) are FGFR3-mutant. Selective targeting of FGFR3 hotspot mutations with tyrosine kina...
Bladder cancerCancer imagingCancer screeningMachine learningTumour biomarkers
10.1038/S41467-024-55331-6
ISSN:2041-1723
Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma
Ye Chen•Liang Xu•Anand Mayakonda•Mo-Li Huang•Deepika Kanojia等 18 人
Nature Communications
2019
•2019/3/22
•Vol.10 No.1 p.1-14
Liposarcomas (LPSs) are a group of malignant mesenchymal tumors showing adipocytic differentiation. Here, to gain insight into the enhancer dysregulation and transcriptional addiction in this disease, we chart super-enhancer structures in both LPS tissues and cell lines. We identify a bromodomain an...
Gene regulationSarcoma
10.1038/S41467-019-09257-Z
ISSN:2041-1723
Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities
Luciano Garofano•Simona Migliozzi•Young Taek Oh•Fulvio D’Angelo•Ryan D. Najac等 22 人
Nature Cancer
2021
•2021/1/11
•Vol.2 No.2 p.141-156
The transcriptomic classification of glioblastoma (GBM) has failed to predict survival and therapeutic vulnerabilities. A computational approach for unbiased identification of core biological traits of single cells and bulk tumors uncovered four tumor cell states and GBM subtypes distributed along n...
CancerCancer metabolismCNS cancer
10.1038/S43018-020-00159-4
ISSN:2662-1347
Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer
Ailith Ewing•Alison Meynert•Ryan Silk•Stuart Aitken•Devin P. Bendixsen等 39 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-14
Deciphering the structural variation across tumour genomes is crucial to determine the events driving tumour progression and better understand tumour adaptation and evolution. High grade serous ovarian cancer (HGSOC) is an exemplar tumour type showing extreme, but poorly characterised structural div...
CancerCancer genomicsDNA damage and repairMitochondriaOvarian cancer
10.1038/S41467-025-60655-Y
ISSN:2041-1723
Negative trade-off between neoantigen repertoire breadth and the specificity of HLA-I molecules shapes antitumor immunity
Máté Manczinger•Balázs Koncz•Gergő Mihály Balogh•Benjamin Tamás Papp•Leó Asztalos等 8 人
Nature Cancer
2021
•2021/7/8
•00 p.1-12
Human leukocyte antigen class I (HLA-I) genes shape our immune response against pathogens and cancer. Certain HLA-I variants can bind a wider range of peptides than others, a feature that could be favorable against a range of viral diseases. However, the implications of this phenomenon on cancer imm...
CancerCancer genomicsCancer immunotherapyTumour immunology
10.1038/S43018-021-00226-4
ISSN:2662-1347
Ectopic JAK–STAT activation enables the transition to a stem-like and multilineage state conferring AR-targeted therapy resistance
Deng Su•Wang Choushi•Wang Yunguan•Xu Yaru•Li Xiaoling等 26 人
Nature Cancer
2022
•2022/9/5
•Vol.3 No.9 p.1071-1087
Emerging evidence indicates that various cancers can gain resistance to targeted therapies by acquiring lineage plasticity. Although various genomic and transcriptomic aberrations correlate with lineage plasticity, the molecular mechanisms enabling the acquisition of lineage plasticity have not been...
CancerCancer therapeutic resistanceProstate cancerTargeted therapiesTumour heterogeneity
10.1038/S43018-022-00431-9
ISSN:2662-1347
SMAD4-armed oncolytic adenovirus therapy potentiates the chemotherapy effects in NSCLC through suppression of the Wnt/β-catenin pathway
Chuanjing Dai•Yaru Zhao•Huili Zhang•Sultan Muhammad Haris•Biao Huang等 10 人
Cancer Gene Therapy
2025
•2025/10/14
•00 p.1-14
Non-small cell lung cancer (NSCLC) represents between 80 and 90% of primary lung cancer cases. Despite progress targeting oncogenic drivers, there are no therapies targeting tumor-suppressor loss. This study confirmed a significant downregulation of SMAD4 expression in both NSCLC tissues and cell li...
Non-small-cell lung cancerTumour virus infections
10.1038/S41417-025-00976-8
ISSN:0929-1903
FBXO7, a tumor suppressor in endometrial carcinoma, suppresses INF2-associated mitochondrial division
Hui Zhang•Yiting Zhao•Jie Wang•Jinyun Li•Jingyi Xia等 13 人
Cell Death & Disease
2023
•2023/6/21
•Vol.14 No.6 p.1-16
Endometrial carcinoma (ECa) is the most common malignant gynecological cancer, with an increased incidence and fatality rate worldwide, while the pathogenesis is still largely unknown. In this study, we confirmed that FBXO7, a gene coding FBXO7 E3 ubiquitin ligase, is significantly downregulated and...
Cancer geneticsOncogenes
10.1038/S41419-023-05891-0
ISSN:2041-4889
APOBEC affects tumor evolution and age at onset of lung cancer in smokers
Tongwu Zhang•Jian Sang•Phuc H. Hoang•Wei Zhao•Jennifer Rosenbaum等 31 人
Nature Communications
2025
•2025/5/21
•Vol.16 No.1 p.1-17
Most solid tumors harbor somatic mutations attributed to off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B). However, how APOBEC3A/B enzymes affect tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, multi-omics profiling of 309 lung cancers from smo...
Cancer genomicsNon-small-cell lung cancer
10.1038/S41467-025-59923-8
ISSN:2041-1723
PDK1-dependent metabolic reprogramming regulates stemness and tumorigenicity of osteosarcoma stem cells through ATF3
Kazuya Tokumura•Kazuya Fukasawa•Jiro Ichikawa•Koki Sadamori•Manami Hiraiwa等 6 人
Cell Death & Disease
2025
•2025/7/29
•Vol.16 No.1 p.1-14
Osteosarcoma stem cells (OSCs) are characterized by their self-renewal and multilineage differentiation abilities, contributing to osteosarcoma malignancy. The Warburg effect describes cancer cells’ preference for glycolysis over mitochondrial oxidative phosphorylation (OXPHOS) for energy production...
Bone cancer
10.1038/S41419-025-07903-7
ISSN:2041-4889
The impact of rare germline variants on human somatic mutation processes
Vali-Pour Mischan•Lehner Ben•Supek Fran
Nature Communications
2022
•2022/6/28
•Vol.13 No.1 p.1-21
Somatic mutations are an inevitable component of ageing and the most important cause of cancer. The rates and types of somatic mutation vary across individuals, but relatively few inherited influences on mutation processes are known. We perform a gene-based rare variant association study with divers...
Cancer geneticsCancer genomicsComputational biology and bioinformaticsRare variants
10.1038/S41467-022-31483-1
ISSN:2041-1723
AXIN1 boosts antiviral response through IRF3 stabilization and induced phase separation
Dan-Ling Dai•Chu Xie•Lan-Yi Zhong•Shang-Xin Liu•Le-Le Zhang等 30 人
Signal Transduction And Targeted Therapy
2024
•2024/10/9
•Vol.9 No.1 p.1-17
Axis inhibition protein 1 (AXIN1), a scaffold protein interacting with various critical molecules, plays a vital role in determining cell fate. However, its impact on the antiviral innate immune response remains largely unknown. Here, we identify that AXIN1 acts as an effective regulator of antivira...
Innate immunityMicrobiology
10.1038/S41392-024-01978-Y
ISSN:2059-3635
Single-cell RNA sequencing reveals the effects of chemotherapy on human pancreatic adenocarcinoma and its tumor microenvironment
Werba Gregor•Weissinger Daniel•Kawaler Emily A.•Zhao Ende•Kalfakakou Despoina等 23 人
Nature Communications
2023
•2023/2/13
•Vol.14 No.1 p.1-16
The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression; however, in-depth single cell characterization of the PDAC TME and its role in response to therapy is lacking. Here, we perform single-cell RNA sequencing on freshly coll...
BioinformaticsCancer microenvironmentPancreatic cancer
10.1038/S41467-023-36296-4
ISSN:2041-1723
SOCS5-RBMX stimulates SREBP1-mediated lipogenesis to promote metastasis in steatotic HCC with HBV-related cirrhosis
Youpeng Wang•Ziyin Zhao•Tingting Guo•Tiansong Wu•Mao Zhang等 12 人
Npj Precision Oncology
2024
•2024/3/1
•Vol.8 No.1 p.1-16
Abnormal lipid metabolism promotes hepatocellular carcinoma (HCC) progression, which engenders therapeutic difficulties owing to unclear mechanisms of the phenomenon. We precisely described a special steatotic HCC subtype with HBV-related cirrhosis and probed its drivers. Hematoxylin-eosin (HE) stai...
Cancer metabolismHepatocellular carcinomaOncogenes
10.1038/S41698-024-00545-6
ISSN:2397-768X
Epigenetic fingerprints link early-onset colon and rectal cancer to pesticide exposure
Silvana C. E. Maas•Iosune Baraibar•Lea Lemler•Maria Butjosa-Espín•Odei Blanco Irazuegui等 8 人
Nature Medicine
2026
•2026/4/21
•00 p.1-11
The incidence of colorectal cancer (CRC) is rising rapidly in people younger than 50 years. Although this increase parallels shifts in lifestyle and environmental factors—collectively termed the exposome—whether these are indeed linked to the development of early-onset CRC (EOCRC) remains uninvestig...
Cancer epidemiologyColorectal cancerData integrationDNA methylationRisk factors
10.1038/S41591-026-04342-5
ISSN:1078-8956
circIPO7 dissociates caprin-1 from ribosomes and inhibits gastric cancer cell proliferation by suppressing EGFR and mTOR
Liu Jing•Niu Liling•Hao Jiaru•Yao Yuan•Yan Meinan等 6 人
Oncogene
2023
•2023/2/3
•00 p.1-14
Circular RNA (circRNA) is a novel RNA molecule characterized by covalently closed loop structure. Since its discovery, researchers have shown that circRNA is not “splicing noise” but a participant of various pathophysiological processes through unique mechanisms. circIPO7, which was identified as an...
Cell growthGastric cancerNon-coding RNAsTranslation
10.1038/S41388-023-02610-Z
ISSN:0950-9232
Targeted methylation of cg24067911 suppresses colorectal cancer metastasis through BCL6-ATXN1-CDH1 axis
Lu-Ping Yang•Jia-Qian Huang•Chiu-Wing Yeung•Qi-Hua Zhang•Xiao-Li Wei等 18 人
Oncogene
2025
•2025/12/2
•00 p.1-12
DNA methylation plays a crucial role in the progression and metastasis of colorectal cancer (CRC), yet the mechanisms underlying its effect at specific loci remain poorly understood. We previously identified cg24067911 hypomethylation as a potential biomarker associated with poor CRC prognosis. To i...
Colorectal cancerExtracellular matrix
10.1038/S41388-025-03638-Z
ISSN:0950-9232
Genetic and epigenetic basis of hepatoblastoma diversity
Nagae Genta•Yamamoto Shogo•Fujita Masashi•Fujita Takanori•Nonaka Aya等 23 人
Nature Communications
2021
•2021/9/20
•Vol.12 No.1 p.1-16
Hepatoblastoma (HB) is the most common pediatric liver malignancy; however, hereditary predisposition and acquired molecular aberrations related to HB clinicopathological diversity are not well understood. Here, we perform an integrative genomic profiling of 163 pediatric liver tumors (154 HBs and n...
Cancer genomicsEmbryonal neoplasmsPaediatric cancer
10.1038/S41467-021-25430-9
ISSN:2041-1723
Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins
Kerryn Elliott•Vinod Kumar Singh•Martin Boström•Erik Larsson
Nature Communications
2023
•2023/5/11
•Vol.14 No.1 p.1-10
Decades ago, it was shown that proteins binding to DNA can quantitatively alter the formation of DNA damage by UV light. This established the principle of UV footprinting for non-intrusive study of protein-DNA contacts in living cells, albeit at limited scale and precision. Here, we perform deep bas...
Gene regulationGenomics
10.1038/S41467-023-38266-2
ISSN:2041-1723
Systematically decoding pathological morphologies and molecular profiles with unified multimodal embedding
Peng Zhang•Chaofei Gao•Kui Hua•Zhuoyu Zhang•Shao Li
Nature Methods
2026
•2026/4/24
•00 p.1-6
Systematic cross-modality inference and integration of pathological morphologies and multilayer molecular profiles have advanced disease biology; however, methodological challenges remain in multimodal learning. Here, we present Multi-Embed, a unified and interpretable framework for multimodal learn...
Computational modelsMachine learning
10.1038/S41592-026-03070-5
ISSN:1548-7091
Multi-omic analysis reveals a CAF-stemness-governed classification in HCC liver transplant recipients beyond the Milan criteria
Sunbin Ling•Jiongjie Yu•Qifan Zhan•Mingwei Gao•Peng Liu等 26 人
Nature Communications
2025
•2025/5/12
•Vol.16 No.1 p.1-13
In patients with hepatocellular carcinoma (HCC) meeting the Milan criteria, liver transplantation (LT) is an effective therapy. This study aims to define the survival-related molecular biological features helping precisely identifying the patients with HCC beyond the Milan criteria who have acceptab...
Cancer genomicsHepatocellular carcinoma
10.1038/S41467-025-59745-8
ISSN:2041-1723
Prediction models for hormone receptor status in female breast cancer do not extend to males: further evidence of sex-based disparity in breast cancer
Subarnarekha Chatterji•Jan Moritz Niehues•Marko van Treeck•Chiara Maria Lavinia Loeffler•Oliver Lester Saldanha等 11 人
Npj Breast Cancer
2023
•2023/11/8
•Vol.9 No.1 p.1-10
Breast cancer prognosis and management for both men and women are reliant upon estrogen receptor alpha (ERα) and progesterone receptor (PR) expression to inform therapy. Previous studies have shown that there are sex-specific binding characteristics of ERα and PR in breast cancer and, counterintuiti...
Breast cancerPrognostic markers
10.1038/S41523-023-00599-Y
ISSN:2374-4677
Chromosome arm aneuploidies shape tumour evolution and drug response
Ankit Shukla•Thu H. M. Nguyen•Sarat B. Moka•Jonathan J. Ellis•John P. Grady等 13 人
Nature Communications
2020
•2020/1/23
•Vol.11 No.1 p.1-14
Chromosome arm aneuploidies (CAAs) are pervasive in cancers. However, how they affect cancer development, prognosis and treatment remains largely unknown. Here, we analyse CAA profiles of 23,427 tumours, identifying aspects of tumour evolution including probable orders in which CAAs occur and CAAs p...
Cancer therapeutic resistanceChemotherapyMachine learningMetastasisSystems biology
10.1038/S41467-020-14286-0
ISSN:2041-1723
PRMT inhibition induces a viral mimicry response in triple-negative breast cancer
Wu Qin•Nie David Y.•Ba-alawi Wail•Ji YiShuai•Zhang ZiWen等 29 人
Nature Chemical Biology
2022
•2022/5/16
•00 p.1-10
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with the worst prognosis and few effective therapies. Here we identified MS023, an inhibitor of type I protein arginine methyltransferases (PRMTs), which has antitumor growth activity in TNBC. Pathway analysis of TNBC ...
Cancer therapyChemical geneticsRNA splicingScreening
10.1038/S41589-022-01024-4
ISSN:1552-4450
Comprehensive characterization of distinct genetic alterations in metastatic breast cancer across various metastatic sites
Soojin Cha•Esak Lee•Hong-Hee Won
Npj Breast Cancer
2021
•2021/7/16
•Vol.7 No.1 p.1-11
Metastasis is the major cause of death in breast cancer patients. Although previous large-scale analyses have identified frequently altered genes specific to metastatic breast cancer (MBC) compared with those in primary breast cancer (PBC), metastatic site-specific altered genes in MBC remain largel...
Breast cancerCancer epidemiologyCancer genomics
10.1038/S41523-021-00303-Y
ISSN:2374-4677
Knockdown of TACC3 inhibits tumor cell proliferation and increases chemosensitivity in pancreatic cancer
Saimeng Shi•Duancheng Guo•Longyun Ye•Tianjiao Li•Qinglin Fei等 9 人
Cell Death & Disease
2023
•2023/11/27
•Vol.14 No.11 p.1-18
Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant digestive tract tumor with limited clinical treatments. Transforming acidic coiled-coil-containing protein 3 (TACC3) is a component of the centrosome axis and a member of the TACC family, which affect mitosis and regulate chromosome stabi...
Mitotic spindlePancreatic cancer
10.1038/S41419-023-06313-X
ISSN:2041-4889
TP63 as a modulator of ferroptosis in TP53 mutations glioblastoma
Haiping Cai•Jiahao Yang•Feifei Luo•Wu Gan•Yanwen Li等 11 人
Cell Death & Disease
2025
•2025/8/13
•Vol.16 No.1 p.1-13
Glioblastoma (GBM) is a highly aggressive brain tumor with limited effective treatment options. Ferroptosis, a form of regulated cell death driven by iron-dependent lipid peroxidation, has emerged as a potential vulnerability in GBM, yet its regulatory mechanisms remain poorly defined. In this study...
CNS cancerTumour biomarkers
10.1038/S41419-025-07938-W
ISSN:2041-4889
Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility
Wen Wanqing•Chen Zhishan•Bao Jiandong•Long Quan•Shu Xiao-ou等 7 人
Nature Communications
2021
•2021/9/13
•Vol.12 No.1 p.1-12
Identifying transcription factors (TFs) whose DNA bindings are altered by genetic variants that regulate susceptibility genes is imperative to understand transcriptional dysregulation in disease etiology. Here, we develop a statistical framework to analyze extensive ChIP-seq and GWAS data and identi...
