Genome Sequence Archive for Human
English
China, Fuzhou
the National Genomics Data Center
数据描述
The Genome Sequence Archive for Human (GSA-Human), as a part of GSA in the National Genomics Data Center, is a data repository specialized for human genetic related data derived from biomedical researches. Aside from basic data archive services, GSA-Human features: • Specializing in human related omics data archives. • Supplying controlled-access data management services. • Providing secure online data request services.
ngdc.cncb.ac.cn
IP: 124.16.164.109
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相关论文
305Proteogenomics of different urothelial bladder cancer stages reveals distinct molecular features for papillary cancer and carcinoma in situ
Zhenmei Yao•Ning Xu•Guoguo Shang•Haixing Wang•Hui Tao等 19 人
Nature Communications
2023
•2023/9/13
•Vol.14 No.1 p.1-25
The progression of urothelial bladder cancer (UC) is a complicated multi-step process. We perform a comprehensive multi-omics analysis of 448 samples from 190 UC patients, covering the whole spectrum of disease stages and grades. Proteogenomic integration analysis indicates the mutations of HRAS reg...
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10.1038/S41467-023-41139-3
ISSN:2041-1723
UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing
Yun Li•Zheng Huang•Lubin Xu•Yanling Fan•Jun Ping等 27 人
Nature Methods
2025
•2025/1/20
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The use of single-cell combinatorial indexing sequencing via droplet microfluidics presents an attractive approach for balancing cost, scalability, robustness and accessibility. However, existing methods often require tailored protocols for individual modalities, limiting their automation potential ...
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10.1038/S41592-024-02586-Y
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Cellular hierarchy insights reveal leukemic stem-like cells and early death risk in acute promyelocytic leukemia
Wen Jin•Yuting Dai•Li Chen•Honghu Zhu•Fangyi Dong等 12 人
Nature Communications
2024
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Acute promyelocytic leukemia (APL) represents a paradigm for targeted differentiation therapy, with a minority of patients experiencing treatment failure and even early death. We here report a comprehensive single-cell analysis of 16 APL patients, uncovering cellular compositions and their impact on...
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Genetically engineered mesenchymal stem cells with dopamine synthesis for Parkinson’s disease in animal models
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Npj Parkinson's Disease
2022
•2022/12/22
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Although striatal delivery of three critical genes for dopamine synthesis by viruses is a potential clinical approach for treating Parkinson’s disease (PD), the approach makes it difficult to finely control dopamine secretion amounts and brings safety concerns. Here, we generate genetically engineer...
Parkinson's disease
10.1038/S41531-022-00440-6
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Single-cell sequencing uncovers disrupted stromal-macrophage communication as a driver of intrauterine adhesion progression
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Communications Biology
2025
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Intrauterine adhesions (IUA), characterized by endometrial fibrosis, pose a serious threat to women’s reproductive health, yet their molecular mechanisms remain poorly understood. Here, we use single-cell RNA sequencing (scRNA-seq) to profile 139,395 single cells from nine individuals in the prolife...
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Single-cell EpiChem jointly measures drug–chromatin binding and multimodal epigenome
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Studies of molecular and cellular functions of small-molecule inhibitors in cancer treatment, eliciting effects by targeting genome and epigenome associated proteins, requires measurement of drug-target engagement in single-cell resolution. Here we present EpiChem for in situ single-cell joint mappi...
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10.1038/S41592-024-02360-0
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LINE-1 transcription activates long-range gene expression
Xiufeng Li•Luyao Bie•Yang Wang•Yaqiang Hong•Ziqiang Zhou等 19 人
Nature Genetics
2024
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Long interspersed nuclear element-1 (LINE-1 or L1) is a retrotransposon group that constitutes 17% of the human genome and shows variable expression across cell types. However, the control of L1 expression and its function in gene regulation are incompletely understood. Here we show that L1 transcri...
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LKB1 inactivation promotes epigenetic remodeling-induced lineage plasticity and antiandrogen resistance in prostate cancer
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Cell Research
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Epigenetic regulation profoundly influences the fate of cancer cells and their capacity to switch between lineages by modulating essential gene expression, thereby shaping tumor heterogeneity and therapy response. In castration-resistant prostate cancer (CRPC), the intricacies behind androgen recept...
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10.1038/S41422-024-01025-Z
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A molecular glue induces aberrant STING oligomerization and inhibits autoinflammatory diseases
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Signal Transduction And Targeted Therapy
2026
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Dysregulated activation of the stimulator of interferon genes (STING) pathway underlies various inflammatory and autoimmune pathologies. Since STING oligomerization is fundamental to its biological function, targeted modulation of this polymerization process presents a promising therapeutic approach...
Target validation
10.1038/S41392-026-02863-6
ISSN:2059-3635
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
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•00 p.1-15
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CDK7-YAP-LDHD axis promotes D-lactate elimination and ferroptosis defense to support cancer stem cell-like properties
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Signal Transduction And Targeted Therapy
2023
•2023/8/16
•Vol.8 No.1 p.1-19
Reprogrammed cellular metabolism is essential for maintaining cancer stem cells (CSCs) state. Here, we report that mitochondrial D-lactate catabolism is a necessary initiating oncogenic event during tumorigenesis of esophageal squamous cell carcinoma (ESCC). We discover that cyclin-dependent kinase ...
Cancer metabolismCancer stem cells
10.1038/S41392-023-01555-9
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Proteogenomic characterization of skull-base chordoma
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Nature Communications
2024
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Nature Biomedical Engineering
2024
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Cell Research
2025
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Npj Precision Oncology
2022
•2022/1/13
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Several clinical trials have shown the safety and effectiveness of PD-1/PD-L1 inhibitors in neoadjuvant therapy in resectable non-small cell lung cancer (NSCLC). However, 18–83% patients can benefit from it. In this study, we aimed to assess the association of PD-L1 expression, tumor mutation burden...
ImmunologyPredictive markers
10.1038/S41698-021-00244-6
ISSN:2397-768X
YL1004 is a SARS-CoV-2 papain-like protease inhibitor with immunomodulatory and antiviral activity in mice
Jinshan Nan•Huiping Shuai•Jingxin Qiao•Rui Zeng•Lianzhao Du等 22 人
Nature Communications
2026
•2026/1/26
•Vol.17 No.1 p.20350
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A genomic and epigenomic atlas of prostate cancer in Asian populations
Jing Li•Chuanliang Xu•Hyung Joo Lee•Shancheng Ren•Xiaoyuan Zi等 55 人
Nature
2020
•2020/3/25
•Vol.580 No.7801 p.93-99
Prostate cancer is the second most common cancer in men worldwide1. Over the past decade, large-scale integrative genomics efforts have enhanced our understanding of this disease by characterizing its genetic and epigenetic landscape in thousands of patients2,3. However, most tumours profiled in the...
Cancer genomicsProstate cancer
10.1038/S41586-020-2135-X
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The cytokine CSBF inhibits the IL-17A and TNF-α inflammatory pathways via SUSD2-ACT1 in keratinocytes and alleviates IMQ-induced psoriasis
Xixi Li•Kai Zhang•Xiulan Yang•Yingying Cheng•Sihua Huang等 14 人
Cellular & Molecular Immunology
2025
•2025/8/14
•Vol.22 No.9 p.1109-1122
Overactivation of inflammatory signaling in keratinocytes is critical for psoriatic skin inflammation, but its regulatory mechanisms remain incompletely understood. Here, we demonstrate that the cytokine CSBF inhibits both individual and synergistic proinflammatory signaling induced by IL-17A and TN...
AutoimmunityCytokinesInflammationNF-kappaB
10.1038/S41423-025-01325-3
ISSN:2042-0226
Interleukin-33 (IL-33) promotes DNA damage-resistance in lung cancer
Haoge Luo•Liping Liu•Xiaoping Liu•Yingdong Xie•Xin Huang等 8 人
Cell Death & Disease
2025
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•Vol.16 No.1 p.1-14
Resistance to DNA damage is one of the primary mechanisms by which tumor cells evade the effects of standard chemotherapeutic agents and radiotherapy. Dynamic and complex interactions between the tumor microenvironment (TME) and tumor cells critically influence the DNA damage response. Interleukin-3...
Cancer microenvironmentCell death and immune responseExtracellular signalling moleculesInterleukins
10.1038/S41419-025-07624-X
ISSN:2041-4889
Remodeling of maternal mRNA through poly(A) tail orchestrates human oocyte-to-embryo transition
Liu Yusheng•Zhao Han•Shao Fanghong•Zhang Yiwei•Nie Hu等 13 人
Nature Structural & Molecular Biology
2023
•2023/1/16
•Vol.30 No.2 p.200-215
Poly(A)-tail-mediated post-transcriptional regulation of maternal mRNAs is vital in the oocyte-to-embryo transition (OET). Nothing is known about poly(A) tail dynamics during the human OET. Here, we show that poly(A) tail length and internal non-A residues are highly dynamic during the human OET, us...
ReprogrammingRNA metabolismRNA modification
10.1038/S41594-022-00908-2
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A pilot study of neoadjuvant combination of anti-PD-1 camrelizumab and VEGFR2 inhibitor apatinib for locally advanced resectable oral squamous cell carcinoma
Ju Wu-tong•Xia Rong-hui•Zhu Dong-wang•Dou Sheng-jin•Zhu Guo-pei等 20 人
Nature Communications
2022
•2022/9/14
•Vol.13 No.1 p.1-11
Novel neoadjuvant therapy regimens are warranted for oral squamous cell carcinoma (OSCC). In this phase I trial (NCT04393506), 20 patients with locally advanced resectable OSCC receive three cycles of camrelizumab (200 mg, q2w) and apatinib (250 mg, once daily) before surgery. The primary endpoints ...
ImmunotherapyOral cancer
10.1038/S41467-022-33080-8
ISSN:2041-1723
Genomic features reveal potential benefit of adding anti-PD-1 immunotherapy to treat non-upper aerodigestive tract natural killer/T-cell lymphoma
Zegeng Chen•He Huang•Huageng Huang•Le Yu•Huawei Weng等 22 人
Leukemia
2024
•2024/2/20
•Vol.38 No.4 p.829-839
Natural killer/T-cell lymphoma (NKTCL) is a highly heterogeneous disease with a poor prognosis. However, the genomic characteristics and proper treatment strategies for non-upper aerodigestive tract NKTCL (NUAT-NKTCL), a rare subtype of NKTCL, remain largely unexplored. In this study, 1589 patients ...
Cancer genomicsCancer immunotherapyT-cell lymphoma
10.1038/S41375-024-02171-4
ISSN:0887-6924
Parvovirus B19 targets hematopoietic stem cells to disrupt multilineage differentiation and drive pancytopenia
Xu-Ying Pei•Zhuo-Jun Liu•Qiang Fu•Hsiang-Ying Lee•Qi Hu等 14 人
Cell Death & Differentiation
2026
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•00 p.1-11
Human parvovirus B19 (B19V) infection is a significant but underrecognized complication, commonly linked not only to aplastic anemia but also pancytopenia, especially in hematopoietic stem cell transplantation (HSCT) recipients. While B19V’s tropism for erythroid progenitor cells (EPCs) is well-docu...
Haematological diseasesInfectious diseases
10.1038/S41418-026-01671-3
ISSN:1350-9047
Safety and feasibility of CRISPR-edited T cells in patients with refractory non-small-cell lung cancer
You Lu•Jianxin Xue•Tao Deng•Xiaojuan Zhou•Kun Yu等 38 人
Nature Medicine
2020
•2020/4/27
•Vol.26 No.5 p.732-740
Clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 editing of immune checkpoint genes could improve the efficacy of T cell therapy, but the first necessary undertaking is to understand the safety and feasibility. Here, we report results from a first-in-human phase I clinical tri...
Cancer immunotherapyGenetic engineeringNon-small-cell lung cancerPhase I trials
10.1038/S41591-020-0840-5
ISSN:1078-8956
Single-cell analysis unravels divergent gene signatures shaping seminoma stemness and metastasis
Zhouliang Bian•Biying Chen•Jiahui Guo•Jiamin Zhang•Guangye Du等 13 人
Cell Death Discovery
2025
•2025/11/7
•Vol.11 No.1 p.1-13
Seminoma is the most common solid malignant tumor of the testis in young males, significantly impacting fertility. Approximately 20% of seminomas metastasize, markedly increasing recurrence risk and compromising quality of life. To investigate the poorly understood mechanisms driving seminoma metast...
MetastasisRNA sequencingTesticular cancer
10.1038/S41420-025-02802-4
ISSN:2058-7716
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
Refined risk stratification helps guiding transplantation choice in adult BCR::ABL1-positive acute lymphoblastic leukemia
Cheng Wang•Jianfeng Li•Weiyang Liu•Lingling Zhao•Han Yan等 15 人
Blood Cancer Journal
2024
•2024/4/24
•Vol.14 No.1 p.1-5
Acute lymphocytic leukaemiaCancer genomics
10.1038/S41408-024-01055-1
ISSN:2044-5385
The m6A methyltransferase METTL14 promotes cell proliferation via SETBP1-mediated activation of PI3K-AKT signaling pathway in myelodysplastic neoplasms
Lingxu Jiang•Yudi Zhang•Jiejing Qian•Xinping Zhou•Liya Ma等 20 人
Leukemia
2024
•2024/7/25
•00 p.1-13
N6-methyladenosine (m6A) is the most prevalent epitranscriptomic modification in mammalian mRNA. Recent studies have revealed m6A is involved in the pathogenesis of various malignant tumors including hematologic neoplasms. Nevertheless, the specific roles of m6A modification and m6A regulators in my...
Myelodysplastic syndromeOncogenesOncogenesis
10.1038/S41375-024-02350-3
ISSN:0887-6924
Involvement of striatal motoric subregions in familial frontotemporal dementia with parkinsonism harboring the C9orf72 repeat expansions
Liu Li•Liu Shuying•Chu Min•Wang Jingjuan•Xie Kexin等 13 人
Npj Parkinson's Disease
2022
•2022/10/6
•Vol.8 No.1 p.1-7
The chromosome 9 open reading frame 72 (C9ORF72) has been proposed as the causative gene of frontotemporal dementia with parkinsonism (FTDP), but its pathophysiological mechanism of parkinsonism is poorly understood. To explore the roles of striatal motor subdivisions in the pathogenesis of parkinso...
Movement disordersNeurodegenerative diseases
10.1038/S41531-022-00398-5
ISSN:2373-8057
The C-type lectin COLEC10 is predominantly produced by hepatic stellate cells and involved in the pathogenesis of liver fibrosis
Mengfan Zhang•Yang Jing•Wenze Xu•Xiaojing Shi•Wenguang Zhang等 10 人
Cell Death & Disease
2023
•2023/11/30
•Vol.14 No.11 p.1-17
Hepatic stellate cell is one of the major nonparenchymal cell types in liver. It has been proved the hepatic stellate cells are activated upon liver injury and produce excessive extracellular matrix to induce liver fibrosis. Single-cell RNA sequencing has been introduced to identify the subpopulatio...
Chronic inflammationDiagnostic markers
10.1038/S41419-023-06324-8
ISSN:2041-4889
Ratio of the interferon-γ signature to the immunosuppression signature predicts anti-PD-1 therapy response in melanoma
Chuanliang Cui•Canqiang Xu•Wenxian Yang•Zhihong Chi•Xinan Sheng等 12 人
Npj Genomic Medicine
2021
•2021/2/4
•Vol.6 No.1 p.1-12
Immune checkpoint inhibitor (ICI) treatments produce clinical benefit in many patients. However, better pretreatment predictive biomarkers for ICI are still needed to help match individual patients to the treatment most likely to be of benefit. Existing gene expression profiling (GEP)-based biomarke...
Gene ontologyPrognostic markers
10.1038/S41525-021-00169-W
ISSN:2056-7944
Spatial transcriptomics analysis of esophageal squamous precancerous lesions and their progression to esophageal cancer
Xuejiao Liu•Simin Zhao•Keke Wang•Liting Zhou•Ming Jiang等 17 人
Nature Communications
2023
•2023/8/8
•Vol.14 No.1 p.1-20
Esophageal squamous precancerous lesions (ESPL) are the precursors of esophageal squamous cell carcinoma (ESCC) including low-grade and high-grade intraepithelial neoplasia. Due to the absence of molecular indicators, which ESPL will eventually develop into ESCC and thus should be treated is not wel...
BiomarkersOesophageal cancerOncogenesisTranscriptomics
10.1038/S41467-023-40343-5
ISSN:2041-1723
Genotypic and phenotypic characteristics of sodium channel—associated epilepsy in Chinese population
Rui Dong•Ruifeng Jin•Hongwei Zhang•Haiyan Zhang•Min Xue等 11 人
Journal Of Human Genetics
2024
•2024/6/17
•00 p.1-13
Variants in voltage-gated sodium channel (VGSC) genes are implicated in seizures, epilepsy, and neurodevelopmental disorders, constituting a significant aspect of hereditary epilepsy in the Chinese population. Through retrospective analysis utilizing next-generation sequencing (NGS), we examined the...
Genetics researchNeurological disorders
10.1038/S10038-024-01257-2
ISSN:1434-5161
Single-cell transcriptomic analysis in a mouse model deciphers cell transition states in the multistep development of esophageal cancer
Jiacheng Yao•Qionghua Cui•Wenyi Fan•Yuling Ma•Yamei Chen等 19 人
Nature Communications
2020
•2020/7/24
•Vol.11 No.1 p.1-13
Esophageal squamous cell carcinoma (ESCC) is prevalent in some geographical regions of the world. ESCC development presents a multistep pathogenic process from inflammation to invasive cancer; however, what is critical in these processes and how they evolve is largely unknown, obstructing early diag...
Cancer microenvironmentOesophageal cancer
10.1038/S41467-020-17492-Y
ISSN:2041-1723
Integrated proteogenomic characterization of ampullary adenocarcinoma
Qiao Zhang•Xiaomeng Xu•Dongxian Jiang•Yunzhi Wang•Haixing Wang等 19 人
Cell Discovery
2025
•2025/1/7
•Vol.11 No.1 p.1-25
Ampullary adenocarcinoma (AMPAC) is a rare and heterogeneous malignancy. Here we performed a comprehensive proteogenomic analysis of 198 samples from Chinese AMPAC patients and duodenum patients. Genomic data illustrate that 4q loss causes fatty acid accumulation and cell proliferation. Proteomic an...
Gastrointestinal cancerMolecular biology
10.1038/S41421-024-00742-4
ISSN:2056-5968
Single-cell multi-omic landscape reveals anatomical-specific immune features in adult and pediatric sepsis
Qian Ye•Xiaofei Lai•Yuliang Liu•Zhengtao Zhang•Yueqiang Fu等 18 人
Nature Immunology
2025
•2025/12/3
•00 p.1-16
The anatomical source of infection is a major determinant of sepsis outcomes; however, how distinct sites shape immunity remains unclear. Here we applied multi-omic profiling, integrating single-cell transcriptomics, single-cell T cell receptor and B cell receptor sequencing, CITE-seq, bulk RNA sequ...
Immunological disordersImmunology
10.1038/S41590-025-02345-X
ISSN:1529-2908
Single-cell profiling unveils nephritis-related circulating immunological signatures in systemic lupus erythematosus patients
Qun Liu•Linjie Wu•Sha Hao•Yiyao Deng•Xiaomin Liu等 20 人
Communications Biology
2026
•2026/1/5
•Vol.9 No.1 p.1550
Lupus nephritis (LN), the most severe complication of systemic lupus erythematosus (SLE), arises from systemic immune dysregulation and renal damage. While renal immune perturbations are well-studied, systemic signatures specific to LN pathogenesis remain unclear. Integrated single-cell RNA and immu...
AutoimmunityLupus nephritis
10.1038/S42003-025-09431-8
ISSN:2399-3642
Deficient extravillous trophoblast invasion caused by impaired sialylation–Siglec-7 interaction contributes to recurrent pregnancy loss
Linyu Zhang•Ying Feng•Peng Wu•Liuyan Chen•Nan Jiang等 10 人
Cell Death & Disease
2026
•2026/3/2
•Vol.17 No.1 p.2910
Successful pregnancy requires precise immune interactions between fetal extravillous trophoblasts (EVT) and maternal decidual immune cells at the maternal–fetal interface. Glycosylation, particularly terminal sialylation, is emerging as a key modulator of these interactions; however, its functional ...
CytokinesDevelopmental biologyDiseasesGlycobiology
10.1038/S41419-026-08503-9
ISSN:2041-4889
Targeting YRDC blocks codon-biased FABP7 translation and lipid droplet formation to overcome chemoresistance in glioblastoma
Yuchao Zhang•Xuesong Yang•Xixi Li•Chen Zheng•Xuechao Zeng等 17 人
Oncogene
2026
•2026/4/21
•00 p.1-16
Dysregulation of transfer RNA (tRNA) modification and reprogramming of codon-biased translation are commonly associated with cancer initiation and progression. However, their roles in chemoresistance and tumor recurrence remain poorly understood, especially in glioblastoma (GBM). This study establis...
Cancer stem cellsCNS cancerVirtual screening
10.1038/S41388-026-03801-0
ISSN:0950-9232
Single-cell sequencing reveals immune features of treatment response to neoadjuvant immunochemotherapy in esophageal squamous cell carcinoma
Zhenlin Yang•He Tian•Xiaowei Chen•Bozhao Li•Guangyu Bai等 13 人
Nature Communications
2024
•2024/10/22
•Vol.15 No.1 p.1-18
Neoadjuvant immunochemotherapy (nICT) has dramatically changed the treatment landscape of operable esophageal squamous cell carcinoma (ESCC), but factors influencing tumor response to nICT are not well understood. Here, using single-cell RNA sequencing paired with T cell receptor sequencing, we prof...
Cancer genomicsCancer immunotherapyCancer microenvironmentOesophageal cancerTumour biomarkers
10.1038/S41467-024-52977-0
ISSN:2041-1723
Effects of poor sleep on the immune cell landscape as assessed by single-cell analysis
Liu Xiuxing•Chen Binyao•Huang Zhaohao•Duan Runping•Li He等 11 人
Communications Biology
2021
•2021/11/25
•Vol.4 No.1 p.1-15
Poor sleep has become an important public health issue. With loss of sleep durations, poor sleep has been linked to the increased risks for diseases. Here we employed mass cytometry and single-cell RNA sequencing to obtain a comprehensive human immune cells landscape in the context of poor sleep, wh...
AutoimmunityInflammationRisk factors
10.1038/S42003-021-02859-8
ISSN:2399-3642
Long-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study
Yanhua Li•Shijie Qin•Lei Dong•Shitong Qiao•Xiao Wang等 14 人
Nature Communications
2024
•2024/3/19
•Vol.15 No.1 p.1-18
There have been reports of long coronavirus disease (long COVID) and breakthrough infections (BTIs); however, the mechanisms and pathological features of long COVID after Omicron BTIs remain unclear. Assessing long-term effects of COVID-19 and immune recovery after Omicron BTIs is crucial for unders...
Molecular medicineOutcomes researchSARS-CoV-2Viral infection
10.1038/S41467-024-46692-Z
ISSN:2041-1723
Characterization of genome-wide STR variation in 6487 human genomes
Shi Yirong•Niu Yiwei•Zhang Peng•Luo Huaxia•Liu Shuai等 12 人
Nature Communications
2023
•2023/4/12
•Vol.14 No.1 p.1-18
Short tandem repeats (STRs) are abundant and highly mutagenic in the human genome. Many STR loci have been associated with a range of human genetic disorders. However, most population-scale studies on STR variation in humans have focused on European ancestry cohorts or are limited by sequencing dept...
BioinformaticsGenetic variation
10.1038/S41467-023-37690-8
ISSN:2041-1723
Multimodal single-cell protein and RNA profiling unveils dysregulated immature neutrophil dynamics in gestational diabetes mellitus
Junyu Xu•Caixia Zhu•Lepei Xie•Yiping Liu•Jinheng Li等 12 人
Communications Biology
2026
•2026/1/7
•Vol.9 No.1 p.3160
Neutrophils are the most abundant leukocytes in human peripheral blood, yet their heterogeneity in pregnancy, especially in gestational diabetes mellitus (GDM), remains incompletely understood. Here, we employed InfinityFlow-based surface marker profiling and single-cell RNA sequencing (scRNA-seq) t...
