Genome Sequence Archive - CNCB-NGDC
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China, Fuzhou
the National Genomics Data Center
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相关论文
410A missense mutation in Pitx2 leads to early-onset glaucoma via NRF2-YAP1 axis
Yang Yeming•Li Xiao•Wang Jieping•Tan Junkai•Fitzmaurice Bernie等 12 人
Cell Death & Disease
2021
•2021/10/29
•Vol.12 No.11 p.1-15
Glaucoma is a leading cause of blindness, affecting 70 million people worldwide. Owing to the similarity in anatomy and physiology between human and mouse eyes and the ability to genetically manipulate mice, mouse models are an invaluable resource for studying mechanisms underlying disease phenotype...
Disease modelNeurodegeneration
10.1038/S41419-021-04331-1
ISSN:2041-4889
Single-cell EpiChem jointly measures drug–chromatin binding and multimodal epigenome
Chao Dong•Xiaoxuan Meng•Tong Zhang•Zhifang Guo•Yaxi Liu等 12 人
Nature Methods
2024
•2024/7/18
•00 p.1-10
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...
Biological techniquesBiotechnology
10.1038/S41592-024-02360-0
ISSN:1548-7091
Genome structure and evolution of Antirrhinum majus L
Miaomiao Li•Dongfen Zhang•Qiang Gao•Yingfeng Luo•Hui Zhang等 35 人
Nature Plants
2019
•2019/1/28
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Snapdragon (Antirrhinum majus L.), a member of the Plantaginaceae family, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a near-complete genome assembly of A. majus cultivar JI7 (A. majus cv....
GenomicsPlant sciences
10.1038/S41477-018-0349-9
ISSN:2055-0278
Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing
Han Dong•Yongsheng Gao•Zhengyi Cai•Yi Li•Xing Li等 7 人
Nature Communications
2026
•2026/1/14
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Despite the extensive studies of individual RNA modifications, the lack of methods to detect multiple modification types simultaneously has left the global epitranscriptomic landscape and its underlying crosstalk largely unexplored. Here, we present ORCA (Omni-RNA modification Characterization and A...
Gene expressionRNA modificationRNA sequencingRNA splicing
10.1038/S41467-026-68419-Y
ISSN:2041-1723
Jag1/2 maintain esophageal homeostasis and suppress foregut tumorigenesis by restricting the basal progenitor cell pool
Haidi Huang•Yu Jiang•Jiangying Liu•Dan Luo•Jianghong Yuan等 20 人
Nature Communications
2024
•2024/5/15
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Basal progenitor cells are crucial for maintaining foregut (the esophagus and forestomach) homeostasis. When their function is dysregulated, it can promote inflammation and tumorigenesis. However, the mechanisms underlying these processes remain largely unclear. Here, we employ genetic mouse models ...
Adult stem cellsCell proliferationDifferentiationOesophageal cancer
10.1038/S41467-024-48347-5
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Eastern coastal Chinese diet associated with reduced obesity and improved cardiometabolic health
Yuwei Shi•Juntao Kan•Yuji Yu•Xiaoguang Yang•Wei He等 20 人
Nature Health
2026
•2026/3/2
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The dietary habits from eastern coastal China have recently garnered widespread attention for their potential health benefits; however, empirical evidence remains limited. Here we applied unsupervised clustering to dietary data from 8,931 participants in the WELL-China cohort from the eastern coasta...
BacteriaCardiovascular diseasesHealth policyNutrition
10.1038/S44360-026-00079-0
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Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study
Yukun Zhang•Xiaoxue Zhang•Chong Li•Huibin Tian•Xiuxiu Weng等 16 人
Npj Biofilms And Microbiomes
2024
•2024/11/17
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Rumen microbiotas are known to influence the fat deposition (FD) in sheep, but controversy over causality remains unresolved. Here, we performed microbiome-wide association studies (MWAS), microbiome genome-wide association analysis (mbGWAS) and bidirectional mendelian randomization (MR) analyses on...
MicrobiomeNext-generation sequencing
10.1038/S41522-024-00606-5
ISSN:2055-5008
A multi-omics molecular landscape of 30 tissues in aging female rhesus macaques
Gong-Hua Li•Xiang-Qing Zhu•Fu-Hui Xiao•Xilong Zhao•Longbao Lv等 18 人
Nature Methods
2025
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A systematic investigation of aging patterns across virtually all major tissues in nonhuman primates, our evolutionarily closest relatives, can provide valuable insights into tissue aging in humans, which is still elusive largely due to the difficulty in sampling. Here, we generated and analyzed mul...
Genetic modelsProteomicsSequencingTranscriptomicsZoology
10.1038/S41592-025-02912-Y
ISSN:1548-7091
In vivo prime editing rescues photoreceptor degeneration in nonsense mutant retinitis pigmentosa
Yidian Fu•Xiaoyu He•Liang Ma•Xin D. Gao•Pengpeng Liu等 12 人
Nature Communications
2025
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The next-generation gene editing tool, prime editing (PE), is adept at correcting point mutations precisely with high editing efficiency and rare off-target events and shows promising therapeutic value in treating hereditary diseases. Retinitis pigmentosa (RP) is the most common type of inherited re...
CRISPR-Cas9 genome editingGenetic engineeringHereditary eye disease
10.1038/S41467-025-57628-6
ISSN:2041-1723
IL-17a induces age-related olfactory dysfunction by impairing regeneration and promoting respiratory metaplasia in mice
Shenglei Wang•Xudong Cha•Yingqi Xie•Zengyi Xu•Boyu Cai等 12 人
Nature Communications
2025
•2025/12/29
0The olfactory epithelium (OE) undergoes life-long renewal and regeneration. This process is supported by the globose basal cells (GBC) during the homeostatic state, as well as horizontal basal cells (HBC) during severe damage. Inflamm-aging refers to the low-grade, chronic and progressive state of h...
InterleukinsMucosal immunologyOlfactory systemRegenerationRespiratory tract diseases
10.1038/S41467-025-67786-2
ISSN:2041-1723
The long noncoding RNA Synage regulates synapse stability and neuronal function in the cerebellum
Fei Wang•Qianqian Wang•Baowei Liu•Lisheng Mei•Sisi Ma等 14 人
Cell Death & Differentiation
2021
•2021/3/24
•00 p.1-17
The brain is known to express many long noncoding RNAs (lncRNAs); however, whether and how these lncRNAs function in modulating synaptic stability remains unclear. Here, we report a cerebellum highly expressed lncRNA, Synage, regulating synaptic stability via at least two mechanisms. One is through ...
Cell biologyMolecular biologyNeuroscienceRNA
10.1038/S41418-021-00774-3
ISSN:1350-9047
Transcriptomic response analysis of rubber tree saplings to water-deficit stress at single-cell resolution
Chengwen Gao•Changli Mao•Ziyan Liu•Cheng Zheng•Ni Liu等 10 人
Communications Biology
2025
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The rubber tree (Hevea brasiliensis) is increasingly affected by climate change, particularly by intensified water-deficit stress, which impacts latex yield and plantation productivity. Understanding how rubber trees adapt to water-deficit stress at the molecular level is crucial for improving their...
DroughtPlant molecular biology
10.1038/S42003-025-09046-Z
ISSN:2399-3642
Chitinase-like proteins de-N-glycosylating CD36 modify cholesterol metabolism in atherosclerotic macrophages
Yu Wang•Jing Zhang•Meiyang Fan•Xianbin Hou•Xiaomeng Li等 21 人
Nature Communications
2026
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0Polymorphisms of mouse chitinase-like protein 3 (Chil3), a member of the mammalian chitinase-like protein (CLP) family, have been demonstrated to be associated with inflammatory diseases by regulating lipid metabolism. However, the specific immunomodulatory impacts of CLPs, mainly mouse CHIL3 and it...
AtherosclerosisCardiovascular diseasesFoam cellsGlycosylationInnate immunity
10.1038/S41467-026-71388-X
ISSN:2041-1723
Single-cell transcriptional responses of T cells during microsporidia infection
Yunlin Tang•Lu Cao•Jiangyan Jin•Tangxin Li•Yebo Chen等 11 人
Communications Biology
2025
•2025/4/5
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T cells have been reported to play critical roles in preventing of microsporidia dissemination. However, there roles and functions of each subset remain unclear. Here in the study, we performed a thorough analysis of murine splenic T-cell response analysis via single-cell RNA sequencing during micro...
Fungal infectionInfectionPathogens
10.1038/S42003-025-07990-4
ISSN:2399-3642
TIE1 acts as a maternal brake on fertilization-independent endosperm development by associating with PRC2 to enforce imprinting
Zeliang Zhang•Xinxue Wang•Rongrong Yuan•Yiyi Li•Yige Pan等 8 人
Nature Plants
2026
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•00 p.1-13
Fully autonomous apomixis with fertilization-independent embryo and endosperm development enables the production of clonal seeds to fix crop hybrid vigour. However, the mechanisms underlying autonomous endosperm development remain unclear. Here we show that TIE1 acts as a maternally expressed transc...
Plant embryogenesisSeed development
10.1038/S41477-026-02344-2
ISSN:2055-0278
Decoding the genomic landscape of chromatin-associated biomolecular condensates
Zhaowei Yu•Qi Wang•Qichen Zhang•Yawen Tian•Guo Yan等 8 人
Nature Communications
2024
•2024/8/13
•Vol.15 No.1 p.1-16
Biomolecular condensates play a significant role in chromatin activities, primarily by concentrating and compartmentalizing proteins and/or nucleic acids. However, their genomic landscapes and compositions remain largely unexplored due to a lack of dedicated computational tools for systematic identi...
BioinformaticsData miningGenomics
10.1038/S41467-024-51426-2
ISSN:2041-1723
Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens
Zhang Yunhua•Cai Tingwei•Yuan Maojun•Li Zhao•Jin Ruoheng等 14 人
Npj Biofilms And Microbiomes
2023
•2023/1/12
•Vol.9 No.1 p.1-8
Microbiome-mediated insecticide resistance is an emerging phenomenon found in insect pests. However, microbiome composition can vary by host genotype and environmental factors, but how these variations may be associated with insecticide resistance phenotype remains unclear. In this study, we compare...
Microbial ecologyMicrobiome
10.1038/S41522-023-00369-5
ISSN:2055-5008
Generation of live mice from haploid ESCs with germline-DMR deletions or switch
Yongjian Ma•Meng Yan•Zhenfei Xie•Hongling Zhang•Zhoujie Li等 10 人
Cell Discovery
2025
•2025/1/21
•Vol.11 No.1 p.1-14
Genomic imprinting is required for sexual reproduction and embryonic development of mammals, in which, differentially methylated regions (DMRs) regulate the parent-specific monoallelic expression of imprinted genes. Numerous studies on imprinted genes have highlighted their critical roles in develop...
DNA methylationEmbryonic stem cellsEpigenetic memoryReprogramming
10.1038/S41421-024-00757-X
ISSN:2056-5968
Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data
Xingtan Zhang•Shengcheng Zhang•Qian Zhao•Ray Ming•Haibao Tang
Nature Plants
2019
•2019/8/5
•Vol.5 No.8 p.833-845
Construction of chromosome-level assembly is a vital step in achieving the goal of a ‘Platinum’ genome, but it remains a major challenge to assemble and anchor sequences to chromosomes in autopolyploid or highly heterozygous genomes. High-throughput chromosome conformation capture (Hi-C) technology ...
BioinformaticsComparative genomicsDNA sequencingPolyploidy in plants
10.1038/S41477-019-0487-8
ISSN:2055-0278
The m 6 A methylome of SARS-CoV-2 in host cells
Jun’e Liu•Yan-Peng Xu•Kai Li•Qing Ye•Hang-Yu Zhou等 17 人
Cell Research
2021
•2021/1/28
•Vol.31 No.4 p.404-414
The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency because of its rapid spread and high mortality. The molecular mechanism of interaction between host and viral genomic RNA is yet unclear. We demonstrate herein that SARS-CoV-2 ...
Mechanisms of diseaseRNA modification
10.1038/S41422-020-00465-7
ISSN:1001-0602
Improving erectile function in diabetic male mice by rescuing depalmitoylated FBP1 to reduce cavernosal lactate
Ming Xiao•Wanyang Guo•Ruijiang Zeng•Shuiqing Wu•Xin Jin
Nature Communications
2026
•2026/1/16
•Vol.17 No.1 p.17400
The high prevalence of diabetes mellitus-induced erectile dysfunction (DMED) in males and the limited efficacy of existing therapies necessitate deeper mechanistic insights. We identify pathological lactate accumulation in the corpus cavernosum as a major driver of DMED in male mice, promoting struc...
Erectile dysfunctionPathogenesis
10.1038/S41467-026-68443-Y
ISSN:2041-1723
P-selectin overexpression impairs hematopoietic stem cell homeostasis via inflammatory receptor-mediated proliferation and differentiation
Wei He•Huandi Qiu•Yunyu Feng•Qiang Qiu•Li Zheng等 10 人
Cell Death & Disease
2025
•2025/10/21
•Vol.16 No.1 p.1-15
Hematopoietic stem cells (HSC) sustain lifelong blood and immune system homeostasis. This study identifies P-selectin as a pivotal regulator of HSC function under aging and inflammatory stress. We observed pronounced Selp upregulation in aged HSC and inflammatory contexts, which drives excessive pro...
Chronic inflammationChronic lymphocytic leukaemiaHaematopoietic stem cellsSenescence
10.1038/S41419-025-08050-9
ISSN:2041-4889
Inhibition of immunoglobulin E attenuates pulmonary hypertension
Shu Ting•Liu Ying•Zhou Yitian•Zhou Zhou•Li Bolun等 19 人
Nature Cardiovascular Research
2022
•2022/7/7
•Vol.1 No.7 p.665-678
Pulmonary hypertension (PH) is a severe cardiopulmonary disease characterized by pulmonary vascular remodeling. Immunoglobulin E (IgE) is known to participate in aortic vascular remodeling, but whether IgE mediates pulmonary vascular disease is unknown. In the present study, we found serum IgE eleva...
Adaptive immunityImmunotherapyTranslational researchVascular diseases
10.1038/S44161-022-00095-9
ISSN:2731-0590
Structural basis for linker histone H5–nucleosome binding and chromatin fiber compaction
Wenyan Li•Jie Hu•Feng Song•Juan Yu•Xin Peng等 26 人
Cell Research
2024
•2024/8/5
•00 p.1-18
The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin ...
Chromatin structureCryoelectron microscopy
10.1038/S41422-024-01009-Z
ISSN:1748-7838
Single-cell profiling reveals the trajectory of FOLR2-expressing tumor-associated macrophages to regulatory T cells in the progression of lung adenocarcinoma
Chan Xiang•Min Zhang•Zhanxian Shang•Shengnan Chen•Jikai Zhao等 15 人
Cell Death & Disease
2023
•2023/8/2
•Vol.14 No.8 p.1-12
An immunosuppressive microenvironment enriched with regulatory CD4+ T lymphocytes (Tregs) facilitates the progression of lung adenocarcinoma (LUAD). This study aims to investigate the cellular mechanism underlying the formation of the immunosuppressive microenvironment in LUAD. LUAD samples (n = 12)...
Cancer microenvironmentNon-small-cell lung cancer
10.1038/S41419-023-06021-6
ISSN:2041-4889
Natural degradation of RNA polymerase II is essential for oocyte chromatin reorganization and maternal-to-zygotic transition
Jing Wang•Wang Li•Jing Guo•Xiaoming Xu•Ge Lin等 7 人
Nature Communications
2025
•2025/12/12
0The final step of oocyte growth, which reorganizes chromatin from the non-surrounded nucleolus (NSN) to the surrounded nucleolus (SN) configuration is essential for embryonic development after meiotic maturation and fertilization. The underlying mechanisms remain unknown. We identify RNA polymerase ...
Nuclear organizationOogenesis
10.1038/S41467-025-67476-Z
ISSN:2041-1723
Maternal vitamin B1 is a determinant for the fate of primordial follicle formation in offspring
Wen-Xiang Liu•Hai-Ning Liu•Zhan-Ping Weng•Qi Geng•Yue Zhang等 9 人
Nature Communications
2023
•2023/11/16
•Vol.14 No.1 p.1-17
The mediation of maternal-embryonic cross-talk via nutrition and metabolism impacts greatly on offspring health. However, the underlying key interfaces remain elusive. Here, we determined that maternal high-fat diet during pregnancy in mice impaired preservation of the ovarian primordial follicle po...
InfertilityNutrition disordersOogenesis
10.1038/S41467-023-43261-8
ISSN:2041-1723
Phenotypic plasticity co-varies with elevational range in two avian species of elevational migrants in the Himalayas
Boning Xue•Huishang She•Lirong Zuo•John M. Bates•Zachary A. Cheviron等 9 人
Nature Communications
2025
•2025/6/18
•Vol.16 No.1 p.1-13
Montane birds represent a large proportion of global avian biodiversity and are highly sensitive to seasonal climatic shifts. Many montane species undertake elevational migration in response to seasonal climate change, but how they cope with disparate environmental pressures along the elevational gr...
Evolutionary ecologyMolecular ecologyMolecular evolution
10.1038/S41467-025-60770-W
ISSN:2041-1723
Targeting Cend1-Atp5f1b interaction rescues mitochondrial dysfunction and ameliorates ischemic brain injury
Hao Li•Yi Yang•Meng Zhang•Eric Guo•Zeheng Li等 10 人
Communications Biology
2025
•2025/12/31
0Mitochondrial dysfunction is a critical contributor to neuronal damage in acute ischemic stroke (AIS), and targeting mitochondrial function represents a promising therapeutic strategy. This study unveils the pivotal role of Cend1 protein in ischemic stroke and elucidates its underlying mechanisms. U...
StrokeTarget identification
10.1038/S42003-025-09419-4
ISSN:2399-3642
Modeling post-gastrula development via bidirectional pluripotent stem cells
Kuisheng Liu•Zihui Yan•Dandan Bai•Rui Jiang•Yan Bi等 30 人
Cell Research
2025
•2025/8/29
•Vol.35 No.12 p.954-969
The absence of stem cells capable of efficiently generating both trophoblast and epiblast lineages has hindered precise recapitulation of embryonic development. Through high-content chemical screening, we established an (AS and LY) AL medium to generate mouse bidirectional pluripotent stem cell...
PluripotencyPluripotent stem cells
10.1038/S41422-025-01172-X
ISSN:1748-7838
A first-in-class pulsatile FXR agonist for bile-acid-related liver diseases
Yi Zang•Jingjing Shi•Guanguan Zhao•Bixi Tang•Mingliang Liu等 21 人
Nature
2026
•2026/6/10
•00 p.1-11
Nuclear receptors are central regulators of metabolism1, yet therapeutic strategies that enforce continuous receptor activation frequently lead to reduced efficacy and unacceptable toxicity. Here we report a first-principles drug design strategy that aligns pharmacokinetics with physiological signal...
Drug discoveryMetabolic diseases
10.1038/S41586-026-10633-1
ISSN:0028-0836
Transcriptomic and spatial GABAergic neuron subtypes in zona incerta mediate distinct innate behaviors
Mengyue Zhu•Jieqiao Peng•Mi Wang•Shan Lin•Huiying Zhang等 12 人
Nature Communications
2025
•2025/4/1
•Vol.16 No.1 p.1-19
Understanding the anatomical connection and behaviors of transcriptomic neuron subtypes is critical to delineating cell type-specific functions in the brain. Here we integrated single-nucleus transcriptomic sequencing, in vivo circuit mapping, optogenetic and chemogenetic approaches to dissect the m...
Cellular neuroscienceNeural circuits
10.1038/S41467-025-57896-2
ISSN:2041-1723
NF-κB-activated oncogene inhibition strategy for cancer gene therapy
Wei Dai•Jian Wu•Yingchun Shui•Qiuyue Wu•Jinke Wang等 6 人
Cancer Gene Therapy
2024
•2024/9/3
•00 p.1-14
NF-κB is a promising target for cancer treatment because of its overactivation in almost all cancers but countless NF-κB inhibitors rarely became clinical drugs due to side effects. In contrast to traditional cancer treatments aimed at inhibiting NF-κB activity, this study develop a novel approach t...