Breast cancerCancer epigenetics
10.1038/S41467-021-25670-9
ISSN:2041-1723
Systematic investigation of chemo-immunotherapy synergism to shift anti-PD-1 resistance in cancer
Yue Wang•Dhamotharan Pattarayan•Haozhe Huang•Yueshan Zhao•Sihan Li等 9 人
Nature Communications
2024
•2024/4/12
•Vol.15 No.1 p.1-16
Chemo-immunotherapy combinations have been regarded as one of the most practical ways to improve immunotherapy response in cancer patients. In this study, we integrate the transcriptomics data from anti-PD-1-treated tumors and compound-treated cancer cell lines to systematically screen for chemo-imm...
Computational biology and bioinformaticsImmunotherapyTumour immunology
10.1038/S41467-024-47433-Y
ISSN:2041-1723
PBRM1 loss defines a nonimmunogenic tumor phenotype associated with checkpoint inhibitor resistance in renal carcinoma
Xian-De Liu•Wen Kong•Christine B. Peterson•Daniel J. McGrail•Anh Hoang等 18 人
Nature Communications
2020
•2020/5/1
•Vol.11 No.1 p.1-14
A non-immunogenic tumor microenvironment (TME) is a significant barrier to immune checkpoint blockade (ICB) response. The impact of Polybromo-1 (PBRM1) on TME and response to ICB in renal cell carcinoma (RCC) remains to be resolved. Here we show that PBRM1/Pbrm1 deficiency reduces the binding of bra...
TranscriptomicsTumour immunology
10.1038/S41467-020-15959-6
ISSN:2041-1723
PLAAT2 suppresses gastric cancer progression by facilitating cMyc ubiquitination and inhibiting MEK/ERK signaling
Mingfei Chu•Xialing Shi•Zhantai Shi•Yu Liang
Cell Death & Disease
2026
•2026/3/18
•Vol.17 No.1 p.3140
Gastric cancer (GC) is a significant global public health issue due to its high incidence and limited therapeutic options. This study aimed to explore the role of phospholipase A and acyltransferase 2 (PLAAT2) in GC progression and its molecular mechanisms. A total of 116 pairs of GC and adjacent ti...
Gastric cancerUbiquitylation
10.1038/S41419-026-08546-Y
ISSN:2041-4889
Inhibition of iRhom1 by CD44-targeting nanocarrier for improved cancer immunochemotherapy
Zhangyi Luo•Yixian Huang•Neelu Batra•Yuang Chen•Haozhe Huang等 18 人
Nature Communications
2024
•2024/1/4
•Vol.15 No.1 p.1-20
The multifaceted chemo-immune resistance is the principal barrier to achieving cure in cancer patients. Identifying a target that is critically involved in chemo-immune-resistance represents an attractive strategy to improve cancer treatment. iRhom1 plays a role in cancer cell proliferation and its ...
Cancer therapyDrug deliveryNucleic-acid therapeuticsTumour immunology
10.1038/S41467-023-44572-6
ISSN:2041-1723
Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias
Ricardo de Matos Simoes•Ryosuke Shirasaki•Sondra L. Downey-Kopyscinski•Geoffrey M. Matthews•Benjamin G. Barwick等 41 人
Nature Cancer
2023
•2023/5/26
•Vol.4 No.5 p.754-773
Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dis...
CancerCancer genomicsMyeloma
10.1038/S43018-023-00550-X
ISSN:2662-1347
Osteosarcoma cells promote intracellular iron detoxification to mitigate GPX4-mediated ferroptosis
Md Abdullah•Donghee Lee•Eslenur Nipa•Jessy Castellanos-Gell•Ann M. Chan等 10 人
Cancer Gene Therapy
2026
•2026/3/23
•00 p.1-11
Osteosarcoma is an aggressive and highly metastatic cancer that arises in bones. Ferroptosis, an iron-dependent form of cell death, is critically controlled by glutathione peroxidase 4 (GPX4). In this study, we characterized GPX4 and its upstream regulator xCT across five osteosarcoma cell lines (U2...
BiomarkersBone cancerCell biologyGene expression
10.1038/S41417-026-01021-Y
ISSN:0929-1903
Development and validation of a deep learning algorithm for improving Gleason scoring of prostate cancer
Kunal Nagpal•Davis Foote•Yun Liu•Po-Hsuan Cameron Chen•Ellery Wulczyn等 19 人
Npj Digital Medicine
2019
•2019/6/7
•Vol.2 No.1 p.1-10
For prostate cancer patients, the Gleason score is one of the most important prognostic factors, potentially determining treatment independent of the stage. However, Gleason scoring is based on subjective microscopic examination of tumor morphology and suffers from poor reproducibility. Here we pres...
Prostate cancer
10.1038/S41746-019-0112-2
ISSN:2398-6352
Uncovering critical transitions and molecule mechanisms in disease progressions using Gaussian graphical optimal transport
Wenbo Hua•Ruixia Cui•Heran Yang•Jingyao Zhang•Chang Liu等 6 人
Communications Biology
2025
•2025/4/6
•Vol.8 No.1 p.1-18
Understanding disease progression is crucial for detecting critical transitions and finding trigger molecules, facilitating early diagnosis interventions. However, the high dimensionality of data and the lack of aligned samples across disease stages have posed challenges in addressing these tasks. W...
Computational modelsDynamic networksMachine learningPrognostic markersTime series
10.1038/S42003-025-07995-Z
ISSN:2399-3642
DRAM1 promotes the stability of lysosomal VAMP8 to enhance autolysosome formation and facilitates the extravasation
Rui Zhang•Xin Zhang•Hua Bai•Qiuyu Cheng•Xia Yao等 24 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-22
Autophagy classically functions to protect cells and organisms during stressful conditions by catabolizing intracellular components to maintain energy homeostasis. Lysosome-autophagosome fusion is a critical step in emptying degraded unwanted contents. However, the mechanism of autophagosome fusion ...
Cancer preventionMacroautophagyPost-translational modifications
10.1038/S41467-025-60887-Y
ISSN:2041-1723
Proteogenomic characterization identifies clinical subgroups in EGFR and ALK wild-type never-smoker lung adenocarcinoma
Hyondeog Kim•Wonyeop Lee•Youngwook Kim•Sang-Jin Lee•Wonyoung Choi等 11 人
Experimental & Molecular Medicine
2024
•2024/9/19
•Vol.56 No.9 p.2082-2095
Patients with lung adenocarcinoma who have never smoked (NSLA) and lack key driver mutations, such as those in the EGFR and ALK genes, face limited options for targeted therapies. They also tend to have poorer outcomes with immune checkpoint inhibitors than lung cancer patients who have a history of...
Cancer genomicsFunctional clusteringProteome informaticsTranscriptomics
10.1038/S12276-024-01320-0
ISSN:2092-6413
Integrative proteogenomic characterization of Wilms tumor
Cheng Cheng•Li Zhang•Xiaofeng Chang•Kai Chen•Tian He等 20 人
Nature Communications
2025
•2025/8/19
•Vol.16 No.1 p.1-20
Wilms tumor (WT), the most common pediatric renal malignancy, exhibits a relatively low mutational burden compared to adult cancers, which hinders the development of targeted therapies. To elucidate the molecular landscape of WT, we perform integrative proteomic, phosphoproteomic, transcriptomic, an...
Cancer genomicsPaediatric cancerTumour heterogeneityWilms tumour
10.1038/S41467-025-62234-7
ISSN:2041-1723
A spectrum of nonsense-mediated mRNA decay efficiency along the degree of mutational constraint
Young-gon Kim•Hyunju Kang•Beomki Lee•Hyeok-Jae Jang•Jong-ho Park等 8 人
Communications Biology
2024
•2024/11/7
•Vol.7 No.1 p.1-9
Despite its importance for regulating gene expression, nonsense-mediated mRNA decay (NMD) remains poorly understood. Here, we extend the findings of a previous landmark study that proposed several factors associated with NMD efficiency using matched genome and transcriptome data from The Cancer Geno...
Gene regulationMolecular medicine
10.1038/S42003-024-07136-Y
ISSN:2399-3642
Integrating spatial gene expression and breast tumour morphology via deep learning
Bryan He•Ludvig Bergenstråhle•Linnea Stenbeck•Abubakar Abid•Alma Andersson等 9 人
Nature Biomedical Engineering
2020
•2020/6/22
•Vol.4 No.8 p.827-834
Spatial transcriptomics allows for the measurement of RNA abundance at a high spatial resolution, making it possible to systematically link the morphology of cellular neighbourhoods and spatially localized gene expression. Here, we report the development of a deep learning algorithm for the predicti...
BiotechnologyComputational biology and bioinformatics
10.1038/S41551-020-0578-X
ISSN:2157-846X
KIF20A inhibits TRIM21-dependent ubiquitination of DHX9 to boost SOX2 stability, enhancing OSCC stemness and ferroptosis resistance
Ziyun Zhang•Yi Li•Jingjiang Hu•Xingjie Tang•Zhanpeng Li等 17 人
Cell Death & Disease
2026
•2026/2/11
•Vol.17 No.1 p.2180
Oral squamous cell carcinoma (OSCC) is an aggressive malignancy characterized by poor prognosis, largely attributable to cancer stem cell (CSC) persistence and ferroptosis resistance. However, the molecular mechanisms that coordinately regulate stemness maintenance and ferroptosis suppression in OSC...
Oral cancer
10.1038/S41419-026-08467-W
ISSN:2041-4889
Evolutionary fingerprints of epithelial-to-mesenchymal transition
Luigi Perelli•Li Zhang•Sarah Mangiameli•Francesca Giannese•Krishnan K. Mahadevan等 36 人
Nature
2025
•2025/3/5
•00 p.1-10
Mesenchymal plasticity has been extensively described in advanced epithelial cancers; however, its functional role in malignant progression is controversial1–5. The function of epithelial-to-mesenchymal transition (EMT) and cell plasticity in tumour heterogeneity and clonal evolution is poorly under...
Cancer geneticsCancer modelsGastrointestinal cancer
10.1038/S41586-025-08671-2
ISSN:0028-0836
Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities
Sejin Oh•Jeonghun Yeom•Hee Jin Cho•Ju-Hwa Kim•Seon-Jin Yoon等 25 人
Nature Communications
2020
•2020/7/3
•Vol.11 No.1 p.1-16
The prognostic and therapeutic relevance of molecular subtypes for the most aggressive isocitrate dehydrogenase 1/2 (IDH) wild-type glioblastoma (GBM) is currently limited due to high molecular heterogeneity of the tumors that impedes patient stratification. Here, we describe a distinct binary class...
CNS cancerProteomic analysis
10.1038/S41467-020-17139-Y
ISSN:2041-1723
Spi-1 proto-oncogene regulates mRNA hypertranscription and malignant progression in head and neck cancer
Zheran Liu•Zijian Qin•Huilin Li•Lili Zhu•Ling He等 10 人
Signal Transduction And Targeted Therapy
2026
•2026/3/18
•Vol.11 No.1 p.1020
Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent and lethal cancers worldwide. Despite multimodal therapeutic advances, long-term survival remains poor, underscoring the need to identify novel molecular drivers of disease aggressiveness. Hypertranscription is a genome-wide ...
Cancer genomicsHead and neck cancerTumour biomarkers
10.1038/S41392-026-02669-6
ISSN:2059-3635
Selective therapeutic strategy for p53-deficient cancer by targeting dysregulation in DNA repair
Justin Zonneville•Moyi Wang•Mohammed M. Alruwaili•Brandon Smith•Megan Melnick等 11 人
Communications Biology
2021
•2021/7/12
•Vol.4 No.1 p.1-12
Breast carcinomas commonly carry mutations in the tumor suppressor p53, although therapeutic efforts to target mutant p53 have previously been unfruitful. Here we report a selective combination therapy strategy for treatment of p53 mutant cancers. Genomic data revealed that p53 mutant cancers exhibi...
Breast cancerChemotherapy
10.1038/S42003-021-02370-0
ISSN:2399-3642
Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations
Elizaveta Besedina•Fran Supek
Nature Communications
2024
•2024/7/20
•Vol.15 No.1 p.1-20
Cancer driver genes can undergo positive selection for various types of genetic alterations, including gain-of-function or loss-of-function mutations and copy number alterations (CNA). We investigated the landscape of different types of alterations affecting driver genes in 17,644 cancer exomes and ...
Cancer genomicsGenetic interactionGenome evolutionStatistical methods
10.1038/S41467-024-50552-1
ISSN:2041-1723
Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images
Javad Noorbakhsh•Saman Farahmand•Ali Foroughi pour•Sandeep Namburi•Dennis Caruana等 9 人
Nature Communications
2020
•2020/12/11
•Vol.11 No.1 p.1-14
Histopathological images are a rich but incompletely explored data type for studying cancer. Manual inspection is time consuming, making it challenging to use for image data mining. Here we show that convolutional neural networks (CNNs) can be systematically applied across cancer types, enabling com...
CancerCancer genomicsComputational biology and bioinformaticsData miningTumour heterogeneity
10.1038/S41467-020-20030-5
ISSN:2041-1723
VSTM2L protects prostate cancer cells against ferroptosis via inhibiting VDAC1 oligomerization and maintaining mitochondria homeostasis
Juan Yang•Xiao Lu•Jing-Lan Hao•Lan Li•Yong-Tong Ruan等 9 人
Nature Communications
2025
•2025/1/29
•Vol.16 No.1 p.1-21
Ferroptosis is a form of iron-dependent programmed cell death, which is distinct from apoptosis, necrosis, and autophagy. Mitochondria play a critical role in initiating and amplifying ferroptosis in cancer cells. Voltage-Dependent Anion Channel 1 (VDAC1) embedded in the mitochondrial outer membrane...
Cell deathProstate cancer
10.1038/S41467-025-56494-6
ISSN:2041-1723
An integrative analysis of the age-associated multi-omic landscape across cancers
Kasit Chatsirisupachai•Tom Lesluyes•Luminita Paraoan•Peter Van Loo•João Pedro de Magalhães
Nature Communications
2021
•2021/4/20
•Vol.12 No.1 p.1-17
Age is the most important risk factor for cancer, as cancer incidence and mortality increase with age. However, how molecular alterations in tumours differ among patients of different age remains largely unexplored. Here, using data from The Cancer Genome Atlas, we comprehensively characterise genom...
Cancer genomicsComputational biology and bioinformatics
10.1038/S41467-021-22560-Y
ISSN:2041-1723
TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states
Ilaria Panzeri•Luca Fagnocchi•Stefanos Apostle•Megan Tompkins•Emily Wolfrum等 17 人
Nature Cancer
2025
•2025/1/24
•Vol.6 No.2 p.385-403
Mutations in cancer risk genes increase susceptibility, but not all carriers develop cancer. Indeed, while DNA mutations are necessary drivers of cancer, only a small subset of mutated cells go on to cause the disease. To date, the mechanisms underlying individual cancer susceptibility remain unclea...
CancerCancer epigeneticsDNA methylation
10.1038/S43018-024-00900-3
ISSN:2662-1347
Genomic characterization of rare molecular subclasses of hepatocellular carcinoma
Damrauer Jeffrey S.•Smith Markia A.•Walter Vonn•Thennavan Aatish•Mose Lisle E.等 7 人
Communications Biology
2021
•2021/10/4
•Vol.4 No.1 p.1-13
Primary liver cancer, consisting of both cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC), is the second leading cause of cancer deaths worldwide. Our goal is to genomically characterize rare HCC subclasses to provide insight into disease biology. Leveraging The Cancer Genome Atlas (TCGA)...
Cancer genomicsHepatocellular carcinoma
10.1038/S42003-021-02674-1
ISSN:2399-3642
Deep learning on tertiary lymphoid structures in hematoxylin-eosin predicts cancer prognosis and immunotherapy response
Ziqiang Chen•Xiaobing Wang•Zelin Jin•Bosen Li•Dongxian Jiang等 26 人
Npj Precision Oncology
2024
•2024/3/22
•Vol.8 No.1 p.1-11
Tertiary lymphoid structures (TLSs) have been associated with favorable immunotherapy responses and prognosis in various cancers. Despite their significance, their quantification using multiplex immunohistochemistry (mIHC) staining of T and B lymphocytes remains labor-intensive, limiting its clinica...
Prognostic markersTumour biomarkers
10.1038/S41698-024-00579-W
ISSN:2397-768X
Frequent CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression
Miklos Diossy•Viktoria Tisza•Hua Li•Pranshu Sahgal•Jia Zhou等 35 人
Npj Precision Oncology
2024
•2024/9/19
•Vol.8 No.1 p.1-13
We analyzed genomic data from the prostate cancer of African- and European American men to identify differences contributing to racial disparity of outcome. We also performed FISH-based studies of Chromodomain helicase DNA-binding protein 1 (CHD1) loss on prostate cancer tissue microarrays. We creat...
CancerComputational biology and bioinformaticsPrognostic markers
10.1038/S41698-024-00705-8
ISSN:2397-768X
Integrated molecular and clinical analysis of BRAF-mutant glioma in adults
Schreck Karisa C.•Langat Pinky•Bhave Varun M.•Li Taibo•Woodward Eleanor等 8 人
Npj Precision Oncology
2023
•2023/2/28
•Vol.7 No.1 p.1-11
BRAF mutations are a significant driver of disease in pediatric low-grade glioma, but the implications of BRAF alterations on the clinical course and treatment response in adult glioma remain unclear. Here, we characterize a multi-institutional cohort of more than 300 patients (>200 adults) with ...
