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相关论文
74Cell-type-aware transcriptome-wide association studies identify 91 independent risk genes for Alzheimer’s disease dementia
Qiang Liu•Randy L. Parrish•Shizhen Tang•Shinya Tasaki•David A. Bennett等 10 人
Communications Biology
2026
•2026/4/22
0Most existing transcriptome wide association studies (TWASs) of Alzheimer’s Disease (AD) dementia only use bulk RNA-seq data and a single statistical method. Here, we utilize an omnibus TWAS (TWAS-O) pipeline that leverages multiple complementary statistical methods to integrate the snRNA-seq datase...
Alzheimer's diseaseGene expressionGenetic association study
10.1038/S42003-026-10030-4
ISSN:2399-3642
Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer’s disease
Zhi Huang•Gennifer E. Merrihew•Eric B. Larson•Jea Park•Deanna Plubell等 12 人
Nature Communications
2023
•2023/5/12
•Vol.14 No.1 p.1-14
Resilience to Alzheimer’s disease is an uncommon combination of high disease burden without dementia that offers valuable insights into limiting clinical impact. Here we assessed 43 research participants meeting stringent criteria, 11 healthy controls, 12 resilience to Alzheimer’s disease and 20 Alz...
Alzheimer's diseaseProteomic analysis
10.1038/S41467-023-38376-X
ISSN:2041-1723
Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers
Zhao Zhang•Youqiong Ye•Jing Gong•Hang Ruan•Chun-Jie Liu等 12 人
Communications Biology
2018
•2018/12/21
•Vol.1 No.1 p.1-11
The protein translational system, including transfer RNAs (tRNAs) and several categories of enzymes, plays a key role in regulating cell proliferation. Translation dysregulation also contributes to cancer development, though relatively little is known about the changes that occur to the translationa...
CancerCancer genomicsComputational biology and bioinformatics
10.1038/S42003-018-0239-8
ISSN:2399-3642
Stemness signature and targeted therapeutic drugs identification for Triple Negative Breast Cancer
Samina Gul•Jianyu Pang•Hongjun Yuan•Yongzhi Chen•Qian yu等 7 人
Scientific Data
2023
•2023/11/20
•Vol.10 No.1 p.1-14
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and carries the worst prognosis, characterized by the lack of progesterone, estrogen, and HER2 gene expression. This study aimed to analyze cancer stemness-related gene signature to determine patients’ risk stratifi...
Breast cancerCancer stem cellsData mining
10.1038/S41597-023-02709-8
ISSN:2052-4463
Genome-wide association study provides insights into the genetic basis of Lewy body dementia
Ping Zhu•Zhengxin Jin•Shiyang Wu•Shan Gao•Yijie He等 11 人
Molecular Psychiatry
2025
•2025/10/9
•00 p.1-15
Lewy body dementia (LBD) is the second most prevalent dementia, however most genetic risk remains uncharacterized. Here, we performed the largest LBD genome-wide association study (GWAS) meta-analysis including 4252 LBD cases and 189,290 controls. We confirmed four previously known risk loci APOE, G...
GeneticsNeuroscience
10.1038/S41380-025-03295-4
ISSN:1359-4184
Aberrant neural stem cell quiescence is the gateway to autism development linked to Arid1b
Byounggook Cho•Hongwon Kim•Saemin An•Yerim Hwang•Daeyeol Kwon等 8 人
Molecular Psychiatry
2025
•2025/8/30
•00 p.1-16
Autism spectrum disorder is a neurodevelopmental disorder with social communication deficits, repetitive behaviors, and restricted interests. While previous studies have demonstrated a close link between aberrant neurogenesis and the development of autism, a fundamental question remains unresolved: ...
Autism spectrum disordersStem cells
10.1038/S41380-025-03174-Y
ISSN:1359-4184
Proteogenomic insights into early-onset endometrioid endometrial carcinoma: predictors for fertility-sparing therapy response
Zhe Hu•Zimeng Wu•Wei Liu•Yan Ning•Jingbo Liu等 35 人
Nature Genetics
2024
•2024/4/2
•00 p.1-15
Endometrial carcinoma remains a public health concern with a growing incidence, particularly in younger women. Preserving fertility is a crucial consideration in the management of early-onset endometrioid endometrial carcinoma (EEEC), particularly in patients under 40 who maintain both reproductive ...
Endometrial cancerPersonalized medicineTumour biomarkers
10.1038/S41588-024-01703-Z
ISSN:1061-4036
Large-scale plasma proteomic profiling unveils diagnostic biomarkers and pathways for Alzheimer’s disease
Gyujin Heo•Ying Xu•Erming Wang•Muhammad Ali•Hamilton Se-Hwee Oh等 38 人
Nature Aging
2025
•2025/5/20
•00 p.1-18
Proteomic studies have been instrumental in identifying brain, cerebrospinal fluid and plasma proteins associated with Alzheimer’s disease (AD). Here, we comprehensively examined 6,905 aptamers corresponding to 6,106 unique proteins in plasma in more than 3,300 well-characterized individuals to iden...