Gene therapyTargeted therapies
10.1038/S41417-024-00828-X
ISSN:0929-1903
Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition
Yusha Liu•Peter Carbonetto•Jason Willwerscheid•Scott A. Oakes•Kay F. Macleod等 6 人
Nature Genetics
2025
•2025/1/2
•00 p.1-11
Profiling tumors with single-cell RNA sequencing has the potential to identify recurrent patterns of transcription variation related to cancer progression, and to produce therapeutically relevant insights. However, strong intertumor heterogeneity can obscure more subtle patterns that are shared acro...
CancerComputational biology and bioinformaticsStatistics
10.1038/S41588-024-01997-Z
ISSN:1061-4036
Genome evolution and diversity of wild and cultivated potatoes
Tang Dié•Jia Yuxin•Zhang Jinzhe•Li Hongbo•Cheng Lin等 19 人
Nature
2022
•2022/6/8
•Vol.606 No.7914 p.535-541
Potato (Solanum tuberosum L.) is the world’s most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and producti...
Agricultural geneticsAgricultureEvolutionary geneticsGenomicsPlant breeding
10.1038/S41586-022-04822-X
ISSN:0028-0836
Whole genome sequencing identifies genetic variants associated with neurogenic inflammation in rosacea
Zhili Deng•Mengting Chen•Zhixiang Zhao•Wenqin Xiao•Tangxiele Liu等 20 人
Nature Communications
2023
•2023/7/5
•Vol.14 No.1 p.1-15
Rosacea is a chronic inflammatory skin disorder with high incidence rate. Although genetic predisposition to rosacea is suggested by existing evidence, the genetic basis remains largely unknown. Here we present the integrated results of whole genome sequencing (WGS) in 3 large rosacea families and w...
Acne vulgarisChronic inflammationDisease geneticsNeuroimmunology
10.1038/S41467-023-39761-2
ISSN:2041-1723
NAD+ dependent UPRmt activation underlies intestinal aging caused by mitochondrial DNA mutations
Liang Yang•Zifeng Ruan•Xiaobing Lin•Hao Wang•Yanmin Xin等 15 人
Nature Communications
2024
•2024/1/16
•Vol.15 No.1 p.1-15
Aging in mammals is accompanied by an imbalance of intestinal homeostasis and accumulation of mitochondrial DNA (mtDNA) mutations. However, little is known about how accumulated mtDNA mutations modulate intestinal homeostasis. We observe the accumulation of mtDNA mutations in the small intestine of ...
MitochondriaMutationStem cells
10.1038/S41467-024-44808-Z
ISSN:2041-1723
Small RNA sequencing analysis of exosomes derived from umbilical plasma in IUGR lambs
Jiawei Lu•Huixia Li•Xiaomin Zheng•Yuan Liu•Peng Zhao
Communications Biology
2023
•2023/9/15
•Vol.6 No.1 p.1-13
During the summer, pregnant ewes experience heat stress, leading to the occurrence of IUGR lambs. This study aims to explore the biomarkers of exosomal miRNAs derived from umbilical plasma in both IUGR and normal Hu lambs. We establish a heat-stressed Hu sheep model during mid-late gestation and sel...
Diagnostic markersIntrauterine growth
10.1038/S42003-023-05276-1
ISSN:2399-3642
Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
Xiao Feng•Qipian Chen•Weihong Wu•Jiexin Wang•Guohong Li等 12 人
Nature Communications
2024
•2024/2/22
•Vol.15 No.1 p.1-15
Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we prese...
Evolutionary biologyEvolutionary geneticsGenome evolutionPlant evolution
10.1038/S41467-024-46080-7
ISSN:2041-1723
O-GlcNAc and phosphorylation modifications on HtL1/FBA10 regulate wheat vernalization for flowering
Pengfang Yang•Yangyang Liu•Qi Dong•Yuting Miao•Jianlong Zhang等 13 人
Nature Communications
2025
•2025/12/27
0Vernalization-regulated flowering is vital for wheat yield and geographical distribution, and the diversity of flowering time genes is essential for the breeding of climate-resilient varieties. Sugars have long been recognized in regulating flowering; however, the intrinsic connection between carboh...
Plant developmentPlant geneticsVernalization
10.1038/S41467-025-67734-0
ISSN:2041-1723
The rise of baobab trees in Madagascar
Jun-Nan Wan•Sheng-Wei Wang•Andrew R. Leitch•Ilia J. Leitch•Jian-Bo Jian等 22 人
Nature
2024
•2024/5/15
•00 p.1-9
The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight ex...
BiodiversityConservation genomicsPhylogeneticsPlant evolution
10.1038/S41586-024-07447-4
ISSN:0028-0836
Characteristics and significance of peripheral blood T-cell receptor repertoire features in patients with indeterminate lung nodules
Luo Huaichao•Zu Ruiling•Huang Ziru•Li Yingqiang•Liao Yulin等 11 人
Signal Transduction And Targeted Therapy
2022
•2022/10/10
•Vol.7 No.1 p.1-4
Lung cancerPredictive markers
10.1038/S41392-022-01169-7
ISSN:2059-3635
Efficient assembly of nanopore reads via highly accurate and intact error correction
Ying Chen•Fan Nie•Shang-Qian Xie•Ying-Feng Zheng•Qi Dai等 15 人
Nature Communications
2021
•2021/1/4
•Vol.12 No.1 p.1-10
Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences d...
Computational modelsDNA sequencingGenome assembly algorithms
10.1038/S41467-020-20236-7
ISSN:2041-1723
CREB suppresses PGRP-SC2 to drive age-related immune senescence and gut dysbiosis in Drosophila
Saifei Wang•Bohan Qi•Peng Ma•Yao Zhang•Youjie Yin等 7 人
Cell Death Discovery
2026
•2026/2/24
•Vol.12 No.1 p.1080
The maintenance of immune homeostasis is critical for tissue health and longevity, yet the regulatory mechanisms linking immune modulation to aging remain poorly understood. Here we found that the transcription factor cAMP response element-binding protein (CREB), activated by JNK signaling in aging ...
Cell death and immune responseGene regulation in immune cellsImmunogenetics
10.1038/S41420-026-02955-W
ISSN:2058-7716
The m6A reader PRRC2A is essential for meiosis I completion during spermatogenesis
Tan Xinshui•Zheng Caihong•Zhuang Yinghua•Jin Pengpeng•Wang Fengchao
Nature Communications
2023
•2023/3/24
•Vol.14 No.1 p.1-18
N6-methyladenosine (m6A) and its reader proteins YTHDC1, YTHDC2, and YTHDF2 have been shown to exert essential functions during spermatogenesis. However, much remains unknown about m6A regulation mechanisms and the functions of specific readers during the meiotic cell cycle. Here, we show that the m...
EpigeneticsRNA modificationSpermatogenesis
10.1038/S41467-023-37252-Y
ISSN:2041-1723
Physiological premature aging of ovarian blood vessels leads to decline in fertility in middle-aged mice
Lu Mu•Ge Wang•Xuebing Yang•Jing Liang•Huan Tong等 13 人
Nature Communications
2025
•2025/1/2
•Vol.16 No.1 p.1-17
Ovarian function declines significantly as females enter middle-age, but the mechanisms underlying this decline remain unclear. Here, we utilize whole-organ imaging to observe a notable decrease in ovarian blood vessel (oBV) density and angiogenesis intensity of middle-aged mice. This leads to a dim...
AgeingDrug developmentMenopause
10.1038/S41467-024-55509-Y
ISSN:2041-1723
GATA2 promotes castration-resistant prostate cancer development by suppressing IFN-β axis-mediated antitumor immunity
Zige Jin•Hanling Wang•Ruxian Tang•Biying Pan•Hui-Ju Lee等 9 人
Oncogene
2024
•2024/7/27
•00 p.1-16
Castration-resistant prostate cancer (CRPC) nearly inevitably develops after long-term treatment with androgen deprivation therapy (ADT), leading to significant mortality. Investigating the mechanisms driving CRPC development is imperative. Here, we determined that the pioneer transcription factor G...
ImmunosurveillanceProstate cancer
10.1038/S41388-024-03107-Z
ISSN:0950-9232
AMPK-PDZD8-GLS1 axis mediates calorie restriction-induced lifespan extension
Mengqi Li•Yu Wang•Xiaoyan Wei•Wei-Feng Cai•Yan-Hui Liu等 16 人
Cell Research
2024
•2024/9/19
•00 p.1-4
AgeingNutrient signallingStress signalling
10.1038/S41422-024-01021-3
ISSN:1748-7838
Prostaglandin E2-driven dedifferentiation of Schwann cells leads to perineural invasion in pancreatic ductal adenocarcinoma
Ling Wang•Qicai Liu•Zhibo Zhang•Shizhong Yang•Juan Tang等 12 人
Signal Transduction And Targeted Therapy
2026
•2026/4/7
•Vol.11 No.1 p.1220
Perineural invasion (PNI), a prominent pathological feature of pancreatic ductal adenocarcinoma (PDAC), is closely associated with poor prognosis. Clarifying its mechanism is therefore critical for developing new therapies. Recent research has focused on the crosstalk between tumors and Schwann cell...
Gastrointestinal cancer
10.1038/S41392-026-02648-X
ISSN:2059-3635
Fat mass and obesity-associated protein regulates RNA methylation associated with depression-like behavior in mice
Liu Shu•Xiu Jianbo•Zhu Caiyun•Meng Kexin•Li Chen等 13 人
Nature Communications
2021
•2021/11/26
•Vol.12 No.1 p.1-13
Post-transcriptional modifications of RNA, such as RNA methylation, can epigenetically regulate behavior, for instance learning and memory. However, it is unclear whether RNA methylation plays a critical role in the pathophysiology of major depression disorder (MDD). Here, we report that expression ...
DepressionMolecular neuroscienceRNA modification
10.1038/S41467-021-27044-7
ISSN:2041-1723
Intestinal DHA-PA-PG axis promotes digestive organ expansion by mediating usage of maternally deposited yolk lipids
Zhengfang Chen•Mudan He•Houpeng Wang•Xuehui Li•Ruirui Qin等 12 人
Nature Communications
2024
•2024/11/12
•Vol.15 No.1 p.1-15
Although the metabolism of yolk lipids such as docosahexaenoic acid (DHA) is pivotal for embryonic development, the underlying mechanism remains elusive. Here we find that the zebrafish hydroxysteroid (17-β) dehydrogenase 12a (hsd17b12a), which encodes an intestinal epithelial-specific enzyme, is es...
Cell deathDevelopmentOrganogenesis
10.1038/S41467-024-54258-2
ISSN:2041-1723
Post-transcriptional control of endogenous retroviruses by L1td1 suppresses totipotency acquisition in pluripotent stem cells
Yi Wu•Yang Liu•Yile Huang•Zhihong Hao•Wenxin Li等 11 人
Cell Discovery
2026
•2026/1/20
•Vol.12 No.1 p.70
Cell biologyStem cells
10.1038/S41421-025-00864-3
ISSN:2056-5968
In vivo adenine base editing reverts C282Y and improves iron metabolism in hemochromatosis mice
Rovai Alice•Chung BoMee•Hu Qingluan•Hook Sebastian•Yuan Qinggong等 14 人
Nature Communications
2022
•2022/9/5
•Vol.13 No.1 p.1-10
Hemochromatosis is one of the most common inherited metabolic diseases among white populations and predominantly originates from a homozygous C282Y mutation in the HFE gene. The G > A transition at position c.845 of the gene causes misfolding of the HFE protein, ultimately resulting in its absenc...
CRISPR-Cas9 genome editingHepatologyMetabolic disordersMolecular medicine
10.1038/S41467-022-32906-9
ISSN:2041-1723
ASO therapy rescues NOTCH2NLC GGC repeat expansion-induced genomic damage, 3D chromatin structural abnormalities, and senescence
Mengjie Li•Mibo Tang•Xiaoyan Hao•Zhengwei Hu•Dongrui Ma等 28 人
Nature Communications
2026
•2026/4/7
0Neuronal intranuclear inclusion disease is caused by abnormal GGC repeat expansion in the NOTCH2NLC gene, though its pathogenic mechanism remains incompletely understood. This study shows that the abnormally expanded polyG-uN2C protein, encoded by the repeat sequence, contains intrinsically disorder...
Chromatin structureDNA damage and repairProtein aggregationSenescence
10.1038/S41467-026-71516-7
ISSN:2041-1723
Zebularine potentiates anti-tumor immunity by inducing tumor immunogenicity and improving antigen processing through cGAS-STING pathway
Yong Zhang•Heng Zhao•Weili Deng•Junzhong Lai•Kai Sang等 6 人
Communications Biology
2024
•2024/5/16
•Vol.7 No.1 p.1-16
DNA methylation is an important epigenetic mechanism involved in the anti-tumor immune response, and DNA methyltransferase inhibitors (DNMTi) have achieved impressive therapeutic outcomes in patients with certain cancer types. However, it is unclear how inhibition of DNA methylation bridges the inna...
Cancer microenvironmentCell death and immune response
10.1038/S42003-024-06271-W
ISSN:2399-3642
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
Comprehensive multi omics explore the microbial function in metabolic pathway flow during altered diet
Yiming Zhao•Siqi Yao•Abdulrahim Umar•Jing Huang•Shuijiao Chen等 6 人
Npj Science Of Food
2025
•2025/10/29
•Vol.9 No.1 p.1-10
High-protein diet (HPD) and high-fiber diet (HFiD) are two common types of diet, and the transition from HPD to HFiD frequently happens in people who perform diet control. Gut microbiota provide a bridge between diet and health. However, most of the research left out the metabolic landscape change a...
Microbial communitiesMicrobiota
10.1038/S41538-025-00575-9
ISSN:2396-8370
Systems biological assessment of altered cytokine responses to bacteria and fungi reveals impaired immune functionality in schizophrenia
Gao Yuan•Fan Yajuan•Yang Zai•Ma Qingyan•Zhao Binbin等 14 人
Molecular Psychiatry
2021
•2021/11/2
•00 p.1-12
Evidence suggests that complex interactions between the immune system and brain have important etiological and therapeutic implications in schizophrenia. However, the detailed cellular and molecular basis of immune dysfunction in schizophrenia remains poorly characterized. To better understand the i...
Biological techniquesCell biologyMolecular biology
10.1038/S41380-021-01362-0
ISSN:1359-4184
Integrating spatial and single-cell transcriptomics reveals tumor heterogeneity and intercellular networks in colorectal cancer
Jing Xiao•Xinyang Yu•Fanlin Meng•Yuncong Zhang•Wenbin Zhou等 12 人
Cell Death & Disease
2024
•2024/5/10
•Vol.15 No.5 p.1-11
Single cell RNA sequencing (scRNA-seq), a powerful tool for studying the tumor microenvironment (TME), does not preserve/provide spatial information on tissue morphology and cellular interactions. To understand the crosstalk between diverse cellular components in proximity in the TME, we performed s...
Cancer microenvironmentCell adhesion
10.1038/S41419-024-06598-6
ISSN:2041-4889
Voluntary wheel running exercise attenuates VPA-induced ASD-like behaviors in male rats: implication of the vagal pathway of the gut-brain axis
Yinhua Li•Jiugen Zhong•Yingying Shen•Jiaheng Gong•Yanqing Feng等 7 人
Npj Biofilms And Microbiomes
2026
•2026/3/20
0Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder with elusive pathogenesis and lack of targeted therapies. While exercise can ameliorate ASD-like behaviors, its underlying mechanisms remain unclear. Recent studies have identified dysbiosis of gut microbiota and altered level...
DiseasesMicrobiologyNeurologyNeuroscience
10.1038/S41522-026-00962-4
ISSN:2055-5008
Evolution of coastal forests based on a full set of mangrove genomes
He Ziwen•Feng Xiao•Chen Qipian•Li Liangwei•Li Sen等 27 人
Nature Ecology & Evolution
2022
•2022/4/28
•00 p.1-12
Genomic studies are now poised to explore whole communities of species. The ~70 species of woody plants that anchor the coastal ecosystems of the tropics, collectively referred to as mangroves, are particularly suited to this exploration. In this study, we de novo sequenced the whole genomes of 32 m...
BiodiversityConservation biologyPhylogeneticsPopulation dynamics
10.1038/S41559-022-01744-9
ISSN:2397-334X
Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
Jiadong Hu•Shi Qiu•Feiyan Wang•Qing Li•Chun-Lei Xiang等 20 人
Nature Communications
2023
•2023/8/4
•Vol.14 No.1 p.1-16
The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia and exhibit taxonomic chemical diversity among lineages. To eluci...
Plant evolutionSecondary metabolismTaxonomy
10.1038/S41467-023-40401-Y
ISSN:2041-1723
Conversion of placental hemogenic endothelial cells to hematopoietic stem and progenitor cells
Guixian Liang•Shicheng Liu•Chunyu Zhou•Mengyao Liu•Yifan Zhang等 9 人
Cell Discovery
2025
•2025/1/28
•Vol.11 No.1 p.1-12
Hematopoietic stem and progenitor cells (HSPCs) are critical for the treatment of blood diseases in clinic. However, the limited source of HSPCs severely hinders their clinical application. In the embryo, hematopoietic stem cells (HSCs) arise from hemogenic endothelial (HE) cells lining the major ar...
Haematopoietic stem cells
10.1038/S41421-024-00760-2
ISSN:2056-5968
Lipid metabolism dysfunction induced by age-dependent DNA methylation accelerates aging
Li Xin•Wang Jiaqiang•Wang LeYun•Gao Yuanxu•Feng Guihai等 17 人
Signal Transduction And Targeted Therapy
2022
•2022/5/25
•Vol.7 No.1 p.1-12
Epigenetic alterations and metabolic dysfunction are two hallmarks of aging. However, the mechanism of how their interaction regulates aging, particularly in mammals, remains largely unknown. Here we show ELOVL fatty acid elongase 2 (Elovl2), a gene whose epigenetic alterations are most highly corre...
AgeingBioinformaticsEpigenetics
10.1038/S41392-022-00964-6
ISSN:2059-3635
Injectable therapeutic system incorporating neurogenesis-programmed stem cells concomitantly promoting muscle regeneration treats stress urinary incontinence
Wenzhuo Fang•Xuan Du•Ranxing Yang•Meng Liu•Ming Yang等 9 人
Nature Communications
2025
•2025/9/25
•Vol.16 No.1 p.1-21
Stress urinary incontinence (SUI) remains a significant clinical challenge due to the lack of strategies that simultaneously address muscle degeneration, neurogenic atrophy, and vascular deficits. Here, we report an innovative injectable system that combines a thermo-responsive poly(N-isopropylacryl...
Biomaterials – cellsMesenchymal stem cellsRNA sequencingStem-cell differentiationUrinary incontinence
10.1038/S41467-025-63421-2
ISSN:2041-1723
RNA m6A regulates the transcription and heterochromatin state of retrotransposons in Arabidopsis
Peizhe Song•Zhihe Cai•Subiding Tayier•Enlin Tian•Zixin Chen等 8 人
Nature Plants
2025
•2025/10/24
•00 p.1-19
Chromatin and transcription states are crucial for establishing and maintaining gene regulation and genome integrity, governed by a complex network of epigenetic modifications. Despite significant advancements, the interplay between epitranscriptomic and epigenetic modifications in transcriptional r...
EpigeneticsEpigenomicsPlant geneticsPlant molecular biology
10.1038/S41477-025-02137-Z
ISSN:2055-0278
Polystyrene-degrading bacteria in the gut microbiome of marine benthic polychaetes support enhanced digestion of plastic fragments
Sufang Zhao•Renju Liu•Shiwei Lv•Benjuan Zhang•Juan Wang等 6 人
Communications Earth & Environment
2024
•2024/3/28
•Vol.5 No.1 p.1-12
Polystyrene foam, which is used as a buoyant material in mariculture, is a common constituent of marine plastic debris. Here, we conduct analyses on polystyrene foam debris collected on the east coast of Xiamen Island, China, and associated plastic-burrowing clamworms. We apply interferometry, mass ...
Environmental impactMarine biology
10.1038/S43247-024-01318-6
ISSN:2662-4435
Mechanical unloading promotes adult cardiomyocyte proliferation through epicardial NRG1–ERBB4 signaling
Chenyu Jiang•Tianyu Liu•Zihao Dai•Li Xiang•Yifan Zhu等 19 人
Nature Cardiovascular Research
2026
•2026/8/5
•Vol.5 No.8 p.705-724
In mammals, the postnatal increase in cardiac workload coincides with the loss of cardiomyocyte proliferative capacity, rendering adult cardiomyocytes permanently post-mitotic. Whether reducing load can restore regenerative potential in the adult heart remains unknown. Here we use a heterotopic hear...