Cancer geneticsCNS cancerOncogenes
10.1038/S41698-023-00359-Y
ISSN:2397-768X
A vision–language foundation model for precision oncology
Jinxi Xiang•Xiyue Wang•Xiaoming Zhang•Yinghua Xi•Feyisope Eweje等 18 人
Nature
2025
•2025/1/8
•00 p.1-10
Clinical decision-making is driven by multimodal data, including clinical notes and pathological characteristics. Artificial intelligence approaches that can effectively integrate multimodal data hold significant promise in advancing clinical care1,2. However, the scarcity of well-annotated multimod...
Machine learningOutcomes researchPathologyPrognosis
10.1038/S41586-024-08378-W
ISSN:0028-0836
Crucial immunological roles of the invasion front in innate and adaptive immunity in cervical cancer
Yuhya Hirahara•Kanako Shimizu•Satoru Yamasaki•Tomonori Iyoda•Shogo Ueda等 12 人
British Journal Of Cancer
2024
•2024/10/29
•00 p.1-13
The immunostimulatory actions of innate and adaptive immune responses play a crucial role in the cancer-immunity cycle. Although cervical cancer (CC) exhibits a high recurrence rate, the relation with lymphocytes in the tumor tissue have not been analyzed. We analyzed NKT, NK, and T cells, not only ...
Cervical cancerInnate immune cells
10.1038/S41416-024-02877-3
ISSN:0007-0920
Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood
Shantao Li•Forrest W. Crawford•Mark B. Gerstein
Nature Communications
2020
•2020/7/17
•Vol.11 No.1 p.1-12
Multiple mutational processes drive carcinogenesis, leaving characteristic signatures in tumor genomes. Determining the active signatures from a full repertoire of potential ones helps elucidate mechanisms of cancer development. This involves optimally decomposing the counts of cancer mutations, tab...
Cancer genomicsMachine learningSoftwareStatistical methods
10.1038/S41467-020-17388-X
ISSN:2041-1723
Multimodal fusion model for prognostic prediction and radiotherapy response assessment in head and neck squamous cell carcinoma
Ruxian Tian•Feng Hou•Haicheng Zhang•Guohua Yu•Ping Yang等 22 人
Npj Digital Medicine
2025
•2025/5/23
•Vol.8 No.1 p.1-14
Accurate prediction of prognosis and postoperative radiotherapy response is critical for personalized treatment in head and neck squamous cell carcinoma (HNSCC). We developed a multimodal deep learning model (MDLM) integrating computed tomography, whole-slide images, and clinical features from 1087 ...
Data integrationHead and neck cancerTranslational research
10.1038/S41746-025-01712-0
ISSN:2398-6352
The role of IGF2BP3/SPOP/c-Myc loop in paclitaxel resistance of endometrial cancer
Yidong Ge•Lili Kong•Yuxuan Li•Zongdong Yu•Fengguang Zhai等 19 人
Communications Biology
2025
•2025/4/17
•Vol.8 No.1 p.1-15
Paclitaxel combination therapy is the main chemotherapy regimen for endometrial cancer (EC); however, subsequent drug resistance is a bottleneck limiting its widespread clinical application. We found that human insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) was abnormally elevated in ...
Cancer therapeutic resistanceEndometrial cancer
10.1038/S42003-025-08065-0
ISSN:2399-3642
Colorectal cancer risk stratification on histological slides based on survival curves predicted by deep learning
Julia Höhn•Eva Krieghoff-Henning•Christoph Wies•Lennard Kiehl•Martin J. Hetz等 17 人
Npj Precision Oncology
2023
•2023/9/26
•Vol.7 No.1 p.1-12
Studies have shown that colorectal cancer prognosis can be predicted by deep learning-based analysis of histological tissue sections of the primary tumor. So far, this has been achieved using a binary prediction. Survival curves might contain more detailed information and thus enable a more fine-gra...
Colorectal cancerMathematics and computingPrognostic markers
10.1038/S41698-023-00451-3
ISSN:2397-768X
The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity
Alexander Joschua Ohnmacht•Anantharamanan Rajamani•Göksu Avar•Ginte Kutkaite•Emanuel Gonçalves等 7 人
Communications Biology
2023
•2023/8/9
•Vol.6 No.1 p.1-11
Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic...
Data integrationDNA methylationDrug developmentPredictive markers
10.1038/S42003-023-05198-Y
ISSN:2399-3642
SLC13A3 is a major effector downstream of activated β-catenin in liver cancer pathogenesis
Wennan Zhao•Xue Wang•Lifeng Han•Chunze Zhang•Chenxi Wang等 16 人
Nature Communications
2024
•2024/8/30
•Vol.15 No.1 p.1-21
Activated Wnt/β-catenin pathway is a key genetic event in liver cancer development. Solute carrier (SLC) transporters are promising drug targets. Here, we identify SLC13A3 as a drug-targetable effector downstream of β-catenin in liver cancer. SLC13A3 expression is elevated in human liver cancer samp...
Hepatocellular carcinomaMechanisms of diseaseTarget identification
10.1038/S41467-024-51860-2
ISSN:2041-1723
Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness
Geut Galai•Xie He•Barak Rotblat•Shai Pilosof
Nature Communications
2023
•2023/10/7
•Vol.14 No.1 p.1-11
Cancer cells alter the expression levels of metabolic enzymes to fuel proliferation. The mitochondrion is a central hub of metabolic reprogramming, where chaperones service hundreds of clients, forming chaperone-client interaction networks. How network structure affects its robustness to chaperone t...
Cancer modelsEcological networks
10.1038/S41467-023-41906-2
ISSN:2041-1723
Multimodal fusion of pathology and radiology foundation models for WHO 2021 glioma subtyping
Camillo Saueressig•Daniel Scholz•Philipp Raffler•Claire Delbridge•Benedikt Wiestler等 6 人
Npj Precision Oncology
2026
•2026/3/12
•Vol.10 No.1 p.1180
Molecular subtyping of gliomas is a common clinical task, yet challenging to perform on histology or radiology images alone. To address this challenge, we developed a multimodal classification framework that integrates histopathology and magnetic resonance imaging (MRI) using foundation models as un...
BiomarkersCancerComputational biology and bioinformaticsMedical researchOncology
10.1038/S41698-026-01366-5
ISSN:2397-768X
GZMK expression within activated intratumoral T-cell subsets reflects differentiation efficiency and predicts response to cancer immunotherapy
Cem M. Sievers•Tian-Gen Chang•Yvette Robbins•Jay Friedman•Marco Craveiro等 17 人
Npj Precision Oncology
2026
•2026/4/18
0Neoadjuvant immunotherapies (NITs) have demonstrated clinical benefit in head and neck carcinoma and other cancers by enhancing T cell-mediated anti-tumor immunity. However, disease recurrence remains a major challenge in a significant proportion of patients. Characterization of T cell dynamics unde...
CancerImmunologyOncology
10.1038/S41698-026-01437-7
ISSN:2397-768X
Combining AI to reveal CCDC3-mediated pathways of colorectal cancer liver metastasis
Runze Huang•Qinyu Liu•Xin Jin•Xuanci Bai•Yibin Wu等 12 人
Npj Digital Medicine
2026
•2026/3/7
0In colorectal cancer liver metastases, chromosomal instability (CIN) serves as a critical hallmark linked to tumor aggressiveness and poor prognosis. This study integrated single-cell RNA sequencing, weighted gene co-expression network analysis, and non-negative matrix factorization to construct a c...
CancerComputational biology and bioinformaticsOncology
10.1038/S41746-026-02457-0
ISSN:2398-6352
DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis
Wei Liu•Jun Li•Yitao Tang•Yining Zhao•Chaozhong Liu等 12 人
Nature Communications
2025
•2025/3/6
•Vol.16 No.1 p.1-6
Functional proteomics provides critical insights into cancer mechanisms, facilitating the discovery of novel biomarkers and therapeutic targets. We have developed a comprehensive cancer functional proteomics resource using reverse phase protein arrays, incorporating data from nearly 8000 patient sam...
CancerComputational platforms and environmentsProteomics
10.1038/S41467-025-57430-4
ISSN:2041-1723
Evolutionary histories of breast cancer and related clones
Tomomi Nishimura•Nobuyuki Kakiuchi•Kenichi Yoshida•Takaki Sakurai•Tatsuki R. Kataoka等 40 人
Nature
2023
•2023/7/26
•00 p.1-8
Recent studies have documented frequent evolution of clones carrying common cancer mutations in apparently normal tissues, which are implicated in cancer development1–3. However, our knowledge is still missing with regard to what additional driver events take place in what order, before one or more ...
AgeingBreast cancerCancer genomicsEvolutionary genetics
10.1038/S41586-023-06333-9
ISSN:0028-0836
Neuronal substance P drives metastasis through an extracellular RNA–TLR7 axis
Veena Padmanaban•Isabel Keller•Ethan S. Seltzer•Benjamin N. Ostendorf•Zachary Kerner等 6 人
Nature
2024
•2024/8/7
•00 p.1-9
Tumour innervation is associated with worse patient outcomes in multiple cancers1,2, which suggests that it may regulate metastasis. Here we observed that highly metastatic mouse mammary tumours acquired more innervation than did less-metastatic tumours. This enhanced innervation was driven by expre...
Breast cancerCancer microenvironmentMetastasis
10.1038/S41586-024-07767-5
ISSN:0028-0836
Boosting pathology foundation models via few-shot prompt-tuning for rare cancer subtyping
Dexuan He•Xiao Zhou•Wenbin Guan•Liyuan Zhang•Xiaoman Zhang等 15 人
Nature Communications
2026
•2026/4/11
0Rare cancers comprise 20–25% of malignancies (over 70% in pediatric oncology) but face major diagnostic challenges due to limited expert availability. While pathology vision-language models show promising zero-shot capabilities for common cancers, their performance on rare cancers remains limited. E...
CancerCancer imagingPathology
10.1038/S41467-026-71715-2
ISSN:2041-1723
Prediction and analysis of tumor infiltrating lymphocytes across 28 cancers by TILScout using deep learning
Huibo Zhang•Lulu Chen•Lan Li•Yang Liu•Barnali Das等 11 人
Npj Precision Oncology
2025
•2025/3/19
•Vol.9 No.1 p.1-15
The density of tumor-infiltrating lymphocytes (TILs) serves as a valuable indicator for predicting anti-tumor responses, but its broad impact across various types of cancers remains underexplored. We introduce TILScout, a pan-cancer deep-learning approach to compute patch-level TIL scores from whole...
Cancer microenvironmentComputational biology and bioinformaticsTumour immunology
10.1038/S41698-025-00866-0
ISSN:2397-768X
BRN2 is a non-canonical melanoma tumor-suppressor
Michael Hamm•Pierre Sohier•Valérie Petit•Jérémy H. Raymond•Véronique Delmas等 24 人
Nature Communications
2021
•2021/6/17
•Vol.12 No.1 p.1-16
While the major drivers of melanoma initiation, including activation of NRAS/BRAF and loss of PTEN or CDKN2A, have been identified, the role of key transcription factors that impose altered transcriptional states in response to deregulated signaling is not well understood. The POU domain transcripti...
Gene expressionMechanisms of diseaseMelanoma
10.1038/S41467-021-23973-5
ISSN:2041-1723
The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences
Jia-Wern Pan•Muhammad Mamduh Ahmad Zabidi•Pei-Sze Ng•Mei-Yee Meng•Siti Norhidayu Hasan等 13 人
Nature Communications
2020
•2020/12/22
•Vol.11 No.1 p.1-12
Molecular profiling of breast cancer has enabled the development of more robust molecular prognostic signatures and therapeutic options for breast cancer patients. However, non-Caucasian populations remain understudied. Here, we present the mutational, transcriptional, and copy number profiles of 56...
Breast cancerCancer genomics
10.1038/S41467-020-20173-5
ISSN:2041-1723
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors
Zapata Luis•Caravagna Giulio•Williams Marc J.•Lakatos Eszter•AbdulJabbar Khalid等 15 人
Nature Genetics
2023
•2023/3/9
•Vol.55 No.3 p.451-460
In cancer, evolutionary forces select for clones that evade the immune system. Here we analyzed >10,000 primary tumors and 356 immune-checkpoint-treated metastases using immune dN/dS, the ratio of nonsynonymous to synonymous mutations in the immunopeptidome, to measure immune selection in cohorts...
ImmunogeneticsImmunotherapyTumour biomarkers
10.1038/S41588-023-01313-1
ISSN:1061-4036
Age-specific tumor-associated macrophage biomarkers underlie metastasis and immune dysregulation in thyroid cancer
Tianyao Chu•Shenglong Xu•Hongyan Chen•Xinlei Zhang•Yan Zhao等 6 人
Npj Aging
2025
•2025/10/9
•Vol.11 No.1 p.1-6
Thyroid cancer (THCA) shows rising incidence and aggressiveness in young-onset cases. Through integrated single-cell, transcriptomic, and proteomic analyses, we identified age-specific tumor-associated macrophage (TAM) genes, including OLR1 and SIGLEC1, linked to metastasis and immune dysfunction. T...
BiomarkersCancerRisk factors
10.1038/S41514-025-00270-9
ISSN:2731-6068
Integrative analysis of genomic and epigenomic regulation reveals miRNA mediated tumor heterogeneity and immune evasion in lower grade glioma
Zhen Yang•Xiaocen Liu•Hao Xu•Andrew E. Teschendorff•Lingjie Xu等 14 人
Communications Biology
2024
•2024/7/6
•Vol.7 No.1 p.1-20
The expression dysregulation of microRNAs (miRNA) has been widely reported during cancer development, however, the underling mechanism remains largely unanswered. In the present work, we performed a systematic integrative study for genome-wide DNA methylation, copy number variation and miRNA express...
Cancer microenvironmentData integrationGene regulatory networksTumour heterogeneity
10.1038/S42003-024-06488-9
ISSN:2399-3642
Rewiring of cortical glucose metabolism fuels human brain cancer growth
Andrew J. Scott•Anjali Mittal•Baharan Meghdadi•Alexandra O’Brien•Justine Bailleul等 41 人
Nature
2025
•2025/9/3
•00 p.1-10
The brain avidly consumes glucose to fuel neurophysiology1. Cancers of the brain, such as glioblastoma, relinquish physiological integrity and gain the ability to proliferate and invade healthy tissue2. How brain cancers rewire glucose use to drive aggressive growth remains unclear. Here we infused ...
Cancer metabolismCNS cancerTranslational research
10.1038/S41586-025-09460-7
ISSN:0028-0836
Acetyl-CoA synthetase 2 contributes to a better prognosis for liver cancer by switching acetate-glucose metabolism
Kyung Hee Jung•Sujin Lee•Han Sun Kim•Jin-Mo Kim•Yun Ji Lee等 11 人
Experimental & Molecular Medicine
2024
•2024/3/25
•00 p.1-13
Acetyl-CoA synthetase 2 (ACSS2)-dependent acetate usage has generally been associated with tumorigenesis and increased malignancy in cancers under nutrient-depleted conditions. However, the nutrient usage and metabolic characteristics of the liver differ from those of other organs; therefore, the me...
Cancer metabolismTargeted therapies
10.1038/S12276-024-01185-3
ISSN:2092-6413
Cancer cell genetics shaping of the tumor microenvironment reveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma
Christel F. A. Ramirez•Daniel Taranto•Masami Ando-Kuri•Marnix H. P. de Groot•Efi Tsouri等 13 人
Nature Communications
2024
•2024/3/22
•Vol.15 No.1 p.1-24
Myeloid cells are abundant and plastic immune cell subsets in the liver, to which pro-tumorigenic, inflammatory and immunosuppressive roles have been assigned in the course of tumorigenesis. Yet several aspects underlying their dynamic alterations in hepatocellular carcinoma (HCC) progression remain...
Cancer microenvironmentHepatocellular carcinomaTumour immunology
10.1038/S41467-024-46835-2
ISSN:2041-1723
ULK1 inhibition overcomes compromised antigen presentation and restores antitumor immunity in LKB1 -mutant lung cancer
Jiehui Deng•Aatish Thennavan•Igor Dolgalev•Ting Chen•Jie Li等 38 人
Nature Cancer
2021
•2021/5/17
•Vol.2 No.5 p.503-514
Inactivating mutations in LKB1/STK11 are present in roughly 20% of nonsmall cell lung cancers (NSCLC) and portend poor response to anti-PD-1 immunotherapy. Unexpectedly, we found that LKB1 deficiency correlated with elevated tumor mutational burden (TMB) in NSCLCs from nonsmokers and genetically eng...
CancerCancer therapyLung cancerTumour immunology
10.1038/S43018-021-00208-6
ISSN:2662-1347
UroFusion-X: a unified multimodal deep learning framework for robust diagnosis, subtyping, and prognosis of urological cancers
Yingming Xiao•Shengke Yang•Mingjing He•Li Chen•Yi Wu等 6 人
Npj Digital Medicine
2026
•2026/1/19
•Vol.9 No.1 p.1170
Multimodal clinical data, including imaging, pathology, omics, and laboratory tests, are often fragmented in routine practice, leading to inconsistent decision-making in the management of urological cancers. We propose UroFusion-X, a unified multimodal framework for integrated diagnosis, molecular s...
CancerComputational biology and bioinformaticsOncology
10.1038/S41746-025-02295-6
ISSN:2398-6352
HMMR promotes prostate cancer proliferation and metastasis via AURKA/mTORC2/E2F1 positive feedback loop
Guo Kaixuan•Liu Cheng•Shi Juanyi•Lai Cong•Gao Ze等 10 人
Cell Death Discovery
2023
•2023/2/7
•Vol.9 No.1 p.1-12
Although dysregulated HMMR is linked to prostate cancer (PCa) prognosis, the precise mechanisms remain unclear. Here, we sought to elucidate the role of HMMR in PCa progression as well as underlying mechanism. Herein, we found that upregulation of HMMR frequently observed in PCa samples and was asso...