Alzheimer's diseaseDiagnostic markers
10.1038/S43587-025-00872-8
ISSN:2662-8465
Cross-ancestry genome-wide association study and systems-level integrative analyses implicate new risk genes and therapeutic targets for depression
Yifan Li•Xinglun Dang•Rui Chen•Zhaowei Teng•Junyang Wang等 16 人
Nature Human Behaviour
2025
•2025/2/24
•00 p.1-18
Deciphering the genetic architecture of depression is pivotal for characterizing the associated pathophysiological processes and development of new therapeutics. Here we conducted a cross-ancestry genome-wide meta-analysis on depression (416,437 cases and 1,308,758 controls) and identified 287 risk ...
DepressionGenome-wide association studies
10.1038/S41562-024-02073-6
ISSN:2397-3374
Systems genetic dissection of brain gene expression reveals excitotoxic mechanisms of Alzheimer’s disease
Pinghan Zhao•Omar El Fadel•Anh Le•Carl Grant Mangleburg•Justin Dhindsa等 17 人
Molecular Psychiatry
2026
•2026/2/14
•00 p.1-20
Gene expression changes likely mediate the impact of Alzheimer’s disease (AD) neuropathology on cognition, but there are challenges to resolve the proximal causal pathways from postmortem brain transcriptome profiles which lack temporal resolution and are further confounded by mixed pathologies. Her...
GeneticsNeurosciencePsychiatric disorders
10.1038/S41380-026-03479-6
ISSN:1359-4184
XunZi, an AI biologist, reveals disease-modifying targets
Xinhe Huang•Junhong Qin•Fei Tang•Chenyu Yang•Linhua Xu等 18 人
Nature Biomedical Engineering
2026
•2026/8/4
•00 p.1-19
Hypothesis generation in biomedicine is constrained by human cognitive limitations in synthesizing insights from fragmented biomedical knowledge and multimodal data sources. Here we introduce XunZi, an AI biologist that integrates logical reasoning and multimodal data fusion to autonomously generate...
Data integrationParkinson's disease
10.1038/S41551-026-01769-6
ISSN:2157-846X
Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration
Ryan Sean K.•Zelic Matija•Han Yingnan•Teeple Erin•Chen Luoman等 23 人
Nature Neuroscience
2022
•2022/12/19
•Vol.26 No.1 p.12-26
Iron dysregulation has been implicated in multiple neurodegenerative diseases, including Parkinson’s disease (PD). Iron-loaded microglia are frequently found in affected brain regions, but how iron accumulation influences microglia physiology and contributes to neurodegeneration is poorly understood...
Cell deathMicrogliaNeurodegenerationNeuroimmunologyParkinson's disease
10.1038/S41593-022-01221-3
ISSN:1097-6256
Proteomic signatures of the APOE ε4 and APOE ε2 genetic variants and Alzheimer’s disease
Lina Lu•Alexa Pichet Binette•Ines Hristovska•Shorena Janelidze•Bart Smets等 17 人
Nature Aging
2026
•2026/5/15
•00 p.1-20
The APOE locus is the strongest genetic factor for Alzheimer’s disease, with ε4 increasing and ε2 decreasing risk, yet the basis of these opposing effects remains unclear. Here we performed a multicohort proteomic analysis across plasma and cerebrospinal fluid in GNPC, BioFINDER-2, ADNI, UK BioBank,...
AgeingAlzheimer's diseaseBiomarkersCognitive ageingGenetic association study
10.1038/S43587-026-01123-0
ISSN:2662-8465
Combined burden and functional impact tests for cancer driver discovery using DriverPower
Shimin Shuai•Steven Gallinger•Lincoln Stein
Nature Communications
2020
•2020/2/5
•Vol.11 No.1 p.1-12
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a sof...
Medical genomicsOncogenes
10.1038/S41467-019-13929-1
ISSN:2041-1723
Bridging clinic and wildlife care with AI-powered pan-species computational pathology
AbdulJabbar Khalid•Castillo Simon P.•Hughes Katherine•Davidson Hannah•Boddy Amy M.等 15 人
Nature Communications
2023
•2023/4/26
•Vol.14 No.1 p.1-13
Cancers occur across species. Understanding what is consistent and varies across species can provide new insights into cancer initiation and evolution, with significant implications for animal welfare and wildlife conservation. We build a pan-species cancer digital pathology atlas (panspecies.ai) an...
Cancer imagingMachine learningPathologyTumour immunologyZoology
10.1038/S41467-023-37879-X
ISSN:2041-1723
Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age
Yufei Wang•Ronghong Li•Renyang Tong•Taiwei Chen•Mingze Sun等 22 人
Nature Immunology
2025
•2025/1/29
•Vol.26 No.2 p.308-322
A comprehensive understanding of the evolution of the immune landscape in humans across the entire lifespan at single-cell transcriptional and protein levels, during development, maturation and senescence is currently lacking. We recruited a total of 220 healthy volunteers from the Shanghai Pudong C...