Cardiac regenerationCardiology
10.1038/S44161-026-00841-3
ISSN:2731-0590
Distinct effects of different Bacteroides strains on depressive-like behavior via a gut-Th1/Th17 cells-brain axis
Zhiyu Li•Peilin Qin•Zuoli Sun•Liangkang Li•Peng Liang等 9 人
Communications Biology
2026
•2026/1/13
•Vol.9 No.1 p.2470
Extensive evidence links gut microbiota to the pathogenesis of major depressive disorder (MDD), yet the specific microbial species involved remain unclear. Here, we identify distinct roles of three Bacteroides species—B. uniformis, B. vulgatus, and B. thetaiotaomicron—in depression. B. uniformis inc...
Adaptive immunityBacteria
10.1038/S42003-026-09525-X
ISSN:2399-3642
Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq
Yan Wang•Yijun Chen•Junpeng Gao•Haoling Xie•Yuqing Guo等 13 人
Cell Discovery
2024
•2024/3/5
•Vol.10 No.1 p.1-22
Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means the inability to detect both alleles simultaneously in an individual diploid cell, largely restricts the application of these methods particularly for medical appl...
ChromosomesDevelopmental biologyWhole genome amplification
10.1038/S41421-023-00638-9
ISSN:2056-5968
The recovery of the microbial community after plaque removal depends on periodontal health status
Xiaoqing Li•Cheng Yu•Bing Zhang•Xiaogang Shan•Wenjun Mao等 10 人
Npj Biofilms And Microbiomes
2023
•2023/10/7
•Vol.9 No.1 p.1-12
Plaque accumulation and microbial community changes are important causes of periodontal disease. Cleaned plaque microorganisms will reattach to form biofilms, but the recovery and outcome of plaque microbial communities in different periodontal health states remain unknown. In this study, we tracked...
BiofilmsClinical microbiologyPlaque
10.1038/S41522-023-00441-0
ISSN:2055-5008
Donor MHC-specific thymus vaccination allows for immunocompatible allotransplantation
Yang Liu•Hexi Feng•Ke Li•Ruiyi Li•Xiao-Jie Zhang等 10 人
Cell Research
2025
•2025/1/3
•00 p.1-13
Organ transplantation is the last-resort option to treat organ failure. However, less than 10% of patients benefit from this only option due to lack of major histocompatibility complex (MHC)-matched donor organs and 25%–80% of donated organs could not find MHC-matched recipients. T cell allorecognit...
Embryonic stem cellsImmunology
10.1038/S41422-024-01049-5
ISSN:1748-7838
Single-cell RNA sequencing revealed cell landscape of tongue dorsal mucosa in rats with gastric intestinal metaplasia
Jiao Xiang•Jing Han•Jianping Wu•Shuo Xu•Chun Cheng等 6 人
Cell Death Discovery
2025
•2025/3/16
•Vol.11 No.1 p.1-11
The formation of tongue coating is closely related with the differentiation of the lingual dorsal mucosa, and a great deal of evidence shows that the variation of tongue coating reflects the pathological and physiological state of the gastric mucosa. However, the detailed mechanism remains elusive. ...
GastritisGastroenteritis
10.1038/S41420-025-02386-Z
ISSN:2058-7716
A comprehensive investigation of Glycoprotein-based nucleic acid vaccines for Hantaan Virus
Jiaxing Zhang•Junqi Zhang•Yanbo Wang•Yubo Sun•Yongkai Wang等 21 人
Npj Vaccines
2024
•2024/10/23
•Vol.9 No.1 p.1-15
Hemorrhagic fever with renal syndrome (HFRS) occurs throughout Eurasia with considerable morbidity and mortality. Currently, the absence of specific treatments or effective antiviral drugs for hantavirus infection makes developing safe and effective vaccines a high priority. Here, we report the deve...
DNA vaccinesRNA vaccines
10.1038/S41541-024-00991-0
ISSN:2059-0105
Knocking out OsPht1;9-1;10 genes decreases arsenic accumulation in rice (Oryza sativa) grains
Huayuan Feng•Chentong Chen•Mengyang Xu•Dan Sun•Xuexia Su等 13 人
Communications Biology
2026
•2026/2/26
•Vol.9 No.1 p.5180
Globally, 94–220 million people in regions with arsenic (As)-contaminated soil or groundwater face significant health risks. Rice, the primary staple food in these areas, is the main source of As exposure for a large portion of this population. Developing low-As rice cultivars provides a sustainable...
Environmental biotechnologyMolecular engineering in plantsPlant physiology
10.1038/S42003-026-09741-5
ISSN:2399-3642
A mobile DELLA controls Medicago truncatula root cortex patterning to host arbuscular mycorrhizal fungi
Jianyong An•Liu Fang•Willem Cremers•Kornelija Aleksejeva•Yiyang Wang等 12 人
Nature Plants
2025
•2025/10/6
•00 p.1-12
Cell division and specification are crucial for plant development and coping with diverse environmental cues. Most land plants rely on symbiosis with arbuscular mycorrhizal (AM) fungi to cope with soil nutrient limitations by forming arbuscules in root inner cortex cells. What determines the AM susc...
Arbuscular mycorrhizaCell fateRoot apical meristem
10.1038/S41477-025-02114-6
ISSN:2055-0278
Systematic mining and quantification reveal the dominant contribution of non-HLA variations to acute graft-versus-host disease
Shuang Liang•Yu-Jian Kang•Mingrui Huo•De-Chang Yang•Min Ling等 17 人
Cellular & Molecular Immunology
2025
•2025/3/4
•00 p.1-11
Human leukocyte antigen (HLA) disparity between donors and recipients is a key determinant triggering intense alloreactivity, leading to a lethal complication, namely, acute graft-versus-host disease (aGVHD), after allogeneic transplantation. Moreover, aGVHD remains a cause of mortality after HLA-ma...
Bone marrow transplantationImmunogenetics
10.1038/S41423-025-01273-Y
ISSN:2042-0226
Serpina3c protects against metabolic dysfunction-associated steatotic liver disease in offspring induced by prenatal prednisone exposure
Yongguo Dai•Zhengjie Lu•Yu Peng•Kexin Liu•Xiaoqian Lu等 17 人
Signal Transduction And Targeted Therapy
2026
•2026/2/18
•Vol.11 No.1 p.710
Metabolic dysfunction-associated steatotic liver disease (MASLD) has become a major global public health problem, and its occurrence is associated with adverse environmental exposures during development. In this study, we investigated the impact of the use of prednisone (a synthetic glucocorticoid d...
Endocrine system and metabolic diseasesMetabolic disorders
10.1038/S41392-025-02569-1
ISSN:2059-3635
Impaired mitochondria-initiated crosstalk with lysosomes reciprocally aggravates mitochondrial defect through LManVI
Shengnan Li•Zhaoliang Shan•Guochun Zhao•Yuwei Li•Minghui Du等 11 人
Nature Communications
2025
•2025/8/7
•Vol.16 No.1 p.1-19
Mitochondria coordinate with lysosomes to maintain cellular homeomstasis. However, in mitochondrial defect condition, how they communicate is less clear. Here, utilizing dMterf4 RNAi fly model, we find that expression of lysosomal alpha-mannosidase VI (LManVI) is significantly downregulated. Mechani...
Gene regulationTranscription
10.1038/S41467-025-62147-5
ISSN:2041-1723
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation
Tong Xiaoling•Han Min-Jin•Lu Kunpeng•Tai Shuaishuai•Liang Shubo等 57 人
Nature Communications
2022
•2022/9/24
•Vol.13 No.1 p.1-15
The silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read...
Comparative genomicsEntomologyEvolutionary geneticsGenome evolution
10.1038/S41467-022-33366-X
ISSN:2041-1723
Developmental chronology of mouse embryo from 2-cell stage through birth
Shangtao Cao•Lihui Lin•Huijian Feng•Pan Chen•Guangming Wu等 36 人
Nature Cell Biology
2026
•2026/6/1
•00 p.1-11
Current single-cell atlases of mouse embryos are limited in temporal resolution and cellular or sequencing depth coverage. Here we report the mouse developmental Cell and Lineage Atlas (mdCLA), which covers 37 time points across the entire embryonic development from the 2-cell stage (E1.5) to birth ...
Cell growthCell lineageMultipotent stem cellsRNA sequencing
10.1038/S41556-026-01971-3
ISSN:1465-7392
Full-length circular RNA profiling by nanopore sequencing with CIRI-long
Hou Lingling•Zhang Jinyang•Zhao Fangqing
Nature Protocols
2023
•2023/4/12
•00 p.1-19
Circular RNAs (circRNAs) have important roles in regulating developmental processes and disease progression. As most circRNA sequences are highly similar to their cognate linear transcripts, the current short-read sequencing-based methods rely on the back-spliced junction signal for distinguishing c...
Data miningGene expression analysis
10.1038/S41596-023-00815-W
ISSN:1754-2189
Evolutionary origin of the chordate nervous system revealed by amphioxus developmental trajectories
Yichen Dai•Yanhong Zhong•Rongrong Pan•Liang Yuan•Yongheng Fu等 16 人
Nature Ecology & Evolution
2024
•2024/7/18
•00 p.1-18
The common ancestor of all vertebrates had a highly sophisticated nervous system, but questions remain about the evolution of vertebrate neural cell types. The amphioxus, a chordate that diverged before the origin of vertebrates, can inform vertebrate evolution. Here we develop and analyse a single-...
Evolutionary developmental biologyMolecular evolution
10.1038/S41559-024-02469-7
ISSN:2397-334X
Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats
Li-Ying Lan•Tai-Cong Liu•Shao-Ming Gao•Qi Li•Li Yang等 13 人
Npj Biofilms And Microbiomes
2025
•2025/2/14
•Vol.11 No.1 p.1-11
Wild animals face numerous challenges in less ideal habitats, including the lack of food as well as changes in diet. Understanding how the gut microbiomes of wild animals adapt to changes in food resources within suboptimal habitats is critical for their survival. Therefore, we conducted a longitudi...
BacteriaMicrobial ecologyMicrobiome
10.1038/S41522-025-00653-6
ISSN:2055-5008
Double-hit of MIA and Nod2 deficiency induces sex-specific offspring behavioral abnormalities through placental dysregulation
Zhen Cao•Xinyu Zhang•Fengjie Gao•Chuyao Wang•Zixuan Zhang等 9 人
Translational Psychiatry
2025
•2025/11/16
0The pathogenesis of neuropsychiatric disorders, including autism spectrum disorder and schizophrenia, originates from complex interactions between genetic susceptibility and early environmental exposure. Infectious challenges during pregnancy are well-known environmental risk factors for neurodevelo...
Autism spectrum disordersSchizophrenia
10.1038/S41398-025-03747-Z
ISSN:2158-3188
PCaseek: ultraspecific urinary tumor DNA detection using deep learning for prostate cancer diagnosis and Gleason grading
Gaojie Li•Ye Wang•Ying Wang•Baojun Wang•Yuan Liang等 15 人
Cell Discovery
2024
•2024/9/3
•Vol.10 No.1 p.1-3
Prostate cancerTumour biomarkers
10.1038/S41421-024-00710-Y
ISSN:2056-5968
JAK/STAT signaling maintains an intermediate cell population during prostate basal cell fate determination
Wangxin Guo•Xiaoyu Zhang•Lin Li•Pengfei Shao•Chao Liang等 16 人
Nature Genetics
2024
•2024/11/13
•00 p.1-14
Unipotent basal and luminal stem cells maintain prostate homeostasis, with an intermediate cell population emerging during prostate inflammation or cancer. However, the identities of basal stem cell and intermediate cell population remain unclear. Here we identified a rare intermediate cell populati...
Prostate cancerProstatitisStem cells
10.1038/S41588-024-01979-1
ISSN:1061-4036
Dynamic genomic changes in methotrexate-resistant human cancer cell lines beyond DHFR amplification suggest potential new targets for preventing drug resistance
Xiang-Ning Meng•Jin-Fa Ma•Yang-He Liu•Si-Qing Li•Xu Wang等 19 人
British Journal Of Cancer
2024
•2024/4/9
•00 p.1-9
Although DHFR gene amplification has long been known as a major mechanism for methotrexate (MTX) resistance in cancer, the early changes and detailed development of the resistance are not yet fully understood. We performed genomic, transcriptional and proteomic analyses of human colon cancer cells w...
Cancer epigeneticsCancer genomics
10.1038/S41416-024-02664-0
ISSN:0007-0920
Dynamic interactions between gut microbiome and host lipidome in antenatal depression: a large longitudinal study
Fan Li•Yunhaonan Yang•Yuanqing Fu•Shanshan Zhang•Ping Wu等 24 人
Molecular Psychiatry
2026
•2026/2/16
•00 p.1-13
Temporal alterations in the host lipidome and gut microbiome, and their dynamic interactions, in the progression of antenatal depression remain poorly understood. Here, we characterized the maternal lipidome and gut microbiome in 1086 Chinese pregnant women from the Tongji-Huaxi-Shuangliu Birth Coho...
DepressionDiagnostic markers
10.1038/S41380-026-03472-Z
ISSN:1359-4184
NRF2 signaling plays an essential role in cancer progression through the NRF2-GPX2-NOTCH3 axis in head and neck squamous cell carcinoma
Xiaoye Jin•Xiayuan Lou•Haoxiang Qi•Chao Zheng•Bo Li等 11 人
Oncogenesis
2024
•2024/9/27
•Vol.13 No.1 p.350
The activation of nuclear factor erythroid 2–related factor 2 (NRF2) has been observed in various cancers. Yet its exact contribution to the development of head and neck squamous cell carcinoma (HNSCC) remains undetermined. We previously found that NRF2 signaling is critical for the differentiation ...
ApoptosisHead and neck cancer
10.1038/S41389-024-00536-Z
ISSN:2157-9024
Parabacteroides distasonis ameliorates hepatic fibrosis potentially via modulating intestinal bile acid metabolism and hepatocyte pyroptosis in male mice
Zhao Qi•Dai Man-Yun•Huang Ruo-Yue•Duan Jing-Yi•Zhang Ting等 13 人
Nature Communications
2023
•2023/4/1
•Vol.14 No.1 p.1-18
Parabacteroides distasonis (P. distasonis) plays an important role in human health, including diabetes, colorectal cancer and inflammatory bowel disease. Here, we show that P. distasonis is decreased in patients with hepatic fibrosis, and that administration of P. distasonis to male mice improves th...
Liver fibrosisMicrobiome
10.1038/S41467-023-37459-Z
ISSN:2041-1723
Transfer cells mediate nitrate uptake to control root nodule symbiosis
Qi Wang•Yige Huang•Zhijie Ren•Xiaxia Zhang•Jing Ren等 12 人
Nature Plants
2020
•2020/6/8
•Vol.6 No.7 p.800-808
Root nodule symbiosis enables nitrogen fixation in legumes and, therefore, improves crop production for sustainable agriculture1,2. Environmental nitrate levels affect nodulation and nitrogen fixation, but the mechanisms by which legume plants modulate nitrate uptake to regulate nodule symbiosis rem...
Plant transportersRhizobial symbiosis
10.1038/S41477-020-0683-6
ISSN:2055-0278
Mitochondrial damage in muscle specific PolG mutant mice activates the integrated stress response and disrupts the mitochondrial folate cycle
Simon T. Bond•Emily J. King•Shannen M. Walker•Christine Yang•Yingying Liu等 26 人
Nature Communications
2025
•2025/3/8
•Vol.16 No.1 p.1-21
During mitochondrial damage, information is relayed between the mitochondria and nucleus to coordinate precise responses to preserve cellular health. One such pathway is the mitochondrial integrated stress response (mtISR), which is known to be activated by mitochondrial DNA (mtDNA) damage. However,...
Endocrine system and metabolic diseasesMitochondria
10.1038/S41467-025-57299-3
ISSN:2041-1723
Analysis of the genomic landscape of yolk sac tumors reveals mechanisms of evolution and chemoresistance
Xuan Zong•Ying Zhang•Xinxin Peng•Dongyan Cao•Mei Yu等 10 人
Nature Communications
2021
•2021/6/11
•Vol.12 No.1 p.1-13
Yolk sac tumors (YSTs) are a major histological subtype of malignant ovarian germ cell tumors with a relatively poor prognosis. The molecular basis of this disease has not been thoroughly characterized at the genomic level. Here we perform whole-exome and RNA sequencing on 41 clinical tumor samples ...
CancerCancer genomicsComputational biology and bioinformatics
10.1038/S41467-021-23681-0
ISSN:2041-1723
Amynthas corticis genome reveals molecular mechanisms behind global distribution
Xing Wang•Yi Zhang•Yufeng Zhang•Mingming Kang•Yuanbo Li等 11 人
Communications Biology
2021
•2021/1/29
•Vol.4 No.1 p.1-13
Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis...
Ecological geneticsGenomeGenomic analysis
10.1038/S42003-021-01659-4
ISSN:2399-3642
The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs
Heng Du•Lei Zhou•Zhen Liu•Yue Zhuo•Meilin Zhang等 10 人
Nature Communications
2024
•2024/11/22
•Vol.15 No.1 p.1-18
Pigs play a central role in human livelihoods in China, but a lack of systematic large-scale whole-genome sequencing of Chinese domestic pigs has hindered genetic studies. Here, we present the 1000 Chinese Indigenous Pig Genomes Project sequencing dataset, comprising 1011 indigenous individuals from...
Agricultural geneticsEvolutionary geneticsHaplotypesRare variants
10.1038/S41467-024-54471-Z
ISSN:2041-1723
Macrophage ferroptosis potentiates GCN2 deficiency induced pulmonary venous arterialization
Jingyuan Zhang•Pei Mao•Tengfei Zhou•Bingqing Yue•Yaning Li等 10 人
Nature Communications
2025
•2025/9/22
•Vol.16 No.1 p.1-19
Pulmonary veno-occlusive disease (PVOD) is a fatal disease characterized by the remodelling of pulmonary veins and haemosiderin accumulation in macrophages. Although (General Control Nonderepressible 2) GCN2 deficiency has been reported in PVOD patients, the underlying mechanism by which GCN2 defici...
Cell death and immune responseDiseasesMedical researchMonocytes and macrophagesTranslational immunology
10.1038/S41467-025-64035-4
ISSN:2041-1723
Identification of increased dedifferentiation along the Prom1+ cancer cells in Müllerian adenosarcoma with sarcomatous overgrowth
Xingming Ye•Jianfeng Zheng•Dan Hu•Li Liu•Fukun Chen等 11 人
British Journal Of Cancer
2025
•2025/2/7
•Vol.132 No.5 p.438-449
Müllerian adenosarcoma (MA) is a rare tumour accounts for 5–7% of uterine sarcomas. Tumours with sarcomatous overgrowth (MASO) or high-grade tend to be aggressive. However, the tumour aetiology is elusive. Single-cell RNA sequencing and bioinformatics were used to analyse the MASO and paired normal ...
CancerCell biology
10.1038/S41416-025-02943-4
ISSN:0007-0920
Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding
Hu Jihong•Chen Biyun•Zhao Jing•Zhang Fugui•Xie Ting等 23 人
Nature Genetics
2022
•2022/4/28
•00 p.1-11
Rapeseed (Brassica napus L.) is an important oil-producing crop for the world. Its adaptation, yield and quality have been considerably improved in recent decades, but the genomic basis underlying successful breeding selection remains unclear. Hence, we conducted a comprehensive genomic assessment o...
Genome-wide association studiesPlant genetics
10.1038/S41588-022-01055-6
ISSN:1061-4036
In situ osteogenic activation of mesenchymal stem cells by the blood clot biomimetic mechanical microenvironment
Wangxiao He•Fan Ding•Liqiang Zhang•Wenjia Liu
Nature Communications
2025
•2025/1/30
•Vol.16 No.1 p.1-16
Blood clots (BCs) play a crucial biomechanical role in promoting osteogenesis and regulating mesenchymal stem cell (MSC) function and fate. This study shows that BC formation enhances MSC osteogenesis by activating Itgb1/Fak-mediated focal adhesion and subsequent Runx2-mediated bone regeneration. No...