Prostate cancerTOR signalling
10.1038/S41420-023-01341-0
ISSN:2058-7716
Using somatic variant richness to mine signals from rare variants in the cancer genome
Saptarshi Chakraborty•Arshi Arora•Colin B. Begg•Ronglai Shen
Nature Communications
2019
•2019/12/3
•Vol.10 No.1 p.1-9
To date, the vast preponderance of somatic variants observed in the cancer genome have been rare variants, and it is common in practice to encounter in a new tumor variants that have not been observed previously. Here we focus on probability estimation for encountering such hitherto unseen variants....
Cancer genomicsStatistical methods
10.1038/S41467-019-13402-Z
ISSN:2041-1723
PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven acquired resistance in preclinical cancer models
Chun Wai Wong•Christos Evangelou•Kieran N. Sefton•Rotem Leshem•Wei Zhang等 24 人
Nature Communications
2023
•2023/9/26
•Vol.14 No.1 p.1-21
Resistance mechanisms to immune checkpoint blockade therapy (ICBT) limit its response duration and magnitude. Paradoxically, Interferon γ (IFNγ), a key cytokine for cellular immunity, can promote ICBT resistance. Using syngeneic mouse tumour models, we confirm that chronic IFNγ exposure confers resi...
Cancer therapeutic resistanceTumour immunology
10.1038/S41467-023-41737-1
ISSN:2041-1723
Task-driven framework using large models for digital pathology
Jiahui Yu•Tianyu Ma•Feng Chen•Jing Zhang•Yingke Xu
Communications Biology
2024
•2024/12/4
•Vol.7 No.1 p.1-6
Microscopy is an indispensable tool for collecting biomedical information in pathological diagnosis, but manual annotation, measurement and interpretation are labor-intensive and costly. Here, we propose a task-driven framework powered by large models that excel in visual analysis and real-time cont...
Cancer imagingCancer screening
10.1038/S42003-024-07303-1
ISSN:2399-3642
Metabolomic differentiation of benign vs malignant pulmonary nodules with high specificity via high-resolution mass spectrometry analysis of patient sera
Yao Yao•Wang Xueping•Guan Jian•Xie Chuanbo•Zhang Hui等 19 人
Nature Communications
2023
•2023/4/24
•Vol.14 No.1 p.1-12
Differential diagnosis of pulmonary nodules detected by computed tomography (CT) remains a challenge in clinical practice. Here, we characterize the global metabolomes of 480 serum samples including healthy controls, benign pulmonary nodules, and stage I lung adenocarcinoma. The adenocarcinoma demon...
BiomarkersCancer
10.1038/S41467-023-37875-1
ISSN:2041-1723
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis
Jennifer A. Karlow•Benpeng Miao•Xiaoyun Xing•Ting Wang•Bo Zhang
Communications Biology
2021
•2021/5/21
•Vol.4 No.1 p.1-16
Trends in altered DNA methylation have been defined across human cancers, revealing global loss of methylation (hypomethylation) and focal gain of methylation (hypermethylation) as frequent cancer hallmarks. Although many cancers share these trends, little is known about the specific differences in ...
CNS cancerDNA methylationEndometrial cancer
10.1038/S42003-021-02094-1
ISSN:2399-3642
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics
Danh-Tai Hoang•Gal Dinstag•Eldad D. Shulman•Leandro C. Hermida•Doreen S. Ben-Zvi等 31 人
Nature Cancer
2024
•2024/7/3
•00 p.1-13
Advances in artificial intelligence have paved the way for leveraging hematoxylin and eosin-stained tumor slides for precision oncology. We present ENLIGHT–DeepPT, an indirect two-step approach consisting of (1) DeepPT, a deep-learning framework that predicts genome-wide tumor mRNA expression from s...
CancerCancer imagingComputational biology and bioinformatics
10.1038/S43018-024-00793-2
ISSN:2662-1347
Global DNA methylation differences involving germline structural variation impact gene expression in pediatric brain tumors
Fengju Chen•Yiqun Zhang•Wei Li•Fritz J. Sedlazeck•Lanlan Shen等 6 人
Nature Communications
2025
•2025/5/21
•Vol.16 No.1 p.1-17
The extent of genetic variation and its influence on gene expression across multiple tissue and cellular contexts is still being characterized, with germline Structural Variants (SVs) being historically understudied. DNA methylation also represents a component of normal germline variation across ind...
Cancer genomicsCNS cancerEpigenomicsGene regulationMethylation analysis
10.1038/S41467-025-60110-Y
ISSN:2041-1723
FUT3 mediated GRP78 fucosylation promotes colorectal cancer survival and proliferation under glucose restriction via PERK/ATF4/STC2 axis
Kaiwen Qin•Haonan Zhang•Yulu Shi•Ruo Wu•Changjie Wu等 16 人
Npj Precision Oncology
2025
•2025/12/14
0Tumor competition for nutrients within the microenvironment triggers stress responses to adapt to adverse conditions; however, the mechanism by which a glucose-depleted environment influences tumor fucosylation to promote endoplasmic reticulum (ER) stress remains unclear. In this study, we demonstra...
Cancer geneticsCancer microenvironmentColorectal cancer
10.1038/S41698-025-01216-W
ISSN:2397-768X
Cancer aneuploidies are shaped primarily by effects on tumour fitness
Juliann Shih•Shahab Sarmashghi•Nadja Zhakula-Kostadinova•Shu Zhang•Yohanna Georgis等 17 人
Nature
2023
•2023/6/28
•00 p.1-8
Aneuploidies—whole-chromosome or whole-arm imbalances—are the most prevalent alteration in cancer genomes1,2. However, it is still debated whether their prevalence is due to selection or ease of generation as passenger events1,2. Here we developed a method, BISCUT, that identifies loci subject to fi...
Cancer genomicsCancer modelsCytogeneticsEvolutionary geneticsGenome informatics
10.1038/S41586-023-06266-3
ISSN:0028-0836
Integrative proteomic characterization of adenocarcinoma of esophagogastric junction
Li Shengli•Yuan Li•Xu Zhi-Yuan•Xu Jing-Li•Chen Gui-Ping等 19 人
Nature Communications
2023
•2023/2/11
•Vol.14 No.1 p.1-19
The incidence of adenocarcinoma of the esophagogastric junction (AEG) has been rapidly increasing in recent decades, but its molecular alterations and subtypes are still obscure. Here, we conduct proteomics and phosphoproteomics profiling of 103 AEG tumors with paired normal adjacent tissues (NATs),...
Data miningOesophageal cancerProteome informatics
10.1038/S41467-023-36462-8
ISSN:2041-1723
Cross-species comparison reveals therapeutic vulnerabilities halting glioblastoma progression
Leo Carl Foerster•Oguzhan Kaya•Valentin Wüst•Diana-Patricia Danciu•Vuslat Akcay等 25 人
Nature Communications
2025
•2025/8/6
•Vol.16 No.1 p.1-20
The growth of a tumor is tightly linked to the distribution of its cells along a continuum of activation states. Here, we systematically decode the activation state architecture (ASA) in a glioblastoma (GBM) patient cohort through comparison to adult murine neural stem cells. Modelling of these data...
CNS cancerComputational biology and bioinformaticsNeural stem cells
10.1038/S41467-025-62528-W
ISSN:2041-1723
Senescence as a dictator of patient outcomes and therapeutic efficacies in human gastric cancer
Zhou Lulin•Niu Zubiao•Wang Yuqi•Zheng You•Zhu Yichao等 14 人
Cell Death Discovery
2022
•2022/1/10
•Vol.8 No.1 p.1-14
Senescence is believed to be a pivotal player in the onset and progression of tumors as well as cancer therapy. However, the guiding roles of senescence in clinical outcomes and therapy selection for patients with cancer remain obscure, largely due to the absence of a feasible senescence signature. ...
Cancer immunotherapyChemotherapyGastric cancerPrognostic markersSenescence
10.1038/S41420-021-00769-6
ISSN:2058-7716
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression
Cao Shaolong•Wang Jennifer R.•Ji Shuangxi•Yang Peng•Dai Yaoyi等 40 人
Nature Biotechnology
2022
•2022/6/13
•00 p.1-10
Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expressi...
Computational modelsTumour heterogeneity
10.1038/S41587-022-01342-X
ISSN:1087-0156
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma
Man Hsin Hung•Joo Sang Lee•Chi Ma•Laurence P. Diggs•Sophia Heinrich等 14 人
Nature Communications
2021
•2021/3/5
•Vol.12 No.1 p.1-15
T-cell exhaustion denotes a hypofunctional state of T lymphocytes commonly found in cancer, but how tumor cells drive T-cell exhaustion remains elusive. Here, we find T-cell exhaustion linked to overall survival in 675 hepatocellular carcinoma (HCC) patients with diverse ethnicities and etiologies. ...
Cancer metabolismCancer microenvironmentHepatocellular carcinomaImmunoediting
10.1038/S41467-021-21804-1
ISSN:2041-1723
Deubiquitinase USP35 stabilizes BRPF1 to activate mevalonate (MVA) metabolism during prostate tumorigenesis
Lin Guowen•Huang Tianrun•Zhang Xiaobo•Wang Gangmin
Cell Death Discovery
2022
•2022/11/10
•Vol.8 No.1 p.1-13
The mutual interplay between epigenetic modifications and metabolic rewiring contributes to malignant features of prostate adenocarcinoma (PRAD). This study aimed to uncover the biological roles of deubiquitylase USP35 in PRAD and find effective epigenetic or metabolic targets. Bioinformatic tools o...
Prostate cancerUbiquitylation
10.1038/S41420-022-01231-X
ISSN:2058-7716
Clinical sequencing of soft tissue and bone sarcomas delineates diverse genomic landscapes and potential therapeutic targets
Nacev Benjamin A.•Sanchez-Vega Francisco•Smith Shaleigh A.•Antonescu Cristina R.•Rosenbaum Evan等 47 人
Nature Communications
2022
•2022/6/15
•Vol.13 No.1 p.1-15
The genetic, biologic, and clinical heterogeneity of sarcomas poses a challenge for the identification of therapeutic targets, clinical research, and advancing patient care. Because there are > 100 sarcoma subtypes, in-depth genetic studies have focused on one or a few subtypes. Herein, we report...
Cancer genomicsSarcomaTumour biomarkersTumour heterogeneity
10.1038/S41467-022-30453-X
ISSN:2041-1723
Benchmarking foundation models as feature extractors for weakly supervised computational pathology
Peter Neidlinger•Omar S. M. El Nahhas•Hannah Sophie Muti•Tim Lenz•Michael Hoffmeister等 16 人
Nature Biomedical Engineering
2025
•2025/10/1
•00 p.1-11
Numerous pathology foundation models have been developed to extract clinically relevant information. There is currently limited literature independently evaluating these foundation models on external cohorts and clinically relevant tasks to uncover adjustments for future improvements. Here we benchm...
Cancer imagingTumour biomarkers
10.1038/S41551-025-01516-3
ISSN:2157-846X
Targeting ALK averts ribonuclease 1-induced immunosuppression and enhances antitumor immunity in hepatocellular carcinoma
Chunxiao Liu•Chenhao Zhou•Weiya Xia•Yifan Zhou•Yufan Qiu等 15 人
Nature Communications
2024
•2024/2/2
•Vol.15 No.1 p.1-18
Tumor-secreted factors contribute to the development of a microenvironment that facilitates the escape of cancer cells from immunotherapy. In this study, we conduct a retrospective comparison of the proteins secreted by hepatocellular carcinoma (HCC) cells in responders and non-responders among a co...
Cancer therapyHepatocellular carcinomaTumour immunology
10.1038/S41467-024-45215-0
ISSN:2041-1723
A novel defined pyroptosis-related gene signature for predicting the prognosis of ovarian cancer
Ying Ye•Qinjin Dai•Hongbo Qi
Cell Death Discovery
2021
•2021/4/7
•Vol.7 No.1 p.1-11
Ovarian cancer (OC) is a highly malignant gynaecological tumour that has a very poor prognosis. Pyroptosis has been demonstrated in recent years to be an inflammatory form of programmed cell death. However, the expression of pyroptosis-related genes in OC and their correlations with prognosis remain...
Ovarian cancerTranscriptomics
10.1038/S41420-021-00451-X
ISSN:2058-7716
Identification of diagnostic biomarkers in prostate cancer-related fatigue by construction of predictive models and experimental validation
Ming Chen•Siqi Zhou•Xiongwei He•Haiyan Wen
British Journal Of Cancer
2024
•2024/12/15
•00 p.1-12
Cancer-related fatigue (CRF) is a prominent cancer-related complication occurring in Prostate cancer (PCa) patients, profoundly affecting prognosis. The lack of diagnostic criteria and biomarkers hampers the management of CRF. The CRF-related data and PCa single-cell data were retrieved from the GEO...
Cancer modelsComputational modelsTumour biomarkers
10.1038/S41416-024-02922-1
ISSN:0007-0920
Cancer diagnosis with DNA molecular computation
Chao Zhang•Yumeng Zhao•Xuemei Xu•Rui Xu•Haowen Li等 10 人
Nature Nanotechnology
2020
•2020/5/25
•Vol.15 No.8 p.709-715
Early and precise cancer diagnosis substantially improves patient survival. Recent work has revealed that the levels of multiple microRNAs in serum are informative as biomarkers for the diagnosis of cancers. Here, we designed a DNA molecular computation platform for the analysis of miRNA profiles in...
Analytical chemistryDNA nanotechnologyNanobiotechnology
10.1038/S41565-020-0699-0
ISSN:1748-3387
Linc00707 regulates autophagy and promotes the progression of triple negative breast cancer by activation of PI3K/AKT/mTOR pathway
Hongli Li•Qinghua Liu•Yaqiong Hu•Chonggao Yin•Yunxiang Zhang等 6 人
Cell Death Discovery
2024
•2024/3/14
•Vol.10 No.1 p.1-14
Triple-negative breast cancer (TNBC) is a pathological subtype of breast cancer (BC) with high malignancy, strong invasiveness and poor prognosis. Long non-coding RNA (LncRNA) plays an important role during tumorigenesis. We identified that Linc00707 was upregulated in TNBC tissues by TCGA database ...
Breast cancerLong non-coding RNAs
10.1038/S41420-024-01906-7
ISSN:2058-7716
The ubiquitin ligase RNF5 determines acute myeloid leukemia growth and susceptibility to histone deacetylase inhibitors
Khateb Ali•Deshpande Anagha•Feng Yongmei•Finlay Darren•Lee Joo Sang等 25 人
Nature Communications
2021
•2021/9/13
•Vol.12 No.1 p.1-17
Acute myeloid leukemia (AML) remains incurable, largely due to its resistance to conventional treatments. Here, we find that increased abundance of the ubiquitin ligase RNF5 contributes to AML development and survival. High RNF5 expression in AML patient specimens correlates with poor prognosis. RNF...
Acute myeloid leukaemiaMechanisms of diseaseUbiquitylation
10.1038/S41467-021-25664-7
ISSN:2041-1723
IgA transcytosis and antigen recognition govern ovarian cancer immunity
Subir Biswas•Gunjan Mandal•Kyle K. Payne•Carmen M. Anadon•Chandler D. Gatenbee等 23 人
Nature
2021
•2021/2/3
•Vol.591 No.7850 p.464-470
Most ovarian cancers are infiltrated by prognostically relevant activated T cells1–3, yet exhibit low response rates to immune checkpoint inhibitors4. Memory B cell and plasma cell infiltrates have previously been associated with better outcomes in ovarian cancer5,6, but the nature and functional re...
Ovarian cancerTumour immunology
10.1038/S41586-020-03144-0
ISSN:0028-0836
Deep learning infers clinically relevant protein levels and drug response in breast cancer from unannotated pathology images
Hui Liu•Xiaodong Xie•Bin Wang
Npj Breast Cancer
2024
•2024/2/27
•Vol.10 No.1 p.1-11
The computational pathology has been demonstrated to effectively uncover tumor-related genomic alterations and transcriptomic patterns. Although proteomics has indeed shown great potential in the field of precision medicine, few studies have focused on the computational prediction of protein levels ...
Breast cancerCancer imagingTranslational research
10.1038/S41523-024-00620-Y
ISSN:2374-4677
Identification of breast cancer subtypes and drug response prediction through forward and reverse translation
Julie Karam•Paul A. Rejto•Jadwiga Renata Bienkowska•Xinmeng Jasmine Mu•Whijae Roh
Npj Precision Oncology
2025
•2025/7/31
•Vol.9 No.1 p.1-10
Breast cancer (BRCA) is the most frequently diagnosed cancer among women and the second leading cause of cancer-related mortality worldwide. Biomarkers that predict therapeutic response can guide the choice of treatment modality and improve patient outcomes. We applied the bulk gene expression decon...
Breast cancerCancerCancer genomicsCancer modelsCancer therapyOncology+1
10.1038/S41698-025-01062-W
ISSN:2397-768X
A visual–omics foundation model to bridge histopathology with spatial transcriptomics
Weiqing Chen•Pengzhi Zhang•Tu N Tran•Yiwei Xiao•Shengyu Li等 20 人
Nature Methods
2025
•2025/5/29
•00 p.1-15
Artificial intelligence has revolutionized computational biology. Recent developments in omics technologies, including single-cell RNA sequencing and spatial transcriptomics, provide detailed genomic data alongside tissue histology. However, current computational models focus on either omics or imag...