Endocrine reproductive disordersNeutrophils
10.1038/S42003-025-09468-9
ISSN:2399-3642
DNA of neutrophil extracellular traps promote NF-κB-dependent autoimmunity via cGAS/TLR9 in chronic obstructive pulmonary disease
Jun Chen•Tao Wang•Xiaoou Li•Lijuan Gao•Ke Wang等 10 人
Signal Transduction And Targeted Therapy
2024
•2024/6/17
•Vol.9 No.1 p.1-16
Chronic obstructive pulmonary disease (COPD) is characterised by persistent airway inflammation even after cigarette smoking cessation. Neutrophil extracellular traps (NETs) have been implicated in COPD severity and acute airway inflammation induced by short-term cigarette smoke (CS). However, wheth...
InflammationRespiratory tract diseases
10.1038/S41392-024-01881-6
ISSN:2059-3635
Integrative proteogenomic characterization reveals therapeutic targets in poorly differentiated and anaplastic thyroid cancers
Zongfu Pan•Zhuo Tan•Ning Xu•Zhenmei Yao•Chuanming Zheng等 31 人
Nature Communications
2025
•2025/4/16
•Vol.16 No.1 p.1-20
Poorly differentiated thyroid cancer (PDTC) and anaplastic thyroid cancer (ATC) present major challenges in treatment owing to extreme aggressiveness and high heterogeneity. In this study, deep-scale analyses spanning genomic, proteomic, and phosphoproteomic data are performed on 348 thyroid-cancer ...
Cancer genomicsThyroid cancer
10.1038/S41467-025-58910-3
ISSN:2041-1723
Comprehensive genomic and transcriptomic analyses reveal prognostic stratification for esophageal squamous cell carcinoma
Jian Gao•Qiming Wang•Fangqiu Fu•Yue Zhao•Teng Yang等 30 人
Signal Transduction And Targeted Therapy
2025
•2025/7/17
•Vol.10 No.1 p.1-15
Recent large-scale multi-omics studies have characterized the heterogeneity of esophageal squamous cell carcinoma (ESCC), but inconsistent clinical management has hindered the identification of prognostic markers and patient stratification. Here, we conducted genomic and transcriptomic profiling of ...
Cancer genomicsPrognostic markersTumour heterogeneity
10.1038/S41392-025-02306-8
ISSN:2059-3635
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
Single-cell RNA sequencing identifies the prolactin receptor as a therapeutic target in adenomyosis
Runze Wang•Shuai Xu•Qionghua Cui•Xin Chen•Xuelian Wang等 13 人
Signal Transduction And Targeted Therapy
2025
•2025/8/13
•Vol.10 No.1 p.1-13
Adenomyosis is a complex gynecological disease characterized by endometrial tissue invasion into the myometrium. Current interventions, such as hormonal therapy or hysterectomy, are associated with significant side effects and compromise fertility, underscoring the urgent need for safe and effective...
Molecular medicineReproductive disorders
10.1038/S41392-025-02339-Z
ISSN:2059-3635
Integrating single-nucleus barcoding with spatial transcriptomics via Stamp-seq to reveal immunotherapy response-enhancing functional modules in NSCLC
Yitong Pan•Huan Yan•Jinhuan Han•Rui Wu•Caiming Xu等 19 人
Cell Discovery
2026
•2026/2/5
•Vol.12 No.1 p.100
Deciphering the spatial organization of cell states is fundamental for understanding development, tissue homeostasis and disease. Emerging advances in spatial transcriptomic profiling techniques allow transcript localization but face limitations in unambiguous cell state assignments due to cellular ...
BioinformaticsCancer immunotherapyCancer microenvironmentNon-small-cell lung cancer
10.1038/S41421-025-00861-6
ISSN:2056-5968
Single-cell profiling reveals molecular basis of malignant phenotypes and tumor microenvironments in small bowel adenocarcinomas
Yang Jingwei•Zhou Xin•Dong Ji•Wang Wendong•Lu Yongqu等 15 人
Cell Discovery
2022
•2022/9/14
•Vol.8 No.1 p.1-23
Small bowel adenocarcinomas (SBAs) are rare malignant tumors with a high mortality rate, and their molecular characteristics are still largely unexplored. Here we performed single-cell RNA sequencing for tumor samples from 12 SBA patients and predicted drug candidates for SBA. We identified four pre...
Cancer microenvironmentGastrointestinal cancer
10.1038/S41421-022-00434-X
ISSN:2056-5968
SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation
Xu Gang•Li Ying•Zhang Shengyuan•Peng Haoran•Wang Yunyun等 21 人
Cell Research
2021
•2021/10/18
•00 p.1-14
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the ongoing global pandemic that poses substantial challenges to public health worldwide. A subset of COVID-19 patients experience systemic inflammatory response, known as cytokine storm, ...
Cell biologyMechanisms of disease
10.1038/S41422-021-00578-7
ISSN:1001-0602
Dual epitope anti-LILRB4 synthetic T-cell receptor and antigen receptor (STAR)-T-cell therapy for relapsed/refractory acute myeloid leukemia
Meng Lv•Hongli Zheng•Xuying Pei•Lei Lei•Wenbo Chen等 16 人
Signal Transduction And Targeted Therapy
2026
•2026/6/1
•Vol.11 No.1 p.2030
Acute myeloid leukemia (AML) is a rapidly progressive malignancy with poor prognosis. To date, chimeric antigen receptor (CAR) T-cell therapy in AML has been limited by the lack of antigens with high specificity for AML cells. Here, we developed a synthetic T-cell receptor and antigen receptor-T (ST...
ImmunotherapyTranslational research
10.1038/S41392-026-02765-7
ISSN:2059-3635
Olverembatinib, a multikinase inhibitor that modulates lipid metabolism, in advanced succinate dehydrogenase-deficient gastrointestinal stromal tumors: a phase 1b study and translational research
Hai-Bo Qiu•Zhiyan Liang•Jing Yang•Ye Zhou•Zhi-Wei Zhou等 19 人
Signal Transduction And Targeted Therapy
2025
•2025/11/4
•Vol.10 No.1 p.1-12
Succinate dehydrogenase (SDH)-deficient gastrointestinal stromal tumors (GISTs) are generally resistant to targeted therapy with tyrosine kinase inhibitors (TKIs), such as imatinib, and there are no standard therapeutic options for advanced SDH-deficient GISTs. The precise oncogenic mechanisms of SD...
Gastrointestinal cancerMolecular medicineSarcoma
10.1038/S41392-025-02456-9
ISSN:2059-3635
SAMSN1 restrains NK cell mediated anti-tumor immunity in hepatocellular carcinoma
Ruifeng Wang•Huidi Chen•Hanyang Liu•Qiang Li•Guojing Yao等 11 人
Nature Communications
2026
•2026/1/21
•Vol.17 No.1 p.19030
NK cells are critical mediators of anti-tumor immunity whose function is frequently compromised in the tumor microenvironment. Here we identify SAM domain, SH3 domain and nuclear localization signals 1 (SAMSN1) as a previously unrecognized immune checkpoint that predominantly regulates NK cell funct...
Hepatocellular carcinomaImmunosuppressionLymphocyte activationNK cells
10.1038/S41467-026-68661-4
ISSN:2041-1723
Single-cell landscape identified SERPINB9 as a key player contributing to stemness and metastasis in non-seminomas
Zhouliang Bian•Biying Chen•Guohai Shi•Haihua Yuan•Yue Zhou等 9 人
Cell Death & Disease
2024
•2024/11/11
•Vol.15 No.11 p.1-13
Embryonal carcinoma (EC), characterized by a high degree of stemness similar to that of embryonic stem cells, is the most malignant subtype within non-seminomatous testicular germ cell tumors (TGCTs). However, the mechanisms underlying its malignancy remain unknown. In this study, we employed single...
Cell biologyGerm cell tumours
10.1038/S41419-024-07220-5
ISSN:2041-4889
CD300E+ macrophages facilitate liver regeneration after splenectomy in decompensated cirrhotic patients
Tao Yang•Yuan Zhang•Chujun Duan•Hui Liu•Dong Wang等 12 人
Experimental & Molecular Medicine
2025
•2025/1/1
•00 p.1-14
Liver cirrhosis is prognostically associated with poor life expectancy owing to subsequent liver failure. Thus, understanding liver regeneration processes during cirrhotic injury is highly important. This study explored the role of macrophage heterogeneity in liver regeneration following splenectomy...
Cell proliferationLiver cirrhosis
10.1038/S12276-024-01371-3
ISSN:2092-6413
Exome-wide genetic risk score (ExGRS) to predict high myopia across multi-ancestry populations
Jian Yuan•Ruowen Qiu•Yuhan Wang•Zhen Ji Chen•Haojun Sun等 14 人
Communications Medicine
2024
•2024/12/30
•Vol.4 No.1 p.1-10
High myopia (HM), characterized by a severe myopic refractive error, stands as a leading cause of visual impairment and blindness globally. HM is a multifactorial ocular disease that presents high genetic heterogeneity. Employing a genetic risk score (GRS) is useful for capturing genetic susceptibil...
Eye diseasesPopulation genetics
10.1038/S43856-024-00718-1
ISSN:2730-664X
Population-level analyses identify host and environmental variables influencing the vaginal microbiome
Lang Qin•Tianyong Sun•Xiao Li•Shigang Zhao•Zheng Liu等 36 人
Signal Transduction And Targeted Therapy
2025
•2025/2/19
•Vol.10 No.1 p.1-15
The vaginal microbiome is critical for the reproductive health of women, yet the differential impacts exerted by the host and by ambient environmental variables on the vaginal microbiome remain largely unknown. Here, we conducted a comprehensive cross-sectional study of the relationships between the...
Genome informaticsReproductive disorders
10.1038/S41392-025-02152-8
ISSN:2059-3635
GPR56 facilitates hepatocellular carcinoma metastasis by promoting the TGF-β signaling pathway
Yiming Luo•Junli Lu•Zhen Lei•Dean Rao•Tiantian Wang等 11 人
Cell Death & Disease
2024
•2024/10/1
•Vol.15 No.10 p.1-14
The metastasis of hepatocellular carcinoma (HCC) poses a significant threat to the survival of patients. G protein-coupled receptor 56 (GPR56) has garnered extensive attention within malignant tumor research and plays a crucial role in cellular surface signal transmission. Nonetheless, its precise f...
Liver cancerMetastasisTargeted therapies
10.1038/S41419-024-07095-6
ISSN:2041-4889
Two noncompeting human neutralizing antibodies targeting MPXV B6 show protective effects against orthopoxvirus infections
Runchu Zhao•Lili Wu•Junqing Sun•Dezhi Liu•Pu Han等 14 人
Nature Communications
2024
•2024/5/31
•Vol.15 No.1 p.1-11
The recent outbreak of mpox epidemic, caused by monkeypox virus (MPXV), poses a new threat to global public health. Here, we initially assessed the preexisting antibody level to the MPXV B6 protein in vaccinia vaccinees born before the end of the immunization program and then identified two monoclon...
AntibodiesCryoelectron microscopyMousePox virus
10.1038/S41467-024-48312-2
ISSN:2041-1723
Olfactomedin 4 orchestrates TGF-β/CEACAM6 axis, promoting cell-autonomous epithelial to mesenchymal transition during gallbladder epithelium carcinogenesis
Songlin Yang•Wenwen Huang•Qingju Zeng•Xiaodan Wang•Shucheng Lin等 17 人
Oncogene
2026
•2026/4/29
•00 p.1-16
Gallbladder cancer (GBC) is a highly lethal disease which is usually diagnosed at advanced stage owing to unavailable screening tools and effective therapies. Persistent inflammation induced by various risk factors is the main cause of GBC, however, the molecular program remains elusive. Unveiling t...
MetastasisTumour biomarkers
10.1038/S41388-026-03808-7
ISSN:0950-9232
Lipocalin-2 drives brain metastatic progression through reciprocal tumor-microenvironment interactions in lung cancer
Yixiang Zhu•Jian Zhang•Danming He•Hongqing Cai•Yan He等 15 人
Signal Transduction And Targeted Therapy
2025
•2025/12/24
•Vol.10 No.1 p.4170
Brain metastasis is a major contributor to mortality in patients with lung cancer. The unique microenvironment of the brain plays a critical role in the initiation and progression of brain metastases (BM), yet the molecular mechanisms underlying tumor-microenvironment interactions remain poorly unde...
Lung cancerMetastasis
10.1038/S41392-025-02514-2
ISSN:2059-3635
Double-dose firmonertinib as first-line treatment in patients with locally advanced or metastatic non-small-cell lung cancer harboring EGFR L858R mutation: a prospective, multicenter, phase II study (FIRM)
Bo Shen•Chun Wang•Liqin Zhang•Yingying Zhu•Xing Zhang等 13 人
Nature Communications
2026
•2026/1/19
•Vol.17 No.1 p.18400
Progression-free survival (PFS) with first-line third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors remains suboptimal in EGFR L858R-mutated advanced non-small-cell lung cancer (NSCLC), highlighting a need for strategies to delay resistance. This single-arm, phase II ...
Cancer therapyLung cancerPhase II trials
10.1038/S41467-026-68554-6
ISSN:2041-1723
CSTF2 mediated mRNA N6-methyladenosine modification drives pancreatic ductal adenocarcinoma m6A subtypes
Yanfen Zheng•Xingyang Li•Shuang Deng•Hongzhe Zhao•Ying Ye等 21 人
Nature Communications
2023
•2023/10/10
•Vol.14 No.1 p.1-17
N6-methyladenosine (m6A) modification of gene transcripts plays critical roles in cancer. Here we report transcriptomic m6A profiling in 98 tissue samples from 65 individuals with pancreatic ductal adenocarcinoma (PDAC). We identify 17,996 m6A peaks with 195 hyper-methylated and 93 hypo-methylated i...
Cancer epigeneticsPancreatic cancer
10.1038/S41467-023-41861-Y
ISSN:2041-1723
Spatially resolved C1QC+ macrophage-CD4+ T cell niche in colorectal cancer microenvironment: implications for immunotherapy response
Hangyu Zhang•Libing Hong•Zhen Dong•Shan Xin•Bo Lin等 26 人
Cell Discovery
2025
•2025/7/1
•Vol.11 No.1 p.1-21
Colorectal cancer (CRC), including both microsatellite instability (MSI) and microsatellite stability (MSS) subtypes, frequently exhibits intrinsic resistance to immunotherapy. However, the spatial tumor microenvironment (TME) and its role in distinguishing immunotherapy responders from non-responde...
Cancer microenvironmentColorectal cancer
10.1038/S41421-025-00811-2
ISSN:2056-5968
Dynamics of TCR repertoire and T cell function in COVID-19 convalescent individuals
Luo Lingjie•Liang Wenhua•Pang Jianfeng•Xu Gang•Chen Yingying等 22 人
Cell Discovery
2021
•2021/9/28
•Vol.7 No.1 p.1-17
SARS-CoV-2 outbreak has been declared by World Health Organization as a worldwide pandemic. However, there are many unknowns about the antigen-specific T-cell-mediated immune responses to SARS-CoV-2 infection. Here, we present both single-cell TCR-seq and RNA-seq to analyze the dynamics of TCR reper...
Cell biologyImmunology
10.1038/S41421-021-00321-X
ISSN:2056-5968
Targeting a super-enhancer induced aldehyde dehydrogenase metabolic loop mitigates CDK4/6 inhibitor resistance in estrogen receptor-positive cancers
Xiaochuan Chen•Shini Liu•Dandong Luo•Dezheng Lin•Jun Liu等 9 人
Nature Communications
2026
•2026/3/27
0CDK4/6 inhibitors (CDK4/6i) have shown striking clinical potential in hormone receptor-positive breast cancers (BC) and endometrial cancers (EC), whereas resistance hinders their clinical utilization. The role of epigenetic alterations in CDK4/6i resistance remains poorly elucidated. Herein, through...
Cancer genomicsCancer therapeutic resistance
10.1038/S41467-026-71144-1
ISSN:2041-1723
Nuclear m6A modification regulates satellite transcription and chromosome segregation
Chenyang Huang•Xiao Shu•Siting Zhou•Yujie Mi•Hanxiao Bian等 17 人
Nature Chemical Biology
2025
•2025/5/22
•00 p.1-13
The precise location and functions of N6-methyladenosine (m6A) modification on mammalian nuclear noncoding RNA remain largely unknown. Here we developed nuclear-m6A-label-seq to directly map human and mouse cell nuclear RNA m6A methylome at single-base resolution. Specifically, m6A modifications hav...
Chemical modificationNon-coding RNAsRNA
10.1038/S41589-025-01900-9
ISSN:1552-4450
Lake-centred sedentary lifestyle of early Tibetan Plateau Indigenous populations at high elevation 4,400 years ago
Xiaoyan Yang•Yu Gao•Shargan Wangdue•Jingkun Ran•Qing Wang等 38 人
Nature Ecology & Evolution
2024
•2024/9/16
•00 p.1-12
The onset of sedentism on the Tibetan Plateau is often presumed to be associated with the dispersal of agriculture or farmers from archaeological sites located in the low elevation margins of the plateau. Previous studies of the plateau assumed that all foragers were probably mobile, but few systema...
ArchaeologyEvolutionary genetics
10.1038/S41559-024-02539-W
ISSN:2397-334X
Single cell immunoprofile of synovial fluid in rheumatoid arthritis with TNF/JAK inhibitor treatment
Xuyang Xia•Chenjia He•Zhinan Xue•Yuelan Wang•Yun Qin等 22 人
Nature Communications
2025
•2025/3/4
•Vol.16 No.1 p.1-23
Numerous patients with rheumatoid arthritis (RA) manifest severe syndromes, including elevated synovial fluid volumes (SF) with abundant immune cells, which can be controlled by TNF/JAK inhibitors. Here, we apply single-cell RNA sequencing (scRNA-seq) and subsequent validations in SF from RA patient...
CD4-positive T cellsGene regulation in immune cellsMonocytes and macrophagesRheumatoid arthritisRNA sequencing
10.1038/S41467-025-57361-0
ISSN:2041-1723
Glucose uptake capacity of leukaemia cells in vitro correlates with response to induction therapy in acute myeloid leukaemia
Suqi Deng•Juan Du•Kexiu Huang•Robert Peter Gale•Danqi Pan等 16 人
Leukemia
2024
•2024/11/18
•00 p.1-3
Acute myeloid leukaemiaCancer imagingCancer metabolism
10.1038/S41375-024-02469-3
ISSN:0887-6924
Distinct aneuploid evolution of astrocytoma and glioblastoma during recurrence
Jinsen Zhang•Yuan Feng•Guanghao Li•Jianhua Zhang•Xin Zhang等 17 人
Npj Precision Oncology
2023
•2023/9/23
•Vol.7 No.1 p.1-10
Astrocytoma and glioblastoma (GB) are reclassified subtypes of adult diffuse gliomas based on distinct isocitrate dehydrogenase (IDH) mutation in the fifth edition of the WHO Classification of Tumors of the Central Nervous System. The recurrence of gliomas is a common and inevitable challenge, and a...
Cancer genomicsCNS cancer
10.1038/S41698-023-00453-1
ISSN:2397-768X
Uncovering the genetic variation spectrum of colorectal polyposis from a multicentre cohort in China
Mengyuan Yang•Ding Zhang•Zhijun Yuan•Daici Chen•Haixing Ju等 12 人
Npj Precision Oncology
2025
•2025/3/15
•Vol.9 No.1 p.1-9
This multicentre study addresses the genetic spectrum of colorectal polyposis in China. We analyzed 120 patients with over 10 adenomas using a 139-gene next-generation sequencing panel and multiplex ligation-dependent probe amplification. Findings revealed that 89 patients carried pathogenic germlin...
Cancer genomicsDisease genetics
10.1038/S41698-025-00864-2
ISSN:2397-768X
Virus-human chromatin interactions reorganise 3D genome and hijack KDM5B for promoting metastasis in nasopharyngeal carcinoma
Dittman Lai-Shun Chung•Zhaozheng Hou•Ying Wang•Kazi Anisha Islam•Songran Liu等 27 人
Nature Communications
2025
•2025/8/4
•Vol.16 No.1 p.1-21
Epstein–Barr virus, the first identified human DNA tumour virus, is detectable in more than 90% of nasopharyngeal carcinoma patients in endemic regions. The 3D chromosome conformation analysis reveals that virus‒host chromatin interactions induce the spatial reorganisation of loops and compartments,...
Head and neck cancerMetastasisTumour virus infections
10.1038/S41467-025-61597-1
ISSN:2041-1723
Gut microbiota modulation via repeated donor fecal transplantation improves motor and gastrointestinal symptoms in drug-naïve Parkinson’s disease: a randomized phase 2 trial
Rui Zhang•Renyi Feng•Jiuqi Wang•Yongkang Chen•Han Liu等 15 人
Signal Transduction And Targeted Therapy
2026
•2026/3/13
•Vol.11 No.1 p.940
The gut-brain axis is increasingly recognized as a critical contributor to Parkinson’s disease (PD) pathogenesis, yet the therapeutic impact of microbiota modulation remains unclear due to lack of clinical trials in drug-naïve patients. We conducted a randomized, double-blind, placebo-controlled pha...
Neurodevelopmental disordersNeuroimmunology
10.1038/S41392-026-02604-9
ISSN:2059-3635
Navoximod modulates local HSV-1 replication to reshape tumor immune microenvironment for enhanced immunotherapy via an injectable hydrogel
Qiuyu Zhuang•Binyu Zhao•Zhiwen Lin•Yuzhi Liang•Qingfu Zhao等 13 人
Communications Biology
2023
•2023/6/9
•Vol.6 No.1 p.1-13
Oncolytic virotherapy can lead to tumor lysis and systemic anti-tumor immunity, but the therapeutic potential in humans is limited due to the impaired virus replication and the insufficient ability to overcome the immunosuppressive tumor microenvironment (TME). To solve the above problems, we identi...
Cancer immunotherapyCancer therapy
10.1038/S42003-023-04983-Z
ISSN:2399-3642
Prevention of cancer initiation by augmenting MHC-I antigen presentation via EZH2 inhibition
Wei Ding•Zihan Ding•Qinghong Zeng•Yan Qiu•Christopher R. Donnelly等 27 人
Oncogene
2025
•2025/11/24
•Vol.44 No.50 p.4878-4894
Early intervention of precancers is significant for improving cancer outcome. EZH2-mediated epigenetic modification was responsible for the immune escape of cancers; besides, tumor immune evasion is correlated with the impaired MHC-I antigen presentation machinery (APM). Oral potentially malignant d...
Cancer preventionPredictive markers
10.1038/S41388-025-03646-Z
ISSN:0950-9232
Single-cell meta-analysis of inflammatory bowel disease with scIBD
Hu Nie•Peilu Lin•Yu Zhang•Yihong Wan•Jiesheng Li等 7 人
Nature Computational Science
2023
•2023/6/15
•Vol.3 No.6 p.522-531
Understanding the heterogeneous intestinal microenvironment is critical to uncover the pathogenesis of inflammatory bowel disease (IBD). Recent advances in single-cell RNA sequencing (scRNA-seq) have identified certain cell types and genes that could contribute to IBD; however, a comprehensively int...
Computational platforms and environmentsData integrationInflammatory bowel diseaseRNA sequencing
10.1038/S43588-023-00464-9
ISSN:2662-8457
Epigenetic regulation of ACSL4 via H2A monoubiquitylation connects lipid metabolism to BAP1-mediated ferroptosis
Kexin Fan•Shuting Zhou•Yakun Ren•Jingwen Xiong•Hua Wang等 16 人
Cell Death & Differentiation
2025
•2025/11/27
•00 p.1-16
The tumor suppressor BRCA1-associated protein 1 (BAP1) encodes a nuclear deubiquitinase that specifically removes H2A monoubiquitination at Lys119 (H2Aub) and plays a crucial role in the epigenetic regulation of gene expression through cooperating with several transcriptional factors and chromatin-m...