Cell biologyImmunologyPathogenesis
10.1038/S41590-024-02059-6
ISSN:1529-2908
Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging
Ziming Du•Jia-Ren Lin•Rumana Rashid•Zoltan Maliga•Shu Wang等 9 人
Nature Protocols
2019
•2019/9/18
•Vol.14 No.10 p.2900-2930
Multiplexed tissue imaging enables precise, spatially resolved enumeration and characterization of cell types and states in human resection specimens. A growing number of methods applicable to formalin-fixed, paraffin-embedded (FFPE) tissue sections have been described, the majority of which rely on...
BiomarkersCancer microenvironmentFluorescence imagingSingle-cell imagingTumour immunology
10.1038/S41596-019-0206-Y
ISSN:1754-2189
Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies
Khunsriraksakul Chachrit•McGuire Daniel•Sauteraud Renan•Chen Fang•Yang Lina等 14 人
Nature Communications
2022
•2022/6/7
•Vol.13 No.1 p.1-15
Transcriptome-wide association studies (TWAS) are popular approaches to test for association between imputed gene expression levels and traits of interest. Here, we propose an integrative method PUMICE (Prediction Using Models Informed by Chromatin conformations and Epigenomics) to integrate 3D geno...
EpigenomicsGene regulationGenome-wide association studiesTranscriptomics
10.1038/S41467-022-30956-7
ISSN:2041-1723
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
The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients
Francesc Muyas•Manuel José Gómez Rodriguez•Rita Cascão•Angela Afonso•Carolin M. Sauer等 8 人
Nature Communications
2024
•2024/1/2
•Vol.15 No.1 p.1-14
Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rat...
Cancer genomicsCancer screeningDiagnostic markers
10.1038/S41467-023-44287-8
ISSN:2041-1723
TGF-β-associated extracellular matrix genes link cancer-associated fibroblasts to immune evasion and immunotherapy failure
Ankur Chakravarthy•Lubaba Khan•Nathan Peter Bensler•Pinaki Bose•Daniel D. De Carvalho
Nature Communications
2018
•2018/11/8
•Vol.9 No.1 p.1-10
The extracellular matrix (ECM) is a key determinant of cancer progression and prognosis. Here we report findings from one of the largest pan-cancer analyses of ECM gene dysregulation in cancer. We define a distinct set of ECM genes upregulated in cancer (C-ECM) and linked to worse prognosis. We foun...
CancerTumour immunology
10.1038/S41467-018-06654-8
ISSN:2041-1723
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
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
Bernardo Rodriguez-Martin•Eva G. Alvarez•Adrian Baez-Ortega•Jorge Zamora•Fran Supek等 49 人
Nature Genetics
2020
•2020/2/5
•Vol.52 No.3 p.306-319
About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis...
CancerGenomics
10.1038/S41588-019-0562-0
ISSN:1061-4036
Pan-cancer analysis of whole genomes
Nature
2020
•2020/2/5
•Vol.578 No.7793 p.82-93
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from...
Science, Humanities and Social Sciences, multidisciplinaryScience, multidisciplinary
10.1038/S41586-020-1969-6
ISSN:0028-0836
Comprehensive transcriptomic analysis of cell lines as models of primary tumors across 22 tumor types
K. Yu•B. Chen•D. Aran•J. Charalel•C. Yau等 10 人
Nature Communications
2019
•2019/8/8
•Vol.10 No.1 p.1-11
Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles from The Cancer Genome Atlas and the Cancer Cell Li...
Cancer modelsData miningGene expression
10.1038/S41467-019-11415-2
ISSN:2041-1723
Impact of TP53 mutations in Triple Negative Breast Cancer
Mitri Zahi I.•Abuhadra Nour•Goodyear Shaun M.•Hobbs Evthokia A.•Kaempf Andy等 7 人
Npj Precision Oncology
2022
•2022/9/9
•Vol.6 No.1 p.1-5
Identifying triple negative breast cancer (TNBC) patients expected to have poor outcomes provides an opportunity to enhance clinical management. We applied an Evolutionary Action Score to functionally characterize TP53 mutations (EAp53) in 96 TNBC patients and observed that EAp53 stratification may ...
Breast cancerPrognostic markers
10.1038/S41698-022-00303-6
ISSN:2397-768X
Identifying individuals with high risk of Alzheimer’s disease using polygenic risk scores
Ganna Leonenko•Emily Baker•Joshua Stevenson-Hoare•Annerieke Sierksma•Mark Fiers等 8 人
Nature Communications
2021
•2021/7/23
•Vol.12 No.1 p.1-10
Polygenic Risk Scores (PRS) for AD offer unique possibilities for reliable identification of individuals at high and low risk of AD. However, there is little agreement in the field as to what approach should be used for genetic risk score calculations, how to model the effect of APOE, what the optim...
Alzheimer's diseaseGeneticsGenome-wide association studiesNeurology
10.1038/S41467-021-24082-Z
ISSN:2041-1723
Identification of markers for neurescence through transcriptomic profiling of postmortem human brains
Shiva Kazempour Dehkordi•Sogand Sajedi•Amirreza Heshmat•Miranda E. Orr•Habil Zare
Npj Aging
2025
•2025/7/1
•Vol.11 No.1 p.1-11
Neuronal senescence (i.e., neurescence) is an important hallmark of aging and neurodegeneration, but it remains poorly characterized in the human brain due to the lack of reliable markers. This study aimed to identify neurescence markers based on single-nucleus transcriptome data from postmortem hum...