Molecular medicineRegeneration
10.1038/S41467-025-56513-6
ISSN:2041-1723
Gut microbial ammonia enhances colonic acetylcholine levels to regulate intestinal motility
Hao Chen•Zhen Wang•Yiming Zhao•Wenyu Yang•Jing Huang等 6 人
Nature Microbiology
2026
•2026/2/20
•Vol.11 No.4 p.907-919
Intestinal motility is a function of the enteric nervous system involving secretion of the excitatory neurotransmitter acetylcholine (ACh). Although gut commensal bacteria are key regulators of intestinal physiology, the molecular mechanisms underlying microbial influence on intestinal peristalsis a...
Bacterial host responseIntestinal diseasesMetagenomicsMicrobiome
10.1038/S41564-026-02269-8
ISSN:2058-5276
DNA methylome and transcriptome landscapes revealed differential characteristics of dioecious flowers in papaya
Ping Zhou•Xiaodan Zhang•Mahpara Fatima•Xinyi Ma•Hongkun Fang等 7 人
Horticulture Research
2020
•2020/6/1
•Vol.7 No.1 p.1-15
Separate sexes in dioecious plants display different morphology and physiological characteristics. The differences between the two sexes lie in their highly differentiated floral characteristics and in sex-related phenotype, which is genetically determined and epigenetically modified. In dioecious p...
EpigenomicsPlant evolution
10.1038/S41438-020-0298-0
ISSN:2662-6810
Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos
Jiaqiang Wang•Yiwei Zhang•Jiaze Gao•Guihai Feng•Chao Liu等 13 人
Nature Structural & Molecular Biology
2024
•2024/4/24
•00 p.1-14
The heterogeneity of CARM1 controls first cell fate bias during early mouse development. However, how this heterogeneity is established is unknown. Here, we show that Carm1 mRNA is of a variety of specific exon-skipping splicing (ESS) isoforms in mouse two-cell to four-cell embryos that contribute t...
Alternative splicingLong non-coding RNAsReprogramming
10.1038/S41594-024-01292-9
ISSN:1545-9993
Allelic variation in UVR8 modulates thermotolerance-yield tradeoffs in plants
Zeqi Li•Yi Zhang•Shiquan Li•Chengyi Qu•Daren Luo等 28 人
Cell Research
2026
•2026/5/14
•00 p.1-14
Industrial activities have driven stratospheric ozone depletion, increasing surface UV-B radiation while exacerbating global warming. These changes limit crop productivity, alter species distributions, and disrupt plant metabolic processes, but the mechanisms linking energy signaling to heat-stress ...
Plant molecular biologyPlant signalling
10.1038/S41422-026-01253-5
ISSN:1748-7838
Immune pathogenic response landscape of acute posterior multifocal placoid pigment epitheliopathy revealed by scRNA sequencing
Jingyang Liu•Qingge Guo•Guangming Liu•Weiping Wang•Xiuxiu Jin等 7 人
Genes & Immunity
2025
•2025/1/7
•Vol.26 No.2 p.75-90
Acute posterior multifocal placoid pigment epitheliopathy (APMPPE) is an exceptionally rare inflammatory disorder affecting choroid and retinal pigment epithelial (RPE) cells. Although recent studies suggest an immune-driven nature, the underlying etiology of APMPPE remains elusive. In this study, w...
Acute inflammationAutoimmunity
10.1038/S41435-024-00316-0
ISSN:1476-5470
NEK8 kinase-mediated lactate increase impairs antitumor immunity decreasing radiotherapy sensitivity in colorectal cancer
Mingzhou Li•Yunfei Ni•Jieqiong Wu•Xin Zou•Yining Chen等 16 人
Nature Communications
2026
•2026/3/28
0Radiotherapy effectively treats colorectal cancer (CRC), but local recurrence remains common and abscopal effects—regression of tumors distant from irradiated sites—are rarely observed even with immune checkpoint inhibitors. Here we show that the protein kinase NEK8, highly expressed in CRC, promote...
Cancer microenvironmentColorectal cancerRadiotherapy
10.1038/S41467-026-70657-Z
ISSN:2041-1723
High stability and metabolic capacity of bacterial community promote the rapid reduction of easily decomposing carbon in soil
Huang Ruilin•Crowther Thomas W.•Sui Yueyu•Sun Bo•Liang Yuting
Communications Biology
2021
•2021/12/8
•Vol.4 No.1 p.1-12
Irreversible climate change alters the decomposition and sequestration of soil carbon (C). However, the stability of C components in soils with different initial organic matter contents and its relationship with the response of major decomposers to climate warming are still unclear. In this study, w...
Climate-change ecologyMicrobial ecology
10.1038/S42003-021-02907-3
ISSN:2399-3642
Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally
Ziheng Peng•Xun Qian•Yu Liu•Xiaomeng Li•Hang Gao等 16 人
Nature Communications
2024
•2024/4/29
•Vol.15 No.1 p.1-13
Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural l...
BiodiversityBiogeochemistryCommunity ecologyEnvironmental impactMicrobial ecology
10.1038/S41467-024-47348-8
ISSN:2041-1723
Lysyl-tRNA synthetase orchestrates translation and hormone signaling during reproduction in Aedes aegypti mosquitoes
Shan Li•Xueli Wang•Haoran Lu•Alexander S. Raikhel•Zhen Zou
Communications Biology
2025
•2025/7/2
•Vol.8 No.1 p.1-15
The regulation of mosquito reproduction at the transcriptional level is well understood, but the translational mechanisms remain unclear. Here, we find that lysyl-tRNA synthetase (KARS) is essential for translational regulation and governs mosquito fecundity in a hormone-dependent manner. RNA interf...
EntomologyReproductive biology
10.1038/S42003-025-08428-7
ISSN:2399-3642
Longitudinal serum proteome mapping reveals biomarkers for healthy ageing and related cardiometabolic diseases
Jun Tang•Liang Yue•Ying Xu•Fengzhe Xu•Xue Cai等 20 人
Nature Metabolism
2025
•2025/1/13
•00 p.1-16
The blood proteome contains biomarkers of ageing and age-associated diseases, but such markers are rarely validated longitudinally. Here we map the longitudinal proteome in 7,565 serum samples from a cohort of 3,796 middle-aged and elderly adults across three time points over a 9-year follow-up peri...
AgeingBiomarkersMetabolismProteomic analysis
10.1038/S42255-024-01185-7
ISSN:2522-5812
A high-quality bread wheat genome unravels the adaptive evolution of wheat end-use quality
Xinyou Cao•Jijin Zhang•Yafei Guo•Yuhong Huang•Lei Guo等 24 人
Nature Plants
2026
•2026/5/7
•00 p.1-14
Understanding the genetics of superior dough performance is essential for improving wheat end-use quality. Here we present a de novo assembly of the genome of JM44, a Chinese wheat cultivar known for its exceptional end-use quality. The JM44 genome achieved reference-level quality (with a quality va...
GenomicsPlant geneticsPopulation genetics
10.1038/S41477-026-02288-7
ISSN:2055-0278
cTAGE5 is essential for adipogenesis and adipose tissue development
Junwan Fan•Tiantian Ma•Xiaoping Ren•Zhilin Chang•Dan Zhang等 13 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-16
White adipocytes serve as primary energy reservoirs and their malfunction is linked to different metabolic disorders, yet the mechanisms underlying cellular specialization, a critical step during adipogenesis remain unknown. Here, we reveal the indispensable role of cutaneous T-cell lymphoma-associa...
DifferentiationMetabolism
10.1038/S41467-025-60698-1
ISSN:2041-1723
Dynamic reorganization of three-dimensional genome architecture during Populus diversification
Tingting Shi•Tao Long•Jiali Wu•Xinying Zeng•Yiman Zhu等 11 人
Nature Ecology & Evolution
2026
•2026/4/24
•00 p.1-16
Advancements in sequencing technology enable the investigation of genomic information within its three-dimensional (3D) spatial structure, offering new insights into genome organization and function. However, the role of higher-order chromatin architecture in species divergence and speciation remain...
Adaptive radiationComparative genomicsEvolutionary genetics
10.1038/S41559-026-03069-3
ISSN:2397-334X
Population genomics of Quercus gilva provides insights into the conservation of fengshui forests
Xiao-Long Jiang•Meng-Xiao WU•Yoko SAITO•Shi-Shi LUO•Xion-Sheng LIU等 9 人
Communications Biology
2026
•2026/3/13
0Human-driven environmental changes threaten the region's dominant trees. China’s fengshui forests harbor ancient trees with cultural and ecological significance, yet their climate resilience remains uncertain. By integrating genome and resequencing data, we investigate the structural variants, demog...
Ecological geneticsPopulation genetics
10.1038/S42003-026-09846-X
ISSN:2399-3642
Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars
Cheng Zhongyi•Zheng Qiang•Shi Jiachun•He Yan•Yang Xueling等 8 人
Isme Communications
2023
•2023/2/22
•Vol.3 No.1 p.1-13
Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying...
Environmental sciencesSoil microbiology
10.1038/S43705-023-00213-Z
ISSN:2730-6151
Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19
Yongzhi Lu•Qi Yang•Ting Ran•Guihua Zhang•Wenqi Li等 24 人
Nature Communications
2024
•2024/11/23
•Vol.15 No.1 p.1-16
The RNA-dependent RNA polymerase (RdRp), 3C-like protease (3CLpro), and papain-like protease (PLpro) are pivotal components in the viral life cycle of SARS-CoV-2, presenting as promising therapeutic targets. Currently, all FDA-approved antiviral drugs against SARS-CoV-2 are RdRp or 3CLpro inhibitors...
SARS-CoV-2Structure-based drug design
10.1038/S41467-024-54462-0
ISSN:2041-1723
Cryoablation plus sintilimab and lenvatinib in advanced or metastatic intrahepatic cholangiocarcinoma: a phase 2 trial
Sijia Gu•Qiyu Luo•Yalei Zhang•Ling Qian•Kun Chen等 15 人
Nature Cancer
2025
•2025/11/1
•00 p.1-20
Treatment options for advanced or metastatic intrahepatic cholangiocarcinoma (ICC) are limited. In this single-arm, phase 2 trial (CASTLE-01, NCT05010668 ), 28 participants with advanced or metastatic ICC who have progressed after chemotherapy were treated with cryoablation, followed by anti-PD1 sin...
Biliary tract cancerCancerCancer immunotherapyGastrointestinal cancer
10.1038/S43018-025-01058-2
ISSN:2662-1347
Optimizing the NGS-based discrimination of multiple lung cancers from the perspective of evolution
Ziyang Wang•Xiaoqiu Yuan•Kunkun Sun•Fang Wu•Ke Liu等 18 人
Npj Precision Oncology
2025
•2025/1/14
•Vol.9 No.1 p.1-15
Next-generation sequencing (NGS) offers a promising approach for differentiating multiple primary lung cancers (MPLC) from intrapulmonary metastasis (IPM), though panel selection and clonal interpretation remain challenging. Whole-exome sequencing (WES) data from 80 lung cancer samples were utilized...
Cancer genomicsGenetic testingNon-small-cell lung cancer
10.1038/S41698-024-00786-5
ISSN:2397-768X
Modeling SHANK3-associated autism spectrum disorder in Beagle dogs via CRISPR/Cas9 gene editing
Rui Tian•Yuan Li•Hui Zhao•Wen Lyu•Jianping Zhao等 17 人
Molecular Psychiatry
2023
•2023/10/17
•00 p.1-12
Despite intensive studies in modeling neuropsychiatric disorders especially autism spectrum disorder (ASD) in animals, many challenges remain. Genetic mutant mice have contributed substantially to the current understanding of the molecular and neural circuit mechanisms underlying ASD. However, the t...
Autism spectrum disordersNeuroscience
10.1038/S41380-023-02276-9
ISSN:1359-4184
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
Wuliangye Baijiu but not ethanol reduces cardiovascular disease risks in a zebrafish thrombosis model
Zhu Hui•Lan Chaohua•Zhao Dong•Wang Ning•Du Di等 12 人
Npj Science Of Food
2022
•2022/12/5
•Vol.6 No.1 p.1-8
Understanding how Baijiu facilitates blood circulation and prevents blood stasis is crucial for revealing the mechanism of Baijiu for cardiovascular disease (CVD) risk reduction. Here we established a zebrafish thrombosis model induced using arachidonic acid (AA) to quantitatively evaluate the antit...
Cardiovascular diseasesTranscriptomics
10.1038/S41538-022-00170-2
ISSN:2396-8370
Hypoxia-induced autophagic degradation of HIF-1α attenuates cellular aging and extends mammalian lifespan
Chen Yang•Zeng Xu•Sha-Tong He•Gen-Jiang Zheng•Jian-Xi Wang等 25 人
Nature Aging
2026
•2026/5/12
•00 p.1-21
Organs age at different rates, yet the protective mechanisms contributing to decelerated aging in certain tissues remain unclear. Applying cross-tissue comparisons to molecular readouts of aging, here we report that the intervertebral disc (IVD) ages slowly. We link the rate of aging to the persiste...
AgeingAutophagySenescence
10.1038/S43587-026-01124-Z
ISSN:2662-8465
A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat
Shoucheng Liu•Kui Li•Xiuru Dai•Guochen Qin•Dongdong Lu等 21 人
Nature Genetics
2025
•2025/4/7
•Vol.57 No.4 p.1008-1020
The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telom...
GenomicsPlant genetics
10.1038/S41588-025-02137-X
ISSN:1061-4036
Dynamic gut responses to sepsis uncovered by multi-omics profiling in a rodent model
Jingchao Lei•Jing Qi•Jia Zhai•Ziying Chen•Nanyi Li等 8 人
Communications Biology
2026
•2026/3/27
0Sepsis reflects an immune dysregulation in response to infection, and the intestine functions as the largest immune organ in the human body. However, the multidimensional dynamic changes within the gut environment during the progression of sepsis remain incompletely understood. Here, we show the alt...
Cellular signalling networksInfectious diseasesMicrobiologyTranscriptomics
10.1038/S42003-026-09940-0
ISSN:2399-3642
Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils
Chaoyang Liu•Meitong Jiang•Mengting Maggie Yuan•Ertao Wang•Yang Bai等 16 人
Nature Food
2023
•2023/10/2
•00 p.1-13
Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to cr...
AgroecologyMicrobial ecology
10.1038/S43016-023-00848-0
ISSN:2662-1355
The Phoebe genome sheds light on the evolution of magnoliids
Shi-Pin Chen•Wei-Hong Sun•Yuan-Fang Xiong•Yu-Ting Jiang•Xue-Die Liu等 20 人
Horticulture Research
2020
•2020/9/1
•Vol.7 No.1 p.1-13
Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genom...
GenomeGenome evolution
10.1038/S41438-020-00368-Z
ISSN:2662-6810
The dynamics of microbiome and virome in migratory birds of southwest China
Qingqing Luo•Hongyan Gao•Yujia Xiang•Jian Li•Lin Dong等 13 人
Npj Biofilms And Microbiomes
2025
•2025/4/23
•Vol.11 No.1 p.1-12
Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus...
Metagenomics
10.1038/S41522-025-00703-Z
ISSN:2055-5008
Engineered outer membrane vesicles enhance solid tumour CAR-T cell therapy
Xianjun Li•Xuehan Li•Jiaqi Shi•Yingjing Li•Hanyu Zhang等 15 人
Nature Biomedical Engineering
2026
•2026/1/7
•00 p.1-16
Major challenges facing chimeric antigen receptor (CAR)-T cell therapy for solid tumours include the immunosuppressive tumour microenvironment and the heterogeneity of antigen expression. Bacterial outer membrane vesicles (OMVs) naturally activate the immune system and can be engineered for drug del...
Biomedical engineeringCancerCancer immunotherapy
10.1038/S41551-025-01575-6
ISSN:2157-846X
Oncolytic adenoviruses expressing checkpoint inhibitors for cancer therapy
Daoyuan Xie•Yaomei Tian•Die Hu•Yuanda Wang•Yuling Yang等 13 人
Signal Transduction And Targeted Therapy
2023
•2023/11/29
•Vol.8 No.1 p.1-16
Despite the remarkable success of immune checkpoint inhibitors (ICIs), primary resistance to ICIs causes only subsets of patients to achieve durable responses due to the complex tumor microenvironment (TME). Oncolytic viruses (OVs) can overcome the immunosuppressive TME and promote systemic antitumo...
Drug developmentTumour immunology
10.1038/S41392-023-01683-2
ISSN:2059-3635
Leveraging a phased pangenome for haplotype design of hybrid potato
Lin Cheng•Nan Wang•Zhigui Bao•Qian Zhou•Andrea Guarracino等 24 人
Nature
2025
•2025/1/22
•00 p.1-10
The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)1,2 dictate a slow, non-accumulative breeding mode of the most important tuber crop. Transitioning potato breeding to a seed-propagated hybrid system based on diploid inbred lines has the potential to greatly...
Agricultural geneticsGenomicsPlant breedingPlant domesticationStructural variation
10.1038/S41586-024-08476-9
ISSN:0028-0836
Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors
Xuan An•Leyan Mao•Yinjia Wang•Qinqin Xu•Xi Liu等 20 人
Nature Ecology & Evolution
2024
•2024/1/9
•00 p.1-13
Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai–Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia ...
Evolutionary geneticsGenome evolution
10.1038/S41559-023-02275-7
ISSN:2397-334X
Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
Xiaoming Song•Jingjing Hu•Tong Wu•Qihang Yang•Xuehuan Feng等 14 人
Horticulture Research
2021
•2021/3/1
•Vol.8 No.1 p.1-21
Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 spe...
Gene expressionHeatNon-coding RNAsRNA sequencing
10.1038/S41438-021-00484-4
ISSN:2662-6810
NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice
Jingying Zhang•Yong-Xin Liu•Na Zhang•Bin Hu•Tao Jin等 21 人
Nature Biotechnology
2019
•2019/4/29
•Vol.37 No.6 p.676-684
Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 japonica varieties grown in the field. We find that indica and japonica recruit distinct root microbiota. Notab...
MicrobiologyPlant sciences
10.1038/S41587-019-0104-4
ISSN:1087-0156
Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics
Denian Wang•Yishang Duan•Lijuan He•Juan Jiang•Jinghong Xian等 18 人
Communications Biology
2025
•2025/5/26
•Vol.8 No.1 p.1-12
The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveol...
Bacterial infectionMolecular medicine
10.1038/S42003-025-08234-1
ISSN:2399-3642
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
Discovery of a selective CDK7 PROTAC against acute leukemia with low platelet toxicity
Yutong Tu•Xiaojia Cai•Zhaofan Tao•Ruisen Zhang•Xian Li等 14 人
Leukemia
2026
•2026/3/25
•00 p.1-9
Cyclin-dependent kinase 7 (CDK7), a key regulator of cell cycle progression and transcriptional control, has emerged as a promising therapeutic target in acute leukemia. While CDK7 inhibitors have shown antileukemic activity, their clinical utility is often restricted by dose-dependent thrombocytope...
Acute myeloid leukaemiaDrug development
10.1038/S41375-026-02925-2
ISSN:0887-6924
CARD16 restores tumorigenesis and restraints apoptosis in glioma cells Via FOXO1/TRAIL axis
Ruoheng Xuan•Tianyu Hu•Lingshan Cai•Beichuan Zhao•Erqiao Han等 6 人
Cell Death & Disease
2024
•2024/11/8
•Vol.15 No.11 p.1-14
A hallmark of glioma cells, particularly glioblastoma multiforme (GBM) cells, is their resistance to apoptosis. Accumulating evidences has demonstrated that CARD16, a caspase recruitment domain (CARD) only protein, enhances both anti-apoptotic and tumorigenic properties. Nevertheless, there is a lim...
ApoptosisCNS cancerPrognostic markers
10.1038/S41419-024-07196-2
ISSN:2041-4889
Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding
Li Chunhui•Guan Honghui•Jing Xin•Li Yaoyao•Wang Baobao等 26 人
Nature Plants
2022
•2022/7/18
•Vol.8 No.7 p.750-763
Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic ...