Cancer metabolismEpigenetics
10.1038/S41418-025-01624-2
ISSN:1350-9047
Proteogenomic characterization of MiT family translocation renal cell carcinoma
Qu Yuanyuan•Wu Xiaohui•Anwaier Aihetaimujiang•Feng Jinwen•Xu Wenhao等 23 人
Nature Communications
2022
•2022/12/5
•Vol.13 No.1 p.1-18
Microphthalmia transcription factor (MiT) family translocation renal cell carcinoma (tRCC) is a rare type of kidney cancer, which is not well characterized. Here we show the comprehensive proteogenomic analysis of tRCC tumors and normal adjacent tissues to elucidate the molecular landscape of this d...
ProteomicsRenal cancerRenal cell carcinomaTumour heterogeneity
10.1038/S41467-022-34460-W
ISSN:2041-1723
Spatiotemporal transcriptome atlas of human embryos after gastrulation
Jiexue Pan•Yuejiao Li•Zhongliang Lin•Qing Lan•Ying Zhang等 55 人
Nature
2026
•2026/5/27
•00 p.1-11
The comprehensive spatiotemporal atlas of gene expression during early human embryonic development is critical for insights into embryogenesis1, organogenesis2 and disease origins3,4. Here, leveraging Stereo-seq technology, we generated spatial transcriptomic profiles across 77 sagittal sections of ...
EmbryogenesisOrganogenesisRNA sequencing
10.1038/S41586-026-10545-0
ISSN:0028-0836
GPR4 promotes immune exclusion in colon cancer through LOXL2-mediated extracellular matrix remodeling
Shuheng Bai•Min Chen•Xuan Wang•Ning Lan•Ruijie Meng等 13 人
Nature Communications
2025
•2025/12/24
0Immune exclusion is associated with adverse prognosis in tumors, and this phenomenon may be facilitated by a physical barrier constituted by the extracellular matrix (ECM). Hypoxia and acidity promote immune exclusion, however the detailed mechanism remains unclear. This study demonstrate that G-pro...
Cancer microenvironmentColon cancer
10.1038/S41467-025-67967-Z
ISSN:2041-1723
Individualized therapy guided by single-cell sequencing in anti-GABAAR encephalitis
Yaqing Shu•Yu Huang•Qihui Li•Huilu Li•Zhibin Li等 18 人
Translational Psychiatry
2025
•2025/3/8
•Vol.15 No.1 p.1-8
We presented a patient with refractory anti-GABAA-R encephalitis, and constructed libraries for single-cell sequencing from the patient’s peripheral blood mononuclear cells (PBMCs), cerebrospinal fluid cells, as well as four healthy volunteer’s PBMCs. A distinct group of monoclonal CD8+ T cells and ...
Clinical geneticsMolecular neuroscience
10.1038/S41398-025-03300-Y
ISSN:2158-3188
Multi-omic analysis of gallbladder cancer identifies distinct tumor microenvironments associated with disease progression
Tao Zhou•Yanhong Wu•Shuai Li•Xinyao Qiu•Erdong Liu等 21 人
Nature Genetics
2025
•2025/6/26
•00 p.1-15
Gallbladder carcinoma (GBC) is the most aggressive biliary tract cancer and is associated with a high mortality rate. Treatment of GBC faces therapeutic challenges owing to the elusive nature of in situ drivers within the local tumor microenvironment that drive its progression. Here, we created a si...
Cancer microenvironmentGall bladder cancer
10.1038/S41588-025-02236-9
ISSN:1061-4036
Remodeling the tumor-immune microenvironment by anti-CTLA4 blockade enhanced subsequent anti-PD-1 efficacy in advanced nasopharyngeal carcinoma
Yuxiang Ma•Huaqiang Zhou•Fan Luo•Yang Zhang•Changbin Zhu等 15 人
Npj Precision Oncology
2024
•2024/3/6
•Vol.8 No.1 p.1-11
Sequential immunotherapy has shown certain advantages in malignancy. Here, we aim to evaluate the efficacy of sequential anti-CTLA-4 and anti-PD-1 treatment for recurrent or metastatic nasopharyngeal carcinoma patients (R/M NPC). We retrospectively analysis 2 phase I trial of ipilimumab and camreliz...
Cancer microenvironmentHead and neck cancer
10.1038/S41698-024-00558-1
ISSN:2397-768X
Establishment and molecular characterisation of patient-derived organoids for primary central nervous system lymphoma
Shengjie Li•Jun Ren•Jianing Wu•Zuguang Xia•Yingzhu Li等 7 人
Leukemia
2025
•2025/3/18
•00 p.1-15
Primary central nervous system lymphoma (PCNSL) exhibits substantial intratumoural and intertumoural heterogeneity, complicating the development of effective treatment methods. Existing in vitro models fail to simulate the cellular and mutational diversity of native tumours and require prolonged gen...
B-cell lymphomaCancer models
10.1038/S41375-025-02562-1
ISSN:0887-6924
Whole-exome sequencing of alpha-fetoprotein producing gastric carcinoma reveals genomic profile and therapeutic targets
Jun Lu•Yongfeng Ding•Yanyan Chen•Junjie Jiang•Yiran Chen等 23 人
Nature Communications
2021
•2021/6/24
•Vol.12 No.1 p.1-13
Alpha-fetoprotein producing gastric carcinoma (AFPGC) is a rare and aggressive subtype of gastric cancer. However, little is known about the genomic features of this disease. We perform whole-exome sequencing analysis of AFPGC, and identify 34 significantly mutated genes. Somatic copy number alterat...
Cancer genomicsGastric cancerTargeted therapies
10.1038/S41467-021-24170-0
ISSN:2041-1723
The aldehyde dehydrogenase 2 rs671 variant enhances amyloid β pathology
Xia Wang•Jiayu Wang•Yashuang Chen•Xiaojing Qian•Shiqi Luo等 8 人
Nature Communications
2024
•2024/3/22
•Vol.15 No.1 p.1-21
In the ALDH2 rs671 variant, a guanine changes to an adenine, resulting in a dramatic decrease in the catalytic activity of the enzyme. Population-based data are contradictory about whether this variant increases the risk of Alzheimer’s disease. In East Asian populations, the prevalence of the ALDH2 ...
Alzheimer's diseaseDisease geneticsPost-translational modifications
10.1038/S41467-024-46899-0
ISSN:2041-1723
Genetic subtype-guided immunochemotherapy in relapsed and refractory diffuse large B cell lymphoma: a phase 2 investigator-initiated nonrandomized clinical trial (GUIDANCE-06)
Yi-Ge Shen•Qing Shi•Wei Tang•Peng-Peng Xu•Yi-Wen Cao等 10 人
Signal Transduction And Targeted Therapy
2025
•2025/7/26
•Vol.10 No.1 p.1-11
Improving the outcome of relapsed or refractory diffuse large B-cell lymphoma (R/R DLBCL) remained an unmet need. The aim of this single-center, phase 2 trial was to evaluate the efficacy and safety of genetic subtype-guided immunochemotherapy (R-ICE-X) in patients with R/R DLBCL: R-ICE-zanubrutinib...
Cancer geneticsCancer microenvironmentDrug development
10.1038/S41392-025-02316-6
ISSN:2059-3635
Multi-omics analysis reveals NNMT as a master metabolic regulator of metastasis in esophageal squamous cell carcinoma
Qi Huang•Haiming Chen•Dandan Yin•Jie Wang•Shaodong Wang等 15 人
Npj Precision Oncology
2024
•2024/1/30
•Vol.8 No.1 p.1-17
Metabolic reprogramming has been observed in cancer metastasis, whereas metabolic changes required for malignant cells during lymph node metastasis of esophageal squamous cell carcinoma (ESCC) are still poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq) of paired ESCC tumor...
Cancer epigeneticsCancer metabolismCancer microenvironment
10.1038/S41698-024-00509-W
ISSN:2397-768X
The ASH1L-AS1-ASH1L axis controls NME1-mediated activation of the RAS signaling in gastric cancer
Mengyu Xie•Long Zhang•Linyu Han•Linying Huang•Yizhou Huang等 7 人
Oncogene
2023
•2023/10/7
•00 p.1-11
Gastric cancer (GC) is one of the most leading cause of malignancies. However, the molecular mechanisms underlying stomach carcinogenesis remain incompletely understood. Dysregulated genetic and epigenetic alternations significantly contribute to GC development. Here, we report that ASH1L and its an...
Gastric cancerNon-coding RNAs
10.1038/S41388-023-02855-8
ISSN:0950-9232
STING synergizes with TOX suppressing HO-1 expression to trigger ferroptosis in tumor-infiltrating CD8+ T cell and immunotherapy resistance
Qian Zhu•Jun-bao Zhang•Cai-ping Nie•Xiu-feng Liu•Liang-ping Zhan等 13 人
Nature Communications
2026
•2026/2/9
•Vol.17 No.1 p.25430
CD8+ T cell abundance within the tumor microenvironment is a critical determinant of immunotherapy efficacy. Here we show that CD8⁺ T cells lacking STING or TOX display markedly improved antitumor activity, with enhanced tumor infiltration and elevated IFN-γ and granzyme B production. These STING or...
Cancer immunotherapyImmune cell death
10.1038/S41467-026-69350-Y
ISSN:2041-1723
Genomic and transcriptomic profiling of hepatoid adenocarcinoma of the stomach
Liu Ziyang•Wang Anqiang•Pu Yingying•Li Zhongwu•Xue Ruidong等 11 人
Oncogene
2021
•2021/7/30
•00 p.1-13
Hepatoid adenocarcinoma of the stomach (HAS), a rare subtype of gastric cancer (GC), has a low incidence but a high mortality rate. Little is known about the molecular features of HAS. Here we applied whole-exome sequencing (WES) on 58 tumours and the matched normal controls from 54 HAS patients, tr...
Cancer geneticsCancer genomicsCancer microenvironmentGastric cancerTumour heterogeneity
10.1038/S41388-021-01976-2
ISSN:0950-9232
Longitudinal analysis of retinal cell state transitions in RB1-deficient retinal organoids reveals the nascent cone precursors are the earliest cell-origin of human retinoblastoma
Ke Ye•Yuan Wang•Ping Xu•Bingbing Xie•Shijing Wu等 16 人
Cell Death & Disease
2026
•2026/1/14
•Vol.17 No.1 p.340
All cancers arise from the malignant transformation of normal cells, yet their cells-of-origin remain challenging to identify due to the inability to directly observe dynamic changes in human tumors. Retinoblastoma (Rb), a malignant intraocular cancer, serves as a well-established model for investig...
Eye cancerInduced pluripotent stem cells
10.1038/S41419-025-08191-X
ISSN:2041-4889
Mechanism exploration and model construction for small cell transformation in EGFR-mutant lung adenocarcinomas
Yan Li•Tongji Xie•Shouzheng Wang•Lin Yang•Xuezhi Hao等 11 人
Signal Transduction And Targeted Therapy
2024
•2024/10/2
•Vol.9 No.1 p.1-13
Small-cell lung cancer (SCLC) transformation accounts for 3–14% of resistance in EGFR-TKI relapsed lung adenocarcinomas (LUADs), with unknown molecular mechanisms and optimal treatment strategies. We performed transcriptomic analyses (including bulk and spatial transcriptomics) and multiplex immunof...
Lung cancerTranslational research
10.1038/S41392-024-01981-3
ISSN:2059-3635
TFAM is an autophagy receptor that limits inflammation by binding to cytoplasmic mitochondrial DNA
Hao Liu•Cien Zhen•Jianming Xie•Zhenhuan Luo•Lin Zeng等 27 人
Nature Cell Biology
2024
•2024/5/23
•00 p.1-14
When cells are stressed, DNA from energy-producing mitochondria can leak out and drive inflammatory immune responses if not cleared. Cells employ a quality control system called autophagy to specifically degrade damaged components. We discovered that mitochondrial transcription factor A (TFAM)—a pro...
MitochondriaMitophagy
10.1038/S41556-024-01419-6
ISSN:1465-7392
A fuzzy sequencer for rapid DNA fragment counting and genotyping
Wenxiong Zhou•Li Kang•Shuo Qiao•Haifeng Duan•Chenghong Yin等 23 人
Nature Biomedical Engineering
2025
•2025/7/2
•00 p.1-15
High-throughput sequencing technologies generate a vast number of DNA sequence reads simultaneously, which are subsequently analysed using the information contained within these fragmented reads. The assessment of sequencing technology relies on information efficiency, which measures the amount of i...
Chemical engineeringDNANext-generation sequencing
10.1038/S41551-025-01430-8
ISSN:2157-846X
Bifidobacterium boosts anti-PD-1 effectiveness through JAK pathway in hepatocellular carcinoma
Ran Huo•Quan-guo Xu•Yi-qing You•Yan-lin Chen•Guang-jian Su等 22 人
Npj Precision Oncology
2025
•2025/7/23
•Vol.9 No.1 p.1-15
Hepatocellular carcinoma (HCC) is a prevalent and deadly cancer. Gut microbiota affect tumor immunity and immunotherapy efficacy, but the exact mechanisms are unclear. A study compared gut microbiota in HCC patients and healthy controls (HC) using 16S rDNA analysis and metabolomics. It found higher ...
Cancer immunotherapyDrug development
10.1038/S41698-025-00960-3
ISSN:2397-768X
NDUFA4L2 regulates the progression and chemotherapy sensitivity of HNSCC by inhibiting PANoptosis
Jing-Jing Cui•Yang Yang•Jia-Hao Zhao•Yu-Jia Guo•Meng-Ran Zhao等 9 人
Npj Precision Oncology
2026
•2026/3/5
0Head and neck squamous cell carcinoma (HNSCC) represents a leading global malignancy among head and neck cancers. While chemotherapy serves as a standard adjuvant treatment, cisplatin resistance frequently compromises therapeutic outcomes. PANoptosis is an integrated inflammatory cell death pathway ...
CancerCell biologyDrug discoveryOncology
10.1038/S41698-026-01358-5
ISSN:2397-768X
ABLIM1, a novel ubiquitin E3 ligase, promotes growth and metastasis of colorectal cancer through targeting IĸBα ubiquitination and activating NF-ĸB signaling
Ying He•Qian Shi•Yuhang Ling•Huihui Guo•Yi Fei等 9 人
Cell Death & Differentiation
2024
•2024/1/16
•00 p.1-14
Actin-binding LIM protein 1 (ABLIM1), a member of the LIM-domain protein family, has been reported as a suppressor in several tumors whereas its role in colorectal cancer (CRC) remains unknown. In this study, we find that ABLIM1 is up-regulated in CRC patients and high levels of ABLIM1 predict short...
MetastasisOncogenesUbiquitin ligases
10.1038/S41418-024-01256-Y
ISSN:1350-9047
Whole-genome methylation profiling of extracellular vesicle DNA in gastric cancer identifies intercellular communication features
Bingqian Lin•Zhenna Jiao•Shouquan Dong•Weikai Yan•Jinting Jiang等 11 人
Nature Communications
2025
•2025/8/29
•Vol.16 No.1 p.1-12
Extracellular vesicles (EVs) are promising biomarkers for cancer diagnosis and prognosis due to their ability to carry specific biomolecular cargo, including DNA. However, the clinical utility of DNA methylation-based liquid biopsies using EV-DNA remains underexplored. The low quantity and relativel...
CancerDiagnostic markersMethylation analysis
10.1038/S41467-025-63435-W
ISSN:2041-1723
Integrative multi-omics and drug–response characterization of patient-derived prostate cancer primary cells
Wang Ziruoyu•Li Yanan•Zhao Wensi•Jiang Shuai•Huang Yuqi等 18 人
Signal Transduction And Targeted Therapy
2023
•2023/5/1
•Vol.8 No.1 p.1-16
Prostate cancer (PCa) is the second most prevalent malignancy in males across the world. A greater knowledge of the relationship between protein abundance and drug responses would benefit precision treatment for PCa. Herein, we establish 35 Chinese PCa primary cell models to capture specific charact...
BioinformaticsDrug screeningUrological cancer
10.1038/S41392-023-01393-9
ISSN:2059-3635
TSC22 domain family member 3 links natural killer cells to CD8+ T cell-mediated drug hypersensitivity
Lele Sun•Pengcheng Huai•Zhenzhen Wang•Qing Zhao•Yingjie Lin等 18 人
Signal Transduction And Targeted Therapy
2025
•2025/6/21
•Vol.10 No.1 p.1-14
Severe cutaneous adverse drug reactions (SCARs) are life-threatening diseases, which are associated with human leukocyte antigen (HLA) risk variants. However, the low positive predictive values of HLA variants suggest additional factors influence disease susceptibility. Using dapsone hypersensitivit...
Innate immunity
10.1038/S41392-025-02300-0
ISSN:2059-3635
ZFP42 maintains stemness and rhythmic transcription in human epidermal stem and progenitor cells via CRY1
Shuiying Gao•Hao Tan•Shuqia Xu•Zhaoyu Zhang•Yushuang Sun等 15 人
Communications Biology
2026
•2026/1/21
•Vol.9 No.1 p.2910
The role of circadian rhythm in regulating stemness in adult stem cells remains unclear. We investigated this in human epidermal stem and progenitor cells (EPSCs), finding that ~10% of expressed genes exhibit rhythmicity, with shared genes between fetal and adult EPSCs enriched in critical biologica...
Circadian rhythmsSkin stem cells
10.1038/S42003-026-09576-0
ISSN:2399-3642
Gefitinib (an EGFR tyrosine kinase inhibitor) plus anlotinib (an multikinase inhibitor) for untreated, EGFR-mutated, advanced non-small cell lung cancer (FL-ALTER): a multicenter phase III trial
Hua-Qiang Zhou•Ya-Xiong Zhang•Gang Chen•Qi-Tao Yu•Hua Zhang等 25 人
Signal Transduction And Targeted Therapy
2024
•2024/8/13
•Vol.9 No.1 p.1-12
Dual inhibition of vascular endothelial growth factor and epidermal growth factor receptor (EGFR) signaling pathways offers the prospect of improving the effectiveness of EFGR-targeted therapy. In this phase 3 study (ClinicalTrial.gov: NCT04028778), 315 patients with treatment-naïve, EGFR-mutated, a...
CancerOncology
10.1038/S41392-024-01927-9
ISSN:2059-3635
A single-cell transcriptome atlas of human euploid and aneuploid blastocysts
Shengpeng Wang•Lizhi Leng•Quanlei Wang•Yifan Gu•Jinlu Li等 23 人
Nature Genetics
2024
•2024/6/5
•00 p.1-14
Aneuploidy is frequently detected in early human embryos as a major cause of early pregnancy failure. However, how aneuploidy affects cellular function remains elusive. Here, we profiled the transcriptomes of 14,908 single cells from 203 human euploid and aneuploid blastocysts involving autosomal an...
Cell lineageInfertility
10.1038/S41588-024-01788-6
ISSN:1061-4036
Oncolytic virus VG161 in refractory hepatocellular carcinoma
Yinan Shen•Xueli Bai•Qi Zhang•Xingmei Liang•Xinyan Jin等 40 人
Nature
2025
•2025/3/19
•00 p.1-9
Hepatocellular carcinoma remains a life-threatening malignancy with limited therapeutic options following the failure of second-line treatments1,2. Oncolytic viruses selectively replicate in and lyse cancer cells, releasing neoantigens and stimulating systemic antitumour immunity3, offering a potent...
Drug developmentLiver cancer
10.1038/S41586-025-08717-5
ISSN:0028-0836
A novel engineered IL-21 receptor arms T-cell receptor-engineered T cells (TCR-T cells) against hepatocellular carcinoma
Wei Zhu•Zhiming Zhang•Jinzhang Chen•Xiaolan Chen•Lei Huang等 24 人
Signal Transduction And Targeted Therapy
2024
•2024/4/20
•Vol.9 No.1 p.1-16
Strategies to improve T cell therapy efficacy in solid tumors such as hepatocellular carcinoma (HCC) are urgently needed. The common cytokine receptor γ chain (γc) family cytokines such as IL-2, IL-7, IL-15 and IL-21 play fundamental roles in T cell development, differentiation and effector phases. ...
Drug developmentImmunotherapy
10.1038/S41392-024-01792-6
ISSN:2059-3635
Dynamic reorganisation of intratumoural bacterial florae during colorectal cancer progression
Minghao Li•Yang Li•Chen Li•Anhang Liu•Yang Liu等 13 人
British Journal Of Cancer
2026
•2026/3/6
•00 p.1-15
Colorectal cancer (CRC) exhibits distinct bacterial community compositions compared to healthy mucosae, which intimately correlate with CRC clinical outcomes. There is a lack of explanation for the inducements of microbiota remodelling. FISH experiments and 16S rRNA sequencing were conducted to dete...
Colorectal cancerMetagenomics
10.1038/S41416-026-03344-X
ISSN:0007-0920
The composition dynamics of transposable elements in human blastocysts
Jian Li•Ping Yuan•Guangwei Ma•Ying Liu•Qingxue Zhang等 7 人
Journal Of Human Genetics
2023
•2023/6/12
•00 p.1-8
Transposable elements (TEs) are mobile DNA sequences that can replicate themselves and play significant roles in embryo development and chromosomal structure remodeling. In this study, we investigated the variation of TEs in blastocysts with different parental genetic backgrounds. We analyzed the pr...
Developmental biologyPreclinical research
10.1038/S10038-023-01169-7
ISSN:1434-5161
Single-cell RNA-seq integrated with multi-omics reveals SERPINE2 as a target for metastasis in advanced renal cell carcinoma
Chen Wen-jin•Dong Ke-qin•Pan Xiu-wu•Gan Si-shun•Xu Da等 12 人
Cell Death & Disease
2023
•2023/1/16
•Vol.14 No.1 p.1-13
Tumor growth, metastasis and therapeutic response are believed to be regulated by the tumor and its microenvironment (TME) in advanced renal cell carcinoma (RCC). However, the mechanisms underlying genomic, transcriptomic and epigenetic alternations in RCC progression have not been completely define...
Cancer genomicsMolecular biologyPrognostic markersRenal cell carcinoma
10.1038/S41419-023-05566-W
ISSN:2041-4889
Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small-cell lung cancer
Yilv Yan•Dongqing Sun•Junjie Hu•Yue Chen•Liangdong Sun等 21 人
Nature Genetics
2024
•2024/12/10
•00 p.1-14
Although immune checkpoint blockade (ICB) therapies have shifted the treatment paradigm for non-small-cell lung cancer (NSCLC), many patients remain resistant. Here we characterize the tumor cell states and spatial cellular compositions of the NSCLC tumor microenvironment (TME) by analyzing single-c...
Non-small-cell lung cancerRNA sequencing
10.1038/S41588-024-01998-Y
ISSN:1061-4036
Vaginal microbiome and sexually-transmitted pathogens in Chinese reproductive-age women: a multicentre cross-sectional and longitudinal cohort study
Muxuan Chen•Cancan Qi•Wei Qing•Zuyi Zhou•Yingxuan Zhang等 10 人
Nature Communications
2025
•2025/11/14
•Vol.16 No.1 p.100020
Sexually transmitted infections (STIs) are associated with vaginal dysbiosis, and co-infections are common but understudied. In this study, 6217 reproductive-age women are recruited from 38 study centres across China at baseline and 2738 participants are followed up at 6 months. We profile the vagin...
Microbial communitiesInfectionPublic health
10.1038/S41467-025-64917-7
ISSN:2041-1723
The tumor-enriched small molecule gambogic amide suppresses glioma by targeting WDR1-dependent cytoskeleton remodeling
Jiaorong Qu•Bojun Qiu•Yuxin Zhang•Yan Hu•Zhixing Wang等 12 人
Signal Transduction And Targeted Therapy
2023
•2023/11/8
•Vol.8 No.1 p.1-15
Glioma is the most prevalent brain tumor, presenting with limited treatment options, while patients with malignant glioma and glioblastoma (GBM) have poor prognoses. The physical obstacle to drug delivery imposed by the blood‒brain barrier (BBB) and glioma stem cells (GSCs), which are widely recogni...
Cancer stem cellsCNS cancerDrug developmentTarget identification
10.1038/S41392-023-01666-3
ISSN:2059-3635
Integrative proteogenomic characterization of early esophageal cancer
Li Lingling•Jiang Dongxian•Zhang Qiao•Liu Hui•Xu Fujiang等 24 人
Nature Communications
2023
•2023/3/25
•Vol.14 No.1 p.1-28
Esophageal squamous cell carcinoma (ESCC) is malignant while the carcinogenesis is still unclear. Here, we perform a comprehensive multi-omics analysis of 786 trace-tumor-samples from 154 ESCC patients, covering 9 histopathological stages and 3 phases. Proteogenomics elucidates cancer-driving waves ...