Alzheimer's diseaseBiomarkersDementiaNeurological disordersSenescence
10.1038/S41514-025-00235-Y
ISSN:2731-6068
BTK regulates microglial function and neuroinflammation in human stem cell models and mouse models of multiple sclerosis
Ross C. Gruber•Gregory S. Wirak•Anna S. Blazier•Lan Lee•Michael R. Dufault等 20 人
Nature Communications
2024
•2024/11/22
•Vol.15 No.1 p.1-17
Neuroinflammation in the central nervous system (CNS), driven largely by resident phagocytes, has been proposed as a significant contributor to disability accumulation in multiple sclerosis (MS) but has not been addressed therapeutically. Bruton’s tyrosine kinase (BTK) is expressed in both B-lymphoc...
Innate immunityMicrogliaMultiple sclerosis
10.1038/S41467-024-54430-8
ISSN:2041-1723
Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture
Álvarez Eva G.•Demeulemeester Jonas•Otero Paula•Jolly Clemency•García-Souto Daniel等 43 人
Nature Communications
2021
•2021/11/25
•Vol.12 No.1 p.1-12
Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. Here, using multiplatform sequencing technologies, we identify and characterize a remarkable mutational mechanism in human hepatocellular carcinoma cause...
Cancer genomicsHepatocellular carcinomaTumour virus infections
10.1038/S41467-021-26805-8
ISSN:2041-1723
Autism genes converge on asynchronous development of shared neuron classes
Paulsen Bruna•Velasco Silvia•Kedaigle Amanda J.•Pigoni Martina•Quadrato Giorgia等 28 人
Nature
2022
•2022/2/2
•Vol.602 No.7896 p.268-273
Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1–6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals...
Autism spectrum disordersDevelopmental neurogenesisNeuroscienceStem cells
10.1038/S41586-021-04358-6
ISSN:0028-0836
Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers
Thatikonda Venu•Islam S. M. Ashiqul•Autry Robert J.•Jones Barbara C.•Gröbner Susanne N.等 15 人
Nature Cancer
2023
•2023/1/26
•Vol.4 No.2 p.276-289
Analysis of mutational signatures can reveal underlying molecular mechanisms of the processes that have imprinted the somatic mutations found in cancer genomes. Here, we analyze single base substitutions and small insertions and deletions in pediatric cancers encompassing 785 whole-genome sequenced ...
CancerCancer genomicsFunctional clusteringPaediatric cancer
10.1038/S43018-022-00509-4
ISSN:2662-1347
Integrating apaQTL and eQTL analysis identifies a potential causal variant associated with lung adenocarcinoma risk in the Chinese population
Huiwen Xu•Yutong Wu•Qiong Chen•Yuhui Yu•Qianyao Meng等 14 人
Communications Biology
2024
•2024/7/13
•Vol.7 No.1 p.1-13
Alternative polyadenylation (APA) plays a crucial role in cancer biology. Here, we used data from the 3′aQTL-atlas, GTEx, and the China Nanjing Lung Cancer GWAS database to explore the association between apaQTL/eQTL-SNPs and the risk of lung adenocarcinoma (LUAD). The variant T allele of rs277646 i...
Cancer genomicsNon-small-cell lung cancer
10.1038/S42003-024-06502-0
ISSN:2399-3642
Multiplex cerebrospinal fluid proteomics identifies biomarkers for diagnosis and prediction of Alzheimer’s disease
Yu Guo•Shi-Dong Chen•Jia You•Shu-Yi Huang•Yi-Lin Chen等 15 人
Nature Human Behaviour
2024
•2024/7/10
•00 p.1-20
Recent expansion of proteomic coverage opens unparalleled avenues to unveil new biomarkers of Alzheimer’s disease (AD). Among 6,361 cerebrospinal fluid (CSF) proteins analysed from the ADNI database, YWHAG performed best in diagnosing both biologically (AUC = 0.969) and clinically (AUC = 0.857) defi...
Alzheimer's diseaseDiagnostic markersNeurodegeneration
10.1038/S41562-024-01924-6
ISSN:2397-3374
A quantitative trait locus for reduced microglial APOE expression associates with reduced cerebral amyloid angiopathy
Michael E. Belloy•Jonathan Graff-Radford•Michael D. Greicius
Nature Genetics
2026
•2026/1/26
•Vol.58 No.2 p.271-272
Alzheimer's diseaseGene regulationGenetic association study
10.1038/S41588-025-02472-Z
ISSN:1061-4036
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
Wei Jiao•Gurnit Atwal•Paz Polak•Rosa Karlic•Edwin Cuppen等 13 人
Nature Communications
2020
•2020/2/5
•Vol.11 No.1 p.1-12
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, ...
Cancer genomicsCancer of unknown primary
10.1038/S41467-019-13825-8
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
Directional integration and pathway enrichment analysis for multi-omics data
Mykhaylo Slobodyanyuk•Alexander T. Bahcheli•Zoe P. Klein•Masroor Bayati•Lisa J. Strug等 6 人
Nature Communications
2024
•2024/7/7
•Vol.15 No.1 p.1-14
Omics techniques generate comprehensive profiles of biomolecules in cells and tissues. However, a holistic understanding of underlying systems requires joint analyses of multiple data modalities. We present DPM, a data fusion method for integrating omics datasets using directionality and significanc...