DNA sequencingGenome-wide association studiesPlant breedingPopulation genetics
10.1038/S41477-022-01190-2
ISSN:2055-0278
A viral protein activates the MAPK pathway to promote viral infection by downregulating callose deposition in plants
Lixiao Feng•Xiangwen Luo•Liping Huang•Yu Zhang•Fangfang Li等 17 人
Nature Communications
2024
•2024/12/4
•Vol.15 No.1 p.1-18
Mitogen-activated protein kinase (MAPK) cascades are evolutionarily conserved in both plants and animals and play critical roles in activating innate immunity to defend against various pathogens. However, the role of MAPK cascades in positively regulating or enhancing viral infections in plants is u...
BioticPlant cell biologyVirus–host interactions
10.1038/S41467-024-54467-9
ISSN:2041-1723
Aging-induced immune microenvironment remodeling fosters melanoma in male mice via γδ17-Neutrophil-CD8 axis
Runping Duan•Loujing Jiang•Tianfu Wang•Zhaohuai Li•Xiaoyang Yu等 9 人
Nature Communications
2024
•2024/12/30
•Vol.15 No.1 p.1-19
Aging is associated with increased tumor metastasis and poor prognosis. However, how an aging immune system contributes to the process is unclear. Here, single-cell RNA sequencing reveals that in male mice, aging shifts the lung immune microenvironment towards a premetastatic niche, characterized by...
Cancer microenvironmentMetastasisTumour immunology
10.1038/S41467-024-55164-3
ISSN:2041-1723
Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3
Xin Zheng•Jinyang Zhang•Lipu Song•Xiang Jennie Li•Fangqing Zhao等 6 人
Nature Biotechnology
2025
•2025/10/1
•00 p.1-7
To address recent challenges in circular RNA (circRNA) analysis, we present CIRI3, a tool for circRNA detection and quantification in terabyte-scale RNA-sequencing datasets. Using dynamic multithreaded task partitioning and a blocking search strategy for junction reads, CIRI3 is an order of magnitud...
Data miningGene expression
10.1038/S41587-025-02835-1
ISSN:1087-0156
Chromosome-scale assembly of the Kandelia obovata genome
Min-Jie Hu•Wei-Hong Sun•Wen-Chieh Tsai•Shuang Xiang•Xing-Kai Lai等 17 人
Horticulture Research
2020
•2020/5/2
•Vol.7 No.1 p.1-12
The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. The...
EvolutionGenome
10.1038/S41438-020-0300-X
ISSN:2662-6810
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts
Xu Sunde•Liu Yong-Xin•Cernava Tomislav•Wang Hongkai•Zhou Yaqi等 20 人
Nature Microbiology
2022
•2022/5/26
•Vol.7 No.6 p.831-843
Plant-pathogenic fungi form intimate interactions with their associated bacterial microbiota during their entire life cycle. However, little is known about the structure, functions and interaction mechanisms of bacterial communities associated with fungal fruiting bodies (perithecia). Here we examin...
Applied microbiologyMicrobiology
10.1038/S41564-022-01131-X
ISSN:2058-5276
Oncolytic adenovirus delivery of neoantigens sensitizes low-mutation tumors to anti-PD-1 therapy and prevents metastasis
Ke-Yu Shen•Shi-Zhe Yu•Ying-Han Su•Sun-Zhe Xie•Chen Zhang等 14 人
Signal Transduction And Targeted Therapy
2025
•2025/12/23
•Vol.10 No.1 p.4100
Neoantigen vaccines and oncolytic viruses are emerging immunotherapies that can reshape the tumor microenvironment (TME). However, tumors with low mutation burdens often respond poorly to immunotherapies because of their limited immunogenicity. Developing effective immunotherapy strategies for these...
Drug developmentVaccines
10.1038/S41392-025-02511-5
ISSN:2059-3635
NSUN2 mediates intestinal stem cell expansion and colorectal tumour initiation via MAPK/ERK signalling
Aslihan Bastem Akan•Caroline V. Billard•Szu-Ying Chen•Po-Hsien Huang•Patrizia Cammareri等 13 人
Cell Death & Disease
2026
•2026/3/19
•Vol.17 No.1 p.3220
Colorectal cancer is initiated by loss of APC, which drives expansion of LGR5+ intestinal stem cell (ISC) populations. Whilst LGR5 + ISC expansion is a critical step for tumour initiation and progression, its regulation is poorly understood. Emerging evidence suggests post-transcriptional RNA modifi...
Cancer epigeneticsCancer stem cellsColon cancer
10.1038/S41419-026-08560-0
ISSN:2041-4889
Glucose starvation mimetic aldometanib removes immune barriers permitting mice with hepatocellular carcinoma to live to normal ages
Hui-Hui Hu•Xuefeng Wang•Bin Lan•Haili Cheng•Hong Wen等 24 人
Cell Research
2025
•2025/11/25
•00 p.1-20
Dysregulated metabolism in tumor tissues and para-tumor tissues alike can lead to immunosuppression, which may underlie cancer development. However, metabolic intervention as a therapeutic strategy has been of no avail. In this study, we explored the anti-cancer therapeutic effect of aldometanib, wh...
Cancer microenvironmentNutrient signallingTumour immunology
10.1038/S41422-025-01195-4
ISSN:1748-7838
Epigenetic imprinting in innate lymphoid cell precursors directs the lineage segregation of innate lymphoid cells
Zhen Liu•Fei Shao•Qiang Zhang•Min Zhao•Shuai Gao等 10 人
Nature Immunology
2025
•2025/9/18
•00 p.1-13
Innate lymphoid cells (ILCs) are essential for mucosal homeostasis, but the epigenetic regulation of their lineage segregation remains elusive. Here we simultaneously profiled the single-cell DNA methylome, chromatin accessibility and transcriptome of ILC subsets and ILC precursors (ILCPs) and found...
LymphocytesMucosal immunology
10.1038/S41590-025-02261-0
ISSN:1529-2908
A single mutation underlying phenotypic convergence for hypoxia adaptation on the Qinghai-Tibetan Plateau
Dongming Xu•Cuiping Yang•Qiushuo Shen•Shengkai Pan•Zhen Liu等 15 人
Cell Research
2021
•2021/6/7
•00 p.1-4
Comparative genomicsMolecular biology
10.1038/S41422-021-00517-6
ISSN:1001-0602
Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia
Yang Xu•Zhang Mingzhi•Zhang Yuqing•Wei Hongcheng•Guan Quanquan等 9 人
Npj Biofilms And Microbiomes
2023
•2023/4/3
•Vol.9 No.1 p.1-10
The composition of the gut microbiome was previously found to be associated with clinical responses to dyslipidemia, but there is limited consensus on the dynamic change of the gut microbiota during pregnancy and the specific microbiome characteristics linked to dyslipidemia in pregnant women. We co...
Health careMetagenomics
10.1038/S41522-023-00383-7
ISSN:2055-5008
Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant–soil feedbacks
Lingfei Hu•Kaidi Zhang•Yachun Xu•Xiaoxuan Zheng•Jamie M. Waterman等 15 人
Nature Plants
2025
•2025/5/1
•00 p.1-17
Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant–soil feedbacks, resulting in increased performance o...
HerbivorySecondary metabolism
10.1038/S41477-025-01987-X
ISSN:2055-0278
GZMK-expressing CD8+ T cells promote recurrent airway inflammatory diseases
Feng Lan•Jizhou Li•Wenxuan Miao•Fei Sun•Su Duan等 13 人
Nature
2025
•2025/1/15
•00 p.1-9
Inflammatory diseases are often chronic and recurrent, and current treatments do not typically remove underlying disease drivers1. T cells participate in a wide range of inflammatory diseases such as psoriasis2, Crohn’s disease3, oesophagitis4 and multiple sclerosis5,6, and clonally expanded antigen...
Cytotoxic T cellsImmunopathogenesisInflammation
10.1038/S41586-024-08395-9
ISSN:0028-0836
Parental histone transfer caught at the replication fork
Ningning Li•Yuan Gao•Yujie Zhang•Daqi Yu•Jianwei Lin等 17 人
Nature
2024
•2024/3/6
•00 p.1-8
In eukaryotes, DNA compacts into chromatin through nucleosomes1,2. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin3,4. Here we report cryo-electron microscopy structures of yeast (Saccharomyces cerevisiae) replisomes associated with ...
Cryoelectron microscopyDNA replicationNucleosomes
10.1038/S41586-024-07152-2
ISSN:0028-0836
Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change
Juan Jiang•Jia-Fu Chen•Xin-Tong Li•Li Wang•Jian-Feng Mao等 7 人
Nature Communications
2025
•2025/3/20
•Vol.16 No.1 p.1-12
Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing ...
Conservation biologyEvolutionary geneticsMolecular evolutionPopulation genetics
10.1038/S41467-025-58021-Z
ISSN:2041-1723
3D biomimetic niche modulates embryo development in vitro
Jia Guo•Jiawei Lyu•Zili Gao•Tan Jia•Leyun Wang等 15 人
Nature Communications
2026
•2026/1/2
•Vol.17 No.1 p.12790
Embryo development undergoes critical morphological transformations post-implantation, largely driven by the complex and dynamic microenvironment of the uterus. Despite advances, current 3D culture models inadequately recapitulate the uterine environment necessary for studying embryo-uterus interact...
BiomaterialsEmbryologyGastrulation
10.1038/S41467-025-68039-Y
ISSN:2041-1723
An uncharacterized small protein MicN mediates the transcriptional reprogramming of Salmonella through regulating the RpoS-RNA polymerase interaction
Ruirui Liu•Qi Wang•Xilu Yuan•Yingying Yue•Ping Zhang等 8 人
Communications Biology
2025
•2025/10/23
•Vol.8 No.1 p.1-15
Salmonella adapts its metabolism upon entry into macrophages to survive in the hostile host environment. However, the specific regulatory mechanisms involved remain largely unknown. In this study, we identify a previously uncharacterized small protein, MicN, that is essential for the survival of Sal...
BacteriologyX-ray crystallography
10.1038/S42003-025-08989-7
ISSN:2399-3642
A spatiotemporal transcriptomic atlas of porcine (Sus scrofa) female early gonadal development
Pengcheng He•Wenzhe Xia•Tianzhi Chen•Yaxuan Yan•Dengfeng Gao等 13 人
Communications Biology
2026
•2026/3/30
•Vol.9 No.1 p.4870
The early gonads of mammals contain primordial germ cells (PGCs) and gonadal somatic cells. In females, the gonadal somatic cells promote the specification of PGCs into oogonia and their entry into meiosis, which is crucial for oogenesis. Although single-cell transcriptome sequencing technology hold...
OogenesisRNA sequencing
10.1038/S42003-026-09932-0
ISSN:2399-3642
Ring finger protein 213 regulates B-cell receptor signaling, metabolism, and development in B lymphocytes
Ziyin Zhang•Nanshu Xiang•Qian Liu•Yanfeng Li•Linhua Wang等 13 人
Signal Transduction And Targeted Therapy
2026
•2026/2/18
•Vol.11 No.1 p.590
The development and function of B lymphocytes require the precise integration of signaling, transcriptional networks, and metabolic programs. While interferon (IFN)-inducible proteins can bridge innate and adaptive immunity, their roles in B cells remain poorly defined. Here, we identified RNF213, a...
Adaptive immunityLymphocytes
10.1038/S41392-026-02575-X
ISSN:2059-3635
Modelling late gastrulation in stem cell-derived monkey embryo models
Jie Li•Jie Li•Jing Cao•ShenShen Shang•Liansheng Zhang等 14 人
Nature
2025
•2025/12/3
•00 p.1-12
Stem cell-derived embryo models could greatly facilitate our understanding of embryonic development. Although human and monkey embryo models have reached early gastrulation stage1–7, the development of robust models beyond this time remains to be accomplished8. Here, using an optimized 3D suspension...
Embryonic stem cellsGastrulation
10.1038/S41586-025-09831-0
ISSN:0028-0836
Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy
Liguo Wang•Xuejing Shao•Tianbai Zhong•Yue Wu•Aixiao Xu等 21 人
Nature Chemical Biology
2021
•2021/3/4
•00 p.1-9
The discovery of effective therapeutic treatments for cancer via cell differentiation instead of antiproliferation remains a great challenge. Cyclin-dependent kinase 2 (CDK2) inactivation, which overcomes the differentiation arrest of acute myeloid leukemia (AML) cells, may be a promising method for...
Cancer therapyKinasesMedicinal chemistrySmall molecules
10.1038/S41589-021-00742-5
ISSN:1552-4450
DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions
Jie Wang•Guangpu Zhang•Cheng Sun•Liming Chang•Yingyong Wang等 11 人
Communications Biology
2025
•2025/5/6
•Vol.8 No.1 p.1-16
Size evolution among gigantic genomes involves gain and loss of many gigabases of transposable elements (TEs), sequences that parasitize host genomes. Vertebrates suppress TEs using piRNA and KRAB-ZFP pathways. TEs and hosts coevolve in an arms race, where suppression strength reflects TE fitness co...
Molecular evolutionTransposition
10.1038/S42003-025-08127-3
ISSN:2399-3642
Comprehensive co-expression network reveals the fine-tuning of AsHSFA2c in balancing drought tolerance and growth in oat
Ningkun Liu•Wei Li•Yujie Qin•Yange Yun•Jinjiang Yan等 11 人
Communications Biology
2025
•2025/3/8
•Vol.8 No.1 p.1-17
Persistent activation of drought tolerance is detrimental to plant growth and development. However, the mechanism that balances plant drought tolerance and growth remains largely undetermined. Here, we constructed a comprehensive co-expression network comprising 84 transcriptome datasets associated ...
Gene regulatory networksPlant stress responses
10.1038/S42003-025-07857-8
ISSN:2399-3642
Wnt11 mediates fibroblast–smooth muscle cell interaction to promote neurogenic bladder fibrosis in rats
Qingyu Ge•Junjie Zhang•Zongyao Fan•Yan Wang•Xinglin Chen等 14 人
Communications Biology
2026
•2026/2/9
•Vol.9 No.1 p.1940
Neurogenic bladder (NB) is a lower urinary tract dysfunction caused by lesions in the nervous system that regulate urine storage and micturition. Fibrosis is considered the basic pathological alteration of NB, whereas the underlying mechanism remains unclear. Here, we find that Wnt11 is significantl...
BladderMechanisms of disease
10.1038/S42003-026-09647-2
ISSN:2399-3642
K235 acetylation couples with PSPC1 to regulate the m6A demethylation activity of ALKBH5 and tumorigenesis
Xiao-Lan Zhang•Xin-Hui Chen•Binwu Xu•Min Chen•Song Zhu等 11 人
Nature Communications
2023
•2023/6/27
•Vol.14 No.1 p.1-15
N6-methyladenosine (m6A) modification plays important roles in bioprocesses and diseases. AlkB homolog 5 (ALKBH5) is one of two m6A demethylases. Here, we reveal that ALKBH5 is acetylated at lysine 235 (K235) by lysine acetyltransferase 8 and deacetylated by histone deacetylase 7. K235 acetylation s...
AcetylationRNA modification
10.1038/S41467-023-39414-4
ISSN:2041-1723
Pseudomonas plecoglossicida disrupts intestinal homeostasis through manipulation of palmitoleic acid microbial metabolism
Lixing Huang•Jiajia Wang•Qiu Li•Rongchao He•Weilu Qi等 8 人
Npj Biofilms And Microbiomes
2026
•2026/3/24
0Sickness-associated anorexia (SAA) is a common symptom during bacterial infections in fish that complicates treatment due to reduced oral drug uptake and efficacy. While current research has largely focused on cytokine-mediated pathways affecting the central nervous system, the role of gut microbiot...
BacteriaMicrobiome
10.1038/S41522-026-00963-3
ISSN:2055-5008
Integrating full-length transcriptomics and metabolomics reveals the regulatory mechanisms underlying yellow pigmentation in tree peony (Paeonia suffruticosa Andr.) flowers
Luo Xiaoning•Sun Daoyang•Wang Shu•Luo Sha•Fu Yaqi等 8 人
Horticulture Research
2021
•2021/11/1
•Vol.8 No.1 p.1-15
Tree peony (Paeonia suffruticosa Andr.) is a popular ornamental plant in China due to its showy and colorful flowers. However, yellow-colored flowers are rare in both wild species and domesticated cultivars. The molecular mechanisms underlying yellow pigmentation remain poorly understood. Here, peta...
Gene regulationMetabolomicsSecondary metabolismTranscriptomics
10.1038/S41438-021-00666-0
ISSN:2662-6810
Targeting cancer cell plasticity by HDAC inhibition to reverse EBV-induced dedifferentiation in nasopharyngeal carcinoma
Xie Jiajun•Wang Zifeng•Fan Wenjun•Liu Youping•Liu Fang等 25 人
Signal Transduction And Targeted Therapy
2021
•2021/9/4
•Vol.6 No.1 p.1-17
Application of differentiation therapy targeting cellular plasticity for the treatment of solid malignancies has been lagging. Nasopharyngeal carcinoma (NPC) is a distinctive cancer with poor differentiation and high prevalence of Epstein-Barr virus (EBV) infection. Here, we show that the expression...
Cancer stem cellsHead and neck cancer
10.1038/S41392-021-00702-4
ISSN:2059-3635
Myeloid Mas drives pyruvate kinase M2-mediated Spi1 lactylation to fuel inflammatory senescence in MASLD
Luying Zhao•Shujing Xu•Shikai Qiao•Zhe Wang•Shenglan Wang等 17 人
Signal Transduction And Targeted Therapy
2026
•2026/5/19
•Vol.11 No.1 p.1860
Metabolic dysfunction-associated steatotic liver disease (MASLD) is driven by unresolved inflammation, yet precise mechanisms linking immune metabolism to disease progression remain elusive. Here, we identified myeloid-expressed Mas, a G protein-coupled receptor, as a critical metabolic checkpoint i...
Metabolic disordersTarget identification
10.1038/S41392-026-02704-6
ISSN:2059-3635
Aberrant METTL1-mediated tRNA m7G modification alters B-cell responses in systemic autoimmunity in humans and mice
Shuyi Wang•Hui Han•Yichao Qian•Xinyuan Ruan•Zhangmei Lin等 15 人
Nature Communications
2024
•2024/12/5
•Vol.15 No.1 p.1-25
Upon activation, naive B cells exit their quiescent state and enter germinal center (GC) responses, a transition accompanied by increased protein synthesis. How protein translation efficiency is adequately adjusted to meet the increased demand requires further investigation. Here, we identify the me...
AutoimmunityB cellsMethylation
10.1038/S41467-024-54941-4
ISSN:2041-1723
Phylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China
Jianhai Yu•Xin Zhang•Jiajun Liu•Linlin Xiang•Shen Huang等 18 人
Nature Communications
2023
•2023/12/12
•Vol.14 No.1 p.1-8
The first local mpox outbreak in Guangdong Province, China occurred in June 2023. However, epidemiological data have failed to quickly identify the source and transmission of the outbreak. Here, phylogeny and molecular evolution of 10 monkeypox virus (MPXV) genome sequences from the Guangdong outbre...
EpidemiologyMolecular evolutionPhylogeneticsPox virus
10.1038/S41467-023-44092-3
ISSN:2041-1723
Discovery of candidate functional non-coding mutations in acute myeloid leukemia using single-cell chromatin accessibility sequencing
Ming Zhu•Jiali Zhu•Zhijuan Zhu•Yiding Yang•Jinxian Dai等 8 人
Communications Biology
2025
•2025/5/26
•Vol.8 No.1 p.1-13
Mutations and gene rearrangements are crucial for the diagnosis and subtyping of acute myeloid leukemia (AML). However, the contribution of non-coding genetic variants, particularly those within cis-regulatory elements (CREs), to AML pathophysiology and heterogeneity remains poorly understood. In th...
Acute myeloid leukaemiaComputational biology and bioinformatics
10.1038/S42003-025-08257-8
ISSN:2399-3642
Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems
Ziheng Peng•Marcel G. A. van der Heijden•Yu Liu•Xiaomeng Li•Haibo Pan等 13 人
Nature Food
2025
•2025/1/3
•00 p.1-14
Soils play a critical role in supporting agricultural production. Subsoils, below 20 cm, underpin fundamental agroecosystem sustainability traits including soil carbon storage, climate regulation and water provision. However, little is known about the ecological stability of subsoils in response to ...