Cancer genomicsOesophageal cancerOesophagusProteomics
10.1038/S41467-023-37440-W
ISSN:2041-1723
A body map of somatic mutagenesis in morphologically normal human tissues
Li Ruoyan•Di Lin•Li Jie•Fan Wenyi•Liu Yachen等 21 人
Nature
2021
•2021/8/25
•00 p.1-6
Somatic mutations that accumulate in normal tissues are associated with ageing and disease1,2. Here we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies of 9 organs from 5 donors. We found that somatic mutation accumulations and clonal expansions were widespr...
Cancer genomicsGenetic variationMutationPhylogenetics
10.1038/S41586-021-03836-1
ISSN:0028-0836
Neutrophil activation and clonal CAR-T re-expansion underpinning cytokine release syndrome during ciltacabtagene autoleucel therapy in multiple myeloma
Shuangshuang Yang•Jie Xu•Yuting Dai•Shiwei Jin•Yan Sun等 13 人
Nature Communications
2024
•2024/1/8
•Vol.15 No.1 p.1-16
Cytokine release syndrome (CRS) is the most common complication of chimeric antigen receptor redirected T cells (CAR-T) therapy. CAR-T toxicity management has been greatly improved, but CRS remains a prime safety concern. Here we follow serum cytokine levels and circulating immune cell transcriptome...
ImmunotherapyMyelomaNeutrophilsTranslational research
10.1038/S41467-023-44648-3
ISSN:2041-1723
PRC2 loss impairs small cell lung cancer tumorigenesis and enhances sensitivity to G9a/GLP inhibition
Jawahar Kopparam•Gayathri Chandrasekaran•Danielle Hulsman•Liesa-Marie Pilger•Karen Stevers等 12 人
Communications Biology
2026
•2026/2/21
•Vol.9 No.1 p.4690
Effective targeted therapies for small cell lung cancer (SCLC) remain a significant challenge. Targeting the epigenome to overcome immune evasion and chemoresistance represents a promising strategy to improve treatment outcomes. In this study, we explored the role of Polycomb repressive complex 2 (P...
Small-cell lung cancerTargeted therapies
10.1038/S42003-026-09677-W
ISSN:2399-3642
Multimodal AI model for early detection of hepatocellular carcinoma
Si-yu Jing•Xue-liang Li•Hong Wen•Jing-xuan Cai•Yong-qi Bei等 18 人
Npj Precision Oncology
2026
•2026/4/2
0Detection of early hepatocellular carcinoma (eHCC) is important for timely treatment and improved prognosis. However, it is challenging to distinguish eHCC from pre-malignant high-grade dysplastic nodules (HGDN). Here we developed an artificial intelligence (AI) derived computational framework to id...
Diagnostic markersGastrointestinal cancer
10.1038/S41698-026-01393-2
ISSN:2397-768X
The PLEKHA1-TACC2 fusion gene drives tumorigenesis via vascular mimicry formation in esophageal squamous-cell carcinoma
Ting Yang•Zhi-Rui Lin•Tian-Liang Xia•Shang-Xin Liu•Bo-Yu Yuan等 11 人
Cell Death & Differentiation
2025
•2025/7/5
•00 p.1-17
Despite advancements of diagnosis and multimodality therapies in esophageal squamous-cell carcinoma (ESCC), the survival is still unsatisfactory. Therefore, it is urgent to identify novel targets for efficient therapeutic strategies. Herein, we identify a fusion gene between PLEKHA1 and TACC2 genera...
Cancer geneticsTumour biomarkers
10.1038/S41418-025-01536-1
ISSN:1350-9047
Dynamic molecular atlas of cardiac fibrosis at single-cell resolution shows CD248 in cardiac fibroblasts orchestrates interactions with immune cells
Guohua Li•Cheng Ni•Jiacheng Wang•Feimu Zhang•Zaiyang Fu等 26 人
Nature Cardiovascular Research
2025
•2025/3/27
•00 p.1-17
Post-injury remodeling is a complex process involving temporal specific cellular interactions in the injured tissue where the resident fibroblasts play multiple roles. Here, we performed single-cell and spatial transcriptome analysis in human and mouse infarcted hearts to dissect the molecular basis...
Heart failureUbiquitylation
10.1038/S44161-025-00617-1
ISSN:2731-0590
JAZF1 safeguards human endometrial stromal cells survival and decidualization by repressing the transcription of G0S2
Yingyu Liang•Siying Lai•Lijun Huang•Yulian Li•Shanshan Zeng等 16 人
Communications Biology
2023
•2023/5/27
•Vol.6 No.1 p.1-17
Decidualization of human endometrial stromal cells (hESCs) is essential for the maintenance of pregnancy, which depends on the fine-tuned regulation of hESCs survival, and its perturbation contributes to pregnancy loss. However, the underlying mechanisms responsible for functional deficits in decidu...
ApoptosisDifferentiation
10.1038/S42003-023-04931-X
ISSN:2399-3642
Cerebrospinal fluid circulating tumor DNA profiling for risk stratification and matched treatment of central nervous system metastases
Mei-Mei Zheng•Qing Zhou•Hua-Jun Chen•Ben-Yuan Jiang•Li-Bo Tang等 30 人
Nature Medicine
2025
•2025/2/27
•00 p.1-10
Genomic profiling of central nervous system (CNS) metastases has the potential to guide treatments. In the present study, we included 584 patients with non-small-cell lung cancer and CNS metastases and performed a comprehensive analysis of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) with...
Prognostic markersTranslational research
10.1038/S41591-025-03538-5
ISSN:1078-8956
Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia
Xiaoyang Qiao•Jianxiang Shi•Hongen Xu•Kai Liu•Youwei Pu等 24 人
Communications Biology
2025
•2025/2/22
•Vol.8 No.1 p.1-13
The Central Plains Han Chinese (CPHC) is the typical agricultural population of East Asia. Investigating the genome of the CPHC is crucial to understanding the genetic structure and adaptation of the modern humans in East Asia. Here, we perform whole genome sequencing of 492 CPHC individuals and obt...
GenomePopulation genetics
10.1038/S42003-025-07760-2
ISSN:2399-3642
Platelet-derived exosomal LINC00183 facilitate colorectal cancer malignant progression driven by histone lactylation through stabilizing ENO1
Guoqing Su•Jinghang Qian•Yi Wang•Yu Zhu•Yanyan Chen等 17 人
Cell Death & Disease
2025
•2025/8/7
•Vol.16 No.1 p.1-18
Platelets play a critical role in tumor progression across various cancers. However, little is known about the molecular mechanisms and biological roles of exosomal long non-coding RNAs (lncRNAs) produced from platelets in colorectal cancer (CRC). Using RNA sequencing, we identified LINC00183 as the...
Cancer metabolismPost-translational modifications
10.1038/S41419-025-07914-4
ISSN:2041-4889
Single-cell landscape of immunological responses in patients with COVID-19
Ji-Yuan Zhang•Xiang-Ming Wang•Xudong Xing•Zhe Xu•Chao Zhang等 21 人
Nature Immunology
2020
•2020/8/12
•Vol.21 No.9 p.1107-1118
In coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the relationship between disease severity and the host immune response is not fully understood. Here we performed single-cell RNA sequencing in peripheral blood samples of 5 heal...
Antimicrobial responsesViral infection
10.1038/S41590-020-0762-X
ISSN:1529-2908
Building a Chinese pan-genome of 486 individuals
Li Qiuhui•Tian Shilin•Yan Bin•Liu Chi Man•Lam Tak-Wah等 7 人
Communications Biology
2021
•2021/8/30
•Vol.4 No.1 p.1-14
Pan-genome sequence analysis of human population ancestry is critical for expanding and better defining human genome sequence diversity. However, the amount of genetic variation still missing from current human reference sequences is still unknown. Here, we used 486 deep-sequenced Han Chinese genome...
BioinformaticsGenome assembly algorithms
10.1038/S42003-021-02556-6
ISSN:2399-3642
Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment
Luo Han•Xia Xuyang•Huang Li-Bin•An Hyunsu•Cao Minyuan等 32 人
Nature Communications
2022
•2022/11/4
•Vol.13 No.1 p.1-17
Cancer-associated fibroblasts (CAFs) are the predominant components of the tumor microenvironment (TME) and influence cancer hallmarks, but without systematic investigation on their ubiquitous characteristics across different cancer types. Here, we perform pan-cancer analysis on 226 samples across 1...
Cancer genomicsCancer microenvironmentTumour heterogeneity
10.1038/S41467-022-34395-2
ISSN:2041-1723
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
Clinically associated genomic landscape of pediatric non-Down Syndrome acute megakaryoblastic leukemia in Chinese patients
Kefei Wu•Hui Liu•Wenting Hu•Yuhan Liu•Wenyan Wu等 33 人
Leukemia
2025
•2025/8/11
•00 p.1-5
Acute myeloid leukaemiaCancer genomics
10.1038/S41375-025-02741-0
ISSN:0887-6924
Tumor-draining lymph nodes shape the tumor microenvironment through enrichment of tumor-reactive effector-exhausted CD8+ T cells
Deyang Kong•Lin Feng•Yu Sun•Huiru Zhang•Jialiang Fan等 17 人
Signal Transduction And Targeted Therapy
2026
•2026/7/3
•Vol.11 No.1 p.2730
Tumor-draining lymph nodes are central to anti-tumor immunity and influence the response to immunotherapy. Colorectal cancers with microsatellite instability and microsatellite stability differ substantially in tumor biology, prognosis and sensitivity to immune checkpoint blockade. However, the diff...
Cancer microenvironmentGastrointestinal cancer
10.1038/S41392-026-02858-3
ISSN:2059-3635
NNMT-mediated N6-methyladenosine modification of NR4A3 mRNA facilitates lymphatic metastasis of gastric adenocarcinoma
Xiaoya Zhao•Linsen Bao•Yun Qian•Shimeng Zhou•Chen Chen等 14 人
Oncogene
2025
•2025/6/16
•00 p.1-13
Lymph node (LN) metastasis is a common feature of gastric adenocarcinoma (GAC) and is closely associated with a poor prognosis. Our previous study highlighted the pivotal role of nicotinamide N-methyltransferase (NNMT) in driving GAC carcinogenesis and malignant progression, primarily through its re...
EpigeneticsPrognostic markers
10.1038/S41388-025-03475-0
ISSN:0950-9232
CXCR1+ neutrophil infiltration orchestrates response to third-generation EGFR-TKI in EGFR mutant non-small-cell lung cancer
Haowei Wang•Anwen Xiong•Xiaoxia Chen•Junhong Guo•Zhuoran Tang等 11 人
Signal Transduction And Targeted Therapy
2024
•2024/12/6
•Vol.9 No.1 p.1-15
Although third-generation Epidermal growth factor receptor—tyrosine kinase inhibitors (EGFR-TKI) is standard of care for patients with EGFR-mutant Non-small cell lung cancer (NSCLC), little is known about the predictors of response or resistance. Here, we integrated single-cell RNA (scRNA) sequencin...
Cancer microenvironmentLung cancerTumour biomarkers
10.1038/S41392-024-02045-2
ISSN:2059-3635
TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing
Yuchao Xia•Zijie Jin•Chengsheng Zhang•Linkun Ouyang•Yuhao Dong等 11 人
Nature Communications
2023
•2023/9/23
•Vol.14 No.1 p.1-12
Single-molecule Real-time Isoform Sequencing (Iso-seq) of transcriptomes by PacBio can generate very long and accurate reads, thus providing an ideal platform for full-length transcriptome analysis. We present an integrated computational toolkit named TAGET for Iso-seq full-length transcript data an...
Computational modelsSequence annotationSoftware
10.1038/S41467-023-41649-0
ISSN:2041-1723
Multidisciplinary analyses and ancient DNA reveal social inequality and mobility in the Central Plains during the Eastern Zhou period in China
Baoshuai Zhang•Jiajing Zheng•Lei Sun•Yuanyuan Zhang•Zhenlong Gao等 23 人
Nature Human Behaviour
2025
•2025/12/30
•00 p.1-17
The Eastern Zhou period (771–221 BC), characterized by social stratification, was marked by important inequality. Here the authors analyse 32 skeletons from Songzhuang Cemetery in Henan Province using sex-specific peptides, ancient DNA and isotopes to explore multidimensional inequality in sexes, di...
ArchaeologyBiological anthropologyGenetic variation
10.1038/S41562-025-02356-6
ISSN:2397-3374
Single-cell RNA sequencing reveals tumor heterogeneity in small cell neuroendocrine cervical carcinoma
Xuesong Xiang•Xiang Tao•Keqin Hua•Hua Jiang•Jingxin Ding
Communications Biology
2025
•2025/2/5
•Vol.8 No.1 p.1-15
Small cell neuroendocrine cervical carcinoma (SCNECC) is an aggressive gynecological malignancy with poor prognosis. The precision therapeutic strategies for SCNECC are severely limited by the complex tumor microenvironment. Here, we mapped the single-cell landscape of a total of six samples from ma...
Cancer genomicsCervical cancerTumour heterogeneity
10.1038/S42003-025-07605-Y
ISSN:2399-3642
Platelet-bioengineered hiPSC-sEVs achieve targeted repair of fibrotic sinoatrial node in preclinical SND models
Hanfeng Liu•Yangxi Zeng•Wei Fan•Xi Lan•Can Liu等 10 人
Nature Communications
2025
•2025/12/9
•Vol.16 No.1 p.109740
Sinus node dysfunction, a prevalent arrhythmia in aging populations, is characterized by fibrosis and loss of pacemaker activity, necessitating pacemaker implantation. Current therapies fail to reverse the underlying pathology. Small extracellular vesicles derived from human induced pluripotent stem...
ArrhythmiasInduced pluripotent stem cellsNanoparticles
10.1038/S41467-025-65936-0
ISSN:2041-1723
Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X
Yu Liu•Chunliang Li•Shuhong Shen•Xiaolong Chen•Karol Szlachta等 22 人
Nature Genetics
2020
•2020/7/6
•Vol.52 No.8 p.811-818
We developed cis-X, a computational method for discovering regulatory noncoding variants in cancer by integrating whole-genome and transcriptome sequencing data from a single cancer sample. cis-X first finds aberrantly cis-activated genes that exhibit allele-specific expression accompanied by an ele...
CancerComputational biology and bioinformaticsData miningLeukaemiaSoftware
10.1038/S41588-020-0659-5
ISSN:1061-4036
Accurate, scalable and cross-platform cell identification for high-resolution spatial transcriptomics
Dongqing Sun•Lele Zhang•Tong Han•Qiu Wu•Peng Zhang等 6 人
Nature Genetics
2026
•2026/5/20
•00 p.1-12
Recent advances in spatial transcriptomics (ST) have brought unprecedented insights into cellular diversity and cell–cell interactions within their spatial context. High-resolution ST techniques, including barcoding-based and imaging-based platforms, have achieved remarkable subcellular resolution. ...
Cancer microenvironmentGenome informaticsSoftware
10.1038/S41588-026-02610-1
ISSN:1061-4036
Single-cell transcriptomics reveals aberrant skin-resident cell populations and identifies fibroblasts as a determinant in rosacea
Mengting Chen•Li Yang•Peijie Zhou•Suoqin Jin•Zheng Wu等 21 人
Nature Communications
2024
•2024/10/9
•Vol.15 No.1 p.1-16
Rosacea is a chronic inflammatory skin disorder, whose underlying cellular and molecular mechanisms remain obscure. Here, we generate a single-cell atlas of facial skin from female rosacea patients and healthy individuals. Among keratinocytes, a subpopulation characterized by IFNγ-mediated barrier f...
Chronic inflammationInflammatory diseasesMechanisms of diseaseMolecular medicine
10.1038/S41467-024-52946-7
ISSN:2041-1723
A single-cell transcriptomic landscape of the lungs of patients with COVID-19
Wang Si•Yao Xiaohong•Ma Shuai•Ping Yifang•Fan Yanling等 43 人
Nature Cell Biology
2021
•2021/12/7
•00 p.1-15
The lung is the primary organ targeted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making respiratory failure a leading coronavirus disease 2019 (COVID-19)-related mortality. However, our cellular and molecular understanding of how SARS-CoV-2 infection drives lung pathology is l...
Innate immunitySARS-CoV-2Senescence
10.1038/S41556-021-00796-6
ISSN:1465-7392
The N6-methyladenosine-mediated cLMNB1 degrades FGFR4 to overcome osimertinib resistance in non-small cell lung cancer
Yuxian Qian•Hui Wang•Yipeng Feng•Yijian Zhang•Qianfan Hu等 12 人
Cell Death & Disease
2025
•2025/11/10
•Vol.16 No.1 p.8180
Osimertinib resistance is the main challenge in treating EGFR-mutant lung adenocarcinoma (LUAD). The role of N6-methyladenosine (m6A) modification of circular RNAs (circRNAs) in osimertinib-resistant LUAD remains largely unknown. We used MeRIP-seq and circRNA-seq to screen for potential circRNA cand...
Cancer therapeutic resistanceDrug deliveryNon-small-cell lung cancerRNA
10.1038/S41419-025-08124-8
ISSN:2041-4889
Single-cell and spatial dissection of precancerous lesions underlying the initiation process of oral squamous cell carcinoma
Sun Lulu•Kang Xindan•Wang Chong•Wang Rui•Yang Guizhu等 15 人
Cell Discovery
2023
•2023/3/13
•Vol.9 No.1 p.1-19
Precancerous lesions of the oral mucosa, especially those accompanied by moderate to severe dysplasia, contribute to the initiation of oral squamous cell carcinoma (OSCC). However, the cellular compositions and spatial organization of the precancerous stage and how these factors promote human OSCC i...
Cancer preventionOral cancerTranscriptomics
10.1038/S41421-023-00532-4
ISSN:2056-5968
Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project
Cong Pei-Kuan•Bai Wei-Yang•Li Jin-Chen•Yang Meng-Yuan•Khederzadeh Saber等 26 人
Nature Communications
2022
•2022/5/26
•Vol.13 No.1 p.1-15
We initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing (WGS) individuals and 5,841 high-density genotyping individuals, and identify 81.5 million SNPs and INDELs, of which 38.5% are absent in dbSNP Build 151. We provide a population-specific reference pa...
Genome informaticsNext-generation sequencingPopulation genetics
10.1038/S41467-022-30526-X
ISSN:2041-1723
Distinct immune signatures discriminate between asymptomatic and presymptomatic SARS-CoV-2pos subjects
Yu Shanhe•Di Caixia•Chen Shijun•Guo Mingquan•Yan Jiayang等 20 人
Cell Research
2021
•2021/9/24
•00 p.1-15
Increasing numbers of SARS-CoV-2-positive (SARS-CoV-2pos) subjects are detected at silent SARS-CoV-2 infection stage (SSIS). Yet, SSIS represents a poorly examined time-window wherein unknown immunity patterns may contribute to the fate determination towards persistently asymptomatic or overt diseas...
ImmunologyMechanisms of disease
10.1038/S41422-021-00562-1
ISSN:1001-0602
Single-cell analysis reveals transcriptomic features and therapeutic targets in primary pulmonary lymphoepithelioma-like carcinoma
Binghua Tan•Ke Xu•Yingcheng Lyu•Yicheng Liang•Ruihao Liang等 15 人
Communications Biology
2025
•2025/3/8
•Vol.8 No.1 p.1-14
Primary pulmonary lymphoepithelioma-like carcinoma (PPLELC) is a rare subtype of non-small-cell lung cancer. Duo to the current lack of precise targeted therapies, there is an urgent need to identify novel therapeutic targets. In this study, we perform single-nucleus transcriptome analysis on PPLELC...
Molecular medicineNon-small-cell lung cancerPrognostic markers
10.1038/S42003-025-07819-0
ISSN:2399-3642
M2 polarization of macrophage protects the lung cancer cells from cold atmospheric plasma via alleviating endoplasmic reticulum stress
Yue Feng•Shengjie Peng•Lele Zhao•Renyi Jiang•Chunhua Tan等 10 人
Cell Death Discovery
2025
•2025/10/27
•Vol.11 No.1 p.1-10
Although cold atmospheric plasma (CAP) has been proved to kill various kinds of tumor cells effectively, most previous studies were performed on the in vitro tumor cell model in the absence of tumor microenvironment (TME), resulting in limited insights to its clinical application. Here, we explored ...
ApoptosisCancer immunotherapy
10.1038/S41420-025-02775-4
ISSN:2058-7716
Cryo-EM structure of the human subcortical maternal complex and the associated discovery of infertility-associated variants
Pengliang Chi•Guojin Ou•Sibei Liu•Qianhong Ma•Yuechao Lu等 17 人
Nature Structural & Molecular Biology
2024
•2024/10/8
•00 p.1-10
The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluati...
Cryoelectron microscopyDevelopmental biologyDiseasesPhysiology
10.1038/S41594-024-01396-2
ISSN:1545-9993
Systematic decoding of functional enhancer connectomes and risk variants in human glioma
Jinfang Bi•Weipeng Mo•Man Liu•Yingjie Song•Qian Xiao等 20 人
Nature Cell Biology
2025
•2025/8/19
•00 p.1-10
Genetic and epigenetic variations contribute to the progression of glioma, but the mechanisms underlying these effects, particularly for enhancer-associated genetic variations in non-coding regions, still remain unclear. Here we performed high-throughput CRISPR interference screening to identify pro...
Cancer epigeneticsCNS cancerEpigenomics
10.1038/S41556-025-01737-3
ISSN:1465-7392
β1,4-galactosyltransferase III drives retinoblastoma invasion via activation of integrin-FAK axis
Junjie Tang•Jinmiao Li•Meng Wang•Yaoming Liu•Hetian Sun等 14 人
Cell Death & Disease
2026
•2026/3/23
•Vol.17 No.1 p.3360
Retinoblastoma (RB) is the most common primary intraocular malignancy in children, and its extraocular extension is closely linked to poor prognosis. However, the molecular drivers underlying local invasion remain incompletely defined. Here, we identify β‑1,4‑galactosyltransferase III (B4GALT3) as a...
Eye cancerPaediatric cancer
10.1038/S41419-026-08620-5
ISSN:2041-4889
CYFIP2 deficiency ameliorates renal interstitial fibrosis through attenuating tubular senescence in hypertensive nephropathy
Ming-chen Sun•Fu-wen Zuo•You-zhao Wang•Xiu-li Ren•Hong-shen Lu等 11 人
Acta Pharmacologica Sinica
2026
•2026/5/7
•00 p.1-15
Tubulointerstitial fibrosis is the central pathological feature of hypertensive nephropathy, with cellular senescence being a key driver. Therefore, identifying therapeutic targets in senescent renal tubular epithelial cells is clinically important. The cytoplasmic FMR1-interacting protein (CYFIP) f...
Biomedicine, generalPharmacology/ToxicologyMedical MicrobiologyImmunologyInternal MedicineVaccine
10.1038/S41401-026-01793-X
ISSN:1671-4083
NSUN2 mediated-aberrant 5-methylcytosine methylation regulates autophagy-related ferroptosis in oral squamous cell carcinoma progression
Yunyang Lu•Runze Li•Weidong Du•Jie Wu•Yi He等 12 人
Cell Death & Disease
2025
•2025/12/23
•Vol.16 No.1 p.9030
Oral squamous cell carcinoma (OSCC) is a common malignant tumor with high metastasis rates and poor prognosis. This study investigated the role of NOP2/Sun RNA methyltransferase family member 2 (NSUN2), a key 5-methylcytosine (m5C) methyltransferase, and m5C methylation in the progression of OSCC, p...
Cancer therapeutic resistanceMacroautophagyOral cancer
10.1038/S41419-025-08174-Y
ISSN:2041-4889
Tumor microenvironment delineates differential responders to trastuzumab emtansine in HER2-positive metastatic breast cancer patients previously treated with pyrotinib: an exploratory biomarker analysis of a phase II study (NJMU-BC02)
Hong Pan•Ji Wang•Yue Sun•Fanfan Li•Chang Sun等 14 人
Signal Transduction And Targeted Therapy
2025
•2025/9/29
•Vol.10 No.1 p.1-11
Trastuzumab emtansine (T-DM1) has been approved for the treatment of HER2-positive breast cancer. However, the efficacy of T-DM1 for patients after failure of pyrotinib and/or trastuzumab plus pertuzumab has not been clear. Additionally, no biomarker has been reported to predict the effect of T-DM1....