BiomarkersData integrationProteomicsStatistical methodsTranscriptomics
10.1038/S41467-024-49986-4
ISSN:2041-1723
Deep transcriptome sequencing of subgenual anterior cingulate cortex reveals cross-diagnostic and diagnosis-specific RNA expression changes in major psychiatric disorders
Nirmala Akula•Stefano Marenco•Kory Johnson•Ningping Feng•Kevin Zhu等 21 人
Neuropsychopharmacology
2021
•2021/2/8
•00 p.1-9
Despite strong evidence of heritability and growing discovery of genetic markers for major mental illness, little is known about how gene expression in the brain differs across psychiatric diagnoses, or how known genetic risk factors shape these differences. Here we investigate expressed genes and g...
Gene expressionRNA sequencing
10.1038/S41386-020-00949-5
ISSN:0893-133X
Mapping the microRNA landscape in the older adult brain and its genetic contribution to neuropsychiatric conditions
Selina M. Vattathil•Ekaterina S. Gerasimov•Se Min Canon•Adriana Lori•Sarah Sze Min Tan等 11 人
Nature Aging
2024
•2024/12/6
•00 p.1-14
MicroRNAs (miRNAs) play a crucial role in regulating gene expression and influence many biological processes. Despite their importance, understanding of how genetic variation affects miRNA expression in the brain and how this relates to brain disorders remains limited. Here we investigated these que...
AgeingBrainGene expressionGene regulation
10.1038/S43587-024-00778-X
ISSN:2662-8465
Durvalumab compared to maintenance chemotherapy in metastatic breast cancer: the randomized phase II SAFIR02-BREAST IMMUNO trial
Thomas Bachelot•Thomas Filleron•Ivan Bieche•Monica Arnedos•Mario Campone等 32 人
Nature Medicine
2021
•2021/1/18
•Vol.27 No.2 p.250-255
The impact of single-agent antibodies against programmed death-ligand 1 (PD-L1) as maintenance therapy is unknown in patients with metastatic breast cancer. The SAFIR02-BREAST IMMUNO substudy included patients with human epidermal growth factor receptor type 2 (Her2)-negative metastatic breast cance...
CancerMedical research
10.1038/S41591-020-01189-2
ISSN:1078-8956
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
Lactate dehydrogenase B facilitates disulfidptosis and exhaustion of tumour-infiltrating CD8+ T cells
Jie Wan•Jian-Hong Shi•Min Shi•Haiyan Huang•Zhen Zhang等 17 人
Nature Cell Biology
2025
•2025/6/3
•00 p.1-11
The aberrant accumulation of intracellular disulfides promotes cancer cell disulfidptosis; however, how disulfide stress influences tumour-infiltrating CD8+ T cell function remains unknown. Here we demonstrate that lactate dehydrogenase B (LDHB) facilitates intratumoural CD8+ T cell disulfidptosis a...
Cell deathImmunosurveillanceT cells
10.1038/S41556-025-01673-2
ISSN:1465-7392
Stroke genetics informs drug discovery and risk prediction across ancestries
Mishra Aniket•Malik Rainer•Hachiya Tsuyoshi•Jürgenson Tuuli•Namba Shinichi等 187 人
Nature
2022
•2022/9/30
•Vol.611 No.7934 p.115-123
Previous genome-wide association studies (GWASs) of stroke — the second leading cause of death worldwide — were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 3...
Genetic markersGenome-wide association studiesPredictive markersStroke
10.1038/S41586-022-05165-3
ISSN:0028-0836
Treatment resistance to platinum-based chemotherapy in lung and ovarian cancer is driven by a targetable TGFβ senescent secretome
Estela González-Gualda•Marika A. V. Reinius•David Macias•Samir Morsli•Jianfeng Ge等 29 人
Nature Aging
2026
•2026/2/3
•Vol.6 No.2 p.368-392
Platinum-based chemotherapy is commonly used for non-small cell lung cancer (NSCLC) and high-grade serous ovarian cancer (HGSOC) treatments, yet clinical outcomes remain poor. Cellular senescence and its associated secretory phenotype (SASP) can have multiple tumor-promoting activities, but both are...
AgeingCancer modelsSenescence
10.1038/S43587-025-01054-2
ISSN:2662-8465
Integrative multi-omics networks identify PKCδ and DNA-PK as master kinases of glioblastoma subtypes and guide targeted cancer therapy
Migliozzi Simona•Oh Young Taek•Hasanain Mohammad•Garofano Luciano•D’Angelo Fulvio等 15 人
Nature Cancer
2023
•2023/2/2
•Vol.4 No.2 p.181-202
Despite producing a panoply of potential cancer-specific targets, the proteogenomic characterization of human tumors has yet to demonstrate value for precision cancer medicine. Integrative multi-omics using a machine-learning network identified master kinases responsible for effecting phenotypic hal...