Computational modelsComputational platforms and environmentsMachine learningSoftware
10.1038/S41592-025-02707-1
ISSN:1548-7091
An augmented reality microscope with real-time artificial intelligence integration for cancer diagnosis
Po-Hsuan Cameron Chen•Krishna Gadepalli•Robert MacDonald•Yun Liu•Shiro Kadowaki等 12 人
Nature Medicine
2019
•2019/8/12
•Vol.25 No.9 p.1453-1457
The microscopic assessment of tissue samples is instrumental for the diagnosis and staging of cancer, and thus guides therapy. However, these assessments demonstrate considerable variability and many regions of the world lack access to trained pathologists. Though artificial intelligence (AI) promis...
BiotechnologyEngineeringHealth care
10.1038/S41591-019-0539-7
ISSN:1078-8956
SCISSOR: a framework for identifying structural changes in RNA transcripts
Hyo Young Choi•Heejoon Jo•Xiaobei Zhao•Katherine A. Hoadley•Scott Newman等 10 人
Nature Communications
2021
•2021/1/12
•Vol.12 No.1 p.1-12
High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA vari...
CancerComputational biology and bioinformaticsGenetics
10.1038/S41467-020-20593-3
ISSN:2041-1723
Transcriptional and genetic alterations of cuproptosis-related genes correlated to malignancy and immune-infiltrate of esophageal carcinoma
Jiang Runmin•Huan Yu•Li Yan•Gao Xinyue•Sun Qiang等 7 人
Cell Death Discovery
2022
•2022/8/22
•Vol.8 No.1 p.1-13
Esophageal carcinoma (ESCA) is a common type of cancer with high mortality. Cuproptosis is a new type of cell death and is characterized by the dependence on mitochondrial respiration and protein lipoylation. However, the potential roles of cuproptosis-related genes (CRGs) in ESCA remain elusive. He...
Oesophageal cancerTumour immunology
10.1038/S41420-022-01164-5
ISSN:2058-7716
Accelerating histopathology workflows with generative AI-based virtually multiplexed tumour profiling
Pushpak Pati•Sofia Karkampouna•Francesco Bonollo•Eva Compérat•Martina Radić等 10 人
Nature Machine Intelligence
2024
•2024/9/9
•00 p.1-17
Understanding the spatial heterogeneity of tumours and its links to disease initiation and progression is a cornerstone of cancer biology. Presently, histopathology workflows heavily rely on hematoxylin and eosin and serial immunohistochemistry staining, a cumbersome, tissue-exhaustive process that ...
Cancer imagingMachine learning
10.1038/S42256-024-00889-5
ISSN:2522-5839
m1A-mediated regulation of BIRC2 mRNA stability drives apoptosis evasion and tumor progression in liver cancer
Yingmin Wu•Shenjie Zhang•Shilong Zhang•Jieyu Lu•Yuntao Yang等 12 人
Cell Death & Disease
2026
•2026/4/16
0Liver cancer remains one of the leading causes of cancer-related mortality worldwide, with its progression driven by uncontrolled cell proliferation and evasion of apoptosis. N1-methyladenosine (m1A) is a prevalent RNA modification implicated in cancer progression, yet its role in liver cancer remai...
ApoptosisCancer epigeneticsRNA decay
10.1038/S41419-026-08731-Z
ISSN:2041-4889
A four-gene signature predicts survival and anti-CTLA4 immunotherapeutic responses based on immune classification of melanoma
Ying Mei•Mei-Ju May Chen•Han Liang•Li Ma
Communications Biology
2021
•2021/3/22
•Vol.4 No.1 p.1-12
Cutaneous melanoma is the most malignant skin cancer. Biomarkers for stratifying patients at initial diagnosis and informing clinical decisions are highly sought after. Here we classified melanoma patients into three immune subtypes by single-sample gene-set enrichment analysis. We further identifie...
Cancer immunotherapyComputational models
10.1038/S42003-021-01911-X
ISSN:2399-3642
A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection
Matthew H. Larson•Wenying Pan•Hyunsung John Kim•Ruth E. Mauntz•Sarah M. Stuart等 11 人
Nature Communications
2021
•2021/4/21
•Vol.12 No.1 p.1-11
Cell-free RNA (cfRNA) is a promising analyte for cancer detection. However, a comprehensive assessment of cfRNA in individuals with and without cancer has not been conducted. We perform the first transcriptome-wide characterization of cfRNA in cancer (stage III breast [n = 46], lung [n = 30]) and no...
CancerCancer screening
10.1038/S41467-021-22444-1
ISSN:2041-1723
Integrating histopathology and transcriptomics for spatial tumor microenvironment profiling in a melanoma case study
Óscar Lapuente-Santana•Joan Kant•Federica Eduati
Npj Precision Oncology
2024
•2024/11/7
•Vol.8 No.1 p.1-15
Local structures formed by cells in the tumor microenvironment (TME) play an important role in tumor development and treatment response. This study introduces SPoTLIghT, a computational framework providing a quantitative description of the tumor architecture from hematoxylin and eosin (H&E) slid...
Cancer imagingCancer microenvironmentComputational biology and bioinformaticsSystems biology
10.1038/S41698-024-00749-W
ISSN:2397-768X
Comprehensive characterization of claudin-low breast tumors reflects the impact of the cell-of-origin on cancer evolution
Roxane M. Pommier•Amélien Sanlaville•Laurie Tonon•Janice Kielbassa•Emilie Thomas等 13 人
Nature Communications
2020
•2020/7/9
•Vol.11 No.1 p.1-12
Claudin-low breast cancers are aggressive tumors defined by the low expression of key components of cellular junctions, associated with mesenchymal and stemness features. Although they are generally considered as the most primitive breast malignancies, their histogenesis remains elusive. Here we sho...
BioinformaticsBreast cancerEpigenetics analysisGene expression analysisMethylation analysis
10.1038/S41467-020-17249-7
ISSN:2041-1723
Short H2A histone variants are expressed in cancer
Guo-Liang Chew•Marie Bleakley•Robert K. Bradley•Harmit S. Malik•Steven Henikoff等 7 人
Nature Communications
2021
•2021/1/20
•Vol.12 No.1 p.1-9
Short H2A (sH2A) histone variants are primarily expressed in the testes of placental mammals. Their incorporation into chromatin is associated with nucleosome destabilization and modulation of alternate splicing. Here, we show that sH2As innately possess features similar to recurrent oncohistone mut...
Cancer epigeneticsCancer genomics
10.1038/S41467-020-20707-X
ISSN:2041-1723
Targeting RCC1 to block the human soft-tissue sarcoma by disrupting nucleo-cytoplasmic trafficking of Skp2
Mingzhi Zhuang•Fengyue Li•Hong Liang•Yongfu Su•Lei Cheng等 11 人
Cell Death & Disease
2024
•2024/4/1
•Vol.15 No.4 p.1-13
Soft-tissue sarcomas (STS) emerges as formidable challenges in clinics due to the complex genetic heterogeneity, high rates of local recurrence and metastasis. Exploring specific targets and biomarkers would benefit the prognosis and treatment of STS. Here, we identified RCC1, a guanine-nucleotide e...
Prognostic markersSarcoma
10.1038/S41419-024-06629-2
ISSN:2041-4889
Modeling the effects of EMT-immune dynamics on carcinoma disease progression
Bergman Daniel R.•Karikomi Matthew K.•Yu Min•Nie Qing•MacLean Adam L.
Communications Biology
2021
•2021/8/18
•Vol.4 No.1 p.1-14
During progression from carcinoma in situ to an invasive tumor, the immune system is engaged in complex sets of interactions with various tumor cells. Tumor cell plasticity alters disease trajectories via epithelial-to-mesenchymal transition (EMT). Several of the same pathways that regulate EMT are ...
Bayesian inferenceCellular signalling networksComputational modelsDifferential equationsGene regulatory networks
10.1038/S42003-021-02499-Y
ISSN:2399-3642
Evidence for 28 genetic disorders discovered by combining healthcare and research data
Joanna Kaplanis•Kaitlin E. Samocha•Laurens Wiel•Zhancheng Zhang•Kevin J. Arvai等 22 人
Nature
2020
•2020/10/14
•Vol.586 No.7831 p.757-762
De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes assoc...
Clinical geneticsGenetics researchNeurodevelopmental disordersStatistical methods
10.1038/S41586-020-2832-5
ISSN:0028-0836
Liver-specific gene PGRMC1 blocks c-Myc-induced hepatocarcinogenesis through ER stress-independent PERK activation
Fubo Ji•Jianjuan Zhang•Liping Mao•Yaqi Tan•Meihua Ye等 19 人
Nature Communications
2025
•2025/1/2
•Vol.16 No.1 p.1-17
Roles of liver-specific genes (LSGs) in tumor initiation and progression are rarely explored in hepatocellular carcinoma (HCC). Here we show that LSGs are generally downregulated in HCC tumor tissues compared to non-HCC liver tissues, and low-LSG HCCs show poor prognosis and the activated c-Myc path...
Hepatocellular carcinomaMechanisms of diseaseTumour heterogeneity
10.1038/S41467-024-55745-2
ISSN:2041-1723
MAT2A enhances PARN transcription via SRF to accelerate glycolysis and drive malignant progression in osteosarcoma
Zhinan Ren•Haoming Chen•Qi Qiao•Zehao Xie•Jianhua Hu等 8 人
Communications Biology
2026
•2026/1/13
•Vol.9 No.1 p.2410
Osteosarcoma lacks effective molecular targets, and the biological role of MAT2A in this disease remains unclear. Here we show that MAT2A drives osteosarcoma progression by increasing the transcription of the downstream gene PARN. MAT2A interacts with the transcription factor SRF, promotes its SUMO-...
Mechanisms of diseaseSarcoma
10.1038/S42003-026-09518-W
ISSN:2399-3642
An in situ hydrogel-mediated chemo-immunometabolic cancer therapy
Wang Bo•Chen Jing•Caserto Julia S.•Wang Xi•Ma Minglin
Nature Communications
2022
•2022/7/2
•Vol.13 No.1 p.1-13
Metabolic reprogramming of the tumor microenvironment (TME) and poor immunogenicity are two of the challenges that cancer immunotherapies have to overcome for improved clinical benefits. Among various immunosuppressive metabolites that keep anti-tumor immunity in check, the tryptophan catabolite kyn...
Applied immunologyCancer immunotherapyCancer therapyDrug delivery
10.1038/S41467-022-31579-8
ISSN:2041-1723
Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma
Charlie Saillard•Flore Delecourt•Benoit Schmauch•Olivier Moindrot•Magali Svrcek等 24 人
Nature Communications
2023
•2023/6/13
•Vol.14 No.1 p.1-12
Two tumor (Classical/Basal) and stroma (Inactive/active) subtypes of Pancreatic adenocarcinoma (PDAC) with prognostic and theragnostic implications have been described. These molecular subtypes were defined by RNAseq, a costly technique sensitive to sample quality and cellularity, not used in routin...
Data integrationHistologyMachine learningPancreatic cancerTumour heterogeneity
10.1038/S41467-023-39026-Y
ISSN:2041-1723
Synthetic lethal combination of CHK1 and WEE1 inhibition for treatment of castration-resistant prostate cancer
Yapeng Chao•Yuzhou Chen•Wenxiao Zheng•Kathryn Demanelis•Yu Liu等 9 人
Oncogene
2024
•2024/1/25
•00 p.1-15
WEE1 and CHEK1 (CHK1) kinases are critical regulators of the G2/M cell cycle checkpoint and DNA damage response pathways. The WEE1 inhibitor AZD1775 and the CHK1 inhibitor SRA737 are in clinical trials for various cancers, but have not been thoroughly examined in prostate cancer, particularly castra...
Prostate cancerTargeted therapies
10.1038/S41388-024-02939-Z
ISSN:0950-9232
A costimulatory molecule-related signature in regard to evaluation of prognosis and immune features for clear cell renal cell carcinoma
Hua Xiaoliang•Ge Shengdong•Zhang Jiong•Xiao Haibing•Tai Sheng等 8 人
Cell Death Discovery
2021
•2021/9/18
•Vol.7 No.1 p.1-10
Costimulatory molecules have been proven to enhance antitumor immune responses, but their roles in clear cell renal cell carcinoma (ccRCC) remain unexplored. In this study, we aimed to explore the gene expression profiles of costimulatory molecule genes in ccRCC and construct a prognostic signature ...
Cancer modelsRenal cell carcinoma
10.1038/S41420-021-00646-2
ISSN:2058-7716
Genetic mutation and biological pathway prediction based on whole slide images in breast carcinoma using deep learning
Qu Hui•Zhou Mu•Yan Zhennan•Wang He•Rustgi Vinod K.等 8 人
Npj Precision Oncology
2021
•2021/9/23
•Vol.5 No.1 p.1-11
Breast carcinoma is the most common cancer among women worldwide that consists of a heterogeneous group of subtype diseases. The whole-slide images (WSIs) can capture the cell-level heterogeneity, and are routinely used for cancer diagnosis by pathologists. However, key driver genetic mutations rela...
Breast cancerCancer genomicsCancer imaging
10.1038/S41698-021-00225-9
ISSN:2397-768X
Deep learning-based detection and semi-quantitative model for spread through air spaces (STAS) in lung adenocarcinoma
Yipeng Feng•Hanlin Ding•Xing Huang•Yijian Zhang•Mengyi Lu等 17 人
Npj Precision Oncology
2024
•2024/8/5
•Vol.8 No.1 p.1-12
Tumor spread through air spaces (STAS) is a distinctive metastatic pattern affecting prognosis in lung adenocarcinoma (LUAD) patients. Several challenges are associated with STAS detection, including misdetection, low interobserver agreement, and lack of quantitative analysis. In this research, a to...
Cancer imagingNon-small-cell lung cancer
10.1038/S41698-024-00664-0
ISSN:2397-768X
γδ T cell dichotomy with opposing cytotoxic and wound healing functions in human solid tumors
Cathal Harmon•Alexandra Zaborowski•Haim Moore•Pamela St. Louis•Karen Slattery等 17 人
Nature Cancer
2023
•2023/7/20
•00 p.1-16
γδ T cells are important tissue-resident, innate T cells that are critical for tissue homeostasis. γδ cells are associated with positive prognosis in most tumors; however, little is known about their heterogeneity in human cancers. Here, we phenotyped innate and adaptive cells in human colorectal (C...
Cancer microenvironmentImmunosurveillanceInnate immune cellsTumour immunology
10.1038/S43018-023-00589-W
ISSN:2662-1347
Uncertainty-aware and causal test-time adaptive foundation model for robust colorectal cancer pathology diagnosis
Shenghan Lou•Genshen Mo•Xiao Zhang•Hao Wang•Hao Li等 16 人
Npj Digital Medicine
2025
•2025/12/6
0Colorectal cancer (CRC) is a leading malignancy worldwide, where histopathological assessment of hematoxylin and eosin (H&E) stained whole-slide images remains the diagnostic gold standard. However, current computational pathology models suffer from domain shifts, unreliable uncertainty estimati...
CancerComputational biology and bioinformaticsMathematics and computingOncology
10.1038/S41746-025-02149-1
ISSN:2398-6352
Targeting MMA-induced USP36 methylmalonylation to suppress macrophage polarization and tumor progression in clear-cell renal cell carcinoma
Daojia Miao•Jian Shi•Diaoyi Tan•Chuanyi Zhao•Qingyang Lv等 10 人
Cell Death & Differentiation
2025
•2025/12/15
•00 p.1-19
Metabolic reprogramming is a hallmark of clear-cell renal cell carcinoma (ccRCC), driving tumor progression and altering the tumor microenvironment (TME), making it crucial to understand metabolic dysregulation in ccRCC and to identify new therapeutic targets for patients. In this study, metabolomic...
Cancer metabolismKidney diseasesProteomics
10.1038/S41418-025-01646-W
ISSN:1350-9047
A genome-wide association study identifies an African-specific locus on chromosome 21q22.12 associated with Burkitt lymphoma risk and survival
Diptavo Dutta•Mateus H. Gouveia•Bryan R. Gorman•Atuahene Adu-Gyamfi•Chia-Han Lee等 49 人
Leukemia
2025
•2025/7/11
•00 p.1-11
Burkitt lymphoma (BL) is a B-cell malignancy that disproportionately affects children in sub-Saharan Africa. We performed a genome-wide association study (GWAS) in a combined set of 800 childhood cases and 3865 controls in East Africa, controlling for age, sex, country, population-specific principal...
Cancer epidemiologyGenetics research
10.1038/S41375-025-02690-8
ISSN:0887-6924
Control-independent mosaic single nucleotide variant detection with DeepMosaic
Yang Xiaoxu•Xu Xin•Breuss Martin W.•Antaki Danny•Ball Laurel L.等 17 人
Nature Biotechnology
2023
•2023/1/2
•00 p.1-8
Mosaic variants (MVs) reflect mutagenic processes during embryonic development and environmental exposure, accumulate with aging and underlie diseases such as cancer and autism. The detection of noncancer MVs has been computationally challenging due to the sparse representation of nonclonally expand...
Genomic analysisMachine learningMutation
10.1038/S41587-022-01559-W
ISSN:1087-0156
High-accuracy prostate cancer pathology using deep learning
Yuri Tolkach•Tilmann Dohmgörgen•Marieta Toma•Glen Kristiansen
Nature Machine Intelligence
2020
•2020/7/13
•Vol.2 No.7 p.411-418
Deep learning (DL) is a powerful methodology for the recognition and classification of tissue structures in digital pathology. Its performance in prostate cancer pathology is still under intensive investigation. Here we develop DL-based models for the detection of prostate cancer tissue in whole-sli...