Breast cancerCancer microenvironmentPredictive markersTumour heterogeneityTumour immunology
10.1038/S41392-025-02409-2
ISSN:2059-3635
Single-cell chromatin accessibility and transcriptomic characterization of Behcet’s disease
Wen Shi•Jinguo Ye•Zhuoxing Shi•Caineng Pan•Qikai Zhang等 10 人
Communications Biology
2023
•2023/10/17
•Vol.6 No.1 p.1-17
Behect’s disease is a chronic vasculitis characterized by complex multi-organ immune aberrations. However, a comprehensive understanding of the gene-regulatory profile of peripheral autoimmunity and the diverse immune responses across distinct cell types in Behcet’s disease (BD) is still lacking. He...
Cell biologyDiseases
10.1038/S42003-023-05420-X
ISSN:2399-3642
Tumor-associated macrophage clusters linked to immunotherapy in a pan-cancer census
Chen Wei•Yijie Ma•Mengyu Wang•Siyi Wang•Wenyue Yu等 13 人
Npj Precision Oncology
2024
•2024/8/9
•Vol.8 No.1 p.1-20
Transcriptional heterogeneity of tumor-associated macrophages (TAMs) has been investigated in individual cancers, but the extent to which these states transcend tumor types and represent a general feature of cancer remains unclear. We performed pan-cancer single-cell RNA sequencing analysis across n...
Cancer microenvironmentTumour biomarkers
10.1038/S41698-024-00660-4
ISSN:2397-768X
VEGF-C maturation mediated by CircFOCAD-orchestrated CCBE1 and ADAM10 expression in nuclear-cytoplasmic synergy drives lymphatic metastasis
Daiyin Liu•Mingrui Pang•Yuanlong Li•Zhicong Liu•Yifan Bi等 16 人
Oncogene
2026
•2026/6/18
•00 p.1-16
Lymphangiogenesis is essential for tumor lymphatic metastasis, yet the molecular mechanisms governing the activation of its key cytokine, VEGF-C, remain unclear. Herein, we identified a circRNA, circFOCAD, through VEGF-C maturation-associated multiple transcription sequencing. CircFOCAD is overexpre...
Cancer microenvironmentEpigeneticsMetastasis
10.1038/S41388-026-03857-Y
ISSN:0950-9232
Pathogenic germline variants in Chinese pancreatic adenocarcinoma patients
Xiaoyi Yin•Hui Shen•Huan Wang•Qingchen Wang•Shan Zhang等 39 人
Nature Communications
2025
•2025/3/5
•Vol.16 No.1 p.1-20
Putting pancreatic adenocarcinoma (PAAD) screening into perspective for high-risk individuals could significantly reduce cancer morbidity and mortality. Previous studies have profiled somatic mutations in PAAD. In contrast, the prevalence of mutations in PAAD predisposition genes has not been define...
Cancer geneticsCancer genomicsPancreatic cancer
10.1038/S41467-025-57520-3
ISSN:2041-1723
Unraveling the genetic architecture of congenital vertebral malformation with reference to the developing spine
Sen Zhao•Hengqiang Zhao•Lina Zhao•Xi Cheng•Zhifa Zheng等 28 人
Nature Communications
2024
•2024/2/6
•Vol.15 No.1 p.1-9
Congenital vertebral malformation, affecting 0.13–0.50 per 1000 live births, has an immense locus heterogeneity and complex genetic architecture. In this study, we analyze exome/genome sequencing data from 873 probands with congenital vertebral malformation and 3794 control individuals. Clinical int...
DevelopmentDisease geneticsMedical genomics
10.1038/S41467-024-45442-5
ISSN:2041-1723
Whole-exome sequencing reveals novel genomic signatures and potential therapeutic targets during the progression of rectal neuroendocrine neoplasm
Shi Xu•Zhi Yong Zhai•Ping Zhou•Xiu Fen Xue•Zhao Yu Huang等 17 人
Cell Death & Disease
2024
•2024/11/15
•Vol.15 No.11 p.1-12
Rectal neuroendocrine neoplasms (rNENs) are among the most frequent gastrointestinal neuroendocrine neoplasms and pose a serious challenge for clinical management. The size of the primary neoplasm is considered to be the most important predictor of disease progression, but the genetic alterations th...
Genetics researchRectal cancer
10.1038/S41419-024-07232-1
ISSN:2041-4889
ALCAM is an entry factor for severe community acquired Pneumonia-associated Human adenovirus species B
Yusang Xie•Hong Mei•Wei Wang•Xiao Li•Pengfei Hu等 9 人
Nature Communications
2024
•2024/12/30
•Vol.15 No.1 p.1-13
Human adenovirus (HAdV) is a widely spread respiratory pathogen that can cause infections in multiple tissues and organs. Previous studies have established an association between HAdV species B (HAdV-B) infection and severe community-acquired pneumonia (SCAP). However, the connection between SCAP-as...
AdenovirusPathogensVirus–host interactions
10.1038/S41467-024-55261-3
ISSN:2041-1723
Integrated proteogenomic characterization of localized prostate cancer identifies biological insights and subtype-specific therapeutic strategies
Wei Ou•Xin-Xin Zhang•Bin Li•Ying Tuo•Ren-Xuan Lin等 15 人
Nature Communications
2025
•2025/4/3
•Vol.16 No.1 p.1-17
Localized prostate cancer (PCa) is highly variable in their response to therapies. Although a fraction of this heterogeneity can be explained by clinical factors or genomic and transcriptomic profiling, the proteomic-based profiling of aggressive PCa remains poorly understood. Here, we profiled the ...
Cancer genomicsCancer metabolismProstate cancer
10.1038/S41467-025-58569-W
ISSN:2041-1723
Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor
Hailiang Zhang•Lin Bai•Xin-Qiang Wu•Xi Tian•Jinwen Feng等 23 人
Nature Communications
2023
•2023/7/17
•Vol.14 No.1 p.1-21
The tyrosine kinase inhibitor (TKI) Sunitinib is one the therapies approved for advanced renal cell carcinoma. Here, we undertake proteogenomic profiling of 115 tumors from patients with clear cell renal cell carcinoma (ccRCC) undergoing Sunitinib treatment and reveal the molecular basis of differen...
Cancer genomicsCancer therapyProteomicsRenal cell carcinomaTumour heterogeneity
10.1038/S41467-023-39981-6
ISSN:2041-1723
Reinvigorating COTL1high NK cells via GITR signalling overcomes immune checkpoint blockade resistance in tsMHC-I-impaired tumours
Wenhua You•Chupeng Hu•Yuhan Zhang•Yedi Huang•Jianzhou Yuan等 20 人
Nature Cell Biology
2026
•2026/3/30
•00 p.1-15
Patients with impaired tumour-specific major histocompatibility complex class I (tsMHC-Iimpaired) often fail to respond to immune checkpoint blockade (ICB), presenting a major clinical challenge. However, through our multicentre investigation, we observed that a subset of patients with tsMHC-Iimpair...
Cancer immunotherapyCancer microenvironmentInnate immune cellsTumour immunology
10.1038/S41556-026-01925-9
ISSN:1465-7392
Metagenomic discovery of novel CRISPR-Cas13 systems
Hu Yanping•Chen Yangcan•Xu Jing•Wang Xinge•Luo Shengqiu等 8 人
Cell Discovery
2022
•2022/10/11
•Vol.8 No.1 p.1-4
BioinformaticsCell biology
10.1038/S41421-022-00464-5
ISSN:2056-5968
EGR4 transcriptionally upregulates GDF15 to promote gastric cancer metastasis
Weiwei Liu•Yanyan Li•Lixin Liang•Lisheng Zheng•Rui Zeng等 9 人
Cell Death & Disease
2025
•2025/11/7
•Vol.16 No.1 p.1-13
Gastric cancer (GC) metastasis remains a major cause of poor prognosis, yet its molecular drivers are poorly understood. Here, we integrated single-cell RNA sequencing (scRNA-seq) of primary tumors and matched metastatic lymph nodes from six GC patients to identify a metastatic epithelial subpopulat...
Gastric cancerOncogenesTumour immunology
10.1038/S41419-025-08095-W
ISSN:2041-4889
Gut microbiota-derived metabolite isovalerylcarnitine modulates salt sensitivity of blood pressure and incident hypertension: a multicenter dietary salt intervention trial
Zhennan Lin•Shujie Li•Mengyao Liu•Jianxin Li•Fangchao Liu等 23 人
Nature Communications
2025
•2025/12/26
0This study aims to investigate the roles of gut microbiota and plasma metabolites in salt sensitivity (SS) of blood pressure (SSBP) and hypertension. A 23-day, multicenter, dietary salt intervention trial (the MetaSalt study) recruited 528 participants who underwent a baseline observation, low-salt,...
EpidemiologyHypertensionMetabolic disordersPredictive markersRisk factors
10.1038/S41467-025-67513-X
ISSN:2041-1723
Exploring PDE5A upregulation in bipolar disorder: insights from single-nucleus RNA sequencing of human basal ganglia
Zhixin Bai•Peilong Li•Xu Gao•Gaoyu Zu•Andrew Jiang等 19 人
Translational Psychiatry
2024
•2024/12/18
•Vol.14 No.1 p.1-19
Basal ganglia is proposed to mediate symptoms underlying bipolar disorder (BD). To understand the cell type-specific gene expression and network changes of BD basal ganglia, we performed single-nucleus RNA sequencing of 30,752 nuclei from caudate, putamen, globus pallidus, and substantia nigra of co...
Bipolar disorderMolecular neuroscience
10.1038/S41398-024-03202-5
ISSN:2158-3188
Single-cell multi-omics analysis of human testicular germ cell tumor reveals its molecular features and microenvironment
Xiaojian Lu•Yanwei Luo•Xichen Nie•Bailing Zhang•Xiaoyan Wang等 14 人
Nature Communications
2023
•2023/12/20
•Vol.14 No.1 p.1-17
Seminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we perform a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examina...
Cancer genomicsCancer microenvironmentTesticular cancer
10.1038/S41467-023-44305-9
ISSN:2041-1723
Phylogenetic evidence reveals early Kra-Dai divergence and dispersal in the late Holocene
Yuxin Tao•Yuancheng Wei•Jiaqi Ge•Yan Pan•Wenmin Wang等 12 人
Nature Communications
2023
•2023/10/30
•Vol.14 No.1 p.1-10
Studying language evolution brings a crucial perspective to bear on questions of human prehistory. As the most linguistically diverse region on earth, East and Southeast Asia have witnessed extensive sociocultural and ethnic contacts among different language communities. Especially, the Kra-Dai lang...
AnthropologyCultural evolutionEvolution of languagePhylogenetics
10.1038/S41467-023-42761-X
ISSN:2041-1723
A phase 1b/2 study of first-line anti-PD-L1/ TGF-βRII fusion protein SHR-1701 combined with nab-paclitaxel and gemcitabine for advanced pancreatic ductal adenocarcinoma
Ran Xue•Miaoyan Wei•Jiajia Yuan•Zhihua Li•Yuhong Zhou等 11 人
Signal Transduction And Targeted Therapy
2025
•2025/12/20
•Vol.10 No.1 p.4150
Nab-paclitaxel plus gemcitabine (AG) is the standard first-line chemotherapy for advanced or metastatic pancreatic ductal adenocarcinoma and has limited efficacy. This phase 1b/2 study aimed to evaluate SHR-1701 (an anti-PD-L1/TGF-βRII fusion protein) plus AG in this population (NCT04624217). In pha...
Gastrointestinal cancerPrognostic markers
10.1038/S41392-025-02530-2
ISSN:2059-3635
Metabolism archetype cancer cells induce protumor TREM2+ macrophages via oxLDL-mediated metabolic interplay in hepatocellular carcinoma
Tianhao Chu•Guiqi Zhu•Zheng Tang•Weifeng Qu•Rui Yang等 22 人
Nature Communications
2025
•2025/7/23
•Vol.16 No.1 p.1-25
The functional programs adopted by cancer cells and their impact on the tumor microenvironment are complex and remain unclear. Here, we identify three distinct single-cell archetypes (i.e. metabolism, stemness and inflammation) in hepatocellular carcinoma (HCC) cells, each exhibiting unique spatial ...
Cancer microenvironmentCytotoxic T cellsHepatocellular carcinomaMonocytes and macrophagesTumour immunology
10.1038/S41467-025-62132-Y
ISSN:2041-1723
Glycolysis inhibition induces anti-tumor central memory CD8+T cell differentiation upon combination with microwave ablation therapy
Xinyu Tang•Xinrui Mao•Peiwen Ling•Muxin Yu•Hua Pan等 16 人
Nature Communications
2024
•2024/5/31
•Vol.15 No.1 p.1-20
Minimally invasive thermal therapy is a successful alternative treatment to surgery in solid tumors with high complete ablation rates, however, tumor recurrence remains a concern. Central memory CD8+ T cells (TCM) play important roles in protection from chronic infection and cancer. Here we find, by...
Breast cancerCancer immunotherapyImmunological memoryTumour immunology
10.1038/S41467-024-49059-6
ISSN:2041-1723
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
Stiff matrix-induced KRTAP2-3 expression suppresses ciliogenesis via actin tension-driven chromatin remodeling
Xiying Chen•Li Yi•Guangsong Xie•Hao Jin•Feng Yang等 17 人
Cell Death & Disease
2026
•2026/4/2
0Primary cilia are sensory organelles that project from the cell surface and play vital roles in cell signaling pathways essential for development and homeostasis. However, the mechanotransduction pathways through which cells perceive and respond to matrix rigidity to regulate ciliogenesis remain poo...
Cell biologyCytoskeleton
10.1038/S41419-026-08678-1
ISSN:2041-4889
Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC
Yu Dong•Wenjiao Xia•Zitong Yang•Liangliang Ren•Hongru Wang等 25 人
Npj Digital Medicine
2026
•2026/1/6
•Vol.9 No.1 p.850
Clear cell renal cell carcinoma (ccRCC) is an aggressive malignancy associated with single-nucleotide variants in VHL, PBRM1, and SETD2. However, the role of structural variation (SV)—which have broader genomic impacts—and 3D genome architecture in ccRCC remains inadequately understood. Here, we rep...
CancerComputational biology and bioinformaticsGeneticsOncology
10.1038/S41746-025-02186-W
ISSN:2398-6352
Multiomics approach reveals the ubiquitination-specific processes hijacked by SARS-CoV-2
Xu Gang•Wu Yezi•Xiao Tongyang•Qi Furong•Fan Lujie等 12 人
Signal Transduction And Targeted Therapy
2022
•2022/9/7
•Vol.7 No.1 p.1-13
The Coronavirus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a global pandemic that seriously threatens health and socioeconomic development, but the existed antiviral drugs and vaccines still cannot yet halt the spread of the epidemic. Therefore,...
Infectious diseases
10.1038/S41392-022-01156-Y
ISSN:2059-3635
Clinical and genomic features of Lynch syndrome differ by tumor site and disease spectrum
Shisen Li•Ningning Luo•Gaoxin Jin•Tiantian Han•Xiangyu Yin等 8 人
Nature Communications
2025
•2025/11/19
•Vol.16 No.1 p.101790
Lynch Syndrome (LS) carriers occasionally develop central nervous system (CNS) malignancies or tumors in organs not traditionally linked to the syndrome. These tumors are poorly characterized in the literature, and there is no sufficient consensus on guidelines and management recommendations for the...
Cancer geneticsCancer genomics
10.1038/S41467-025-65164-6
ISSN:2041-1723
FSP1 inhibition enhances olaparib sensitivity in BRCA-proficient ovarian cancer patients via a nonferroptosis mechanism
Huixian Miao•Huangyang Meng•Yashuang Zhang•Tian Chen•Lin Zhang等 6 人
Cell Death & Differentiation
2024
•2024/2/19
•00 p.1-14
Poly ADP-ribose polymerase inhibitors (PARPis) exhibit promising efficacy in patients with BRCA mutations or homologous repair deficiency (HRD) in ovarian cancer (OC). However, less than 40% of patients have HRD, it is vital to expand the indications for PARPis in BRCA-proficient patients. Ferr...
Cancer geneticsGene expressionGene regulationTumour biomarkersTumour-suppressor proteins
10.1038/S41418-024-01263-Z
ISSN:1350-9047
Perioperative tislelizumab plus chemotherapy for locally advanced gastroesophageal junction adenocarcinoma (NEOSUMMIT-03): a prospective, nonrandomized, open-label, phase 2 trial
Run-Cong Nie•Shu-Qiang Yuan•Ya Ding•Yong-Ming Chen•Yuan-Fang Li等 23 人
Signal Transduction And Targeted Therapy
2025
•2025/2/5
•Vol.10 No.1 p.1-9
This prospective, nonrandomized, open-label phase 2 trial (Chinese Clinical Trial Registry, ChiCTR2200061906) aimed to evaluate the effectiveness of adding the PD-1 antibody tislelizumab to perioperative chemotherapy in patients with locally advanced gastroesophageal junction adenocarcinoma (GEJA). ...
Drug developmentGastrointestinal cancer
10.1038/S41392-025-02160-8
ISSN:2059-3635
ACO2 deficiency increases vulnerability to Parkinson’s disease via dysregulating mitochondrial function and histone acetylation-mediated transcription of autophagy genes
Junge Zhu•Fanxi Xu•Hong Lai•Huiyao Yuan•Xu-Ying Li等 9 人
Communications Biology
2023
•2023/11/25
•Vol.6 No.1 p.1-17
Parkinson’s disease (PD) is characterized by α-synuclein aggregation in dopaminergic (DA) neurons, which are sensitive to oxidative stress. Mitochondria aconitase 2 (ACO2) is an essential enzyme in the tricarboxylic acid cycle that orchestrates mitochondrial and autophagic functions to energy metabo...
Cell death in the nervous systemParkinson's disease
10.1038/S42003-023-05570-Y
ISSN:2399-3642
Single-cell transcriptomics identifies PDGFRA+ progenitors orchestrating angiogenesis and periodontal tissue regeneration
Jianing Liu•Junxi He•Ziqi Zhang•Lu Liu•Yuan Cao等 24 人
International Journal Of Oral Science
2025
•2025/7/24
•Vol.17 No.1 p.1-15
Periodontal bone defects, primarily caused by periodontitis, are highly prevalent in clinical settings and manifest as bone fenestration, dehiscence, or attachment loss, presenting a significant challenge to oral health. In regenerative medicine, harnessing developmental principles for tissue repair...
Mesenchymal stem cellsRegeneration
10.1038/S41368-025-00384-6
ISSN:2049-3169
An integrated map of fibroblastic populations in human colon mucosa and cancer tissues
Li Siying•Lu Ran•Shu Linjuan•Chen Yulin•Zhao Jin等 14 人
Communications Biology
2022
•2022/12/3
•Vol.5 No.1 p.1-14
Fibroblasts and myofibroblasts are major mesenchymal cells in the lamina propria of colon mucosa and in colon cancer tissues. Detailed insight into the highly specific populations of fibroblasts and myofibroblasts is required to understand the integrity and homeostasis of human colon mucosa and colo...
Cancer microenvironmentCell biologyColorectal cancer
10.1038/S42003-022-04298-5
ISSN:2399-3642
Epstein-Barr virus drives nasopharyngeal carcinoma metastasis via RNA m5C modification of ICAM-1 mediated by NSUN2 and YBX3
Xiu-Zhi Wang•Jia-Xin Jiang•Yi-Qi Li•Yang Liu•Shuang-Yan Ye等 12 人
Cell Death & Differentiation
2026
•2026/3/18
•00 p.1-12
Epstein-Barr virus (EBV) is a critical epigenetic regulator in nasopharyngeal carcinoma (NPC) pathogenesis, primarily through well-established mechanisms involving DNA methylation and histone modifications. However, the contribution of RNA modifications, especially RNA 5-methylcytosine (m5C), to EBV...
Cancer geneticsMetastasis
10.1038/S41418-026-01719-4
ISSN:1350-9047
Evolutionary route of nasopharyngeal carcinoma metastasis and its clinical significance
Lin Mei•Zhang Xiao-Long•You Rui•Liu You-Ping•Cai Hong-Min等 34 人
Nature Communications
2023
•2023/2/4
•Vol.14 No.1 p.1-21
It is critical to understand factors associated with nasopharyngeal carcinoma (NPC) metastasis. To track the evolutionary route of metastasis, here we perform an integrative genomic analysis of 163 matched blood and primary, regional lymph node metastasis and distant metastasis tumour samples, combi...
Cancer genomicsCancer therapeutic resistanceHead and neck cancerMetastasisTumour heterogeneity
10.1038/S41467-023-35995-2
ISSN:2041-1723
Dual targeting PD-L1 and 4-1BB to overcome dendritic cell-mediated lenalidomide resistance in follicular lymphoma
Zhong Zheng•Jian-Biao Wang•Rui Sun•Nan Wang•Xiang-Qin Weng等 15 人
Signal Transduction And Targeted Therapy
2025
•2025/1/20
•Vol.10 No.1 p.1-13
Immunomodulatory agent lenalidomide is effective in treating follicular lymphoma (FL). We conducted the first trial of immunotherapy rituximab plus lenalidomide in newly diagnosed FL in China (NCT03715309). One-hundred and fifteen patients were enrolled and treated with rituximab 375 mg/m2 intraveno...
Cancer microenvironmentCancer therapy
10.1038/S41392-024-02105-7
ISSN:2059-3635
Hypoxia-driven remodeling of SELENOP+ macrophages shapes T cell dynamics and promotes ovarian cancer metastasis
Qing Liu•Chenzhao Feng•Tianhao Wu•Siyang Zhang•Xinyi Wang等 17 人
Nature Communications
2026
•2026/1/12
•Vol.17 No.1 p.10970
High-grade serous ovarian cancer (HGSOC) is characterized by extensive transcoelomic dissemination and the accumulation of ascites. However, how site-specific tumor microenvironment (TME) drives progression remains unknown. Here we show the co-occurrence and spatial co-localization of SELENOP+ macro...
Cancer microenvironmentData miningMetastasisOvarian cancerTumour heterogeneity
10.1038/S41467-025-67859-2
ISSN:2041-1723
The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing
Gang Xu•Furong Qi•Hanjie Li•Qianting Yang•Haiyan Wang等 13 人
Cell Discovery
2020
•2020/10/20
•Vol.6 No.1 p.1-14
Understanding the mechanism that leads to immune dysfunction in severe coronavirus disease 2019 (COVID-19) is crucial for the development of effective treatment. Here, using single-cell RNA sequencing, we characterized the peripheral blood mononuclear cells (PBMCs) from uninfected controls and COVID...
BioinformaticsImmunology
10.1038/S41421-020-00225-2
ISSN:2056-5968
Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution
Yang Liu•Shuai He•Xi-Liang Wang•Wan Peng•Qiu-Yan Chen等 21 人
Nature Communications
2021
•2021/2/2
•Vol.12 No.1 p.1-18
The heterogeneous nature of tumour microenvironment (TME) underlying diverse treatment responses remains unclear in nasopharyngeal carcinoma (NPC). Here, we profile 176,447 cells from 10 NPC tumour-blood pairs, using single-cell transcriptome coupled with T cell receptor sequencing. Our analyses rev...
Cancer microenvironmentHead and neck cancerTumour heterogeneityTumour immunology
10.1038/S41467-021-21043-4
ISSN:2041-1723
Genomic landscape and molecular subtypes of primary central nervous system lymphoma
Shengjie Li•Danhui Li•Zuguang Xia•Jianing Wu•Jun Ren等 11 人
Blood Cancer Journal
2025
•2025/11/26
•Vol.16 No.1 p.80
The genetic landscape and molecular subtypes of primary central nervous system lymphoma (PCNSL) remain inadequately characterized, presenting a major obstacle to the development of effective therapeutic strategies. We conducted a genomic study of 176 PCNSLs from five tertiary centers with long-term ...