CancerCancer genomicsCNS cancerMachine learning
10.1038/S43018-022-00510-X
ISSN:2662-1347
Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders
Wenqiang Li•Rui Chen•Laipeng Feng•Xinglun Dang•Jiewei Liu等 12 人
Nature Human Behaviour
2023
•2023/11/9
•00 p.1-19
Anxiety disorders are the most prevalent mental disorders. However, the genetic etiology of anxiety disorders remains largely unknown. Here we conducted a genome-wide meta-analysis on anxiety disorders by including 74,973 (28,392 proxy) cases and 400,243 (146,771 proxy) controls. We identified 14 ri...
AnxietyGenomics
10.1038/S41562-023-01746-Y
ISSN:2397-3374
CRISPRi screens in human iPSC-derived astrocytes elucidate regulators of distinct inflammatory reactive states
Leng Kun•Rose Indigo V. L.•Kim Hyosung•Xia Wenlong•Romero-Fernandez Wilber等 20 人
Nature Neuroscience
2022
•2022/10/27
•Vol.25 No.11 p.1528-1542
Astrocytes become reactive in response to insults to the central nervous system by adopting context-specific cellular signatures and outputs, but a systematic understanding of the underlying molecular mechanisms is lacking. In this study, we developed CRISPR interference screening in human induced p...
AstrocyteHigh-throughput screeningNeuroimmunology
10.1038/S41593-022-01180-9
ISSN:1097-6256
High resolution clonal architecture of hypomutated Wilms tumours
Henry Lee-Six•Taryn D. Treger•Manas Dave•Tim HH Coorens•Nathaniel D. Anderson等 27 人
Nature Communications
2025
•2025/5/29
•Vol.16 No.1 p.1-10
A paradigm of childhood cancers is that they have a low mutation burden, with some ostensibly bearing fewer mutations than the normal tissues from which they derive. We set out to resolve this paradox by examining paediatric renal cancers with exceptionally few mutations using high resolution, high ...
Cancer genomicsPaediatric cancerUrological cancer
10.1038/S41467-025-59854-4
ISSN:2041-1723
Contribution of leukocyte telomere length to cardiovascular disease onset from genome-wide cross-trait analysis
Jun Qiao•Qian Wang•Yuhui Zhao•Minjing Chang•Shuo Sun等 17 人
Nature Communications
2025
•2025/9/30
•Vol.16 No.1 p.1-19
Telomere shortening is a well-established marker of cellular aging and genomic instability. While the relationship between leukocyte telomere length and cardiovascular diseases has long been of interest, their genetic interplay remains incompletely understood. In this study, we observe substantial g...
Cardiovascular geneticsGenetic linkage studyGenotype
10.1038/S41467-025-63707-5
ISSN:2041-1723
Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism
Mai Te-Lun•Chen Chia-Ying•Chen Yu-Chen•Chiang Tai-Wei•Chuang Trees-Juen
Molecular Psychiatry
2022
•2022/8/12
•00 p.1-12
Genetic risk variants and transcriptional expression changes in autism spectrum disorder (ASD) were widely investigated, but their causal relationship remains largely unknown. Circular RNAs (circRNAs) are abundant in brain and often serve as upstream regulators of mRNAs. By integrating RNA-sequencin...
Autism spectrum disordersGeneticsNeuroscience
10.1038/S41380-022-01714-4
ISSN:1359-4184
APOE genotype-specific methylation patterns are linked to Alzheimer disease pathology and estrogen response
Rebecca Panitch•Nathan Sahelijo•Junming Hu•Kwangsik Nho•David A. Bennett等 10 人
Translational Psychiatry
2024
•2024/2/29
•Vol.14 No.1 p.1-10
The joint effects of APOE genotype and DNA methylation on Alzheimer disease (AD) risk is relatively unknown. We conducted genome-wide methylation analyses using 2,021 samples in blood (91 AD cases, 329 mild cognitive impairment, 1,391 controls) and 697 samples in brain (417 AD cases, 280 controls). ...
DiseasesGenetics
10.1038/S41398-024-02834-X
ISSN:2158-3188
GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia
Lincoln M. P. Shade•Yuriko Katsumata•Erin L. Abner•Khine Zin Aung•Steven A. Claas等 23 人
Nature Genetics
2024
•2024/10/8
•00 p.1-15
Genome-wide association studies (GWAS) have identified >80 Alzheimer’s disease and related dementias (ADRD)-associated genetic loci. However, the clinical outcomes used in most previous studies belie the complex nature of underlying neuropathologies. Here we performed GWAS on 11 ADRD-related neur...
Alzheimer's diseaseCerebrovascular disordersGenome-wide association studies
10.1038/S41588-024-01939-9
ISSN:1061-4036
Evidence for improved DNA repair in long-lived bowhead whale
Denis Firsanov•Max Zacher•Xiao Tian•Todd L. Sformo•Yang Zhao等 55 人
Nature
2025
•2025/10/29
•00 p.1-9
At more than 200 years, the maximum lifespan of the bowhead whale exceeds that of all other mammals. The bowhead is also the second-largest animal on Earth1, reaching over 80,000 kg. Despite its very large number of cells and long lifespan, the bowhead is not highly cancer-prone, an incongruity term...