Diagnostic markersImage processingProstate cancer
10.1038/S42256-020-0200-7
ISSN:2522-5839
Novel biomarker SARIFA in colorectal cancer: highly prognostic, not genetically driven and histologic indicator of a distinct tumor biology
Nic G. Reitsam•Veselin Grozdanov•Chiara M. L. Löffler•Hannah S. Muti•Bianca Grosser等 7 人
Cancer Gene Therapy
2023
•2023/11/22
•00 p.1-10
SARIFA (Stroma AReactive Invasion Front Areas) has recently emerged as a promising histopathological biomarker for colon and gastric cancer. To elucidate the underlying tumor biology, we assessed SARIFA-status in tissue specimens from The-Cancer-Genome-Atlas (TCGA) cohorts COAD (colonic adenocarcino...
BiomarkersCancer
10.1038/S41417-023-00695-Y
ISSN:0929-1903
Connecting omics signatures and revealing biological mechanisms with iLINCS
Pilarczyk Marcin•Fazel-Najafabadi Mehdi•Kouril Michal•Shamsaei Behrouz•Vasiliauskas Juozas等 26 人
Nature Communications
2022
•2022/8/9
•Vol.13 No.1 p.1-13
There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here we present iLINCS ( http://ilincs.org ), an integrative web-based platform for analysis of omics data ...
Computational platforms and environmentsData miningDrug developmentTarget identificationTranslational research
10.1038/S41467-022-32205-3
ISSN:2041-1723
Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues
Abelin Jennifer G.•Bergstrom Erik J.•Rivera Keith D.•Taylor Hannah B.•Klaeger Susan等 23 人
Nature Communications
2023
•2023/4/3
•Vol.14 No.1 p.1-22
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand prot...
Mass spectrometryPost-translational modificationsProteomic analysisProteomics
10.1038/S41467-023-37547-0
ISSN:2041-1723
Identifying potential risk genes for clear cell renal cell carcinoma with deep reinforcement learning
Dazhi Lu•Yan Zheng•Xianyanling Yi•Jianye Hao•Xi Zeng等 11 人
Nature Communications
2025
•2025/4/15
•Vol.16 No.1 p.1-18
Clear cell renal cell carcinoma (ccRCC) is the most prevalent type of renal cell carcinoma. However, our understanding of ccRCC risk genes remains limited. This gap in knowledge poses challenges to the effective diagnosis and treatment of ccRCC. To address this problem, we propose a deep reinforceme...
Machine learningRenal cell carcinomaTumour biomarkers
10.1038/S41467-025-58439-5
ISSN:2041-1723
Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice
Siqi Ji•Yuanhui Liu•Yuejie Xu•Junzhao Gao•Jingzheng Jin等 14 人
Nature Microbiology
2026
•2026/4/17
•00 p.1-18
Microbiome–host interactions can influence colorectal cancer (CRC) outcomes and the effectiveness of immunotherapy treatment, but the precise mechanisms underlying this are poorly understood. Here we analyse CRC patient cohort data and observe that Facalibacterium prausnitzii abundance in faecal sam...
Cellular microbiologyImmunotherapyTumour-suppressor proteins
10.1038/S41564-026-02326-2
ISSN:2058-5276
Pan-cancer analysis of TRPV2 identifies its potential role as a prognostic and immunologic biomarker in oesophageal cancer
Hang Yi•Yiwen Lin•Xuefei Wang•Yousheng Mao
British Journal Of Cancer
2023
•2023/6/13
•00 p.1-3
Data processingOesophageal cancer
10.1038/S41416-023-02302-1
ISSN:0007-0920
Molecular characteristics of microsatellite stable early-onset colorectal cancer as predictors of prognosis and immunotherapeutic response
Can Lu•Xiaopeng Zhang•Josefine Schardey•Ulrich Wirth•Kathrin Heinrich等 11 人
Npj Precision Oncology
2023
•2023/7/1
•Vol.7 No.1 p.1-12
The incidence of early-onset colorectal cancer (EO-CRC, in patients younger than 50) is increasing worldwide. The specific gene signatures in EO-CRC patients are largely unknown. Since EO-CRC with microsatellite instability is frequently associated with Lynch syndrome, we aimed to comprehensively ch...
Cancer genomicsColorectal cancer
10.1038/S41698-023-00414-8
ISSN:2397-768X
De novo detection of somatic mutations in high-throughput single-cell profiling data sets
Francesc Muyas•Carolin M. Sauer•Jose Espejo Valle-Inclán•Ruoyan Li•Raheleh Rahbari等 8 人
Nature Biotechnology
2023
•2023/7/6
•00 p.1-10
Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism and cell plasticity. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq (assay for transposase-acc...
Cancer genomicsGenetics researchGenomic instabilityStatistical methods
10.1038/S41587-023-01863-Z
ISSN:1087-0156
Insulin receptor expression to predict resistance to axitinib and elucidation of the underlying molecular mechanism in metastatic renal cell carcinoma
Masayuki Takahashi•Kei Daizumoto•Tomoya Fukawa•Yayoi Fukuhara•Yoshimi Bando等 16 人
British Journal Of Cancer
2023
•2023/6/24
•00 p.1-10
The study aimed to examine the significance of insulin receptor (INSR) expression in predicting resistance to axitinib in clear cell renal cell carcinoma (ccRCC). Clinicopathological data were collected from 36 consecutive patients with metastatic RCC who received axitinib. Thirty-three primary tumo...
Molecular biologyRenal cell carcinoma
10.1038/S41416-023-02325-8
ISSN:0007-0920
The genomic landscape of Mongolian hepatocellular carcinoma
Julián Candia•Enkhjargal Bayarsaikhan•Mayank Tandon•Anuradha Budhu•Marshonna Forgues等 11 人
Nature Communications
2020
•2020/9/1
•Vol.11 No.1 p.1-13
Mongolia has the highest incidence of hepatocellular carcinoma (HCC) in the world, but its causative factors and underlying tumor biology remain unknown. Here, we describe molecular characteristics of HCC from 76 Mongolian patients by whole-exome and transcriptome sequencing. We present a comprehens...
Cancer genomicsGene expression profilingHepatocellular carcinoma
10.1038/S41467-020-18186-1
ISSN:2041-1723
Identification of the Notch ligand DLK1 as an immunotherapeutic target and regulator of tumor cell plasticity and chemoresistance in adrenocortical carcinoma
Nai-Yun Sun•Suresh Kumar•Yoo Sun Kim•Diana Varghese•Arnulfo Mendoza等 28 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-15
While immunotherapeutic targeting of cell surface proteins is an increasingly effective cancer therapy, identification of new surface proteins, particularly those with biological importance, is critical. Here, we uncover delta-like non-canonical Notch ligand 1 (DLK1) as a cell surface protein with l...
Adrenal tumoursCancer immunotherapyCancer therapeutic resistanceNeuroendocrine cancer
10.1038/S41467-025-60649-W
ISSN:2041-1723
Multi-omics and single cell characterization of cancer immunosenescence landscape
Qiuxia Wei•Ruizhi Chen•Xue He•Yanan Qu•Changjian Yan等 23 人
Scientific Data
2024
•2024/7/7
•Vol.11 No.1 p.1-16
Cellular senescence (CS) is closely related to tumor progression. However, the studies about CS genes across human cancers have not explored the relationship between cancer senescence signature and telomere length. Additionally, single-cell analyses have not revealed the evolutionary trends of malig...
Cancer microenvironmentRisk factors
10.1038/S41597-024-03562-Z
ISSN:2052-4463
CAD hijacks STING to impair antitumor immunity and radiotherapy efficacy of colorectal cancer
Zhengkun Cai•Zeyuan Cheng•Lu Zhang•Yuhan Zhang•Jinming Shi等 9 人
Cell Death & Disease
2025
•2025/8/23
•Vol.16 No.1 p.1-16
Radiotherapy (RT)-elicited antitumor immunity serves as a pivotal mechanism in RT-mediated tumor control. The strategic integration of RT with immunotherapies, particularly immune checkpoint blockade (ICB), is revolutionizing cancer therapeutics, demonstrating remarkable clinical potential. In this ...
RadiotherapyTranslational research
10.1038/S41419-025-07964-8
ISSN:2041-4889
SOX on tumors, a comfort or a constraint?
Junqing Jiang•Yufei Wang•Mengyu Sun•Xiangyuan Luo•Zerui Zhang等 17 人
Cell Death Discovery
2024
•2024/2/9
•Vol.10 No.1 p.1-18
The sex-determining region Y (SRY)-related high-mobility group (HMG) box (SOX) family, composed of 20 transcription factors, is a conserved family with a highly homologous HMG domain. Due to their crucial role in determining cell fate, the dysregulation of SOX family members is closely associated wi...
Cancer genomicsCancer immunotherapy
10.1038/S41420-024-01834-6
ISSN:2058-7716
Molecular profiling of driver events in metastatic uveal melanoma
Joakim Karlsson•Lisa M. Nilsson•Suman Mitra•Samuel Alsén•Ganesh Vilas Shelke等 16 人
Nature Communications
2020
•2020/4/20
•Vol.11 No.1 p.1-13
Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cas...
CancerCancer geneticsCancer genomicsMetastasisTumour immunology
10.1038/S41467-020-15606-0
ISSN:2041-1723
DSS1 inhibits autophagy to activate epithelial-mesenchymal transition in a pro-metastatic niche of renal cell carcinoma
Xiaoyu Chen•Qingyuan Liu•Jingxian Wu•Pengfei Zhou•Mingming Zhao等 6 人
Nature Communications
2025
•2025/7/23
•Vol.16 No.1 p.1-23
The mechanisms underlying clear cell renal cell carcinoma (ccRCC) metastasis remain largely unexplored. We demonstrate that Deleted in Split hand/Split foot protein 1 (DSS1), a critical cofactor of BRCA2 in DNA repair, is upregulated in metastatic ccRCC and promotes both tumor growth and distant met...
Cancer microenvironmentMacroautophagyRenal cell carcinoma
10.1038/S41467-025-62135-9
ISSN:2041-1723
A systematic pan-cancer study on deep learning-based prediction of multi-omic biomarkers from routine pathology images
Salim Arslan•Julian Schmidt•Cher Bass•Debapriya Mehrotra•Andre Geraldes等 12 人
Communications Medicine
2024
•2024/3/15
•Vol.4 No.1 p.1-15
The objective of this comprehensive pan-cancer study is to evaluate the potential of deep learning (DL) for molecular profiling of multi-omic biomarkers directly from hematoxylin and eosin (H&E)-stained whole slide images. A total of 12,093 DL models predicting 4031 multi-omic biomarkers across ...
Cancer imagingPredictive markersTumour biomarkers
10.1038/S43856-024-00471-5
ISSN:2730-664X
A multimodal whole-slide foundation model for pathology
Tong Ding•Sophia J. Wagner•Andrew H. Song•Richard J. Chen•Ming Y. Lu等 29 人
Nature Medicine
2025
•2025/11/5
•00 p.1-13
The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning. However, translating these advancements to address complex c...
Machine learningPathology
10.1038/S41591-025-03982-3
ISSN:1078-8956
Machine learning identifies TIME subtypes linking EGFR mutations and immune states in lung adenocarcinoma
Zetian Gong•Mingjun Du•Ying Li•Bicheng Ye•Yuming Huang等 10 人
Npj Digital Medicine
2025
•2025/11/26
0Epidermal growth factor receptor (EGFR) mutation is a key oncogenic driver in lung adenocarcinoma (LUAD), but its impact on the tumor immune microenvironment (TIME) remains unclear. By integrating single-cell transcriptomes from 153 LUAD samples using machine learning, we generated an atlas of over ...
CancerComputational biology and bioinformaticsImmunologyOncology
10.1038/S41746-025-02172-2
ISSN:2398-6352
A structurally informed human protein–protein interactome reveals proteome-wide perturbations caused by disease mutations
Dapeng Xiong•Yunguang Qiu•Junfei Zhao•Yadi Zhou•Dongjin Lee等 14 人
Nature Biotechnology
2024
•2024/10/24
•00 p.1-15
To assist the translation of genetic findings to disease pathobiology and therapeutics discovery, we present an ensemble deep learning framework, termed PIONEER (Protein–protein InteractiOn iNtErfacE pRediction), that predicts protein-binding partner-specific interfaces for all known protein interac...
Cancer genomicsProteome informatics
10.1038/S41587-024-02428-4
ISSN:1087-0156
Collagen promotes anti-PD-1/PD-L1 resistance in cancer through LAIR1-dependent CD8 + T cell exhaustion
David H. Peng•Bertha Leticia Rodriguez•Lixia Diao•Limo Chen•Jing Wang等 16 人
Nature Communications
2020
•2020/9/9
•Vol.11 No.1 p.1-18
Tumor extracellular matrix has been associated with drug resistance and immune suppression. Here, proteomic and RNA profiling reveal increased collagen levels in lung tumors resistant to PD-1/PD-L1 blockade. Additionally, elevated collagen correlates with decreased total CD8+ T cells and increased e...
Cancer immunotherapyCancer microenvironmentLung cancerTumour immunology
10.1038/S41467-020-18298-8
ISSN:2041-1723
DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy
Ahmed Khalil•Fran Supek
Nature Communications
2025
•2025/5/13
•Vol.16 No.1 p.1-20
Somatic cells can transform into tumors due to mutations, and the tumors further evolve towards increased aggressiveness and therapy resistance. We develop DiffInvex, a framework for identifying changes in selection acting on individual genes in somatic genomes, drawing on an empirical mutation rate...
Cancer genomicsCancer therapeutic resistanceEvolutionOncogenesStatistical methods
10.1038/S41467-025-59397-8
ISSN:2041-1723
Unconventional human CD61 pairing with CD103 promotes TCR signaling and antigen-specific T cell cytotoxicity
Megat H. B. A. Hamid•Pablo F. Cespedes•Chen Jin•Ji-Li Chen•Uzi Gileadi等 38 人
Nature Immunology
2024
•2024/4/1
•00 p.1-13
Cancer remains one of the leading causes of mortality worldwide, leading to increased interest in utilizing immunotherapy strategies for better cancer treatments. In the past decade, CD103+ T cells have been associated with better clinical prognosis in patients with cancer. However, the specific imm...
Lymphocyte activationT cellsTumour immunology
10.1038/S41590-024-01802-3
ISSN:1529-2908
Cancer-associated fibroblasts drive lung adenocarcinoma progression via THBS2-mediated epithelial-mesenchymal transition
Yuqing Ren•Ruijie Ming•Anning Zuo•Shutong Liu•Yuhao Ba等 17 人
Oncogene
2025
•2025/9/19
•00 p.1-14
The role of cancer-associated fibroblasts (CAFs) in the initiation and invasion phases of human lung adenocarcinoma (LUAD) development is not fully understood. In this study, we utilized single-cell RNA sequencing, spatial transcriptomics, and a combination of in vivo and in vitro models to decode t...
Cancer microenvironmentLung cancer
10.1038/S41388-025-03569-9
ISSN:0950-9232
Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma
Wu Yige•Terekhanova Nadezhda V.•Caravan Wagma•Naser Al Deen Nataly•Lal Preet等 42 人
Nature Communications
2023
•2023/3/27
•Vol.14 No.1 p.1-25
Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we perform snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal cell carcinoma (ccRCC) specimens, respectively, with matched...
Cancer genomicsRenal cell carcinomaTumour biomarkersTumour heterogeneity
10.1038/S41467-023-37211-7
ISSN:2041-1723
Transposable element expression in tumors is associated with immune infiltration and increased antigenicity
Yu Kong•Christopher M. Rose•Ashley A. Cass•Alexander G. Williams•Martine Darwish等 15 人
Nature Communications
2019
•2019/11/19
•Vol.10 No.1 p.1-14
Profound global loss of DNA methylation is a hallmark of many cancers. One potential consequence of this is the reactivation of transposable elements (TEs) which could stimulate the immune system via cell-intrinsic antiviral responses. Here, we develop REdiscoverTE, a computational method for quanti...
Cancer genomicsImmunotherapy
10.1038/S41467-019-13035-2
ISSN:2041-1723
Hepatic stellate cell stearoyl co-A desaturase activates leukotriene B4 receptor 2 - β-catenin cascade to promote liver tumorigenesis
Sonal Sinha•Satoka Aizawa•Yasuhiro Nakano•Alexander Rialdi•Hye Yeon Choi等 18 人
Nature Communications
2023
•2023/5/8
•Vol.14 No.1 p.1-14
Hepatocellular carcinoma (HCC) is the 3rd most deadly malignancy. Activated hepatic stellate cells (aHSC) give rise to cancer-associated fibroblasts in HCC and are considered a potential therapeutic target. Here we report that selective ablation of stearoyl CoA desaturase-2 (Scd2) in aHSC globally s...
Cancer microenvironmentHepatocellular carcinomaLiver cancer
10.1038/S41467-023-38406-8
ISSN:2041-1723
N6-methyladenosine regulated FGFR4 attenuates ferroptotic cell death in recalcitrant HER2-positive breast cancer
Zou Yutian•Zheng Shaoquan•Xie Xinhua•Ye Feng•Hu Xiaoqian等 17 人
Nature Communications
2022
•2022/5/13
•Vol.13 No.1 p.1-18
Intrinsic and acquired anti-HER2 resistance remains a major hurdle for treating HER2-positive breast cancer. Using genome-wide CRISPR/Cas9 screening in vitro and in vivo, we identify FGFR4 as an essential gene following anti-HER2 treatment. FGFR4 inhibition enhances susceptibility to anti-HER2 thera...
CancerCancer therapeutic resistanceCancer therapyCell death
10.1038/S41467-022-30217-7
ISSN:2041-1723
Secreted SULF1 protein modulates CD8 + T cell exhaustion by promoting TAM polarization in gastric cancer
Xiaodan Lu•Di Lu
Genes & Immunity
2026
•2026/4/15
•00 p.1-12
Gastric cancer (GC) progression is linked to immune escape in the tumor microenvironment, yet the molecules regulating tumor-associated macrophage polarization and CD8+ T-cell exhaustion are unclear. This study analyzed TCGA data to examine SULF1 expression and its prognostic role. It used CRISPR/Ca...