B-cell lymphomaCancer genomics
10.1038/S41408-025-01421-7
ISSN:2044-5385
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
CRISPR screens reveal convergent targeting strategies against evolutionarily distinct chemoresistance in cancer
Chunge Zhong•Wen-Jie Jiang•Yingjia Yao•Zexu Li•You Li等 35 人
Nature Communications
2024
•2024/6/29
•Vol.15 No.1 p.1-21
Resistance to chemotherapy has been a major hurdle that limits therapeutic benefits for many types of cancer. Here we systematically identify genetic drivers underlying chemoresistance by performing 30 genome-scale CRISPR knockout screens for seven chemotherapeutic agents in multiple cancer cells. C...
Cancer geneticsCancer genomicsMechanism of action
10.1038/S41467-024-49673-4
ISSN:2041-1723
Phase 1 pilot study for hemophilia-A: AAV8 vector with prophylactic tacrolimus-glucocorticoid achieves therapeutic FVIII activity
Wei Liu•Xiaolei Pei•Tenghui Yu•Bingqi Xu•Xinyue Dai等 17 人
Signal Transduction And Targeted Therapy
2026
•2026/3/11
•Vol.11 No.1 p.880
This prospective phase 1 pilot study evaluated the safety and efficacy of GS001, an adeno-associated virus serotype 8 (AAV8)-based vector encoding B-domain–deleted factor VIII with exploratory assessment of prophylactic immunosuppression. Twelve adult severe hemophilia A participants were enrolled. ...
Clinical trialsHaematological diseases
10.1038/S41392-026-02599-3
ISSN:2059-3635
Sliding-attention transformer neural architecture for predicting T cell receptor–antigen–human leucocyte antigen binding
Ziyan Feng•Jingyang Chen•Youlong Hai•Xuelian Pang•Kun Zheng等 16 人
Nature Machine Intelligence
2024
•2024/9/27
•00 p.1-15
Neoantigens are promising targets for immunotherapy by eliciting immune response and removing cancer cells with high specificity, low toxicity and ease of personalization. However, identifying effective neoantigens remains difficult because of the complex interactions among T cell receptors, antigen...
Computational biology and bioinformaticsImmunology
10.1038/S42256-024-00901-Y
ISSN:2522-5839
Real-time and programmable transcriptome sequencing with PROFIT-seq
Jinyang Zhang•Lingling Hou•Lianjun Ma•Zhengyi Cai•Shujun Ye等 9 人
Nature Cell Biology
2024
•2024/10/23
•00 p.1-12
The high diversity and complexity of the eukaryotic transcriptome make it difficult to effectively detect specific transcripts of interest. Current targeted RNA sequencing methods often require complex pre-sequencing enrichment steps, which can compromise the comprehensive characterization of the en...
Computational biology and bioinformaticsGene expression analysis
10.1038/S41556-024-01537-1
ISSN:1465-7392
A single-cell transcriptomic atlas reveals senescence and inflammation in the post-tuberculosis human lung
Guoqiang Sun•Kuan Li•Jiale Ping•Liyun Zhao•Chao Cui等 25 人
Nature Microbiology
2025
•2025/7/14
•00 p.1-19
Patients with a history of Mycobacterium tuberculosis infection often suffer from irreversible and progressive pulmonary damage, yet the underlying mechanisms are not fully understood. Here we conducted single-cell transcriptomic analysis of human lung tissues including 19 post-tuberculosis lung tis...
Cell biologyInfectionTuberculosis
10.1038/S41564-025-02050-3
ISSN:2058-5276
m6A demethylation of FOSL1 mRNA protects hepatoma cells against necrosis under glucose deprivation
Chun-Rui Wang•Jun-Hua Gong•Zhi-Bo Zhao•Qian Zhu•Bian Shu等 12 人
Cell Death & Differentiation
2024
•2024/5/18
•00 p.1-15
Stress-adaptive mechanisms enabling cancer cells to survive under glucose deprivation remain elusive. N6-methyladenosine (m6A) modification plays important roles in determining cancer cell fate and cellular stress response to nutrient deficiency. However, whether m6A modification functions in the re...
CancerEpigenetics
10.1038/S41418-024-01308-3
ISSN:1350-9047
Lenalidomide-induced pure red cell aplasia is associated with elevated expression of MHC-I molecules on erythrocytes
Qi Hu•Yang Liu•Qiuyu Yue•Shuo Zhou•Xianghong Jin等 11 人
Nature Communications
2024
•2024/11/22
•Vol.15 No.1 p.1-13
The RVd therapy, combining lenalidomide, bortezomib, and dexamethasone, is a mainstay treatment for multiple myeloma. A multiple myeloma patient developed pure red cell aplasia (PRCA) following RVd treatment, despite the absence of common PRCA triggers. In vitro analyses reveal lenalidomide as a piv...
Cytotoxic T cellsGene regulation in immune cellsHaematological diseasesMHC class IMolecular medicine
10.1038/S41467-024-54571-W
ISSN:2041-1723
The long-term effectiveness and mechanism of oncolytic virotherapy combined with anti-PD-L1 antibody in colorectal cancer patient
Hangyu Zhang•Yiqing Ren•Feiyu Wang•Xiaoxuan Tu•Zhou Tong等 12 人
Cancer Gene Therapy
2024
•2024/7/27
•00 p.1-15
Colorectal cancer (CRC) is known to be resistant to immunotherapy. In our phase-I clinical trial, one patient achieved a 313-day prolonged response during the combined treatment of oncolytic virotherapy and immunotherapy. To gain a deeper understanding of the potential molecular mechanisms, we perfo...
Colorectal cancerDrug development
10.1038/S41417-024-00807-2
ISSN:0929-1903
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
DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing
Peng Ni•Fan Nie•Zeyu Zhong•Jinrui Xu•Neng Huang等 13 人
Nature Communications
2023
•2023/7/8
•Vol.14 No.1 p.1-13
Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS ar...
Computational biology and bioinformaticsComputational modelsComputational platforms and environmentsData processingEpigenomics
10.1038/S41467-023-39784-9
ISSN:2041-1723
Defining heterogeneity in core regulatory circuitry reveals HOXB3 condensation as a potential target in glioblastoma
Chuanxia Zhang•Yijing He•Xiudan Zhan•Jiaming Yu•Shao Xu等 13 人
Nature Cell Biology
2025
•2025/9/30
•00 p.1-15
Glioblastoma (GBM) exhibits marked heterogeneity, yet therapeutic strategies effectively targeting this variability remain inadequately developed. Here we employed single-cell CUT&Tag analysis to investigate H3K27ac modifications, uncovering pronounced heterogeneity within the core regulatory ci...
Cancer epigeneticsCancer immunotherapyCNS cancer
10.1038/S41556-025-01758-Y
ISSN:1465-7392
Maternal factor OTX2 regulates human embryonic genome activation and early development
Qiuyan Wang•Chuanxin Zhang•Yanna Dang•Jiaqi Sun•Zhuoning Zou等 16 人
Nature Genetics
2025
•2025/10/27
•00 p.1-13
Transcription factors (TFs) are instrumental in kickstarting embryonic genome activation (EGA) in many species, yet their regulatory roles in human embryos remain poorly understood. Here, we show that OTX2, a maternally provided PRD-like homeobox TF, is required for proper human EGA and early develo...
DNA sequencingEmbryogenesisGene regulationTranscriptomics
10.1038/S41588-025-02350-8
ISSN:1061-4036
Single-cell spatial transcriptomics of tertiary lymphoid organ-like structures in human atherosclerotic plaques
Zhichao Lai•Deqiang Kong•Qingsong Li•Yue Wang•Kang Li等 35 人
Nature Cardiovascular Research
2025
•2025/4/28
•00 p.1-20
Tertiary lymphoid organs have been identified in the arterial adventitia in both mouse models of atherosclerosis and patients with atherosclerosis, yet their role in the disease remains insufficiently explored. Here we present a spatially resolved single-cell transcriptome atlas of human atheroscler...
AtherosclerosisCarotid artery diseaseGene expression analysisLymphangiogenesis
10.1038/S44161-025-00639-9
ISSN:2731-0590
Purine salvage–associated metabolites as biomarkers for early diagnosis of esophageal squamous cell carcinoma: a diagnostic model–based study
Yawen Sun•Wenjuan Liu•Mu Su•Tao Zhang•Xia Li等 12 人
Cell Death Discovery
2024
•2024/3/14
•Vol.10 No.1 p.1-13
Esophageal squamous cell carcinoma (ESCC) remains an important health concern in developing countries. Patients with advanced ESCC have a poor prognosis and survival rate, and achieving early diagnosis remains a challenge. Metabolic biomarkers are gradually gaining attention as early diagnostic biom...
Cancer metabolismCancer preventionCancer screeningDiagnostic markersOesophageal cancer
10.1038/S41420-024-01896-6
ISSN:2058-7716
Spatially resolved multi-omics of human metabolic dysfunction-associated steatotic liver disease
Ziyu Li•Gang Luo•Changpei Gan•Huayu Zhang•Ling Li等 22 人
Nature Genetics
2025
•2025/11/24
•00 p.1-14
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of chronic liver disease worldwide. We generated single-cell and spatial transcriptomic and metabolomic maps from 61 human livers, including controls (n = 10), metabolic dysfunction-associated steatotic liver (MASL) ...
Gene expressionLiver diseases
10.1038/S41588-025-02407-8
ISSN:1061-4036
A tunable human intestinal organoid system achieves controlled balance between self-renewal and differentiation
Li Yang•Xulei Wang•Xingyu Zhou•Hongyu Chen•Sentao Song等 8 人
Nature Communications
2025
•2025/1/2
•Vol.16 No.1 p.1-16
A balance between stem cell self-renewal and differentiation is required to maintain concurrent proliferation and cellular diversification in organoids; however, this has proven difficult in homogeneous cultures devoid of in vivo spatial niche gradients for adult stem cell-derived organoids. In this...
Intestinal stem cellsSelf-renewalStem-cell differentiation
10.1038/S41467-024-55567-2
ISSN:2041-1723
Refined phenotyping of vaccine responses reveals transcriptomic determinants of neutralizing antibody heterogeneity
Qingqin Wu•Huajie Hu•Liuyu Qin•Xupu Ma•Bohao Chen等 13 人
Npj Vaccines
2026
•2026/1/30
•Vol.11 No.1 p.610
Individuals exhibit considerable heterogeneity in vaccine-induced antibody responses, yet commonly used binary classifications may overlook intermediate patterns. More nuanced grouping could better capture inter-individual differences. Here, we analyzed longitudinal neutralizing antibody (NAb) traje...
Computational biology and bioinformaticsImmunology
10.1038/S41541-026-01386-Z
ISSN:2059-0105
CBX3 promotes multidrug resistance by suppressing ferroptosis in colorectal carcinoma via the CUL3/NRF2/GPX2 axis
Xiaoming Bai•Tinghong Duan•Jiaofang Shao•Yutong Zhang•Guangyuan Xing等 14 人
Oncogene
2025
•2025/3/16
•00 p.1-16
Chemoresistance poses a significant challenge in colorectal cancer (CRC) treatment. However, the mechanisms underlying chemoresistance remain unclear. CBX3 promoted proliferation and metastasis in CRC. However, the role and mechanism of CBX3 in chemoresistance remain unknown. Therefore, we aimed to ...
Cancer therapeutic resistanceColorectal cancer
10.1038/S41388-025-03337-9
ISSN:0950-9232
Unraveling cellular and molecular mechanisms of relapse in CD19/CD22 dual-targeting chimeric antigen receptor T-cell therapy for B-cell acute lymphoblastic leukemia
Jiaqi Tan•Fuhong He•Haiyang Hu•Wenyue Cao•Na Wang等 9 人
Leukemia
2026
•2026/5/29
•00 p.1-16
CD19/CD22 dual-target chimeric antigen receptor (CAR19/22) T cell therapies mark a key advance over single-target options for refractory B-cell malignancies. However, over 20% of patients relapse and underlying mechanisms remain less understood. This study evaluated relapse in 91 B-cell acute l...
Acute lymphocytic leukaemiaGenomicsImmunotherapy
10.1038/S41375-026-02978-3
ISSN:0887-6924
Multiomic analysis of cervical squamous cell carcinoma identifies cellular ecosystems with biological and clinical relevance
Junpeng Fan•Funian Lu•Tianyu Qin•Wenju Peng•Xucui Zhuang等 23 人
Nature Genetics
2023
•2023/11/20
•00 p.1-14
Cervical squamous cell carcinoma (CSCC) exhibits a limited response to immune-checkpoint blockade. Here we conducted a multiomic analysis encompassing single-cell RNA sequencing, spatial transcriptomics and spatial proteomics, combined with genetic and pharmacological perturbations to systematically...
Cancer microenvironmentCervical cancer
10.1038/S41588-023-01570-0
ISSN:1061-4036
BMX inhibition overcomes small cell lung cancer chemoresistance by stabilizing E2F1 via ERK1/2-Cyclin D1/CDK4/6 axis
Ting Wu•Shuang Qi•Chenliang Shi•Chao Wu•Qingwang Liu等 12 人
Signal Transduction And Targeted Therapy
2026
•2026/4/8
•Vol.11 No.1 p.1250
Chemotherapy resistance remains a critical bottleneck limiting its clinical efficacy in small cell lung cancer (SCLC), with its core mechanisms and targeted intervention strategies urgently requiring breakthroughs. Our study revealed that the BMX (bone marrow tyrosine kinase on chromosome X)-E2F1 (E...
Lung cancerMolecular medicine
10.1038/S41392-026-02644-1
ISSN:2059-3635
Androgen receptor promotes arachidonic acid metabolism and angiogenic microenvironment in AFP-negative hepatocellular carcinoma
Zhilong Lin•Xiaofei Liu•Houwei Wang•Shumin Li•Ziqiang Miao等 22 人
Nature Communications
2025
•2025/7/12
•Vol.16 No.1 p.1-20
Alpha-fetoprotein (AFP) is a classic biomarker for hepatocellular carcinoma (HCC). AFP-positive HCC (AFP+ HCC) has been intensively investigated; however, the genomic, transcriptomic and microenvironmental characteristics of AFP-negative HCC (AFP− HCC) remain to be deciphered. Here we show that tumo...
Cancer metabolismCellular signalling networksTumour angiogenesisTumour biomarkers
10.1038/S41467-025-61448-Z
ISSN:2041-1723
Combining single-cell RNA sequencing and population-based studies reveals hand osteoarthritis-associated chondrocyte subpopulations and pathways
Hui Li•Xiaofeng Jiang•Yongbing Xiao•Yuqing Zhang•Weiya Zhang等 14 人
Bone Research
2023
•2023/11/2
•Vol.11 No.1 p.1-13
Hand osteoarthritis is a common heterogeneous joint disorder with unclear molecular mechanisms and no disease-modifying drugs. In this study, we performed single-cell RNA sequencing analysis to compare the cellular composition and subpopulation-specific gene expression between cartilage with macrosc...
HomeostasisPathogenesis
10.1038/S41413-023-00292-7
ISSN:2095-6231
TRIM11 potentiates antitumor immunity via inhibition of the IFN-γ/PD-L1 axis
Yingying Xu•Runjie Cai•Maoxuan Liu•Xiaokai Fan•Xiaochun Wan等 8 人
Cell Death & Differentiation
2025
•2025/11/7
•00 p.1-13
PD-L1 serves as the ligand for the immune inhibitory checkpoint protein PD-1, and its expression in tumors can be induced by interferon-γ (IFN-γ), leading to immune evasion. While JAK/STAT signaling is known to mediate IFN-γ-induced PD-L1 expression, the mechanisms governing the negative regulation ...
CancerTumour-suppressor proteins
10.1038/S41418-025-01610-8
ISSN:1350-9047
Combination human umbilical cord perivascular and endothelial colony forming cell therapy for ischemic cardiac injury
Farwah Iqbal•Alexander Johnston•Brandon Wyse•Razieh Rabani•Poonam Mander等 11 人
Npj Regenerative Medicine
2023
•2023/8/25
•Vol.8 No.1 p.1-18
Cell-based therapeutics are promising interventions to repair ischemic cardiac tissue. However, no single cell type has yet been found to be both specialized and versatile enough to heal the heart. The synergistic effects of two regenerative cell types including endothelial colony forming cells (ECF...
Cardiac regenerationHeart failureRegeneration
10.1038/S41536-023-00321-3
ISSN:2057-3995
Exome-wide association study identifies KDELR3 mutations in extreme myopia
Jian Yuan•You-Yuan Zhuang•Xiaoyu Liu•Yue Zhang•Kai Li等 17 人
Nature Communications
2024
•2024/8/7
•Vol.15 No.1 p.1-17
Extreme myopia (EM), defined as a spherical equivalent (SE) ≤ −10.00 diopters (D), is one of the leading causes of sight impairment. Known EM-associated variants only explain limited risk and are inadequate for clinical decision-making. To discover risk genes, we performed a whole-exome sequencing (...
Rare variantsRefractive errors
10.1038/S41467-024-50580-X
ISSN:2041-1723
Increased PRSS56 expression is a causal factor and therapeutic target for human axial high myopia
Boxuan Wu•Weijia Zeng•Kefu Tang•Jiawei Xiong•Xiaofen Mo等 15 人
Cell Research
2026
•2026/4/1
•00 p.1-15
High myopia (HM), characterized by significant ocular axial length elongation, affects hundreds of millions of people and is often inherited, particularly in cases that develop during childhood or adolescence. Although numerous myopia loci (MYP) have been identified, most causative genes remain unde...
Developmental biologyMolecular biology
10.1038/S41422-026-01241-9
ISSN:1748-7838
Single-cell transcriptomics analysis of bullous pemphigoid unveils immune-stromal crosstalk in type 2 inflammatory disease
Tingting Liu•Zhenzhen Wang•Xiaotong Xue•Zhe Wang•Yuan Zhang等 16 人
Nature Communications
2024
•2024/7/15
•Vol.15 No.1 p.1-16
Bullous pemphigoid (BP) is a type 2 inflammation- and immunity-driven skin disease, yet a comprehensive understanding of the immune landscape, particularly immune-stromal crosstalk in BP, remains elusive. Herein, using single-cell RNA sequencing (scRNA-seq) and in vitro functional analyzes, we pinpo...
AutoimmunityGene regulation in immune cellsLangerhans cellsSkin diseasesT-helper 2 cells
10.1038/S41467-024-50283-3
ISSN:2041-1723
Architecture of the neutrophil compartment
Daniela Cerezo-Wallis•Andrea Rubio-Ponce•Mathis Richter•Emanuele Pitino•Immanuel Kwok等 63 人
Nature
2025
•2025/12/3
•00 p.1-10
Neutrophils exhibit remarkable phenotypic and functional diversity across tissues and diseases1,2, yet the lack of understanding of how this immune compartment is globally organized challenges translation to the clinic. Here we performed single-cell transcriptional profiling of neutrophils spanning ...
Computational biology and bioinformaticsNeutrophils
10.1038/S41586-025-09807-0
ISSN:0028-0836
SGF29 nuclear condensates reinforce cellular aging
Kaowen Yan•Qianzhao Ji•Dongxin Zhao•Mingheng Li•Xiaoyan Sun等 15 人
Cell Discovery
2023
•2023/11/7
•Vol.9 No.1 p.1-21
Phase separation, a biophysical segregation of subcellular milieus referred as condensates, is known to regulate transcription, but its impacts on physiological processes are less clear. Here, we demonstrate the formation of liquid-like nuclear condensates by SGF29, a component of the SAGA transcrip...
Cell biologySenescence
10.1038/S41421-023-00602-7
ISSN:2056-5968
Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs
Bo Lu•Yi Yan•Liting Dong•Lingling Han•Yawei Liu等 16 人
Cell Discovery
2021
•2021/3/30
•Vol.7 No.1 p.1-10
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapie...
TranscriptomicsTransposition
10.1038/S41421-021-00248-3
ISSN:2056-5968
Tumor molecular age acceleration is associated with early progression in diffuse large B-cell lymphoma
Jiahao Chen•Yan Zhu•Zi-Yang Shi•Xiang Li•Yun-Ruei Kao等 16 人
Leukemia
2026
•2026/7/27
•00 p.1-5
B-cell lymphomaCancer genomics
10.1038/S41375-026-03076-0
ISSN:0887-6924
Context-dependent tumor-suppressive BMP signaling in diffuse intrinsic pontine glioma regulates stemness through epigenetic regulation of CXXC5
Sun Ye•Yan Kun•Wang Yi•Xu Cheng•Wang Dan等 15 人
Nature Cancer
2022
•2022/8/1
•00 p.1-18
The most lethal subtype of diffuse intrinsic pontine glioma (DIPG) is H3K27M. Although ACVR1 mutations have been implicated in the pathogenesis of this currently incurable disease, the impacts of bone morphogenetic protein (BMP) signaling on more than 60% of H3K27M DIPG carrying ACVR1 wild-type rema...
CNS cancerGrowth factor signallingMechanisms of disease
10.1038/S43018-022-00408-8
ISSN:2662-1347
Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma
Shanzhao Jin•Ruoyan Li•Ming-Yuan Chen•Chao Yu•Lin-Quan Tang等 29 人
Cell Research
2020
•2020/9/8
•Vol.30 No.11 p.950-965
Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignancy with a complex tumor ecosystem. How the interplay between tumor cells, EBV, and the microenvironment contributes to NPC progression and immune evasion remains unclear. Here we performed single-cell RNA sequencing on ...
Cancer genomicsCancer microenvironment
10.1038/S41422-020-00402-8
ISSN:1001-0602
Heat stress targets and degrades BCR::ABL1 oncoproteins to overcome drug-resistance in Philadelphia chromosome-positive acute lymphoblastic leukemia
Chang Yang•Yuan-Yuan Kang•Chen-Ying Zhu•Yafang Ma•Pei-Han Yu等 12 人
Leukemia
2025
•2025/7/22
•00 p.1-12
BCR::ABL1 oncofusion protein drives Philadelphia-chromosome positive acute lymphoblastic leukemia (Ph+ ALL), making it a critical therapeutic target. Tyrosine kinase inhibitors (TKIs) targeting BCR::ABL1 have revolutionized the treatment of Ph+ ALL patients. However, mutations in the kinase domain o...
Acute lymphocytic leukaemiaTargeted therapies
10.1038/S41375-025-02709-0
ISSN:0887-6924
Single-cell RNA-sequencing reveals radiochemotherapy-induced innate immune activation and MHC-II upregulation in cervical cancer
Liu Chao•Li Xiaohui•Huang Qingyu•Zhang Min•Lei Tianyu等 15 人
Signal Transduction And Targeted Therapy
2023
•2023/1/30
•Vol.8 No.1 p.1-15
Radiochemotherapy (RCT) is a powerful treatment for cervical cancer, which affects not only malignant cells but also the immune and stromal compartments of the tumor. Understanding the remodeling of the local ecosystem induced by RCT would provide valuable insights into improving treatment strategie...
Cancer therapyGynaecological cancer
10.1038/S41392-022-01264-9
ISSN:2059-3635
IL-15 overexpression promotes memory program and anti-tumor activity of CD64 CAR T cells in a preclinical AML model
Lingling Shan•Chuo Li•Ting Li•Chongkai Wang•Haidong Cui等 7 人
Communications Biology
2026
•2026/1/15
•Vol.9 No.1 p.2510
The prognosis of relapsed or refractory acute myeloid leukemia (r/r AML) patients remains poor due to lack of novel therapies. We previous demonstrated that chimeric antigen receptor (CAR) T cells targeting CD64 have the potential to treat AML with minimal toxicity to hematopoietic stem/progenitor c...
Cancer immunotherapyMyeloma
10.1038/S42003-026-09528-8
ISSN:2399-3642
Global transcriptomic characterization of T cells in individuals with chronic HIV-1 infection
Wang Xiang-Ming•Zhang Ji-Yuan•Xing Xudong•Huang Hui-Huang•Xia Peng等 22 人
Cell Discovery
2022
•2022/3/28
•Vol.8 No.1 p.1-17
To obtain a comprehensive scenario of T cell profiles and synergistic immune responses, we performed single-cell RNA sequencing (scRNA-seq) on the peripheral T cells of 14 individuals with chronic human immunodeficiency virus 1 (HIV-1) infection, including nine treatment-naive (TP) and eight antiret...