Cancer modelsDouble-strand DNA breaksNon-homologous-end joiningSenescence
10.1038/S41586-025-09694-5
ISSN:0028-0836
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
Evaluating cell lines as models for metastatic breast cancer through integrative analysis of genomic data
Ke Liu•Patrick A. Newbury•Benjamin S. Glicksberg•William Z. D. Zeng•Shreya Paithankar等 7 人
Nature Communications
2019
•2019/5/15
•Vol.10 No.1 p.1-12
Cell lines are widely-used models to study metastatic cancer although the extent to which they recapitulate the disease in patients remains unknown. The recent accumulation of genomic data provides an unprecedented opportunity to evaluate the utility of them for metastatic cancer research. Here, we ...
Breast cancerCancerCancer modelsComputational biology and bioinformaticsMetastasis
10.1038/S41467-019-10148-6
ISSN:2041-1723
Exercise hormone irisin is a critical regulator of cognitive function
Islam Mohammad R.•Valaris Sophia•Young Michael F.•Haley Erin B.•Luo Renhao等 22 人
Nature Metabolism
2021
•2021/8/20
•Vol.3 No.8 p.1058-1070
Identifying secreted mediators that drive the cognitive benefits of exercise holds great promise for the treatment of cognitive decline in ageing or Alzheimer’s disease (AD). Here, we show that irisin, the cleaved and circulating form of the exercise-induced membrane protein FNDC5, is sufficient to ...
MetabolismNeuroscience
10.1038/S42255-021-00438-Z
ISSN:2522-5812
Reply to: a quantitative trait locus for reduced microglial APOE expression associates with reduced cerebral amyloid angiopathy
Lincoln M. P. Shade•Qi Qiao•Yuriko Katsumata•Shubhabrata Mukherjee•Jai G. Broome等 9 人
Nature Genetics
2026
•2026/1/26
•Vol.58 No.2 p.273-274
Alzheimer's diseaseGenetics research
10.1038/S41588-025-02473-Y
ISSN:1061-4036
A molecular cell atlas of the human lung from single-cell RNA sequencing
Kyle J. Travaglini•Ahmad N. Nabhan•Lolita Penland•Rahul Sinha•Astrid Gillich等 18 人
Nature
2020
•2020/11/18
•Vol.587 No.7835 p.619-625
Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1–9, it has been difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-c...
Evolutionary geneticsGene expressionTranscriptomics
10.1038/S41586-020-2922-4
ISSN:0028-0836
Crowdsourced mapping of unexplored target space of kinase inhibitors
Anna Cichońska•Balaguru Ravikumar•Robert J. Allaway•Fangping Wan•Sungjoon Park等 27 人
Nature Communications
2021
•2021/6/3
•Vol.12 No.1 p.1-18
Despite decades of intensive search for compounds that modulate the activity of particular protein targets, a large proportion of the human kinome remains as yet undrugged. Effective approaches are therefore required to map the massive space of unexplored compound–kinase interactions for novel and p...
CheminformaticsKinasesMachine learning
10.1038/S41467-021-23165-1
ISSN:2041-1723
Sex differences in oncogenic mutational processes
Constance H. Li•Stephenie D. Prokopec•Ren X. Sun•Fouad Yousif•Nathaniel Schmitz等 6 人
Nature Communications
2020
•2020/8/28
•Vol.11 No.1 p.1-24
Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here w...
Cancer geneticsCancer genomicsGenome informaticsOncogenes
10.1038/S41467-020-17359-2
ISSN:2041-1723
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Kadir C. Akdemir•Victoria T. Le•Sahaana Chandran•Yilong Li•Roel G. Verhaak等 10 人
Nature Genetics
2020
•2020/2/5
•Vol.52 No.3 p.294-305
Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating different domains have important roles in reinforcing the stability of these f...
CancerData miningGene expression
10.1038/S41588-019-0564-Y
ISSN:1061-4036
Brain Chimeroids reveal individual susceptibility to neurotoxic triggers
Noelia Antón-Bolaños•Irene Faravelli•Tyler Faits•Sophia Andreadis•Rahel Kastli等 15 人
Nature
2024
•2024/6/26
•00 p.1-8
Interindividual genetic variation affects the susceptibility to and progression of many diseases1,2. However, efforts to study how individual human brains differ in normal development and disease phenotypes are limited by the paucity of faithful cellular human models, and the difficulty of scaling c...
Disease modelNeural stem cells
10.1038/S41586-024-07578-8
ISSN:0028-0836
Mechanisms and therapeutic implications of hypermutation in gliomas
Mehdi Touat•Yvonne Y. Li•Adam N. Boynton•Liam F. Spurr•J. Bryan Iorgulescu等 78 人
Nature
2020
•2020/4/15
•Vol.580 No.7804 p.517-523
A high tumour mutational burden (hypermutation) is observed in some gliomas1–5; however, the mechanisms by which hypermutation develops and whether it predicts the response to immunotherapy are poorly understood. Here we comprehensively analyse the molecular determinants of mutational burden and sig...