Immune cell deathImmunoediting
10.1038/S41435-026-00399-X
ISSN:1476-5470
PHF14 enhances DNA methylation of SMAD7 gene to promote TGF-β-driven lung adenocarcinoma metastasis
Tian Han•Liu Chenying•Yu Jianchen•Han Jian•Du Jianan等 19 人
Cell Discovery
2023
•2023/4/18
•Vol.9 No.1 p.1-20
Aberrant activation of TGF-β signaling plays a pivotal role in cancer metastasis and progression. However, molecular mechanisms underlying the dysregulation of TGF-β pathway remain to be understood. Here, we found that SMAD7, a direct downstream transcriptional target and also a key antagonist of TG...
Cell signallingMetastasisNon-small-cell lung cancer
10.1038/S41421-023-00528-0
ISSN:2056-5968
An atlas of genetic effects on cellular composition of the tumor microenvironment
Yimin Cai•Zequn Lu•Can Chen•Ying Zhu•Zhirui Chen等 32 人
Nature Immunology
2024
•2024/9/2
•00 p.1-17
Deciphering the composition of the tumor microenvironment (TME) is critical for understanding tumorigenesis and to design immunotherapies. In the present study, we mapped genetic effects on cell-type proportions using single-cell and bulk RNA sequencing data, identifying 3,494 immunity quantitative ...
Cancer immunotherapyTumour immunology
10.1038/S41590-024-01945-3
ISSN:1529-2908
Integrative multiomics analysis of platelet-related genes unveils molecular subtypes and prognostic signatures in acute myeloid leukemia
Fangmin Zhong•Fangyi Yao•Zihao Wang•Bo Huang•Xiaozhong Wang
Npj Precision Oncology
2025
•2025/11/17
•Vol.9 No.1 p.3530
Acute myeloid leukemia (AML) remains challenging due to molecular heterogeneity and limited prognostic models integrating tumor microenvironment dynamics. While thrombocytopenia correlates with poor outcomes, the roles of platelet-related genes (PRGs) in AML pathogenesis are unclear. We integrated m...
High-throughput screeningPrognostic markers
10.1038/S41698-025-01137-8
ISSN:2397-768X
M2 macrophage exosomal LINC01001 promotes non-small cell lung cancer development by affecting METTL3 and glycolysis pathway
Li Xu•Kang Li•Jia Li•Fang Xu•Shuzhi Liang等 7 人
Cancer Gene Therapy
2023
•2023/9/4
•00 p.1-12
There have been data showing that LINC01001 is highly expressed in lung cancer, but the effect of M2 macrophage exosomal LINC01001 to METTL3, glycolysis and immunity in non-small cell lung cancer (NSCLC) has not been reported. In this study, we aimed to explore the regulatory effect and mechanism of...
BiomarkersNon-small-cell lung cancer
10.1038/S41417-023-00661-8
ISSN:0929-1903
Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma
Rached Alkallas•Mathieu Lajoie•Dan Moldoveanu•Karen Vo Hoang•Philippe Lefrançois等 12 人
Nature Cancer
2020
•2020/6/22
•Vol.1 No.6 p.635-652
The high background tumor mutation burden in cutaneous melanoma limits the ability to identify significantly mutated genes (SMGs) that drive this cancer. To address this, we performed a mutation significance study of over 1,000 melanoma exomes, combined with a multi-omic analysis of 470 cases from T...
CancerCancer genomicsMelanoma
10.1038/S43018-020-0077-8
ISSN:2662-1347
A pan-tissue survey of mosaic chromosomal alterations in 948 individuals
Teng Gao•Maria Eleni Kastriti•Viktor Ljungström•Andreas Heinzel•Arthur S. Tischler等 10 人
Nature Genetics
2023
•2023/10/30
•Vol.55 No.11 p.1901-1911
Genetic mutations accumulate in an organism’s body throughout its lifetime. While somatic single-nucleotide variants have been well characterized in the human body, the patterns and consequences of large chromosomal alterations in normal tissues remain largely unknown. Here, we present a pan-tissue ...
Genome informaticsPopulation genetics
10.1038/S41588-023-01537-1
ISSN:1061-4036
Single-cell atlas reveals the immunosuppressive microenvironment and Treg cells landscapes in recurrent Glioblastoma
Xingdong Wang•Yizhi Ge•Yuting Hou•Xiaodong Wang•Zhengcun Yan等 11 人
Cancer Gene Therapy
2024
•2024/3/1
•00 p.1-12
Patients diagnosed with glioblastoma (GBM) have the most aggressive tumor progression and lethal recurrence. Research on the immune microenvironment landscape of tumor and cerebrospinal fluid (CSF) is limited. At the single-cell level, we aim to reveal the recurrent immune microenvironment of GBM an...
CancerImmunology
10.1038/S41417-024-00740-4
ISSN:0929-1903
Modulating ovarian cancer progression through FDX1-driven autophagy
Chang Liu•Siyu Wang•Jiabao Zhao•Hui Qiu•Hongmei Du
Npj Precision Oncology
2025
•2025/7/8
•Vol.9 No.1 p.1-15
Ferredoxin 1 (FDX1) emerges as a crucial regulator of autophagy and copper metabolism in ovarian cancer (OC), as revealed by this investigation. Predominantly localized to the cytoplasm and mitochondria, FDX1 coordinates autophagic activity by modulating the AMPK and mTOR signaling pathways. Its rol...
Ovarian cancer
10.1038/S41698-025-00994-7
ISSN:2397-768X
Tumor evolutionary trajectories during the acquisition of invasiveness in early stage lung adenocarcinoma
Siwei Wang•Mulong Du•Jingyuan Zhang•Weizhang Xu•Qianyu Yuan等 17 人
Nature Communications
2020
•2020/11/27
•Vol.11 No.1 p.1-8
The evolutionary trajectories of early lung adenocarcinoma (LUAD) have not been fully elucidated. We hypothesize that genomic analysis between pre-invasive and invasive components will facilitate the description of LUAD evolutionary patterns. We micro-dissect malignant pulmonary nodules (MPNs) into ...
Cancer genomicsNon-small-cell lung cancerPreclinical research
10.1038/S41467-020-19855-X
ISSN:2041-1723
Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis
Bo Wen•Kai Li•Yun Zhang•Bing Zhang
Nature Communications
2020
•2020/4/9
•Vol.11 No.1 p.1-14
Genomics-based neoantigen discovery can be enhanced by proteomic evidence, but there remains a lack of consensus on the performance of different quality control methods for variant peptide identification in proteogenomics. We propose to use the difference between accurately predicted and observed re...
CancerMachine learningProteome informaticsProteomics
10.1038/S41467-020-15456-W
ISSN:2041-1723
Self-assembly of hybrid 3D cultures by integrating living and synthetic cells
Nils Piernitzki•Ning Gao•Gilles Gasparoni•Louisa M. Krauß•Julia Schulze-Hentrich等 10 人
Nature Communications
2025
•2025/12/10
•Vol.16 No.1 p.110730
Self-assembly is a fundamental property of living matter that drives the three-dimensional organization of cell collectives such as tissues and organs. Here, the co-assembly of synthetic and natural cells is leveraged to create hybrid living 3D cancer cultures. We screen a range of synthetic cell mo...
Bioinspired materialsCancer models
10.1038/S41467-025-66789-3
ISSN:2041-1723
Passenger mutations link cellular origin and transcriptional identity in human lung adenocarcinomas
Sukanya Panja•Padmaja Mantri•Kofi Ennu Johnson•Juan Sebastian Andrade-Martinez•Soo-Ryum Yang等 17 人
Nature Genetics
2025
•2025/11/27
•00 p.1-9
DNA damage is preferentially repaired in expressed genes; thus, genome-wide correlations between somatic mutation patterns and normal cell transcription may reflect tumor cell origins. Accordingly, we found that aggregate lung adenocarcinoma (LUAD) and squamous cancer (LUSC) somatic mutation density...
GenomicsNon-small-cell lung cancerTranscriptomics
10.1038/S41588-025-02418-5
ISSN:1061-4036
Rational development of gemcitabine-based nanoplatform for targeting SERPINB9/Granzyme B axis to overcome chemo-immune-resistance
Haozhe Huang•Yiqing Mu•Yixian Huang•Beihong Ji•Yifei Wang等 16 人
Nature Communications
2025
•2025/5/5
•Vol.16 No.1 p.1-19
SERPINB9, an endogenous inhibitor of granzyme B (GzmB), has emerged as a critical factor in the resistance to immunotherapy by protecting cancer cells from GzmB-induced cytotoxicity. However, its role in chemosensitivity remains unknown. In this study, we show that gemcitabine (GEM) treatment upregu...
Cancer therapeutic resistanceOligo deliveryPancreatic cancerTargeted therapies
10.1038/S41467-025-59490-Y
ISSN:2041-1723
Molecular mechanisms of MAZ targeting up-regulation of NDUFS3 expression to promote malignant progression in melanoma
Yu Feng•Qinxuan Ni•Na Wu•Taiyu Xie•Fang Yun等 16 人
Communications Biology
2024
•2024/11/12
•Vol.7 No.1 p.1-19
Myc-associated Zinc-finger Protein (MAZ) has been implicated in the malignant progression of various tumors. However, its expression and functional relationship of MAZ in melanoma have not been previously investigated. This study confirms elevated expression of MAZ in melanoma, correlating with poor...
Cancer metabolismMelanomaTranscriptional regulatory elements
10.1038/S42003-024-07209-Y
ISSN:2399-3642
Concurrent delivery of immune checkpoint blockade modulates T cell dynamics to enhance neoantigen vaccine-generated antitumor immunity
Liu Longchao•Chen Jiahui•Zhang Hongyi•Ye Jianfeng•Moore Casey等 9 人
Nature Cancer
2022
•2022/4/7
•00 p.1-16
Neoantigen vaccines aiming to induce tumor-specific T cell responses have achieved promising antitumor effects in early clinical trials. However, the underlying mechanism regarding response or resistance to this treatment is unclear. Here we observe that neoantigen vaccine-generated T cells can syne...
CancerCancer immunotherapyTumour immunologyTumour vaccines
10.1038/S43018-022-00352-7
ISSN:2662-1347
Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers
Rebecca J. Deyell•Yaoqing Shen•Emma Titmuss•Katherine Dixon•Laura M. Williamson等 31 人
Nature Communications
2024
•2024/5/16
•Vol.15 No.1 p.1-15
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in chi...
Cancer geneticsCancer genomicsGene expressionPaediatric cancer
10.1038/S41467-024-48363-5
ISSN:2041-1723
Inhibition of DUSP18 impairs cholesterol biosynthesis and promotes anti-tumor immunity in colorectal cancer
Xiaojun Zhou•Genxin Wang•Chenhui Tian•Lin Du•Edward V. Prochownik等 6 人
Nature Communications
2024
•2024/7/12
•Vol.15 No.1 p.1-19
Tumor cells reprogram their metabolism to produce specialized metabolites that both fuel their own growth and license tumor immune evasion. However, the relationships between these functions remain poorly understood. Here, we report CRISPR screens in a mouse model of colo-rectal cancer (CRC) that im...
Cancer metabolismCancer microenvironmentTumour immunology
10.1038/S41467-024-50138-X
ISSN:2041-1723
PD-1 blockade plus tyrosine kinase inhibitor remodels the tumor microenvironment in advanced renal cell carcinoma
Liangyou Gu•Qi Zhang•Qiyang Liang•Cheng Peng•Yaohui Wang等 18 人
Nature Communications
2026
•2026/3/31
0The combination of tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICIs) has improved clinical outcomes in advanced renal cell carcinoma (aRCC), though therapeutic resistance remains a major challenge. We conducted single-cell transcriptomic analysis on 61 tumor samples from 34 a...
CancerCancer microenvironmentRenal cancer
10.1038/S41467-026-70978-Z
ISSN:2041-1723
A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded
Ozyoruk Kutsev Bengisu•Can Sermet•Darbaz Berkan•Başak Kayhan•Demir Derya等 15 人
Nature Biomedical Engineering
2022
•2022/12/23
•Vol.6 No.12 p.1407-1419
Histological artefacts in cryosectioned tissue can hinder rapid diagnostic assessments during surgery. Formalin-fixed and paraffin-embedded (FFPE) tissue provides higher quality slides, but the process for obtaining them is laborious (typically lasting 12–48 h) and hence unsuitable for intra-operati...
Image processingMachine learningPathology
10.1038/S41551-022-00952-9
ISSN:2157-846X
Efficacy, safety and single-cell analysis of neoadjuvant immunochemotherapy in locally advanced oral squamous cell carcinoma: a phase II trial
Zhongzheng Xiang•Xiaoyuan Wei•Zhuoyuan Zhang•Yueyang Tang•Linyan Chen等 15 人
Nature Communications
2025
•2025/4/28
•Vol.16 No.1 p.1-17
The clinical activity of neoadjuvant immunochemotherapy (NAIC) for treating locally advanced oral squamous cell carcinoma (LA-OSCC) remains uncertain. This single-arm, phase II trial (ChiCTR2200066119) tested 2 cycles of NAIC with camrelizumab plus nab-paclitaxel and cisplatin in LA-OSCC patients. F...
Head and neck cancerOral cancerPhase II trialsPredictive markersTumour immunology
10.1038/S41467-025-59004-W
ISSN:2041-1723
Regulatory T cells crosstalk with tumor cells and endothelium through lymphotoxin signaling
Wenji Piao•Long Wu•Yanbao Xiong•Gregory C. Zapas•Christina M. Paluskievicz等 26 人
Nature Communications
2024
•2024/12/2
•Vol.15 No.1 p.1-18
Regulatory T cells (Tregs) with multifaceted functions suppress anti-tumor immunity by signaling surrounding cells. Here we report Tregs use the surface lymphotoxin (LT)α1β2 to preferentially stimulate LT beta receptor (LTβR) nonclassical NFκB signaling on both tumor cells and lymphatic endothe...
Cancer microenvironmentCell migrationTumour immunology
10.1038/S41467-024-54874-Y
ISSN:2041-1723
Intratumoral heterogeneity and clonal evolution in liver cancer
Bojan Losic•Amanda J. Craig•Carlos Villacorta-Martin•Sebastiao N. Martins-Filho•Nicholas Akers等 28 人
Nature Communications
2020
•2020/1/15
•Vol.11 No.1 p.1-15
Clonal evolution of a tumor ecosystem depends on different selection pressures that are principally immune and treatment mediated. We integrate RNA-seq, DNA sequencing, TCR-seq and SNP array data across multiple regions of liver cancer specimens to map spatio-temporal interactions between cancer and...
CancerGastroenterologyImmunologyOncology
10.1038/S41467-019-14050-Z
ISSN:2041-1723
Mutational signature-based classification uncovers emerging oral cancer subtypes with distinct molecular patterns
Sophie Deneuve•Béatrice Fervers•Julia S. Bruno•Emma Bach•Sergey Senkin等 20 人
International Journal Of Oral Science
2026
•2026/4/24
•Vol.18 No.1 p.380
Tobacco use, alcohol consumption, and infection with human papilloma virus (HPV) are well-established risk factors for head and neck squamous cell carcinomas (HNSCC). However, the incidence of oral cancer, particularly in the mobile tongue, has been rising in non-smoker/non-drinker and HPV-negative ...
Cancer genomicsGenome informaticsOral cancer
10.1038/S41368-026-00437-4
ISSN:2049-3169
MTSS1 suppresses mammary tumor-initiating cells by enhancing RBCK1-mediated p65 ubiquitination
Min Cong•Yuan Wang•Yang Yang•Cheng Lian•Xueqian Zhuang等 14 人
Nature Cancer
2020
•2020/1/20
•Vol.1 No.2 p.222-234
Tumor-initiating cells (TICs) are considered the culprits of cancer development and progression. Dysregulation of metastasis suppressor protein 1 (MTSS1) has been widely observed in tumor metastasis, but its functional contribution and mechanism in cancer is poorly understood. Here we report a role ...
Breast cancerCancerCancer stem cellsUbiquitylation
10.1038/S43018-019-0021-Y
ISSN:2662-1347
Breast cancer homologous recombination deficiency prediction from pathological images with a sufficient and representative Transformer
Haijing Luan•Taiyuan Hu•Jifang Hu•Weier Liu•Kaixing Yang等 14 人
Npj Precision Oncology
2025
•2025/5/30
•Vol.9 No.1 p.1-14
Homologous recombination deficiency (HRD) has been recognized as a key biomarker for poly-ADP ribose polymerase inhibitors (PARPi) and platinum-based chemotherapy in breast cancer (BC). HRD prediction typically relies on molecular biology assays, which have a high turnaround time, and cost. In contr...
Breast cancerDiagnostic markersTumour biomarkers
10.1038/S41698-025-00950-5
ISSN:2397-768X
Single-cell analysis of AIMP2 splice variants informs on drug sensitivity and prognosis in hematologic cancer
Jayoung Ku•Ryul Kim•Dongchan Kim•Daeyoon Kim•Seulki Song等 13 人
Communications Biology
2020
•2020/10/30
•Vol.3 No.1 p.1-13
Aminoacyl-tRNA synthetase-interacting multifunctional protein 2 (AIMP2) is a non-enzymatic component required for the multi-tRNA synthetase complex. While exon 2 skipping alternatively spliced variant of AIMP2 (AIMP2-DX2) compromises AIMP2 activity and is associated with carcinogenesis, its clinical...