AutoimmunityBioinformatics
10.1038/S41421-021-00367-X
ISSN:2056-5968
Genetic variants in UNC93B1 predispose to childhood-onset systemic lupus erythematosus
Mahmoud Al-Azab•Elina Idiiatullina•Ziyang Liu•Meng Lin•Katja Hrovat-Schaale等 25 人
Nature Immunology
2024
•2024/6/3
•Vol.25 No.6 p.969-980
Rare genetic variants in toll-like receptor 7 (TLR7) are known to cause lupus in humans and mice. UNC93B1 is a transmembrane protein that regulates TLR7 localization into endosomes. In the present study, we identify two new variants in UNC93B1 (T314A, located proximally to the TLR7 transmembrane dom...
Systemic lupus erythematosusToll-like receptors
10.1038/S41590-024-01846-5
ISSN:1529-2908
DCTPP1 regulates oxidative stress homeostasis via AUF1 in human villous trophoblasts
Yajuan Lu•Xue Wu•Lei He•Peng Pan•Anqi Zhao等 11 人
Cell Death Discovery
2025
•2025/8/23
•Vol.11 No.1 p.1-11
Placental trophoblast dysfunction is one of the main causes of missed abortion (MA). The expression and regulation of specific molecules play crucial roles in this complex process. Among these, human deoxycytidine triphosphate pyrophosphatase 1 (DCTPP1), a key enzyme, not only participates in nucleo...
Cell growthInfertility
10.1038/S41420-025-02666-8
ISSN:2058-7716
Sintilimab (anti-PD-1 antibody) combined with high-dose methotrexate, temozolomide, and rituximab (anti-CD20 antibody) in primary central nervous system lymphoma: a phase 2 study
Zhiyong Zeng•Apeng Yang•Jingke Yang•Sheng Zhang•Zhen Xing等 29 人
Signal Transduction And Targeted Therapy
2024
•2024/9/4
•Vol.9 No.1 p.1-10
Primary central nervous system lymphoma (PCNSL) is a rare and frequently fatal lymphoma subtype. The programmed death-1 (PD-1) pathway has emerged as a potential therapeutic target, but the effectiveness of PD-1 antibody sintilimab in combination with immunochemotherapy as a frontline treatment for ...
CNS cancerDrug development
10.1038/S41392-024-01941-X
ISSN:2059-3635
Echs1-mediated histone crotonylation facilitates zygotic genome activation and expression of repetitive elements in early mammalian embryos
Yong-feng Wang•Yu-ting Wan•Qian-rong Qi•Qing Tian•Xin-mei Liu等 8 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-21
Histone crotonylation, a conserved post-translational histone modification, plays a crucial role in transcriptional regulation. However, its function in early embryonic development remains largely unexplored. Here, we perform genome-wide mapping of histone crotonylation in mouse and human early embr...
DifferentiationEmbryogenesisEmbryonic stem cells
10.1038/S41467-025-60565-Z
ISSN:2041-1723
Single-cell and spatial transcriptome analyses reveal tertiary lymphoid structures linked to tumour progression and immunotherapy response in nasopharyngeal carcinoma
Yang Liu•Shuang-Yan Ye•Shuai He•Dong-Mei Chi•Xiu-Zhi Wang等 23 人
Nature Communications
2024
•2024/9/4
•Vol.15 No.1 p.1-22
Tertiary lymphoid structures are immune cell aggregates linked with cancer outcomes, but their interactions with tumour cell aggregates are unclear. Using nasopharyngeal carcinoma as a model, here we analyse single-cell transcriptomes of 343,829 cells from 77 biopsy and blood samples and spatially-r...
Cancer immunotherapyCancer microenvironmentHead and neck cancer
10.1038/S41467-024-52153-4
ISSN:2041-1723
Landscape of pathogenic mutations in premature ovarian insufficiency
Ke Hanni•Tang Shuyan•Guo Ting•Hou Dong•Jiao Xue等 19 人
Nature Medicine
2023
•2023/2/2
•Vol.29 No.2 p.483-492
Premature ovarian insufficiency (POI) is a major cause of female infertility due to early loss of ovarian function. POI is a heterogeneous condition, and its molecular etiology is unclear. To identify genetic variants associated with POI, here we performed whole-exome sequencing in a cohort of 1,030...
Disease geneticsEndocrine reproductive disorders
10.1038/S41591-022-02194-3
ISSN:1078-8956
Single-cell landscape of primary central nervous system diffuse large B-cell lymphoma
Nianping Liu•Chen Jiang•Xinfeng Yao•Minghao Fang•Xiaolong Qiao等 13 人
Cell Discovery
2023
•2023/6/12
•Vol.9 No.1 p.1-17
Understanding tumor heterogeneity and immune infiltrates within the tumor-immune microenvironment (TIME) is essential for the innovation of immunotherapies. Here, combining single-cell transcriptomics and chromatin accessibility sequencing, we profile the intratumor heterogeneity of malignant cells ...
Cancer genomicsCNS cancerHaematological cancerTumour immunology
10.1038/S41421-023-00559-7
ISSN:2056-5968
Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes
Li Lingling•Jiang Dongxian•Liu Hui•Guo Chunmei•Zhao Rui等 23 人
Nature Communications
2023
•2023/3/29
•Vol.14 No.1 p.1-24
The subtypes of duodenal cancer (DC) are complicated and the carcinogenesis process is not well characterized. We present comprehensive characterization of 438 samples from 156 DC patients, covering 2 major and 5 rare subtypes. Proteogenomics reveals LYN amplification at the chromosome 8q gain funct...
Cancer genomicsGastrointestinal cancerIntestinal diseasesProteomics
10.1038/S41467-023-37221-5
ISSN:2041-1723
Revealing tumor microenvironmental heterogeneity and prognostic value in angioimmunoblastic T-cell lymphoma via spatial transcriptome sequencing
Xiang Zhang•Yong Sun•Duo Wu•Fang Yu•Hanjin Yang等 16 人
Cell Death & Disease
2026
•2026/1/9
•Vol.17 No.1 p.270
Angioimmunoblastic T-cell lymphoma (AITL) represents the second most prevalent subtype of peripheral T-cell lymphoma, characterized by a dismal prognosis. However, a systematic exploration of tumor microenvironment (TME) features and their prognostic significance in AITL remains notably deficient. T...
Cancer microenvironmentT-cell lymphoma
10.1038/S41419-025-08212-9
ISSN:2041-4889
The dynamic evolution of lineage switch under CD19 CAR-T treatment in non-KMT2A rearranged B-ALL patients
Shaowei Qiu•Yihan Mei•Runxia Gu•Yu Liu•Manling Chen等 21 人
Leukemia
2024
•2024/10/31
•00 p.1-5
Acute lymphocytic leukaemiaAcute myeloid leukaemiaImmunotherapy
10.1038/S41375-024-02449-7
ISSN:0887-6924
SEAD reference panel with 22,134 haplotypes boosts rare variant imputation and genome-wide association analysis in Asian populations
Meng-Yuan Yang•Jia-Dong Zhong•Xin Li•Geng Tian•Wei-Yang Bai等 37 人
Nature Communications
2024
•2024/12/30
•Vol.15 No.1 p.1-14
Limited whole genome sequencing (WGS) studies in Asian populations result in a lack of representative reference panels, thus hindering the discovery of ancestry-specific variants. Here, we present the South and East Asian reference Database (SEAD) panel ( https://imputationserver.westlake.edu.cn/ ),...
Genome-wide association studiesRare variants
10.1038/S41467-024-55147-4
ISSN:2041-1723
Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq
Ziye Xu•Yuexiao Lyu•Haide Chen•Yu Chen•Yongcheng Wang
Nature Protocols
2025
•2025/4/25
•00 p.1-32
Formalin-fixed paraffin-embedded (FFPE) samples represent a vast and valuable resource of patient material, often linked to extensive clinical history and follow-up data. However, achieving single-cell or single-nucleus RNA (sc/snRNA) profiling in these archived tissues remains challenging. To addre...
Gene expression analysisRNA sequencing
10.1038/S41596-025-01170-8
ISSN:1754-2189
Cell-free DNA testing for the detection and prognosis prediction of pancreatic cancer
Jianmin Wu•Xiongfei Xu•Qingzheng Zhang•Peilong Li•Tong Wu等 20 人
Nature Communications
2025
•2025/7/18
•Vol.16 No.1 p.1-14
Pancreatic cancer is known for its lethal condition, with most cases being diagnosed at advanced stage. Recently, liquid biopsy has emerged as a promising tool in cancer detection. Here we develop both an early detection model and a prognostic model for pancreatic cancer using cell-free DNA (cfDNA) ...
Cancer screeningPancreatic cancer
10.1038/S41467-025-61890-Z
ISSN:2041-1723
The integrated genomic and epigenomic landscape of brainstem glioma
Lee H. Chen•Changcun Pan•Bill H. Diplas•Cheng Xu•Landon J. Hansen等 28 人
Nature Communications
2020
•2020/6/17
•Vol.11 No.1 p.1-11
Brainstem gliomas are a heterogeneous group of tumors that encompass both benign tumors cured with surgical resection and highly lethal cancers with no efficacious therapies. We perform a comprehensive study incorporating epigenetic and genomic analyses on a large cohort of brainstem gliomas, includ...
Cancer genomicsCNS cancer
10.1038/S41467-020-16682-Y
ISSN:2041-1723
WASH regulates B cell signaling, metabolism and function through STAT1
Panpan Jiang•Caini Lan•Siyu Zhao•Xin Zhang•Juan Lai等 28 人
Cell Death & Differentiation
2025
•2025/12/23
•00 p.1-14
Actin and actin polymerization factors regulate the immune system in a complex manner. The function in the cytoplasm has been well-established, where they are important components of the cytoskeleton, controlling cell migration, function, and vesicular transport. However, it remains poorly understoo...
B cellsSignal transduction
10.1038/S41418-025-01647-9
ISSN:1350-9047
AZIN1-dependent polyamine synthesis accelerates tumor cell cycle progression and impairs effector T-cell function in osteosarcoma
Jiaming Yu•Chuanxia Zhang•Qinkai Zhang•Bing Lu•Guohao Lu等 12 人
Cell Death & Disease
2025
•2025/4/17
•Vol.16 No.1 p.1-12
Osteosarcoma, the most prevalent malignant bone tumor among adolescents, frequently exhibits limited responsiveness to immunotherapy, a challenge attributed to poorly understood underlying mechanisms. Here, we identify enhanced polyamine biosynthesis as a key driver of osteosarcoma progression and i...
Cancer metabolismImmunosurveillanceImmunotherapy
10.1038/S41419-025-07640-X
ISSN:2041-4889
tRF-27-87R8WP9N1E5 serves as a prognostic biomarker and tumor suppressor in gastric cancer by targeting the WNT4 pathway via Ago2
Xiuchong Yu•Yang Zhou•Jianing Tong•Yaoyao Xie•Jiahe Dai等 7 人
Oncogene
2026
•2026/7/28
•00 p.1-16
Gastric cancer (GC) poses a significant global health burden, creating critical demands for early diagnostic biomarkers and novel therapeutic targets. tRNA-derived fragments (tRFs) have recently emerged as key regulatory molecules in tumorigenesis. However, the roles of tRFs in GC are largely unknow...
Prognostic markerssiRNAs
10.1038/S41388-026-03914-6
ISSN:0950-9232
Massively parallel interrogation of human functional variants modulating cancer immunosurveillance
Ying Liu•Yongshuo Liu•Xuran Niu•Ang Chen•Yizhou Li等 12 人
Signal Transduction And Targeted Therapy
2025
•2025/3/19
•Vol.10 No.1 p.1-18
Anti-PD-1/PD-L1 immune checkpoint blockade (ICB) therapy has revolutionized clinical cancer treatment, while abnormal PD-L1 or HLA-I expression in patients can significantly impact the therapeutic efficacy. Somatic mutations in cancer cells that modulate these critical regulators are closely associa...
Cancer genomicsFunctional genomicsTumour biomarkersTumour immunology
10.1038/S41392-025-02171-5
ISSN:2059-3635
Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations
Xiujia Yang•Haipei Tang•Chunhong Lan•Weiting He•Sen Chen等 10 人
Communications Biology
2026
•2026/1/10
•Vol.9 No.1 p.2400
The development and maturation of B lymphocytes are critical for adaptive immunity, relying on tightly regulated gene programs within specialized microenvironments shaped by extracellular matrix and neighboring cells. However, high-dimensional, integrated analyses of B cell heterogeneity, gene regul...
Computational biology and bioinformaticsLymphopoiesisSenescence
10.1038/S42003-026-09515-Z
ISSN:2399-3642
Single-cell sequencing reveals VEGFR as a potential target for CAR-T cell therapy in chordoma
Huantong Wu•Xinqiang Li•Boyan Zhang•Penghao Liu•Maoyang Qi等 9 人
British Journal Of Cancer
2024
•2024/4/11
•00 p.1-12
Chordomas are rare osseous neoplasms with a dismal prognosis when they recur. Here we identified cell surface proteins that could potentially serve as novel immunotherapeutic targets in patients with chordoma. Fourteen chordoma samples from patients attending Xuanwu Hospital Capital Medical Universi...
Cancer immunotherapyImmunotherapyRNA sequencing
10.1038/S41416-024-02635-5
ISSN:0007-0920
Spatial transcriptomics reveals molecular heterogeneity and subtype-specific therapeutic targets in small cell lung cancer
Tongji Xie•Le Tang•Guangyu Fan•Xiaohong Han•Yuankai Shi
Npj Precision Oncology
2026
•2026/1/16
•Vol.10 No.1 p.810
Small cell lung cancer (SCLC) is a highly aggressive malignancy with strong associations to smoking, characterized by initial platinum sensitivity followed by rapid recurrence and poor long-term survival. The evolutionary processes driving this high plasticity and intratumoral heterogeneity remain i...
BiomarkersCancerComputational biology and bioinformaticsOncology
10.1038/S41698-025-01243-7
ISSN:2397-768X
INCENP and CDCA8 predict neoadjuvant chemotherapy response and outcomes in esophageal squamous cell carcinoma
Xiangyu Wang•Ting Wang•Keke Wang•Chengjuan Zhang•Zhibo Li等 15 人
Nature Communications
2026
•2026/1/21
•Vol.17 No.1 p.16720
Neoadjuvant chemotherapy (NACT), a key strategy for various cancers, markedly improves patient prognosis and 5-year survival rates. However, numerous patients develop resistance to NACT and thus fail to benefit from it. Therefore, identifying reliable biomarkers to predict patient responsivenes...
Cancer therapeutic resistanceOesophageal cancerPredictive markersTumour biomarkers
10.1038/S41467-026-68371-X
ISSN:2041-1723
Neoadjuvant tislelizumab (anti-PD-1 antibody) plus chemotherapy in patients with advanced epithelial ovarian cancer: the exploratory NAIVE trial
Zhigang Zhang•Jing Fei•Sangting Lao•Rui Liu•Xiaoqing Zhu等 15 人
Signal Transduction And Targeted Therapy
2026
•2026/7/3
•Vol.11 No.1 p.2650
The clinical efficacy and immune modulation of neoadjuvant immunochemotherapy for epithelial ovarian cancer (EOC) remain uncertain. To clarify these effects, the NAIVE trial (NCT04815408), a prospective phase II study, evaluated the efficacy of neoadjuvant platinum-based chemotherapy with tislelizum...
Gynaecological cancerTranslational immunologyTranslational research
10.1038/S41392-026-02746-W
ISSN:2059-3635
A patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments
Yanmei Zhang•Qifan Hu•Yuquan Pei•Hao Luo•Zixuan Wang等 21 人
Nature Communications
2024
•2024/4/20
•Vol.15 No.1 p.1-17
Cancer models play critical roles in basic cancer research and precision medicine. However, current in vitro cancer models are limited by their inability to mimic the three-dimensional architecture and heterogeneous tumor microenvironments (TME) of in vivo tumors. Here, we develop an innovative pati...
Cancer modelsTissue engineering
10.1038/S41467-024-47737-Z
ISSN:2041-1723
Stress granules restrain ferroptosis by sequestering ferritin
Zehe Ge•Zihan Wang•Erjie Zhao•Yizhuo Guo•Longxiu Zhang等 31 人
Nature Cell Biology
2026
•2026/5/22
•00 p.1-15
Glioblastoma stem cells (GSCs) are refractory to first-line treatment in the clinic, which includes irradiation (IR) and temozolomide (TMZ). Here we find that disrupting stress granules (SGs) sensitizes GSCs to IR/TMZ through ferroptosis. The profiling of SG proteins reveals the recruitment of iron-...
Cancer therapyCell deathCNS cancerStress granules
10.1038/S41556-026-01953-5
ISSN:1465-7392
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
Tumour circular RNAs elicit anti-tumour immunity by encoding cryptic peptides
Di Huang•Xiaofeng Zhu•Shuying Ye•Jiahui Zhang•Jianyou Liao等 17 人
Nature
2023
•2023/12/13
•00 p.1-10
Emerging data have shown that previously defined noncoding genomes might encode peptides that bind human leukocyte antigen (HLA) as cryptic antigens to stimulate adaptive immunity1,2. However, the significance and mechanisms of action of cryptic antigens in anti-tumour immunity remain unclear. Here ...
Breast cancerTumour immunology
10.1038/S41586-023-06834-7
ISSN:0028-0836
Myofibroblasts derived type V collagen promoting tissue mechanical stress and facilitating metastasis and therapy resistance of lung adenocarcinoma cells
Guangsheng Zhu•Yanan Wang•Yingjie Wang•Hua Huang•Boshi Li等 11 人
Cell Death & Disease
2024
•2024/7/10
•Vol.15 No.7 p.1-13
Lung cancer is a leading cause of cancer-related mortality globally, with a dismal 5-year survival rate, particularly for Lung Adenocarcinoma (LUAD). Mechanical changes within the tumor microenvironment, such as extracellular matrix (ECM) remodeling and fibroblast activity, play pivotal roles in can...
Cancer microenvironmentNon-small-cell lung cancerPrognostic markers
10.1038/S41419-024-06873-6
ISSN:2041-4889
The role of m6A demethylase FTO in chemotherapy resistance mediating acute myeloid leukemia relapse
Zhi-Wei Zhang•Xiao-Su Zhao•Huidong Guo•Xiao-Jun Huang
Cell Death Discovery
2023
•2023/7/5
•Vol.9 No.1 p.1-11
Acute myeloid leukemia (AML) is the most common hematopoietic malignancies, and chemotherapy resistance is one of the main causes of relapse. Because of lower survival rate for patients with relapse, it is pivotal to identify etiological factors responsible for chemo-resistance. In this work, direct...
Acute myeloid leukaemiaEpigenomics
10.1038/S41420-023-01505-Y
ISSN:2058-7716
A phase II clinical trial of toripalimab in advanced solid tumors with polymerase epsilon/polymerase delta (POLE/POLD1) mutation
Ying Jin•Run-Jie Huang•Wen-Long Guan•Zhi-Qiang Wang•Zong-Jiong Mai等 14 人
Signal Transduction And Targeted Therapy
2024
•2024/9/2
•Vol.9 No.1 p.1-11
Patients carrying mutations in polymerase epsilon/polymerase delta have shown positive responses to immune checkpoint inhibitors. Yet, prospective trials exploring the efficacy in those with polymerase epsilon/polymerase delta mutations are still lacking. A phase II clinical trial was initiated to e...
Cancer therapyPredictive markers
10.1038/S41392-024-01939-5
ISSN:2059-3635
Heterogeneity of tumor microenvironment is associated with clinical prognosis of non-clear cell renal cell carcinoma: a single-cell genomics study
Chen Wen-jin•Cao Hao•Cao Jian-wei•Zuo Li•Qu Fa-jun等 15 人
Cell Death & Disease
2022
•2022/1/11
•Vol.13 No.1 p.1-14
Non-clear renal cell carcinomas (nccRCCs) are less frequent in kidney cancer with histopathological heterogeneity. A better understanding of the tumor biology of nccRCC can provide more effective treatment paradigms for different subtypes. To reveal the heterogeneity of tumor microenvironment (TME) ...
Cancer genomicsCancer microenvironmentRenal cell carcinoma
10.1038/S41419-022-04501-9
ISSN:2041-4889
Integrating cytological images and spatial transcriptomics for cell segmentation with DISSECT
Yufeng He•Yanping Zhao•Rui Zhang•Heli Yang•Zongxu Zhang等 14 人
Nature Computational Science
2026
•2026/7/9
•00 p.1-14
Advances in imaging- and sequencing-based spatial transcriptomics have increased molecular throughput and resolution, enabling the measurement and analysis of spatial transcriptomes at single-cell resolution. However, accurate cell segmentation remains challenging because cell morphology, tissue pro...
Computational modelsData miningMachine learning
10.1038/S43588-026-01020-X
ISSN:2662-8457
The translation landscape of ovarian clear cell carcinoma indicates that RBM4 plays a pro-oncogenic role in tumor progression
Yiying Chen•Dongxu Lu•Yaqi Xing•Jing He•Sumei Zhang等 15 人
Oncogene
2026
•2026/6/5
•00 p.1-13
Ovarian clear cell carcinoma (OCCC) is a highly aggressive gynecological malignancy characterized by distinct clinicopathological features and resistance to chemotherapy. Despite advances in multi-omics characterization, the translational regulatory landscape of OCCC remains unexplored. Here, we per...
Ovarian cancerPost-translational modifications
10.1038/S41388-026-03840-7
ISSN:0950-9232
Human papillomavirus integration perspective in small cell cervical carcinoma
Wang Xiaoli•Jia Wenlong•Wang Mengyao•Liu Jihong•Zhou Xianrong等 45 人
Nature Communications
2022
•2022/10/10
•Vol.13 No.1 p.1-10
Small cell cervical carcinoma (SCCC) is a rare but aggressive malignancy. Here, we report human papillomavirus features and genomic landscape in SCCC via high-throughput HPV captured sequencing, whole-genome sequencing, whole-transcriptome sequencing, and OncoScan microarrays. HPV18 infections and i...
Cervical cancerTumour virus infectionsViral infection
10.1038/S41467-022-33359-W
ISSN:2041-1723
Single-cell multiomic analysis unveils the immune landscape dynamics of graves’ ophthalmopathy
Shurui Ke•Zhong Liu•Ming Zhou•Bing Xiao•Qiuling Hu等 9 人
Communications Biology
2025
•2025/5/12
•Vol.8 No.1 p.1-15
Graves’ ophthalmopathy (GO) is an autoimmune disease that occurs concurrently with Graves’ disease, potentially leading to facial disfigurement and irreversible vision loss. However, the molecular characteristics of cellular changes in the peripheral immune environment of GO patients remain unclear....
AutoimmunityEye diseases
10.1038/S42003-025-08115-7
ISSN:2399-3642
First-in-human, phase 1 dose-escalation and dose-expansion study of a RET inhibitor SY-5007 in patients with advanced RET-altered solid tumors
Wei Li•Yongsheng Wang•Anwen Xiong•Ge Gao•Zhengbo Song等 16 人
Signal Transduction And Targeted Therapy
2024
•2024/11/4
•Vol.9 No.1 p.1-11
Oncogenic RET alteration is an important, tissue-agnostic therapeutic target across diverse cancers. We conducted a first-in-human phase 1 study on SY-5007, a potent and selective RET inhibitor, in patients with RET-altered solid tumors. Primary endpoints were safety, maximum tolerated dose (MTD), a...
Clinical trialsDrug development
10.1038/S41392-024-02006-9
ISSN:2059-3635
Metformin escape in prostate cancer by activating the PTGR1 transcriptional program through a novel super-enhancer
Jianheng Ye•Shanghua Cai•Yuanfa Feng•Jinchuang Li•Zhiduan Cai等 17 人
Signal Transduction And Targeted Therapy
2023
•2023/8/16
•Vol.8 No.1 p.1-15
The therapeutic efficacy of metformin in prostate cancer (PCa) appears uncertain based on various clinical trials. Metformin treatment failure may be attributed to the high frequency of transcriptional dysregulation, which leads to drug resistance. However, the underlying mechanism is still unclear....