Cancer genomicsCancer immunotherapyCNS cancerGenomic instability
10.1038/S41586-020-2209-9
ISSN:0028-0836
Histone demethylase KDM5D upregulation drives sex differences in colon cancer
Jiexi Li•Zhengdao Lan•Wenting Liao•James W. Horner•Xueping Xu等 23 人
Nature
2023
•2023/6/21
•00 p.1-8
Sex exerts a profound impact on cancer incidence, spectrum and outcomes, yet the molecular and genetic bases of such sex differences are ill-defined and presumptively ascribed to X-chromosome genes and sex hormones1. Such sex differences are particularly prominent in colorectal cancer (CRC) in which...
Cancer epigeneticsCancer microenvironmentColorectal cancerMetastasis
10.1038/S41586-023-06254-7
ISSN:0028-0836
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
Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology
Dehkordi Shiva Kazempour•Walker Jamie•Sah Eric•Bennett Emma•Atrian Farzaneh等 18 人
Nature Aging
2021
•2021/12/10
•00 p.1-10
Senescent cells contribute to pathology and dysfunction in animal models1. Their sparse distribution and heterogenous phenotype have presented challenges to their detection in human tissues. We developed a senescence eigengene approach to identify these rare cells within large, diverse populations o...
AgeingCellular signalling networksComputational neuroscience
10.1038/S43587-021-00142-3
ISSN:2662-8465
Genomic basis for RNA alterations in cancer
Nature
2020
•2020/2/5
•Vol.578 No.7793 p.129-136
Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneit...
Cancer genomicsData integration
10.1038/S41586-020-1970-0
ISSN:0028-0836
Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases
de Klein Niek•Tsai Ellen A.•Vochteloo Martijn•Baird Denis•Huang Yunfeng等 21 人
Nature Genetics
2023
•2023/2/23
•Vol.55 No.3 p.377-388
Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait l...
Gene expressionGene regulationTranscriptomics
10.1038/S41588-023-01300-6
ISSN:1061-4036
Pathway and network analysis of more than 2500 whole cancer genomes
Matthew A. Reyna•David Haan•Marta Paczkowska•Lieven P. C. Verbeke•Miguel Vazquez等 26 人
Nature Communications
2020
•2020/2/5
•Vol.11 No.1 p.1-17
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as par...
Cancer genomicsCellular signalling networks
10.1038/S41467-020-14367-0
ISSN:2041-1723
Macrophage ferroptosis potentiates GCN2 deficiency induced pulmonary venous arterialization
Jingyuan Zhang•Pei Mao•Tengfei Zhou•Bingqing Yue•Yaning Li等 10 人
Nature Communications
2025
•2025/9/22
•Vol.16 No.1 p.1-19
Pulmonary veno-occlusive disease (PVOD) is a fatal disease characterized by the remodelling of pulmonary veins and haemosiderin accumulation in macrophages. Although (General Control Nonderepressible 2) GCN2 deficiency has been reported in PVOD patients, the underlying mechanism by which GCN2 defici...
Cell death and immune responseDiseasesMedical researchMonocytes and macrophagesTranslational immunology
10.1038/S41467-025-64035-4
ISSN:2041-1723
Acquisition of aneuploidy drives mutant p53-associated gain-of-function phenotypes
Redman-Rivera Lindsay N.•Shaver Timothy M.•Jin Hailing•Marshall Clayton B.•Schafer Johanna M.等 11 人
Nature Communications
2021
•2021/8/31
•Vol.12 No.1 p.1-15
p53 is mutated in over half of human cancers. In addition to losing wild-type (WT) tumor-suppressive function, mutant p53 proteins are proposed to acquire gain-of-function (GOF) activity, leading to novel oncogenic phenotypes. To study mutant p53 GOF mechanisms and phenotypes, we genetically enginee...
OncogenesTumour-suppressor proteins
10.1038/S41467-021-25359-Z
ISSN:2041-1723
Multimodal joint deconvolution and integrative signature selection in proteomics
Yue Pan•Xusheng Wang•Jiao Sun•Chunyu Liu•Junmin Peng等 6 人
Communications Biology
2024
•2024/4/24
•Vol.7 No.1 p.1-9
Deconvolution is an efficient approach for detecting cell-type-specific (cs) transcriptomic signals without cellular segmentation. However, this type of methods may require a reference profile from the same molecular source and tissue type. Here, we present a method to dissect bulk proteome by lever...
Proteome informaticsStatistical methods
10.1038/S42003-024-06155-Z
ISSN:2399-3642
Gene mutant dosage is associated with prognosis and metastatic tropism in 60,000 clinical cancer samples
Nicola Calonaci•Eriseld Krasniqi•Daniel Colic•Stefano Scalera•Giorgia Gandolfi等 13 人
Nature Genetics
2026
•2026/7/31
•00 p.1-12
The interplay between somatic mutations and copy number alterations influences tumor evolution and prognosis. These alterations are often treated independently, overlooking gene mutant dosage (GMD)—a key property of their interaction. Here we develop a computational framework that infers mutation co...
Data miningTumour biomarkers
10.1038/S41588-026-02666-Z
ISSN:1061-4036