AgroecologyEnvironmental health
10.1038/S43016-024-01106-7
ISSN:2662-1355
Identification of a distinct cluster of LY6E+ macrophages in esophageal squamous cell carcinoma: functional phenotype, spatial interaction, and prognostic significance
Kun Chen•Jianjiao Ni•Yida Li•Sijia Gu•Ye Li等 20 人
British Journal Of Cancer
2026
•2026/4/29
•00 p.1-12
Tumor-associated macrophages are key players in cancer progression, but their heterogeneity is not fully understood. This study aims to investigate the role of a specific macrophage subpopulation marked by LY6E in esophageal squamous cell carcinoma (ESCC). We analyzed macrophage subsets in ESCC, foc...
Cancer microenvironmentMonocytes and macrophagesOesophageal cancer
10.1038/S41416-026-03456-4
ISSN:0007-0920
Global diversity and ecological functions of viruses inhabiting oil reservoirs
Liyun An•Xinwu Liu•Jianwei Wang•Jinbo Xu•Xiaoli Chen等 9 人
Nature Communications
2024
•2024/8/8
•Vol.15 No.1 p.1-16
Oil reservoirs, being one of the significant subsurface repositories of energy and carbon, host diverse microbial communities affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil res...
Microbial ecologyViral reservoirs
10.1038/S41467-024-51101-6
ISSN:2041-1723
KAT8-mediated H4K16ac is essential for sustaining trophoblast self-renewal and proliferation via regulating CDX2
Shilei Bi•Lijun Huang•Yongjie Chen•Zhenhua Hu•Shanze Li等 21 人
Nature Communications
2024
•2024/7/3
•Vol.15 No.1 p.1-17
Abnormal trophoblast self-renewal and differentiation during early gestation is the major cause of miscarriage, yet the underlying regulatory mechanisms remain elusive. Here, we show that trophoblast specific deletion of Kat8, a MYST family histone acetyltransferase, leads to extraembryonic ectoderm...
AcetylationReproductive disordersSelf-renewal
10.1038/S41467-024-49930-6
ISSN:2041-1723
Cyprinid Juji (Gobiocypris rarus) as a model fish to study germ cell development and gonadal differentiation
Naike Su•Zhiqin Ren•Houpeng Wang•Chaofan Wang•Yongkang Hao等 8 人
Communications Biology
2025
•2025/12/24
0Although the cyprinid zebrafish has been widely used to study gametogenesis and gonadal differentiation, it has remarkable limitations, such as the loss of sex determinants in laboratory strains, a juvenile ovary stage in both sexes, and oocyte defects generally leading to sex reversal. Here, we dev...
Genetic engineeringGermline developmentModel vertebrates
10.1038/S42003-025-09378-W
ISSN:2399-3642
Astrocytic ALKBH5 in stress response contributes to depressive-like behaviors in mice
Fang Guo•Jun Fan•Jin-Ming Liu•Peng-Li Kong•Jing Ren等 18 人
Nature Communications
2024
•2024/5/21
•Vol.15 No.1 p.1-19
Epigenetic mechanisms bridge genetic and environmental factors that contribute to the pathogenesis of major depression disorder (MDD). However, the cellular specificity and sensitivity of environmental stress on brain epitranscriptomics and its impact on depression remain unclear. Here, we found tha...
DepressionEpigenetics in the nervous systemPrefrontal cortex
10.1038/S41467-024-48730-2
ISSN:2041-1723
High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing
Zhuo-Xing Shi•Zhi-Chao Chen•Jia-Yong Zhong•Kun-Hua Hu•Ying-Feng Zheng等 12 人
Nature Communications
2023
•2023/5/6
•Vol.14 No.1 p.1-13
Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative RNA splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT-scISOseq, a method that removes most artifact cDNAs and concatenates multiple cDNAs for PacBio circular consensus s...
Genome-wide analysis of gene expressionHigh-throughput screeningNext-generation sequencingRNA sequencingTranscriptomics
10.1038/S41467-023-38324-9
ISSN:2041-1723
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
Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat
Hao Zhang•Zhiyuan Jin•Fa Cui•Long Zhao•Xiaoyu Zhang等 18 人
Nature Communications
2023
•2023/12/12
•Vol.14 No.1 p.1-15
The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen co...
Plant breedingPlant developmentPlant stress responses
10.1038/S41467-023-44003-6
ISSN:2041-1723
NOD1/2 signaling in macrophages drives adaptive immune resistance in cancer
Xiduan Wei•Li Yang•Yuting Wang•Kun Wang•Dan Wang等 17 人
Signal Transduction And Targeted Therapy
2026
•2026/7/16
•Vol.11 No.1 p.3000
Therapeutic resistance remains a prevalent and intractable clinical challenge across a broad spectrum of human malignancies. Despite extensive investigations, the intricate molecular networks by which the tumor microenvironment (TME) mediates such resistance are not fully understood. In this study, ...
Cancer microenvironmentTumour immunology
10.1038/S41392-026-02758-6
ISSN:2059-3635
Dual recombinase-mediated intersectional genetics defines the functional heterogeneity of neural stem cells in adult hippocampus
Ziqi Liang•Zhimin Li•Dan Zhang•Xing Luo•Qiang Liu等 11 人
Molecular Psychiatry
2025
•2025/2/24
•00 p.1-17
The Cre-lox site-specific recombinase system is one of the most powerful and versatile technology platforms for studying neural stem cells (NSCs) in adult brain, which is now challenged due to the complex and dynamic nature of in vivo gene expression. In this study, we develop an inducible dual reco...
Cell biologyNeuroscience
10.1038/S41380-025-02937-X
ISSN:1359-4184
Sex differences orchestrated by androgens at single-cell resolution
Fei Li•Xudong Xing•Qiqi Jin•Xiang-Ming Wang•Pengfei Dai等 20 人
Nature
2024
•2024/4/10
•00 p.1-8
Sex differences in mammalian complex traits are prevalent and are intimately associated with androgens1–7. However, a molecular and cellular profile of sex differences and their modulation by androgens is still lacking. Here we constructed a high-dimensional single-cell transcriptomic atlas comprisi...
Cell biologyImmunology
10.1038/S41586-024-07291-6
ISSN:0028-0836
Chromosome-level genome assembly of the predatory stink bug, Eocanthecona furcellata (Wolff)
Qing-Ling Hu•Ji-Chong Zhuo•Chuan-Xi Zhang
Scientific Data
2026
•2026/1/6
•Vol.13 No.1 p.60
The predatory bug Eocanthecona furcellata (Hemiptera: Pentatomidae) is an important natural enemy of agricultural and forest pests. In this study, we assembled a chromosome-level genome of E. furcellata using a combination of Illumina short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C...
DNA sequencingDNA transposable elementsRNA sequencingSequence annotation
10.1038/S41597-025-06312-X
ISSN:2052-4463
Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation
Li Wei•Long Qi•Wu Hao•Zhou Yanshuang•Duan Lifan等 25 人
Nature Communications
2022
•2022/12/2
•Vol.13 No.1 p.1-15
Pluripotent stem cells hold great promise in regenerative medicine and developmental biology studies. Mitochondrial metabolites, including tricarboxylic acid (TCA) cycle intermediates, have been reported to play critical roles in pluripotency. Here we show that TCA cycle enzymes including Pdha1, Pcb...
MitochondriaStem cells
10.1038/S41467-022-35199-0
ISSN:2041-1723
Chronic alcohol consumption disrupts the integrity of the blood-brain barrier through the gut-brain axis
Chenguang Li•Hongxuan Wang•Xinrou Lin•Guanyong Zeng•Xiangpen Li等 12 人
Communications Biology
2025
•2025/11/25
0Chronic alcohol consumption can lead to disruption of the blood-brain barrier. The gut-brain axis may be involved in this pathological process. We investigated the gut microbiota of 30 healthy individuals and 30 alcohol use disorder (AUD) patients and found that at the genus level, AUD patients had ...
Clinical microbiologyNeurotoxicity syndromes
10.1038/S42003-025-09235-W
ISSN:2399-3642
Environmentally relevant lanthanum chloride exposure induces hepatic steatosis in zebrafish larvae via PPARα-dependent ApoB suppression
Keying Li•Xinying Zhao•Zhuoyi Xie•Qiuchen Wu•Wenlu Jia等 13 人
Communications Biology
2026
•2026/2/9
•Vol.9 No.1 p.3900
Lanthanum (La), the second most produced rare earth element, is detected in various environmental and human samples. Epidemiological studies have reported a strong association between La exposure and liver injury. However, the effects of early La exposure on liver development and underlying mechanis...
BiomarkersDevelopmental biologyEndocrine system and metabolic diseases
10.1038/S42003-026-09697-6
ISSN:2399-3642
Gut microbiota alters host bile acid metabolism to contribute to intrahepatic cholestasis of pregnancy
Tang Bo•Tang Li•Li Shengpeng•Liu Shuang•He Jialin等 16 人
Nature Communications
2023
•2023/3/9
•Vol.14 No.1 p.1-17
Intrahepatic cholestasis of pregnancy (ICP) is a female pregnancy-specific disorder that is characterized by increased serum bile acid and adverse fetal outcomes. The aetiology and mechanism of ICP are poorly understood; thus, existing therapies have been largely empiric. Here we show that the gut m...
Liver diseasesMicrobiome
10.1038/S41467-023-36981-4
ISSN:2041-1723
Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement
Weilong Kong•Xiangrui Kong•Zhongqiang Xia•Xiaofeng Li•Fang Wang等 23 人
Nature Genetics
2025
•2025/3/17
•00 p.1-11
The tea plant stands as a globally cherished nonalcoholic beverage crop, but the genetic underpinnings of important agronomic and metabolomic traits remain largely unexplored. Here we de novo deep resequenced 802 tea plants and their relative accessions globally. By integrating public Camellia acces...
Plant geneticsPopulation genetics
10.1038/S41588-025-02135-Z
ISSN:1061-4036
Cancer cell employs a microenvironmental neural signal trans-activating nucleus-mitochondria coordination to acquire stemness
Bin He•Rui Gao•Shasha Lv•Ailin Chen•Junxiu Huang等 23 人
Signal Transduction And Targeted Therapy
2023
•2023/7/19
•Vol.8 No.1 p.1-19
Cancer cell receives extracellular signal inputs to obtain a stem-like status, yet how tumor microenvironmental (TME) neural signals steer cancer stemness to establish the hierarchical tumor architectures remains elusive. Here, a pan-cancer transcriptomic screening for 10852 samples of 33 TCGA cance...
Cancer microenvironmentCancer stem cellsGenome informaticsStem-cell niche
10.1038/S41392-023-01487-4
ISSN:2059-3635
Sialic acids in pancreatic cancer cells drive tumour-associated macrophage differentiation via the Siglec receptors Siglec-7 and Siglec-9
Ernesto Rodriguez•Kelly Boelaars•Kari Brown•R. J. Eveline Li•Laura Kruijssen等 16 人
Nature Communications
2021
•2021/2/24
•Vol.12 No.1 p.1-14
Changes in glycosylation during tumour progression are a key hallmark of cancer. One of the glycan moieties generally overexpressed in cancer are sialic acids, which can induce immunomodulatory properties via binding to Siglec receptors. We here show that Pancreatic Ductal Adenocarcinoma (PDAC) tumo...
GlycobiologyPancreatic cancer
10.1038/S41467-021-21550-4
ISSN:2041-1723
Classification of distinct tendinopathy subtypes for precision therapeutics
Chenqi Tang•Zetao Wang•Yuanhao Xie•Yang Fei•Junchao Luo等 22 人
Nature Communications
2024
•2024/11/1
•Vol.15 No.1 p.1-14
Rotator cuff tendinopathy is the most common tendinopathy type with the worst prognosis. Conventional treatments often elicit heterogeneous drug responses due to the diversity of tendinopathy. Hence, this study attempted a classification of 126 diseased tendons into three distinct subtypes with oppo...
InflammationTendons
10.1038/S41467-024-53826-W
ISSN:2041-1723
HNF4α ubiquitination mediated by Peli1 impairs FAO and accelerates pressure overload-induced myocardial hypertrophy
Yuxing Hou•Pengxi Shi•Haiyang Du•Chenghao Zhu•Chao Tang等 13 人
Cell Death & Disease
2024
•2024/2/12
•Vol.15 No.2 p.1-14
Impaired fatty acid oxidation (FAO) is a prominent feature of metabolic remodeling observed in pathological myocardial hypertrophy. Hepatocyte nuclear factor 4alpha (HNF4α) is closely associated with FAO in both cellular processes and disease conditions. Pellino 1 (Peli1), an E3 ligase containing a ...
Cardiovascular biologyMolecular biology
10.1038/S41419-024-06470-7
ISSN:2041-4889
The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay
Si Cheng•Zhe Xu•Shengzhe Bian•Xi Chen•Yanfeng Shi等 23 人
Cell Discovery
2023
•2023/7/21
•Vol.9 No.1 p.1-20
Ischemic stroke is a leading cause of global mortality and long-term disability. However, there is a paucity of whole-genome sequencing studies on ischemic stroke, resulting in limited knowledge of the interplay between genomic and phenotypic variations among affected patients. Here, we outline the ...
Genome-wide association studiesPopulation genetics
10.1038/S41421-023-00582-8
ISSN:2056-5968
Molecular characteristics of primary pulmonary lymphoepithelioma-like carcinoma based on integrated genomic analyses
Bojiang Chen•Yu Zhang•Sisi Dai•Ping Zhou•Wenxin Luo等 12 人
Signal Transduction And Targeted Therapy
2021
•2021/1/8
•Vol.6 No.1 p.1-10
Primary pulmonary lymphoepithelioma-like carcinoma (pLELC) is a rare non-small cell lung cancer (NSCLC) subtype. Clinical features have been described in our previous report, but molecular characteristics remain unclear. Herein, pLELC genomic features were explored. Among 41,574 lung cancers, 128 pL...
Cancer genomicsLung cancer
10.1038/S41392-020-00382-6
ISSN:2059-3635
Chromosome-level genome assembly of the casuarina moth, Lymantria xylina Swinhoe (1903)
Siyi Liu•Hui Jiang•Tao Ni•Kai Wang•Xia Hu等 8 人
Scientific Data
2026
•2026/2/4
•Vol.13 No.1 p.3520
The casuarina moth, Lymantria xylina, is a serious pest threatening subtropical regions through severe defoliation and strong invasive potential. Despite its economic impact and high invasion risk, a high-quality reference genome remains lacking. To bridge this knowledge gap, we generated a chromoso...
EukaryoteGenome
10.1038/S41597-026-06724-3
ISSN:2052-4463
Bcl11a deficiency in cerebellar Purkinje cells causes ataxia and autistic-like behavior by altering Vav3
Jie Zhang•Yuan-Xin Li•Qian Huang•Yu Yuan•Jun-Yang Chen等 9 人
Molecular Psychiatry
2025
•2025/8/25
•00 p.1-17
BCL11A encodes a transcription factor essential for brain development, with pathogenic variants causing intellectual disability, autism spectrum disorder (ASD), microcephaly, hypotonia, and behavioral abnormalities. While clinical studies have identified cerebellar pathology in patients with BCL11A ...
Autism spectrum disordersNeuroscience
10.1038/S41380-025-03175-X
ISSN:1359-4184
Mapping the zygote-to-adult developmental cell phylogeny in Arabidopsis thaliana reveals a three-cell rule of branching
Fan-Nv Xia•Kehui Liu•Jianguo Wang•Zhan Liu•Ang Li等 8 人
Nature Plants
2026
•2026/4/13
•00 p.1-17
Similar to the evolutionary history of all species on Earth, the developmental lineage history of all cells in a multicellular organism is stored in a phylogenetic tree. Mapping the zygote-to-adult developmental cell phylogeny of a complex organism is of tremendous value but technically challenging....
Molecular engineeringPlant genetics
10.1038/S41477-026-02264-1
ISSN:2055-0278
ZFP612 controls neuropathic pain through epigenetic repression of Il1rl1 within the silencer–promoter loop in primary sensory neurons of male mice
Longfei Ma•Yangyuxin Huang•Meiling Han•Bing Wang•Xinying Guo等 28 人
Nature Communications
2025
•2025/11/28
•Vol.16 No.1 p.107010
Peripheral nerve injury-induced intrinsic immune responses in primary sensory neurons are critical for neuropathic pain genesis. However, the key regulators driving these responses remain elusive. Here, we report that nerve injury-specific downregulation of zinc finger protein 612 (ZFP612) in injure...
Gene silencingMolecular neuroscienceNeuropathic pain
10.1038/S41467-025-65935-1
ISSN:2041-1723
An updated Pig Haplotype Reference Panel (PHARP 4.0) comprising 13,298 haplotypes
Qingyu Wang•Zhenyang Zhang•Xiaowei Ye•Jiamin Gu•Jiabao Sun等 17 人
Communications Biology
2025
•2025/11/20
•Vol.8 No.1 p.16250
High-throughput genome sequencing and genotyping have significantly accelerated genetic research. However, the high cost of whole-genome sequencing (WGS) remains a barrier to large-scale studies like genome-wide association studies (GWAS) and genomic prediction. Genotype imputation offers a cost-eff...
DNA sequencingGenomeGenomicsHaplotypes
10.1038/S42003-025-09052-1
ISSN:2399-3642
Small extracellular vesicle-miR-183-5p mediated crosstalk between tumor cells and macrophages in high-risk pancreatic neuroendocrine tumors
Wuhu Zhang•Junfeng Xu•Dan Huang•Yi Qin•Xin Lou等 17 人
Oncogene
2025
•2025/6/5
•00 p.1-17
High-risk pancreatic neuroendocrine tumors (pNET) are characterized by aggressive progression and metastasis, contributing to poor clinical outcomes. This study explores molecular mechanisms underlying metastasis in high-risk pNETs and evaluates therapeutic interventions. We employed small RNA seque...
MetastasisNeuroendocrine cancer
10.1038/S41388-025-03462-5
ISSN:0950-9232
C/EBPβ activation in vascular smooth muscle cells promotes hyperlipidemia-induced phenotypic transition and arterial stiffness
Jun Ma•Xiangyu Yang•Yanan Li•Xin Zhang•Kai Liu等 21 人
Signal Transduction And Targeted Therapy
2025
•2025/4/2
•Vol.10 No.1 p.1-14
Arterial stiffness is a critical factor in cardiovascular and cerebrovascular events, yet clinical practice lacks specific therapeutic targets and biomarkers for its assessment. Hyperlipidemia closely correlates with arterial stiffness, and we observed elevated CCAAT/enhancer-binding protein β (C/EB...
Cardiovascular diseasesCell biology
10.1038/S41392-025-02196-W
ISSN:2059-3635
The fungistatic mechanism of benzaldehyde against the nematophagous fungus Arthrobotrys oligospora suggests a method for manipulating soil fungistasis
Li-Xue Tan•Ying-Ying Zhang•Zhi-Jian Liu•Yi Cao•Jian-Jin Liu等 7 人
Communications Biology
2026
•2026/3/10
0Germination and growth of biocontrol microorganisms in soil are often inhibited by soil fungistasis (SF), resulting in unsatisfactory control efficacy. Therefore, exploring mechanisms underlying SF is important for developing efficient biocontrol agents. Benzaldehyde has a strong fungistatic effect ...
Antimicrobial resistanceFungal biology
10.1038/S42003-026-09836-Z
ISSN:2399-3642
The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels
Yiming Zhao•Hao Chen•Jing Huang•Ludmila Chistoserdova•Zheng Yu
Nature Communications
2025
•2025/12/2
0Methane, a predominant component of human intestinal gas, has been reported to be associated with a reduction in intestinal transit speed, as well as correlations with elevated body mass index. While the gut methanogenic archaea that produce this gas have been studied, the countervailing role of met...
EndocrinologyMicrobiology
10.1038/S41467-025-66596-W
ISSN:2041-1723
Standing genetic variation and introgression shape the cryptic radiation of Aquilegia in the mountains of Southwest China
Jun-Chu Peng•Ziwen He•Zhi-Qiang Zhang
Communications Biology
2025
•2025/4/30
•Vol.8 No.1 p.1-15
Cryptic diversity in evolutionary radiation offers an excellent system for investigating the intricacies of evolutionary progress. Understanding the evolution of cryptic diversity is imperative for unraveling the hidden complexities of biodiversity. However, empirical evidence elucidating the mechan...