Urological cancerUrology
10.1038/S41392-023-01516-2
ISSN:2059-3635
KRAS-extrachromosomal DNA drives intratumoral heterogeneity in gastric cancer
Rong Guan•Chenxi Li•Xinchun Dai•Yanyan Wang•Yiyuan Zhang等 16 人
Oncogene
2026
•2026/3/5
•Vol.45 No.12 p.1100-1110
Extrachromosomal DNA (ecDNA), autonomously replicating circular DNA outside the chromosomes, exists as critical oncogene driver in approximately 20% of all tumors. Massive ecDNA amplification and its asymmetric segregation during mitotic drive high level oncogene amplification and contribute to tumo...
CancerGenetics
10.1038/S41388-026-03713-Z
ISSN:0950-9232
Single-cell immune profiling and validation of PBMCs in the onset of and recovery from herpes zoster
Shang Zheng•Shuyao Zhang•Xiangyao Li•Yong Fei•Lei Yang等 11 人
Communications Biology
2024
•2024/12/4
•Vol.7 No.1 p.1-15
To gain deeper insights into pathogenesis of herpes zoster, the peripheral blood mononuclear cells (PBMCs) from male patients mostly were subjected to single-cell RNA-seq (scRNA-seq) and ATAC-seq analysis. Here we show a detailed immune cell profile in the onset of and recovery from herpes zoster, r...
Diagnostic markersInfection
10.1038/S42003-024-07289-W
ISSN:2399-3642
Hypoxia-induced MIC19 myristoylation promotes PRKN-dependent VDAC2 ubiquitination and activates mitophagy in non-small cell lung cancer
Hua Huang•Chen Ding•Zexia Zhao•Wenhao Zhao•Guorui He等 10 人
Oncogene
2026
•2026/6/20
•00 p.1-14
Tumor hypoxia drives mitophagy reprogramming to support mitochondrial quality control in non-small cell lung cancer (NSCLC) cells, yet the role of the mitochondrial cristae organizers remains poorly understood. Here, we identified MIC19, a key subunit of mitochondrial contact site and cristae organi...
Predictive markersTumour biomarkers
10.1038/S41388-026-03847-0
ISSN:0950-9232
Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways
Xu Lin•Hong-Mei Xiao•Hui-Min Liu•Wan-Qiang Lv•Jonathan Greenbaum等 32 人
Nature Communications
2023
•2023/10/27
•Vol.14 No.1 p.1-17
Although the gut microbiota has been reported to influence osteoporosis risk, the individual species involved, and underlying mechanisms, remain largely unknown. We performed integrative analyses in a Chinese cohort of peri-/post-menopausal women with metagenomics/targeted metabolomics/whole-genome ...
Applied microbiologyOsteoporosisPredictive markersRisk factors
10.1038/S41467-023-42005-Y
ISSN:2041-1723
A protein-encoding CCDC7 circular RNA inhibits the progression of prostate cancer by up-regulating FLRT3
Qiong Wang•Bisheng Cheng•Sandeep Singh•Yiran Tao•Zhongqiu Xie等 12 人
Npj Precision Oncology
2024
•2024/1/16
•Vol.8 No.1 p.1-15
Circular RNAs (circRNAs) are a family of endogenous RNAs that have become a focus of biological research in recent years. Emerging evidence has revealed that circRNAs exert biological functions by acting as transcriptional regulators, microRNA sponges, and binding partners with RNA-binding proteins....
Drug developmentTumour heterogeneity
10.1038/S41698-024-00503-2
ISSN:2397-768X
Sequencing of cerebrospinal fluid cell-free DNA facilitated early differential diagnosis of intramedullary spinal cord tumors
Ruichao Chai•Songyuan An•Han Lin•Bo Pang•Hao Yan等 14 人
Npj Precision Oncology
2024
•2024/2/22
•Vol.8 No.1 p.1-9
Pre-surgery differential diagnosis is valuable for personalized treatment planning in intramedullary spinal cord tumors. This study assessed the performance of sequencing cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) for differential diagnosis of these tumors. Prospectively enrolling 45 patient...
CNS cancerDiagnostic markersMolecular medicineOncogenesis
10.1038/S41698-024-00541-W
ISSN:2397-768X
Exome sequencing reveals genetic heterogeneity and clinically actionable findings in children with cerebral palsy
Yangong Wang•Yiran Xu•Chongchen Zhou•Ye Cheng•Niu Qiao等 34 人
Nature Medicine
2024
•2024/5/1
•00 p.1-11
Cerebral palsy (CP) is the most common motor disability in children. To ascertain the role of major genetic variants in the etiology of CP, we conducted exome sequencing on a large-scale cohort with clinical manifestations of CP. The study cohort comprised 505 girls and 1,073 boys. Utilizing the cur...
Developmental disordersNeurodevelopmental disorders
10.1038/S41591-024-02912-Z
ISSN:1078-8956
Single-cell and spatial transcriptomics reveal mechanisms of radioresistance and immune escape in recurrent nasopharyngeal carcinoma
Rui You•Qunlun Shen•Chao Lin•Kangning Dong•Xiao Liu等 23 人
Nature Genetics
2025
•2025/7/21
•00 p.1-16
Radiotherapy resistance and immune evasion are prominent features of recurrent nasopharyngeal carcinoma (rNPC). However, their mechanisms remain incompletely understood. Here, we conducted single-cell and spatial transcriptomics analysis of 39 tumors from 24 patients to reveal the microenvironmental...
Cancer microenvironmentHead and neck cancer
10.1038/S41588-025-02253-8
ISSN:1061-4036
Ancient DNA from Shimao city records kinship practices in Neolithic China
Zehui Chen•Jacob D. Gardner•Zhouyong Sun•E. Andrew Bennett•Qian Han等 26 人
Nature
2025
•2025/11/26
•00 p.1-9
The discovery of Shimao city (around 2300–1800 bce1), a premier state-level Neolithic fortified settlement in Shaanxi, China2, played an important role in helping us understand the emergence of socially stratified urban societies. However, key questions remain regarding how ancestry and kinship shap...
ArchaeologyPopulation genetics
10.1038/S41586-025-09799-X
ISSN:0028-0836
Immune checkpoints HLA-E:CD94-NKG2A and HLA-C:KIR2DL1 complementarily shield circulating tumor cells from NK-mediated immune surveillance
Xiaowei Liu•Fengli Zuo•Jinen Song•Leyi Tang•Xueyan Wang等 11 人
Cell Discovery
2024
•2024/2/9
•Vol.10 No.1 p.1-5
ImmunosurveillanceMetastasis
10.1038/S41421-024-00646-3
ISSN:2056-5968
Clinical implications of CSF-ctDNA positivity in newly diagnosed diffuse large B cell lymphoma
Jin-Hua Liang•Yi-Fan Wu•Hao-Rui Shen•Yue Li•Jun-Heng Liang等 19 人
Leukemia
2024
•2024/5/15
•00 p.1-12
The clinical implications of CSF-ctDNA positivity in newly diagnosed diffuse large B cell lymphoma (ND-DLBCL) remains largely unexplored. One hundred ND-DLBCL patients were consecutively enrolled as training cohort and another 26 ND-DLBCL patients were prospectively enrolled in validation cohor...
B-cell lymphomaChemotherapyMetastasis
10.1038/S41375-024-02279-7
ISSN:0887-6924
Poly(ADP-ribosylation) of P-TEFb by PARP1 disrupts phase separation to inhibit global transcription after DNA damage
Fu Huanyi•Liu Rongdiao•Jia Zixuan•Li Ran•Zhu Feifeng等 14 人
Nature Cell Biology
2022
•2022/4/7
•00 p.1-13
DNA damage shuts down genome-wide transcription to prevent transcriptional mutagenesis and to initiate repair signalling, but the mechanism to stall elongating RNA polymerase II (Pol II) is not fully understood. Central to the DNA damage response, poly(ADP-ribose) polymerase 1 (PARP1) initiates DNA ...
DNA damage and repairMolecular biophysicsPolyADP-ribosylationTranscription
10.1038/S41556-022-00872-5
ISSN:1465-7392
A multicenter single-arm clinical study of Chinese children’s cancer group-acute promyelocytic leukemia-2017 (CCCG-APL-2017) protocol
Lixian Chang•Ju Gao•Xiaoying Lei•Yingyi He•Shuquan Zhuang等 21 人
Signal Transduction And Targeted Therapy
2025
•2025/8/22
•Vol.10 No.1 p.1-9
The Realgar-Indigo Naturalis formula (RIF) is a proprietary Chinese medicine, which is one of the important drugs in the treatment of pediatric acute promyelocytic leukemia (APL). However, the dose of RIF in clinical application is not uniform and the long-term effectiveness and safety of combining ...
Haematological cancer
10.1038/S41392-025-02353-1
ISSN:2059-3635
miR-101/METTL3 axis induces autophagy by interrupting FOXG1/EIF3J-AS1 binding in gliomas
Yaping Yan•Shanshan Liu•Ailing Luo•Mansi Cai•Xiaohong Zhang等 11 人
Cell Death & Disease
2025
•2025/12/13
0The role of autophagy in glioma remains controversial, with long non-coding RNAs (lncRNAs) playing a crucial role in its regulation. N6-methyladenosine (m6A) modification influences lncRNA expression and function. Specifically, lncRNA EIF3J-AS1 acts as an oncogene in glioma, yet the mechanisms drivi...
CNS cancerMechanisms of disease
10.1038/S41419-025-08285-6
ISSN:2041-4889
Comparative study on genomic and epigenomic profiles of retinoblastoma or tuberous sclerosis complex via nanopore sequencing and a joint screening framework
Junting Wang•Chengyue Zhang•Li Zhang•Hong-juan Yao•Xiaohong Liu等 10 人
Cancer Gene Therapy
2023
•2023/12/25
•00 p.1-15
Recurrence and extraocular metastasis in advanced intraocular retinoblastoma (RB) are still major obstacles for successful treatment of Chinese children. Tuberous sclerosis complex (TSC) is a very rare, multisystemic genetic disorder characterized by hamartomatous growth. In this study, we aimed to ...
BiomarkersPaediatric cancer
10.1038/S41417-023-00714-Y
ISSN:0929-1903
Lactate derived from macrophages drives skin dermal fibroblasts phenotypic remodeling via MCT1-primed histone H3 lysine 23 lactylation in hypertrophic scar
Yixuan Yuan•Yujie Xiao•Jie Zou•Liang Luo•Mengyang Li等 18 人
Nature Communications
2026
•2026/2/12
•Vol.17 No.1 p.26940
Hypertrophic scar (HS) is a fibroproliferative disorder characterized by fibroblast hyperactivation and aberrant extracellular matrix deposition. This study identifies macrophage-derived lactate as a key mediator of fibroblast phenotypic remodeling via monocarboxylate transporter 1 (MCT1)-mediated h...
Mechanisms of diseasePost-translational modificationsSkin diseases
10.1038/S41467-026-69388-Y
ISSN:2041-1723
Single-cell and proteomic profiling unveil aberrant immune phenotypes in gestational diabetes following assisted reproductive technology
Hui Zhu•Jie Cai•Qinyan Xu•Liqi Xu•Da He等 18 人
Communications Biology
2026
•2026/1/29
•Vol.9 No.1 p.3350
Pregnant women undergoing assisted reproductive technology (ART) have an increased risk of gestational diabetes mellitus (GDM), potentially linked to altered immune regulation, but the underlying circulating immune features remain unclear. Here we show an integrated single-cell transcriptomic, immun...
EndocrinologyImmunology
10.1038/S42003-026-09615-W
ISSN:2399-3642
Targeting ADAR1 with a small molecule for the treatment of prostate cancer
Xiao Wang•Jiaxing Li•Yasheng Zhu•Hongtao Shen•Jiayu Ding等 23 人
Nature Cancer
2025
•2025/2/10
•00 p.1-19
Despite the initial response to androgen signaling therapy, most cases of prostate cancer (PCa) eventually relapse and remain incurable. The specific function of ADAR1 that governs PCa progression and specific inhibitors of ADAR are underexplored. In this study, we demonstrate that highly expressed ...
CancerOncogenesTarget identification
10.1038/S43018-025-00907-4
ISSN:2662-1347
Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese
Dan Zhou•Ming Wu•Qilong Tan•Liyang Sun•Yuanxing Tu等 20 人
Nature Communications
2025
•2025/8/9
•Vol.16 No.1 p.1-15
A substantial portion of lung cancer-associated genetic elements in East Asian populations remains unidentified, underscoring the need for large-scale genome-wide studies, particularly on non-coding regulation. We conducted a whole genome sequencing (WGS)-based genome-wide scan in 13,722 Chinese ind...
Genome-wide association studiesNon-small-cell lung cancer
10.1038/S41467-025-62459-6
ISSN:2041-1723
The bone marrow immune ecosystem shapes daratumumab acquired resistance in plasma cell myeloma
Yun Wang•Shuzhao Chen•Zhijian Liang•Robert Peter Gale•Shutong Liu等 14 人
Leukemia
2025
•2025/8/1
•00 p.1-12
Daratumumab, an anti-CD38 monoclonal antibody, is an effective therapy for plasma cell myeloma (PCM). However, many initial responders relapse. We compared paired samples from subjects pre-therapy and then acquired resistance to daratumumab. We first used single-cell RNA sequencing and digital spati...
Cancer microenvironmentTranslational research
10.1038/S41375-025-02712-5
ISSN:0887-6924
Cancer-associated fibroblasts expressing FSTL3 promote vasculogenic mimicry formation and drive colon cancer malignancy
Leqian Ying•Yini Zhu•Lu Zhang•Min Ji•Meidan Wang等 17 人
Cell Death & Disease
2025
•2025/10/6
•Vol.16 No.1 p.1-18
Anti-angiogenic therapies are commonly employed in colon cancer management, yet many patients eventually develop resistance and experience disease progression. Vasculogenic mimicry (VM)—the formation of tumor-derived vessel-like networks—has been recognized as one mechanism contributing to this resi...
Colon cancerExtracellular signalling moleculesPrognostic markersTargeted therapiesTumour biomarkers
10.1038/S41419-025-08009-W
ISSN:2041-4889
Endoplasmic reticulum stress promotes leukemic plasmacytoid dendritic cell differentiation skewing and immune suppression in acute myeloid leukemia
Xingcheng Yang•Juan Peng•Xia Mao•Lei Zhang•Shaolong He等 10 人
Leukemia
2026
•2026/8/3
•00 p.1-12
Mature plasmacytoid dendritic cell proliferation associated with acute myeloid leukemia (pDC-AML) is a distinct entity with poor prognosis. Yet, the mechanisms underlying the immune evasion and aberrant pDC expansion remain poorly understood. We performed multi-omic profiling of 18 pDC-AML cases, al...
Acute myeloid leukaemiaTumour immunology
10.1038/S41375-026-03080-4
ISSN:0887-6924
High-depth whole-genome sequencing identifies structure variants, copy number variants and short tandem repeats associated with Parkinson’s disease
Chaodong Wang•Hankui Liu•Xu-Ying Li•Jinghong Ma•Zhuqin Gu等 13 人
Npj Parkinson's Disease
2024
•2024/7/23
•Vol.10 No.1 p.1-14
While numerous single nucleotide variants and small indels have been identified in Parkinson’s disease (PD), the contribution of structural variants (SVs), copy number variants (CNVs), and short tandem repeats (STRs) remains poorly understood. Here we investigated the association using the high-dept...
Genome-wide association studiesNext-generation sequencingParkinson's disease
10.1038/S41531-024-00722-1
ISSN:2373-8057
Novel molecular subtypes of METex14 non-small cell lung cancer with distinct biological and clinical significance
Shengnan Chen•Tao Hu•Jikai Zhao•Qian Zhu•Jin Wang等 11 人
Npj Precision Oncology
2024
•2024/7/26
•Vol.8 No.1 p.1-14
Not all MET exon 14 skipping (METex14) NSCLC patients benefited from MET inhibitors. We hypothesized an inter-tumoral heterogeneity in METex14 NSCLC. Investigations at genomic and transcriptomic level were conducted in METex14 NSCLC samples from stage I-III and recurrent/metastatic patients as disco...
Non-small-cell lung cancerTumour heterogeneity
10.1038/S41698-024-00642-6
ISSN:2397-768X
PABPC3 drives ovarian cancer metastasis and drug sensitivity by downregulating CLDN1 expression
Hong Zhang•Yiping Lin•Mintao Ji•Yuhan Guo•Haisheng Liang等 18 人
Cell Death & Disease
2025
•2025/11/17
•Vol.16 No.1 p.8400
Ovarian cancer remains one of the most lethal malignancies affecting women, with its high mortality rate primarily attributed to the aggressive metastatic nature of the disease, leading to late-stage diagnoses. The challenges posed by tumor metastasis and treatment resistance significantly complicat...
Cancer
10.1038/S41419-025-08151-5
ISSN:2041-4889
Profiling and functional characterization of long noncoding RNAs during human tooth development
Xiuge Gu•Wei Wei•Chuan Wu•Jing Sun•Xiaoshan Wu等 14 人
International Journal Of Oral Science
2025
•2025/5/9
•Vol.17 No.1 p.1-12
The regulatory processes in developmental biology research are significantly influenced by long non-coding RNAs (lncRNAs). However, the dynamics of lncRNA expression during human tooth development remain poorly understood. In this research, we examined the lncRNAs present in the dental epithelium (D...
Cell biologyDevelopmental biology
10.1038/S41368-025-00375-7
ISSN:2049-3169
Single-cell transcriptomics reveals hair growth retardation mediated by aberrant connective tissue sheath contraction in male androgenetic alopecia
Guo Li•Li Yang•Shixin Duan•Mengting Chen•Yujin Zhang等 19 人
Nature Communications
2026
•2026/2/26
•Vol.17 No.1 p.32520
Androgenetic alopecia (AGA) manifests as progressive hair follicle (HF) miniaturization; however, its drivers remain poorly elucidated. Combining spatial and single-cell transcriptomics, we generate a concise single-cell atlas of anagen HFs in male AGA, revealing early changes in cell subpopulations...
Skin diseasesSkin stem cells
10.1038/S41467-026-70153-4
ISSN:2041-1723
Heterozygous de novo dominant negative mutation of REXO2 results in interferonopathy
Elina Idiiatullina•Mahmoud Al-Azab•Meng Lin•Katja Hrovat-Schaale•Ziyang Liu等 15 人
Nature Communications
2024
•2024/8/6
•Vol.15 No.1 p.1-15
Mitochondrial RNA (mtRNA) in the cytosol can trigger the innate immune sensor MDA5, and autoinflammatory disease due to type I IFN. Here, we show that a dominant negative mutation in the gene encoding the mitochondrial exonuclease REXO2 may cause interferonopathy by triggering the MDA5 pathway....
Inflammatory diseasesInterferonsRIG-I-like receptorsRNA decay
10.1038/S41467-024-50878-W
ISSN:2041-1723
All-trans retinoic acid suppresses systemic inflammation induced by severe fever with thrombocytopenia syndrome virus in mice
Xin Yu•Jianan Wu•Xiaohong Yin•Mengjia Yue•Yunfa Zhang等 18 人
Nature Microbiology
2026
•2026/7/20
•00 p.1-15
The vitamin A metabolite all-trans retinoic acid (ATRA) has immunoregulatory features, but its systemic role during viral infection is unclear. Here we show that patients infected with severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging tick-borne infection, have depleted serum vi...
Acute inflammationVirus–host interactions
10.1038/S41564-026-02411-6
ISSN:2058-5276
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
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
Elevated glutamate impedes anti-HIV-1 CD8 + T cell responses in HIV-1-infected individuals on antiretroviral therapy
You-Yuan Wang•Cheng Zhen•Wei Hu•Hui-Huang Huang•Yan-Jun Li等 26 人
Communications Biology
2023
•2023/7/7
•Vol.6 No.1 p.1-12
CD8 + T cells are essential for long-lasting HIV-1 control and have been harnessed to develop therapeutic and preventive approaches for people living with HIV-1 (PLWH). HIV-1 infection induces marked metabolic alterations. However, it is unclear whether these changes affect the anti-HIV function of ...
CD8-positive T cellsHIV infections
10.1038/S42003-023-04975-Z
ISSN:2399-3642
The 1000 Chinese Pangenome empowers medical and population genetics
Yifei Wang•Zhongqu Duan•Dan Chen•Dandan Shi•Yi Ding等 21 人
Nature
2026
•2026/4/1
•00 p.1-10
Pangenomes are revolutionizing our ability to resolve genomic regions with complex variations1. However, existing human pangenomes2,3, constrained by small sample sizes, provide limited utility for medical and population genetic applications. Here we generated 1,116 diploid genome assemblies (55 de ...
Genetic association studyGenetic variationGenome assembly algorithmsSequencingStructural variation
10.1038/S41586-026-10315-Y
ISSN:0028-0836
Sintilimab (anti-PD-1 antibody) plus chidamide (histone deacetylase inhibitor) in relapsed or refractory extranodal natural killer T-cell lymphoma (SCENT): a phase Ib/II study
Yan Gao•Haixia He•Xueping Li•Liling Zhang•Wei Xu等 24 人
Signal Transduction And Targeted Therapy
2024
•2024/5/17
•Vol.9 No.1 p.1-9
Anti-PD-1 antibodies are a favorable treatment for relapsed or refractory extranodal natural killer T cell lymphoma (RR-ENKTL), however, the complete response (CR) rate and the duration of response (DOR) need to be improved. This phase 1b/2 study investigated the safety and efficacy of sintilimab, a...
Clinical trialsHaematological cancerPredictive markers
10.1038/S41392-024-01825-0
ISSN:2059-3635
Ancient DNA reveals the population interactions and a Neolithic patrilineal community in Northern Yangtze Region
Tingyu Yang•Jianing He•Chunmei Li•Chao Ning•Tianming Zhang等 17 人
Nature Communications
2025
•2025/9/30
•Vol.16 No.1 p.1-14
The scarcity of ancient genomes of early rice cultivators has hindered our understanding of their genetic profiles and dynamic interactions with millet cultivators. In this study, we analyzed 58 ancient genomes from Baligang, a long-term settlement situated on the northern rim of the Middle Yangtze ...
Population geneticsSocial evolution
10.1038/S41467-025-63743-1
ISSN:2041-1723
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
HLA-A+ tertiary lymphoid structures with reactivated tumor infiltrating lymphocytes are associated with a positive immunotherapy response in esophageal squamous cell carcinoma
Dandan Zhang•Dongxian Jiang•Liping Jiang•Jiakang Ma•Xiaobing Wang等 17 人
British Journal Of Cancer
2024
•2024/5/18
•00 p.1-12
Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. However, the overall response rate to ICB therapy remains low in esophageal squamous cell carcinoma (ESCC). This study aimed to identify biomarkers of ICB therapy for ESCC and interrogate its po...
Cancer microenvironmentOesophageal cancerTumour biomarkersTumour immunology
10.1038/S41416-024-02712-9
ISSN:0007-0920
Single-cell analysis reveals the chemotherapy-induced cellular reprogramming and novel therapeutic targets in relapsed/refractory acute myeloid leukemia
Li Kening•Du Yuxin•Cai Yun•Liu Wenjie•Lv Yan等 20 人
Leukemia
2022
•2022/12/21
•Vol.37 No.2 p.308-325
Chemoresistance and relapse are the leading cause of AML-related deaths. Utilizing single-cell RNA sequencing (scRNA-seq), we dissected the cellular states of bone marrow samples from primary refractory or short-term relapsed AML patients and defined the transcriptional intratumoral heterogeneity. W...
Acute myeloid leukaemiaCell biology
10.1038/S41375-022-01789-6
ISSN:0887-6924
Single-cell transcriptome analysis indicates fatty acid metabolism-mediated metastasis and immunosuppression in male breast cancer
Handong Sun•Lishen Zhang•Zhonglin Wang•Danling Gu•Mengyan Zhu等 43 人
Nature Communications
2023
•2023/9/11
•Vol.14 No.1 p.1-18
Male breast cancer (MBC) is a rare but aggressive malignancy with cellular and immunological characteristics that remain unclear. Here, we perform transcriptomic analysis for 111,038 single cells from tumor tissues of six MBC and thirteen female breast cancer (FBC) patients. We find that that MBC ha...
Breast cancerMechanisms of disease
10.1038/S41467-023-41318-2
ISSN:2041-1723