Alternative splicingAssay systemsDiagnostic markersHaematological cancerPrognostic markers
10.1038/S42003-020-01353-X
ISSN:2399-3642
crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors
Dongsheng Yuan•Robin Jugas•Petra Pokorna•Jaroslav Sterba•Ondrej Slaby等 26 人
Nature Cancer
2025
•2025/6/6
•00 p.1-12
DNA methylation-based classification of (brain) tumors has emerged as a powerful and indispensable diagnostic technique. Initial implementations used methylation microarrays for data generation, while most current classifiers rely on a fixed methylation feature space. This makes them incompatible wi...
CancerCancer of unknown primaryCNS cancerDNA methylationMachine learning
10.1038/S43018-025-00976-5
ISSN:2662-1347
AKT-induced lncRNA VAL promotes EMT-independent metastasis through diminishing Trim16-dependent Vimentin degradation
Han Tian•Rong Lian•Yun Li•Chenying Liu•Shujun Liang等 17 人
Nature Communications
2020
•2020/10/12
•Vol.11 No.1 p.1-15
Despite the importance of AKT overactivation in tumor progression, results from clinical trials of various AKT inhibitors remain suboptimal, suggesting that AKT-driven tumor metastasis needs to be further understood. Herein, based on long non-coding RNA (lncRNA) profiling induced by active AKT, we i...
MetastasisNon-small-cell lung cancer
10.1038/S41467-020-18929-0
ISSN:2041-1723
Tumor fractions deciphered from circulating cell-free DNA methylation for cancer early diagnosis
Zhou Xiao•Cheng Zhen•Dong Mingyu•Liu Qi•Yang Weiyang等 8 人
Nature Communications
2022
•2022/12/13
•Vol.13 No.1 p.1-13
Tumor-derived circulating cell-free DNA (cfDNA) provides critical clues for cancer early diagnosis, yet it often suffers from low sensitivity. Here, we present a cancer early diagnosis approach using tumor fractions deciphered from circulating cfDNA methylation signatures. We show that the estimated...
CancerDiagnostic markersMachine learning
10.1038/S41467-022-35320-3
ISSN:2041-1723
Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication
Liu Yanling•Klein Jonathon•Bajpai Richa•Dong Li•Tran Quang等 33 人
Nature Communications
2023
•2023/4/5
•Vol.14 No.1 p.1-18
Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we...
Cancer geneticsCancer genomicsComputational modelsPaediatric cancer
10.1038/S41467-023-37438-4
ISSN:2041-1723
The level of oncogenic Ras determines the malignant transformation of Lkb1 mutant tissue in vivo
Briana Rackley•Chang-Soo Seong•Evan Kiely•Rebecca E. Parker•Manali Rupji等 11 人
Communications Biology
2021
•2021/1/29
•Vol.4 No.1 p.1-12
The genetic and metabolic heterogeneity of RAS-driven cancers has confounded therapeutic strategies in the clinic. To address this, rapid and genetically tractable animal models are needed that recapitulate the heterogeneity of RAS-driven cancers in vivo. Here, we generate a Drosophila melanogaster ...
Cancer geneticsCancer modelsLung cancerSuper-resolution microscopyTumour-suppressor proteins
10.1038/S42003-021-01663-8
ISSN:2399-3642
Chimeric antibody targeting unique epitope on onco-mucin16 reduces tumor burden in pancreatic and lung malignancies
Ashu Shah•Sanjib Chaudhary•Imayavaramban Lakshmanan•Abhijit Aithal•Sophia G. Kisling等 22 人
Npj Precision Oncology
2023
•2023/8/11
•Vol.7 No.1 p.1-16
Aberrantly expressed onco-mucin 16 (MUC16) and its post-cleavage generated surface tethered carboxy-terminal (MUC16-Cter) domain are strongly associated with poor prognosis and lethality of pancreatic (PC) and non-small cell lung cancer (NSCLC). To date, most anti-MUC16 antibodies are directed towar...
Non-small-cell lung cancerPancreatic cancerTargeted therapies
10.1038/S41698-023-00423-7
ISSN:2397-768X
Exosomal miR-19a and IBSP cooperate to induce osteolytic bone metastasis of estrogen receptor-positive breast cancer
Wu Kerui•Feng Jiamei•Lyu Feng•Xing Fei•Sharma Sambad等 19 人
Nature Communications
2021
•2021/8/31
•Vol.12 No.1 p.1-18
Bone metastasis is an incurable complication of breast cancer. In advanced stages, patients with estrogen-positive tumors experience a significantly higher incidence of bone metastasis (>87%) compared to estrogen-negative patients (<56%). To understand the mechanism of this bone-tropism of ER+ tumor...
Breast cancerCancer
10.1038/S41467-021-25473-Y
ISSN:2041-1723
Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer
Shi Wenhao•Wang Yushen•Xu Chen•Li Yan•Ge Sai等 24 人
Nature Communications
2023
•2023/2/14
•Vol.14 No.1 p.1-22
Diffuse-type gastric cancer (DGC) and intestinal-type gastric cancer (IGC) are the major histological types of gastric cancer (GC). The molecular mechanism underlying DGC and IGC differences are poorly understood. In this research, we carry out multilevel proteomic analyses, including proteome, phos...
Cell signallingGastric cancerProteomicsTumour heterogeneity
10.1038/S41467-023-35797-6
ISSN:2041-1723
Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system
Raúl N. Mateos•Wira Winardi•Kenichi Chiba•Ai Okada•Ayako Suzuki等 7 人
Npj Systems Biology And Applications
2024
•2024/12/6
•Vol.10 No.1 p.1-12
The KEAP1-NRF2 system plays a crucial role in responding to oxidative and electrophilic stress. Its dysregulation can cause the overexpression of downstream genes, a known cancer hallmark. Understanding and detecting abnormal KEAP1-NRF2 activity is essential for understanding disease mechanisms and ...
CancerComputational biology and bioinformatics
10.1038/S41540-024-00475-W
ISSN:2056-7189
Interpreting pathways to discover cancer driver genes with Moonlight
Antonio Colaprico•Catharina Olsen•Matthew H. Bailey•Gabriel J. Odom•Thilde Terkelsen等 17 人
Nature Communications
2020
•2020/1/3
•Vol.11 No.1 p.1-17
Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as genes controlling biological processes. W...
Cancer genomicsOncogenesSoftware
10.1038/S41467-019-13803-0
ISSN:2041-1723
Tumor hypoxia represses γδ T cell-mediated antitumor immunity against brain tumors
Jang Hyun Park•Hyun-Jin Kim•Chae Won Kim•Hyeon Cheol Kim•Yujin Jung等 13 人
Nature Immunology
2021
•2021/2/11
•Vol.22 No.3 p.336-346
The anatomic location and immunologic characteristics of brain tumors result in strong lymphocyte suppression. Consequently, conventional immunotherapies targeting CD8 T cells are ineffective against brain tumors. Tumor cells escape immunosurveillance by various mechanisms and tumor cell metabolism ...
Tumour immunology
10.1038/S41590-020-00860-7
ISSN:1529-2908
Single cell analysis revealed SFRP2 cancer associated fibroblasts drive tumorigenesis in head and neck squamous cell carcinoma
Qiwei Wang•Yinan Zhao•Guolin Tan•JinGang Ai
Npj Precision Oncology
2024
•2024/10/9
•Vol.8 No.1 p.1-15
Understanding the mechanisms of invasion and metastasis in head and neck squamous cell carcinoma (HNSCC) is crucial for effective treatment, particularly in metastatic cases. In this study, we analyzed multicenter bulk sequencing and comprehensive single-cell data from 702,446 cells, leading to the ...
Cancer genomicsCancer microenvironmentHead and neck cancer
10.1038/S41698-024-00716-5
ISSN:2397-768X
Bridging cell morphological behaviors and molecular dynamics in multi-modal spatial omics with MorphLink
Jing Huang•Chenyang Yuan•Jiahui Jiang•Jianfeng Chen•Sunil S. Badve等 14 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-14
Multi-modal spatial omics data are invaluable for exploring complex cellular behaviors in diseases from both morphological and molecular perspectives. Current analytical methods primarily focus on clustering and classification, and do not adequately examine the relationship between cell morphology a...
Computational modelsImage processingStatistical methodsTranscriptomics
10.1038/S41467-025-61142-0
ISSN:2041-1723
TTK promotes mitophagy by regulating ULK1 phosphorylation and pre-mRNA splicing to inhibit mitochondrial apoptosis in bladder cancer
Kang Chen•Jinyu Chen•Yukun Cong•Qingliu He•Chunyu Liu等 11 人
Cell Death & Differentiation
2025
•2025/4/23
•00 p.1-16
Bladder cancer (BC) remains a major global health challenge, with poor prognosis and limited therapeutic options in advanced stages. TTK protein kinase (TTK), a serine/threonine kinase, has been implicated in the progression of various cancers, but its role in BC has not been fully elucidated. In th...
AutophagyKinasesOncogenes
10.1038/S41418-025-01492-W
ISSN:1350-9047
METTL5-mediated rRNA modification controls prostate cancer progression through the IRF7/DNA2 axis and mitophagy regulation
Ruifeng Yang•Qintao Ge•Fengyao Wu•Manmei Long•Bingyu Li等 18 人
Oncogene
2026
•2026/7/13
•00 p.1-14
Prostate cancer progression to advanced disease is accompanied by extensive metabolic rewiring, yet the upstream regulatory mechanisms remain incompletely defined. Here, we showed that the rRNA m6A methyltransferase METTL5 was progressively upregulated during prostate cancer progression and was asso...
Cell biologyProstate cancer
10.1038/S41388-026-03867-W
ISSN:0950-9232
Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA
Bae Mingyun•Kim Gyuhee•Lee Tae-Rim•Ahn Jin Mo•Park Hyunwook等 28 人
Nature Communications
2023
•2023/4/10
•Vol.14 No.1 p.1-15
Multi-cancer early detection remains a key challenge in cell-free DNA (cfDNA)-based liquid biopsy. Here, we perform cfDNA whole-genome sequencing to generate two test datasets covering 2125 patient samples of 9 cancer types and 1241 normal control samples, and also a reference dataset for background...
Cancer genomicsCancer screeningMachine learning
10.1038/S41467-023-37768-3
ISSN:2041-1723
A novel saliva-based miRNA profile to diagnose and predict oral cancer
Jaikrishna Balakittnen•Chameera Ekanayake Weeramange•Daniel F. Wallace•Pascal H. G. Duijf•Alexandre S. Cristino等 13 人
International Journal Of Oral Science
2024
•2024/2/18
•Vol.16 No.1 p.1-13
Oral cancer (OC) is the most common form of head and neck cancer. Despite the high incidence and unfavourable patient outcomes, currently, there are no biomarkers for the early detection of OC. This study aims to discover, develop, and validate a novel saliva-based microRNA signature for early diagn...
Diagnostic markersOral cancer detectionPredictive markers
10.1038/S41368-023-00273-W
ISSN:2049-3169
CCT6A promotes cell proliferation in colon cancer by targeting BIRC5 associated with p53 status
Han Zhang•Taotao Zheng•Chuan Qin•Xinyue Zhang•Han Lin等 13 人
Cancer Gene Therapy
2024
•2024/7/13
•00 p.1-13
Chaperonin-containing TCP1 (CCT) is a multi-subunit complex, known to participate the correct folding of many proteins. Currently, the mechanism underlying CCT subunits in cancer progression is incompletely understood. Based on data analysis, the expression of CCT subunit 6 A (CCT6A) is found higher...
Cancer geneticsOncogenesTumour biomarkers
10.1038/S41417-024-00806-3
ISSN:0929-1903
Tumor-associated macrophages restrict CD8+ T cell function through collagen deposition and metabolic reprogramming of the breast cancer microenvironment
Kevin M. Tharp•Kelly Kersten•Ori Maller•Greg A. Timblin•Connor Stashko等 17 人
Nature Cancer
2024
•2024/6/3
•00 p.1-18
Tumor progression is accompanied by fibrosis, a condition of excessive extracellular matrix accumulation, which is associated with diminished antitumor immune infiltration. Here we demonstrate that tumor-associated macrophages (TAMs) respond to the stiffened fibrotic tumor microenvironment (TME) by ...
CancerCancer immunotherapyCancer metabolismCancer microenvironmentTransforming growth factor beta
10.1038/S43018-024-00775-4
ISSN:2662-1347
Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer
Hamzeh Kayhanian•William Cross•Suzanne E. M. van der Horst•Panagiotis Barmpoutis•Eszter Lakatos等 37 人
Nature Genetics
2024
•2024/7/3
•00 p.1-14
Mismatch repair (MMR)-deficient cancer evolves through the stepwise erosion of coding homopolymers in target genes. Curiously, the MMR genes MutS homolog 6 (MSH6) and MutS homolog 3 (MSH3) also contain coding homopolymers, and these are frequent mutational targets in MMR-deficient cancers. The impac...
CancerTumour immunology
10.1038/S41588-024-01777-9
ISSN:1061-4036
Claudin-7 deficiency induces metabolic reprogramming of neutrophils in the colorectal cancer microenvironment
Xiaoqing Liang•Dajin Yuan•Songyun Zhao•Jianbo Zhou•Kun Wang等 12 人
Cell Death & Disease
2025
•2025/10/16
•Vol.16 No.1 p.1-16
Neutrophils are integral components of the bone marrow and stromal cell network. They express the immune checkpoint molecule PD-L1 and can induce T cell exhaustion, thereby promoting immunosuppression. In this study, we investigated whether tumor-derived Cldn7 deficiency could recruit polymorphonucl...
Gastrointestinal cancerImmune evasion
10.1038/S41419-025-08064-3
ISSN:2041-4889
Prostaglandin E2-driven dedifferentiation of Schwann cells leads to perineural invasion in pancreatic ductal adenocarcinoma
Ling Wang•Qicai Liu•Zhibo Zhang•Shizhong Yang•Juan Tang等 12 人
Signal Transduction And Targeted Therapy
2026
•2026/4/7
•Vol.11 No.1 p.1220
Perineural invasion (PNI), a prominent pathological feature of pancreatic ductal adenocarcinoma (PDAC), is closely associated with poor prognosis. Clarifying its mechanism is therefore critical for developing new therapies. Recent research has focused on the crosstalk between tumors and Schwann cell...
Gastrointestinal cancer
10.1038/S41392-026-02648-X
ISSN:2059-3635
A Golgi apparatus-related signature predicts the immune microenvironment and prognosis of gastric cancer
Changlei Wu•Liang Sun•Wenjie Zhu•Chao Huang•Zhengming Zhu等 6 人
Genes & Immunity
2025
•2025/5/7
•00 p.1-11
In recent years, numerous studies have provided evidence of the involvement of the Golgi apparatus (GA) in various stages of cancer development. Nonetheless, the specific impact of GA-related characteristics on gastric cancer (GC) progression remains ambiguous. We utilized LASSO and multivariate COX...
Cancer geneticsImmune evasion
10.1038/S41435-025-00332-8
ISSN:1476-5470
The concurrence of DNA methylation and demethylation is associated with transcription regulation
Shi Jiejun•Xu Jianfeng•Chen Yiling Elaine•Li Jason Sheng•Cui Ya等 8 人
Nature Communications
2021
•2021/9/6
•Vol.12 No.1 p.1-12
The mammalian DNA methylome is formed by two antagonizing processes, methylation by DNA methyltransferases (DNMT) and demethylation by ten-eleven translocation (TET) dioxygenases. Although the dynamics of either methylation or demethylation have been intensively studied in the past decade, the direc...
Data miningDNA methylationEpigenomicsGene expressionGene regulation
10.1038/S41467-021-25521-7
ISSN:2041-1723
Multi-omics analysis identifies osteosarcoma subtypes with distinct prognosis indicating stratified treatment
Jiang Yafei•Wang Jinzeng•Sun Mengxiong•Zuo Dongqing•Wang Hongsheng等 31 人
Nature Communications
2022
•2022/11/23
•Vol.13 No.1 p.1-17
Osteosarcoma (OS) is a primary malignant bone tumor that most commonly affects children, adolescents, and young adults. Here, we comprehensively analyze genomic, epigenomic and transcriptomic data from 121 OS patients. Somatic mutations are diverse within the cohort, and only TP53 is significantly m...
Cancer genomicsSarcomaTumour biomarkers
10.1038/S41467-022-34689-5
ISSN:2041-1723
Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions
Fabio Alfieri•Giulio Caravagna•Martin H. Schaefer
Nature Communications
2023
•2023/6/16
•Vol.14 No.1 p.1-13
Cancers evolve under the accumulation of thousands of somatic mutations and chromosomal aberrations. While most coding mutations are deleterious, almost all protein-coding genes lack detectable signals of negative selection. This raises the question of how tumors tolerate such large amounts of delet...
Cancer genomicsComputational biology and bioinformaticsEvolutionary theoryGene amplificationTumour heterogeneity
10.1038/S41467-023-39313-8
ISSN:2041-1723
Multimodal analysis suggests differential immuno-metabolic crosstalk in lung squamous cell carcinoma and adenocarcinoma
Leitner Brooks P.•Givechian Kevin B.•Ospanova Shyryn•Beisenbayeva Aray•Politi Katerina等 6 人
Npj Precision Oncology
2022
•2022/1/27
•Vol.6 No.1 p.1-10
Immunometabolism within the tumor microenvironment is an appealing target for precision therapy approaches in lung cancer. Interestingly, obesity confers an improved response to immune checkpoint inhibition in non-small cell lung cancer (NSCLC), suggesting intriguing relationships between systemic m...
Cancer genomicsCancer imagingCancer metabolismNon-small-cell lung cancer
10.1038/S41698-021-00248-2
ISSN:2397-768X