Evolutionary biologyPopulation geneticsSpeciation
10.1038/S42003-025-08120-W
ISSN:2399-3642
The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment
Susu Qu•Xiangyu Zhou•Zhicheng Wang•Yi Wei•Han Zhou等 14 人
Molecular Psychiatry
2023
•2023/11/13
•00 p.1-21
The stimulant methylphenidate (MPH) and the non-stimulant atomoxetine (ATX) are frequently used for the treatment of attention-deficit/hyperactivity disorder (ADHD); however, the function of these drugs in different types of brain cells and their effects on related genes remain largely unknown. To a...
Cell biologyMolecular biologyPsychology
10.1038/S41380-023-02314-6
ISSN:1359-4184
Nuclear FGF2 orchestrates phase separation-mediated rDNA chromatin architecture to control BMSCs cell fate
Hengguo Zhang•Zifei Wang•Zhenqing Liu•Xuan Li•Wansu Sun等 15 人
Bone Research
2025
•2025/9/24
•Vol.13 No.1 p.800
Ribosomal RNA (rRNA) synthesis is intricately tied to cellular growth and proliferation. Basic fibroblast growth factor (FGF2), a pivotal factor for bone marrow mesenchymal stem cells (BMSCs), can stimulates rRNA transcription, though the underlying mechanism remains unknown. Here, we demonstrate th...
BoneBone quality and biomechanics
10.1038/S41413-025-00451-Y
ISSN:2095-6231
Bacillus cereus is a key microbial determinant of intractable otitis media with effusion
Yue Fan•Junru Chen•Shenglong Xu•Hailu Zhou•Yingying Shang等 12 人
Communications Medicine
2025
•2025/5/3
•Vol.5 No.1 p.1-8
Currently, the mechanisms by which otitis media with effusion (OME) progresses to intractable OME is unclear. Since crosstalk between microbiome and host contributes to many diseases, we hypothesized that similar interactions could occur in the middle ear effusion (MEE) samples from patients with OM...
Clinical microbiologyPrognostic markers
10.1038/S43856-025-00876-W
ISSN:2730-664X
Centralized industrialization of pork in Europe and America contributes to the global spread of Salmonella enterica
Heng Li•Yilei Wu•Dan Feng•Quangui Jiang•Shengkai Li等 17 人
Nature Food
2024
•2024/5/9
•00 p.1-10
Salmonella enterica causes severe food-borne infections through contamination of the food supply chain. Its evolution has been associated with human activities, especially animal husbandry. Advances in intensive farming and global transportation have substantially reshaped the pig industry, but thei...
Data miningEvolutionary geneticsPathogens
10.1038/S43016-024-00968-1
ISSN:2662-1355
Regulation of m6A RNA reader protein OsECT3 activity by lysine acetylation in the cold stress response in rice
Nini Ma•Peizhe Song•Ziyang Liu•Yangjie Li•Zhihe Cai等 13 人
Nature Plants
2025
•2025/6/20
•Vol.11 No.6 p.1165-1180
N6-Methyladenosine (m6A) reader proteins, which recognize m6A to regulate RNA metabolism, are important for plant adaptation to the changing environment. It remains unknown how the activities of plant m6A reader proteins are regulated in plant responses to stress. Here we show that the rice m6A read...
AbioticEpigeneticsPlant molecular biology
10.1038/S41477-025-02013-W
ISSN:2055-0278
Warming and resource enhancement shape food webs in South China Sea coral reef system
Zheng Zhang•Min Hui•Jiao Cheng•Zhongli Sha
Communications Earth & Environment
2025
•2025/12/31
0Coral reef ecosystems are being altered by rising ocean temperatures and increasing nutrient inputs, yet their combined influence on food-web structure is not well understood. Here we analyzed 130 coral reef food webs across the South China Sea, constructed from environmental DNA surveys integrated ...
EcologyOcean sciences
10.1038/S43247-025-03147-7
ISSN:2662-4435
Restoration of ethanol-induced Bifidobacterium pseudocatenulatum depletion ameliorates alcohol-associated liver disease
Yating Li•Liya Yang•Hong Xu•Xiaoyuan Bian•Ding Shi等 7 人
Npj Biofilms And Microbiomes
2026
•2026/1/20
•Vol.12 No.1 p.470
Alcohol-associated liver disease (ALD), characterized by gut barrier disruption and microbial dysbiosis, is associated with significant depletion of the genus Bifidobacterium in patients, as evidenced by our cohort of 127 subjects. Functional screening revealed B. pseudocatenulatum as a protective s...
Applied microbiologyMicrobial communitiesHealth careMicrobiology
10.1038/S41522-026-00913-Z
ISSN:2055-5008
Plasma extracellular vesicles-derived microRNAs provide potential biomarkers in distinguishing between focal cortical dysplasia type I and II
Bocheng Zhou•Hao Yu•Chang Liu•Yao Wang•Yi Wang等 15 人
Pediatric Research
2025
•2025/11/2
•00 p.1-11
Preoperative pathological information of focal cortical dysplasia (FCD) is critical for surgical planning, but non-invasive diagnostic methods are currently unavailable. This study aimed to identify potential biomarkers for FCD subtyping by screening microRNAs (miRNAs) in plasma extracellular vesicl...
Medicine/Public Health, generalPediatricsPediatric Surgery
10.1038/S41390-025-04343-Z
ISSN:0031-3998
Peripheral nerve-derived CSF1 induces BMP2 expression in macrophages to promote nerve regeneration and wound healing
Kai Wang•Binyu Song•Yuhan Zhu•Juanli Dang•Tong Wang等 11 人
Npj Regenerative Medicine
2024
•2024/11/21
•Vol.9 No.1 p.350
The precise mechanisms regulating inflammatory and prorepair macrophages have not been fully elucidated, despite the pivotal role played by innate immunity in wound healing. We first employed a denervation wound model to validate the crosstalk between neurons and macrophages. Compared to normal woun...
ImmunologyPeripheral nervous system
10.1038/S41536-024-00379-7
ISSN:2057-3995
XPO1 inhibitor KPT-330 disrupts the core transcriptional regulatory circuitry of dedifferentiated liposarcoma by modulating the translation process
Xiaorui Fan•Ying Zhang•Zhengming Yang•Tuan Zea Tan•Xingze Huang等 14 人
Oncogene
2026
•2026/4/16
•00 p.1-17
Dedifferentiated liposarcoma (DDLPS) is a rare and aggressive subtype of liposarcoma, driven by a core transcriptional regulatory circuitry (CRC) that sustains tumor proliferation. This malignancy poses considerable clinical challenges, marked by high postoperative recurrence and metastatic potentia...
Cancer therapySarcoma
10.1038/S41388-026-03794-W
ISSN:0950-9232
Single-cell RNA sequencing reveals cell landscape following antimony exposure during spermatogenesis in Drosophila testes
Yu Jun•Fu Yangbo•Li Zhiran•Huang Qiuru•Tang Juan等 16 人
Cell Death Discovery
2023
•2023/3/9
•Vol.9 No.1 p.1-14
Antimony (Sb), is thought to induce testicular toxicity, although this remains controversial. This study investigated the effects of Sb exposure during spermatogenesis in the Drosophila testis and the underlying transcriptional regulatory mechanism at single-cell resolution. Firstly, we found that f...
Cell growthCell lineage
10.1038/S41420-023-01391-4
ISSN:2058-7716
Dynamic transcriptional immune landscape in response to NK-cell therapy combined with gemcitabine plus S-1 in advanced pancreatic cancer: a phase 1b/2 trial
Qin Tan•Yifei Li•Caixia Liu•Jing Xu•Jinlian Tong等 12 人
Signal Transduction And Targeted Therapy
2025
•2025/11/21
•Vol.10 No.1 p.3810
Despite advancements in several malignancies, the treatment atlas of natural killer (NK) cell therapy for pancreatic cancer remains inadequate, and the dynamic immune landscape underlying the various responses is still incompletely understood. This phase 1b/2 trial evaluated the safety and efficacy ...
Cancer therapyGastrointestinal cancerImmunotherapy
10.1038/S41392-025-02488-1
ISSN:2059-3635
Human microbiota from drug-naive patients with obsessive-compulsive disorder drives behavioral symptoms and neuroinflammation via succinic acid in mice
Ying-Dan Zhang•Dong-Dong Shi•Bing-Bing Liao•Yi Li•Sen Zhang等 8 人
Molecular Psychiatry
2024
•2024/1/25
•00 p.1-16
Emerging evidence suggests that the gut microbiota is closely related to psychiatric disorders. However, little is known about the role of the gut microbiota in the development of obsessive-compulsive disorder (OCD). Here, to investigate the contribution of gut microbiota to the pathogenesis of OCD,...
NeurosciencePsychiatric disorders
10.1038/S41380-024-02424-9
ISSN:1359-4184
Genomics-driven discovery of superior alleles and genes for yellow rust resistance in wheat
Jianhui Wu•Shengwei Ma•Jianqing Niu•Weihang Sun•Haitao Dong等 24 人
Nature Genetics
2025
•2025/7/22
•00 p.1-11
Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici, poses a significant threat to wheat production worldwide. Breeding resistant cultivars is crucial for managing this disease. However, our understanding of the genetic mechanisms underlying YR resistance remains fragmented. To address t...
DNA sequencingPlant breedingPlant genetics
10.1038/S41588-025-02259-2
ISSN:1061-4036
DNA/RNA-binding protein KIN17 supports esophageal cancer progression via resolving noncanonical STING activation induced by R-loop
Zichao Wei•Ning Zhao•Lu Kuang•Ji Cong•Sujuan Zheng等 7 人
Signal Transduction And Targeted Therapy
2025
•2025/8/15
•Vol.10 No.1 p.1-13
Targeting the DNA damage response (DDR) exhibits potent efficacy in inducing immune activation and enhancing patient prognosis. However, the benefits of DDR regulation are not universally observed across all patients, owing to the intricate compensatory mechanisms operative in certain cancers. There...
Genomic instabilityHead and neck cancerOncogenes
10.1038/S41392-025-02344-2
ISSN:2059-3635
Single-cell RNA sequencing identifies an Il1rn+/Trem1+ macrophage subpopulation as a cellular target for mitigating the progression of thoracic aortic aneurysm and dissection
Liu Xuanyu•Chen Wen•Zhu Guoyan•Yang Hang•Li Wenke等 8 人
Cell Discovery
2022
•2022/2/8
•Vol.8 No.1 p.1-21
Thoracic aortic aneurysm and dissection (TAAD) is a life-threatening condition characterized by medial layer degeneration of the thoracic aorta. A thorough understanding of the regulator changes during pathogenesis is essential for medical therapy development. To delineate the cellular and molecular...
Innate immunityMechanisms of disease
10.1038/S41421-021-00362-2
ISSN:2056-5968
Mapping the spreading routes of lymphatic metastases in human colorectal cancer
Chong Zhang•Lin Zhang•Tianlei Xu•Ruidong Xue•Liang Yu等 13 人
Nature Communications
2020
•2020/4/24
•Vol.11 No.1 p.1-11
Lymphatic metastases are closely associated with tumor relapse and reduced survival in colorectal cancer (CRC). How tumor cells disseminate within the lymphatic network remains largely unknown. Here, we analyze the subclonal structure of 94 tumor samples, covering the primary tumors, lymph node meta...
Cancer genomicsGastrointestinal cancerMetastasis
10.1038/S41467-020-15886-6
ISSN:2041-1723
LIM domain only 7: a novel driver of immune evasion through regulatory T cell differentiation and chemotaxis in pancreatic ductal adenocarcinoma
Shangnan Dai•Yunpeng Peng•Guangfu Wang•Chongfa Chen•Qiuyang Chen等 16 人
Cell Death & Differentiation
2024
•2024/8/14
•00 p.1-20
With advancements in genomics and immunology, immunotherapy has emerged as a revolutionary strategy for tumor treatment. However, pancreatic ductal adenocarcinoma (PDAC), an immunologically “cold” tumor, exhibits limited responsiveness to immunotherapy. This study aimed to address the urgent need to...
Cancer microenvironmentChemokinesEpigeneticsImmune evasionTumour heterogeneity
10.1038/S41418-024-01358-7
ISSN:1350-9047
Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system
Guo Haipeng•Dong Pengsheng•Gao Fan•Huang Lei•Wang Sipeng等 8 人
Npj Biofilms And Microbiomes
2022
•2022/4/11
•Vol.8 No.1 p.1-14
Sucrose is an effective carbon source for creating more reliable and environmentally friendly conditions for shrimp growth by regulating bacteria in biofloc-based culture systems. However, the influence of sucrose addition on the interaction, co-occurrence networks, and assembly mechanisms of bacter...
Microbial ecologyWater microbiology
10.1038/S41522-022-00288-X
ISSN:2055-5008
Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq
Zhifei Shi•Xiyang Chen•Yijia Yang•Ang Wu•Heng Wang等 20 人
Cell Research
2026
•2026/7/13
•00 p.1-18
Mapping of protein-DNA interactions at single-cell resolution remains a central challenge in epigenomics, particularly for transcription factors (TFs), whose sparse binding limits reliable detection. Here, we establish DeChIC-seq (DNA Deaminase-based Chromatin Immuno-Conversion sequencing), a c...
Epigenetic memoryPluripotency
10.1038/S41422-026-01275-Z
ISSN:1748-7838
Lipid metabolism and microbial regulation analyses provide insights into the energy-saving strategies of hibernating snakes
Yuting Wei•Huirong Mao•Qiuhong Liu•Wenjie Fang•Tianxiang Zhang等 10 人
Communications Biology
2025
•2025/1/12
•Vol.8 No.1 p.1-13
Hibernation is a necessary means for animals to maintain survival while coping with low temperatures and food shortages. While most studies have largely focused on mammalian hibernation, its reptilian equivalent has been less studied. In order to provide insights into the energy metabolism and poten...
Animal physiologyHerpetology
10.1038/S42003-025-07493-2
ISSN:2399-3642
Molecular features and clinical implications of the heterogeneity in Chinese patients with HER2-low breast cancer
Lei-Jie Dai•Ding Ma•Yu-Zheng Xu•Ming Li•Yu-Wei Li等 13 人
Nature Communications
2023
•2023/8/22
•Vol.14 No.1 p.1-13
The molecular heterogeneity and distinct features of HER2-low breast cancers, particularly in the Chinese population, are not well understood, limiting its precise management in the era of antibody‒drug conjugates. To address this issue, we established a cohort of 434 Chinese patients with HER2-low ...
Breast cancerCancer genomicsTargeted therapiesTumour heterogeneity
10.1038/S41467-023-40715-X
ISSN:2041-1723
Targeting pericentric non-consecutive motifs for heterochromatin initiation
Runze Ma•Yan Zhang•Jing Zhang•Pinqi Zhang•Zeqi Liu等 9 人
Nature
2024
•2024/7/3
•Vol.631 No.8021 p.678-685
Pericentric heterochromatin is a critical component of chromosomes marked by histone H3 K9 (H3K9) methylation1–3. However, what recruits H3K9-specific histone methyltransferases to pericentric regions in vertebrates remains unclear4, as does why pericentric regions in different species share the sam...
Gene silencingHistone post-translational modifications
10.1038/S41586-024-07640-5
ISSN:0028-0836
Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction
Yuan Lin•Yingying Luo•Yanxia Sun•Wenjia Guo•Xuan Zhao等 12 人
Nature Communications
2020
•2020/11/30
•Vol.11 No.1 p.1-14
Adenocarcinoma at the gastroesophageal junction (ACGEJ) has dismal clinical outcomes, and there are currently few specific effective therapies because of limited knowledge on its genomic and transcriptomic alterations. The present study investigates genomic and transcriptomic changes in ACGEJ from C...
Cancer genomicsOesophageal cancer
10.1038/S41467-020-19949-6
ISSN:2041-1723
Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks
Xi Peng•Shang Wang•Miaoxiao Wang•Kai Feng•Qing He等 12 人
Nature Communications
2024
•2024/9/17
•Vol.15 No.1 p.1-14
Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach ...
Ecological modellingEcological networksMicrobial ecology
10.1038/S41467-024-52532-X
ISSN:2041-1723
Integrative omics of the genetic basis for wheat WUE and drought resilience reveal the function of TaMYB7-A1
Yuxin Zhou•Dongzhi Wang•Hao Wang•Yunzhou Qiao•Peng Zhao等 12 人
Nature Communications
2025
•2025/9/29
•Vol.16 No.1 p.1-19
Improving wheat drought resilience and water use efficiency (WUE) is critical for sustaining productivity under increasing water scarcity. Here, we integrate genome-wide association study (GWAS), expression quantitative trait locus (eQTL) mapping, population-transcriptome analysis, and sum...
Plant geneticsPlant stress responses
10.1038/S41467-025-63642-5
ISSN:2041-1723
Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq
Liu Yusheng•Zhang Yiwei•Wang Jiaqiang•Lu Falong
Nature Protocols
2022
•2022/7/13
•00 p.1-28
Poly(A) tails are added to the 3′ ends of most mRNAs in a non-templated manner and play essential roles in post-transcriptional regulation, including mRNA export, stability and translation. Measuring poly(A) tails is critical for understanding their regulatory roles in almost every aspect of biologi...
RNA metabolismRNA sequencingTranscriptomics
10.1038/S41596-022-00704-8
ISSN:1754-2189
Implications of oral streptococcal bacteriophages in autism spectrum disorder
Tong Zhan•Zhou Xin•Chu Yanan•Zhang Tianxu•Zhang Jie等 12 人
Npj Biofilms And Microbiomes
2022
•2022/11/18
•Vol.8 No.1 p.1-12
Growing evidence suggests altered oral and gut microbiota in autism spectrum disorder (ASD), but little is known about the alterations and roles of phages, especially within the oral microbiota in ASD subjects. We enrolled ASD (n = 26) and neurotypical subjects (n = 26) with their oral hygiene contr...
MetagenomicsMicrobiome
10.1038/S41522-022-00355-3
ISSN:2055-5008
A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits
Guangwei Zhao•Qun Lian•Zhonghua Zhang•Qiushi Fu•Yuhua He等 44 人
Nature Genetics
2019
•2019/11/1
•Vol.51 No.11 p.1607-1615
Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessi...
Computational biology and bioinformaticsGeneticsPlant sciences
10.1038/S41588-019-0522-8
ISSN:1061-4036
Genetic architecture and phenotypic diversity of oocyte and early embryo competence defects in female infertility
Changlong Zhang•Wei Zheng•Honghui Zhang•Shuai Zhao•Huiling Hu等 32 人
Nature Medicine
2025
•2025/10/16
•00 p.1-10
Oocyte and early embryo competence defects (OECD) represent a recently recognized cause of female infertility with the application of assisted reproductive technology, characterized by impaired oocyte or early embryo development. To investigate the genetic landscape and subtypes of OECD, we performe...
Disease geneticsInfertility
10.1038/S41591-025-04001-1
ISSN:1078-8956
Single-cell atlas of reproductive endocrine organs reveals transcriptomic responses to type 1 diabetes mellitus in nonhuman primates
Zheng-Hui Zhao•Ning Xu•Xue-Ying Chen•Cheng-Yan Zhuo•Yong Lu等 9 人
Cell Discovery
2026
•2026/8/4
•Vol.12 No.1 p.580
Type 1 diabetes mellitus characterized by insulin deficiency and hyperglycemia is associated with female subfertility. However, how hyperglycemia affects the hypothalamic-pituitary-ovarian-uterine axis remains poorly understood. In this study, we performed single-cell transcriptomic profiling of the...
Mechanisms of diseaseTranscriptomics
10.1038/S41421-026-00908-2
ISSN:2056-5968
Lenvatinib plus transarterial chemoembolization and PD-1 inhibitors as conversion therapies for unresectable intermediate-advanced hepatocellular carcinoma: a phase 2 trial and exploratory biomolecular study
Xiaoyun Zhang•Haozheng Cai•Wei Peng•Haiqing Wang•JiaYi Wu等 26 人
Signal Transduction And Targeted Therapy
2026
•2026/1/22
•Vol.11 No.1 p.370
Conversion therapy remains an uncommon strategy for managing unresectable hepatocellular carcinoma (uHCC) due to limited evidence supporting its efficacy. To address this gap, we initiated a prospective phase 2 multicenter trial (NCT04997850) comparing the LEN-TAP regimen, combining lenvatinib, tran...
Gastrointestinal cancerOutcomes research
10.1038/S41392-025-02498-Z
ISSN:2059-3635
Treatment of SARS-CoV-2-induced pneumonia with NAD+ and NMN in two mouse models
Jiang Yisheng•Deng Yongqiang•Pang Huanhuan•Ma Tiantian•Ye Qing等 10 人
Cell Discovery
2022
•2022/4/29
•Vol.8 No.1 p.1-17
The global COVID-19 epidemic has spread rapidly around the world and caused the death of more than 5 million people. It is urgent to develop effective strategies to treat COVID-19 patients. Here, we revealed that SARS-CoV-2 infection resulted in the dysregulation of genes associated with NAD+ metabo...
Cell deathMechanisms of disease
10.1038/S41421-022-00409-Y
ISSN:2056-5968
Transcriptome profiles reveal that gibberellin-related genes regulate weeping traits in crape myrtle
Suzhen Li•Tangchun Zheng•Xiaokang Zhuo•Zhuojiao Li•Lulu Li等 11 人
Horticulture Research
2020
•2020/4/1
•Vol.7 No.1 p.1-14
Plant architecture includes vital traits that influence and benefit crops, and economically important trees. Different plant architectures provide natural beauty. Weeping ornamental plants are aesthetically appealing to people. The regulatory mechanism controlling the weeping trait is poorly underst...
Molecular engineering in plantsPlant molecular biology
10.1038/S41438-020-0279-3
ISSN:2662-6810
Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems
Shuo Jiao•Haibo Pan•Pablo García-Palacios•Hairong Tu•Yiran Zhang等 27 人
Nature Food
2026
•2026/5/15
•00 p.1-13
Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired a...
AgroecologyClimate-change mitigation
10.1038/S43016-026-01348-7
ISSN:2662-1355
Gut microbiome predicts personalized responses to dietary fiber in prediabetes: a randomized, open-label trial
Delei Song•Guangli Feng•Yuhang Ma•Yu Shi•Chunfang Qian等 36 人
Nature Communications
2025
•2025/12/13
0Gut microbiota contributes to prediabetes progression, however, whether microbiota features can guide targeted prevention and treatment for diabetes requires validation through large-scale clinical trials. Here, in a randomized, open-label trial, we randomly assigned 802 prediabetic subjects to a us...
MicrobiomePre-diabetes
10.1038/S41467-025-66498-X
ISSN:2041-1723
Resetting histone modifications during human prenatal germline development
Gao Rui•Zeng Shiyang•Yang Dongxu•Li Xiaocui•Liu Wenqiang等 19 人
Cell Discovery
2023
•2023/2/3
•Vol.9 No.1 p.1-15
Histone modifications play critical roles in regulating gene expression and present dynamic changes during early embryo development. However, how they are reprogrammed during human prenatal germline development has not yet been elucidated. Here, we map the genome-wide profiles of three key histone m...
Embryonic germ cells
10.1038/S41421-023-00519-1
ISSN:2056-5968
Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism
Gang Wang•Xingtan Zhang•Edward Allen Herre•Doyle McKey•Carlos A. Machado等 14 人
Nature Communications
2021
•2021/2/2
•Vol.12 No.1 p.1-14
Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast ge...
CoevolutionEvolutionary ecologyPlant evolutionSpeciation
10.1038/S41467-021-20957-3
ISSN:2041-1723
Functional variants at 1p36.23 confer risk of schizophrenia through modulating RERE
Yixing Liu•Junyang Wang•Hong Yang•Yifan Li•Changgai Mu等 16 人
Nature Communications
2026
•2026/1/24
•Vol.17 No.1 p.17420
Genome-wide association studies have identified 1p36.23 as a schizophrenia risk locus. However, the functional variants and genes driving the association remain unknown. Here, we identified two functional variants (i.e., rs159961 and rs301792) at the 1p36.23 risk locus. Both variants reside introns ...
Disease geneticsFunctional genomicsGenetics of the nervous systemSchizophrenia
10.1038/S41467-026-68449-6
ISSN:2041-1723
DNA methylation is involved in sexual differentiation and sex chromosome evolution in the dioecious plant garden asparagus
Li Shu-Fen•Lv Can-Can•Lan Li-Na•Jiang Kai-Lu•Zhang Yu-Lan等 8 人
Horticulture Research
2021
•2021/9/1
•Vol.8 No.1 p.1-14
DNA methylation is a crucial regulatory mechanism in many biological processes. However, limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants. In this study, we investigated the variances in methylation and transcriptional patterns of male ...
DNA methylationPlant reproduction
10.1038/S41438-021-00633-9
ISSN:2662-6810
PCDH17 induces colorectal cancer metastasis by destroying the vascular endothelial barrier
Fengyun Dong•Pinghui Zhou•Feifei Kong•Sijie Cao•Xiaozao Pan等 13 人
Cell Death & Disease
2025
•2025/1/21
•Vol.16 No.1 p.1-12
Compromised vascular integrity facilitates the cancer cells extravasation and metastasis. However, the mechanisms leading to a disruption in vascular integrity in colorectal cancer (CRC) remain unclear. In this study, PCDH17 expression was higher in the vascular endothelial cells of colon cancer wit...
MetastasisPrognostic markers
10.1038/S41419-025-07355-Z
ISSN:2041-4889
TCR-mimic bispecific nanobody-based T cell engager targeting intracellular tumor antigens for cancer immunotherapy
Ziqiang Ding•Shuyang Sun•Xiaomei Yang•Xianing Huang•Xiaoqiong Hou等 8 人
Signal Transduction And Targeted Therapy
2026
•2026/6/25
•Vol.11 No.1 p.2470
T cell engager (TCE) immunotherapies have revolutionized the landscape of cancer treatment; however, their efficacy remains limited by the inaccessibility of intracellular tumor antigens. Conventional bispecific T cell engagers, typically constructed from aggregation-prone single-chain variable frag...
ImmunotherapyTumour immunology
10.1038/S41392-026-02745-X
ISSN:2059-3635
Analysis of the glyco-code in pancreatic ductal adenocarcinoma identifies glycan-mediated immune regulatory circuits
Rodriguez Ernesto•Boelaars Kelly•Brown Kari•Madunić Katarina•van Ee Thomas等 22 人
Communications Biology
2022
•2022/1/11
•Vol.5 No.1 p.1-15
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most aggressive malignancies with a 5-year survival rate of only 9%. Despite the fact that changes in glycosylation patterns during tumour progression have been reported, no systematic approach has been conducted to evaluate its potential fo...
GlycobiologyPancreatic cancer
10.1038/S42003-021-02934-0
ISSN:2399-3642
Lysosomal and mTORC1 signaling dysregulation underpin the pathology of spastic paraplegia type 80
Yiqiang Zhi•Tongtong Zhang•Danping Lu•Shuhuai Lin•Huizhen Su等 16 人
Nature Communications
2025
•2025/11/7
•Vol.16 No.1 p.1-18
Endosomal sorting complex required for transport (ESCRT) is the major membrane remodeling complex, closely associated with endolysosomal repair and hereditary spastic paraplegias (HSP) diseases. Loss of function mutations in the ESCRT-I component UBAP1 causes a rare type of HSP (spastic paraplegia 8...
Cell biologyLysosomesNeuroscience
10.1038/S41467-025-64800-5
ISSN:2041-1723
Human neutrophil α-defensin HNP1 interacts with bacterial OmpA to promote Acinetobacter baumannii biofilm formation
Chongbing Liao•Qihui Liu•Gan Luo•Yinyue Luo•Dan Yao等 11 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-19
Acinetobacter baumannii is the causative agent of a wide range of nosocomial and community-acquired infections that remain extremely difficult to treat due largely to its antibiotic resistance contributed, in part, by biofilm formation. We find that the prototypic human neutrophil α-defensin HNP1, p...
Antimicrobial resistanceBiofilmsPathogens
10.1038/S41467-025-60935-7
ISSN:2041-1723
Chromosome-level genome assembly and population genomics of Robinia pseudoacacia reveal the genetic basis for its wide cultivation
Zefu Wang•Xiao Zhang•Weixiao Lei•Hui Zhu•Shengdan Wu等 7 人
Communications Biology
2023
•2023/7/31
•Vol.6 No.1 p.1-12
Urban greening provides important ecosystem services and ideal places for urban recreation and is a serious consideration for municipal decision-makers. Among the tree species cultivated in urban green spaces, Robinia pseudoacacia stands out due to its attractive flowers, fragrances, high trunks, wi...
Evolutionary geneticsPlant ecology
10.1038/S42003-023-05158-6
ISSN:2399-3642
Aberrant epithelial cell interaction promotes esophageal squamous-cell carcinoma development and progression
Liping Chen•Shihao Zhu•Tianyuan Liu•Xuan Zhao•Tao Xiang等 8 人
Signal Transduction And Targeted Therapy
2023
•2023/12/15
•Vol.8 No.1 p.1-16
Epithelial-mesenchymal transition (EMT) and proliferation play important roles in epithelial cancer formation and progression, but what molecules and how they trigger EMT is largely unknown. Here we performed spatial transcriptomic and functional analyses on samples of multistage esophageal squamous...
Gastrointestinal cancerOncogenes
10.1038/S41392-023-01710-2
ISSN:2059-3635
Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning
Ni Peng•Huang Neng•Nie Fan•Zhang Jun•Zhang Zhi等 11 人
Nature Communications
2021
•2021/10/13
•Vol.12 No.1 p.1-11
In plants, cytosine DNA methylations (5mCs) can happen in three sequence contexts as CpG, CHG, and CHH (where H = A, C, or T), which play different roles in the regulation of biological processes. Although long Nanopore reads are advantageous in the detection of 5mCs comparing to short-read bisulfit...
Computational modelsDNA methylationPlant genetics
10.1038/S41467-021-26278-9
ISSN:2041-1723
Molecular heterogeneity of the non-human primate cochlea
Xin Chen•Yuwei Che•Jieyu Qi•Ming Cen•Shan Gao等 19 人
Nature Communications
2026
•2026/1/17
•Vol.17 No.1 p.16330
Unraveling the intricate composition and function of the cochlea is paramount to comprehending the mechanisms underlying sound perception and the pathogenesis of auditory disorders. The mammalian cochlea displays a highly organized structure, which contributes to the diversity and complexity of audi...
CochleaHair cell
10.1038/S41467-026-68350-2
ISSN:2041-1723
Multiple active-sites editing of adenylation domains of srfA operon for constructing diverse surfactin lipopeptide
Zhaoyang Wang•Li Liu•Jiaxun Wei•Ning Liu•Ming Ying等 7 人
Communications Biology
2026
•2026/1/6
•Vol.9 No.1 p.1260
The srfA operon, which encodes the surfactin synthase SrfA in Bacillus rhizobacteria, is essential for surfactin biosynthesis. As a typical non-ribosomal peptide synthetase (NRPS), the adenylation domain of SrfA determines the structure of the synthesized peptide. A major challenge in the field lies...
Genetic engineeringMicrobiology techniques
10.1038/S42003-025-09405-W
ISSN:2399-3642
PCDHA9 as a candidate gene for amyotrophic lateral sclerosis
Jie Zhong•Chaodong Wang•Dan Zhang•Xiaoli Yao•Quanzhen Zhao等 19 人
Nature Communications
2024
•2024/3/11
•Vol.15 No.1 p.1-22
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease. To identify additional genetic factors, we analyzed exome sequences in a large cohort of Chinese ALS patients and found a homozygous variant (p.L700P) in PCDHA9 in three unrelated patients. We generated Pcdhα9 mutant mic...
Amyotrophic lateral sclerosisCell deathGenetics of the nervous system
10.1038/S41467-024-46333-5
ISSN:2041-1723
Mitochondrial pyruvate carrier-mediated metabolism is dispensable for the classical activation of macrophages
Linyu Ran•Song Zhang•Guosheng Wang•Pei Zhao•Jiaxing Sun等 11 人
Nature Metabolism
2023
•2023/5/15
•00 p.1-17
Glycolysis is essential for the classical activation of macrophages (M1), but how glycolytic pathway metabolites engage in this process remains to be elucidated. Glycolysis leads to production of pyruvate, which can be transported into the mitochondria by the mitochondrial pyruvate carrier (MPC) fol...
Innate immunityMetabolismMetabolomics
10.1038/S42255-023-00800-3
ISSN:2522-5812
Multiomics of parkinsonism cynomolgus monkeys highlights significance of metabolites in interaction between host and microbiota
Jiang-Mei Gao•Shou-Yue Xia•Geoff Hide•Bi-Hai Li•Yi-Yan Liu等 12 人
Npj Biofilms And Microbiomes
2024
•2024/7/26
•Vol.10 No.1 p.1-14
The gut microbiota has been demonstrated to play a significant role in the pathogenesis of Parkinson’s disease (PD). However, conflicting findings regarding specific microbial species have been reported, possibly due to confounding factors within human populations. Herein, our current study investig...
Clinical microbiologySequencing
10.1038/S41522-024-00535-3
ISSN:2055-5008
Empagliflozin and liraglutide ameliorate HFpEF in mice via augmenting the Erbb4 signaling pathway
Xia-yun Ni•Xiao-jun Feng•Zhi-hua Wang•Yang Zhang•Peter J. Little等 9 人
Acta Pharmacologica Sinica
2024
•2024/4/8
•00 p.1-14
Heart failure with preserved ejection fraction (HFpEF) is closely associated with metabolic derangement. Sodium glucose cotransporter-2 inhibitors (SGLT2i) and glucagon-like peptide-1 receptor agonists (GLP-1RA) exert anti-HFpEF effects, but the underlying mechanisms remain unclear. In this study, w...
Biomedicine, generalPharmacology/ToxicologyMedical MicrobiologyImmunologyInternal MedicineVaccine
10.1038/S41401-024-01265-0
ISSN:1671-4083
Single-cell m6A mapping in vivo using picoMeRIP–seq
Yanjiao Li•Yunhao Wang•Maria Vera-Rodriguez•Leif Christopher Lindeman•Linda Ellevog Skuggen等 21 人
Nature Biotechnology
2023
•2023/6/22
•00 p.1-6
Current N6-methyladenosine (m6A) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio, we developed picogram-scale m6A RNA immunoprecipitation and sequencing (picoMeRIP–seq) for studying m6A in vivo in single cells an...
Embryonic inductionEpigenetic memoryEpigenomicsMethylation analysisTranscriptomics
10.1038/S41587-023-01831-7
ISSN:1087-0156
Up-regulation of Ifi27l2a expression in bone marrow monocytes contributes to glucocorticoid-induced bone loss
Zhihang Wang•Chongjun Huang•Shijia Liu•Peilun Xiao•Zeyao Lu等 7 人
Communications Biology
2025
•2025/11/17
•Vol.8 No.1 p.15900
Glucocorticoid-induced osteoporosis (GIO) is the most common complication of prolonged, high-dose glucocorticoid therapy. The enhancement of osteoclast differentiation is a key factor in the pathogenesis of GIO. Osteoclasts originate from the bone marrow, and a disorder of the bone marrow microenvir...
Cell biologyMolecular biology
10.1038/S42003-025-08985-X
ISSN:2399-3642
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
Single-cell RNA-seq reveals keratinocyte and fibroblast heterogeneity and their crosstalk via epithelial-mesenchymal transition in psoriasis
Dianhao Guo•Xiaokang Li•Jing Wang•Xin Liu•Yibo Wang等 7 人
Cell Death & Disease
2024
•2024/3/12
•Vol.15 No.3 p.1-14
The pathogenesis of psoriasis, a chronic inflammatory autoimmune skin disease with a high global prevalence, remains unclear. We performed a high-resolution single-cell RNA sequencing analysis of 94,759 cells from 13 samples, including those from psoriasis model mice and wild-type mice. We presented...
Psoriasis
10.1038/S41419-024-06583-Z
ISSN:2041-4889
Genomic regions under selection in the feralization of the dingoes
Shao-jie Zhang•Guo-Dong Wang•Pengcheng Ma•Liang-liang Zhang•Ting-Ting Yin等 13 人
Nature Communications
2020
•2020/2/3
•Vol.11 No.1 p.1-10
Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demogr...
Comparative genomicsEvolutionary geneticsMolecular evolutionPopulation genetics
10.1038/S41467-020-14515-6
ISSN:2041-1723
Chronic cold stress induced transcriptomic alterations in multi-metabolically active tissues of pigs
Bo Huang•Yurui Bai•Xun Zhou•Xue Tian•Xun Wang等 9 人
Communications Biology
2025
•2025/11/22
0Cold stress poses significant challenges to livestock production; however, the regulatory mechanisms underlying porcine responses to chronic cold stress remain inadequately understood. To address this gap, we characterized the transcriptional responses of five metabolism-related tissues to chronic c...
Agricultural geneticsHomeostasisTranscriptomics
10.1038/S42003-025-09226-X
ISSN:2399-3642
Unveiling the regulatory role of GRP7 in ABA signal-mediated mRNA translation efficiency regulation
Jing Zhang•Wenna Shao•Yongxin Xu•Fa’an Tian•Jinchao Chen等 13 人
Nature Communications
2025
•2025/4/26
•Vol.16 No.1 p.1-18
Abscisic acid (ABA) is a crucial phytohormone involved in plant growth and stress responses. While the transcriptional regulation triggered by ABA is well-documented, its effects on translational regulation have been less studied. Through Ribo-seq and RNA-seq analyses, we find that ABA treatment not...
Plant hormonesPlant stress responsesTranslation
10.1038/S41467-025-59329-6
ISSN:2041-1723
Plin2-mediated lipid droplet mobilization accelerates exit from pluripotency by lipidomic remodeling and histone acetylation
Wu Yi•Chen Keshi•Li Linpeng•Hao Zhihong•Wang Tianyu等 20 人
Cell Death & Differentiation
2022
•2022/5/25
•00 p.1-16
Metabolic switch is critical for cell fate determination through metabolic functions, epigenetic modifications, and gene expression. However, the mechanisms underlying these alterations and their functional roles remain unclear. Here, we show that Plin2-mediated moderate lipid hydrolysis is critical...
BiochemistryCell biology
10.1038/S41418-022-01018-8
ISSN:1350-9047
Surface decoration of bacteria generates robust living therapeutics for improved ulcerative colitis therapy
Junyu Liu•Zhihao Fang•Xiaobin Li•Xiaopeng Zhang•Yun Chen等 16 人
Communications Biology
2026
•2026/2/13
•Vol.9 No.1 p.4280
Oral probiotics have shown great potential in treating ulcerative colitis (UC). However, gastrointestinal obstacles substantially inactivate probiotics, impeding delivery and colonization in the colon. Here, we developed robust oral living therapeutics with high colon-accumulating effect via surface...
BiologicsUlcerative colitis
10.1038/S42003-026-09732-6
ISSN:2399-3642
RYBP/YAF2-PRC1 complexes and histone H1-dependent chromatin compaction mediate propagation of H2AK119ub1 during cell division
Jicheng Zhao•Min Wang•Luyuan Chang•Juan Yu•Aoqun Song等 12 人
Nature Cell Biology
2020
•2020/3/23
•Vol.22 No.4 p.439-452
Stable propagation of epigenetic information is important for maintaining cell identity in multicellular organisms. However, it remains largely unknown how mono-ubiquitinated histone H2A on lysine 119 (H2AK119ub1) is established and stably propagated during cell division. In this study, we found tha...
Gene silencingHistone post-translational modifications
10.1038/S41556-020-0484-1
ISSN:1465-7392
Comparison of fecal and blood metabolome reveals inconsistent associations of the gut microbiota with cardiometabolic diseases
Deng Kui•Xu Jin-jian•Shen Luqi•Zhao Hui•Gou Wanglong等 13 人
Nature Communications
2023
•2023/2/2
•Vol.14 No.1 p.1-12
Blood metabolome is commonly used in human studies to explore the associations of gut microbiota-derived metabolites with cardiometabolic diseases. Here, in a cohort of 1007 middle-aged and elderly adults with matched fecal metagenomic (149 species and 214 pathways) and paired fecal and blood target...
Clinical microbiologyMetabolomicsPolicy and public health in microbiology
10.1038/S41467-023-36256-Y
ISSN:2041-1723
Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber
Jiantao Guan•Xiangsheng Li•Han Miao•Xuemei Yan•Xiaoping Liu等 12 人
Nature Genetics
2026
•2026/7/21
•00 p.1-13
Cucumber (Cucumis sativus L.) is a global vegetable crop and powerful model for sex determination, fruit development and vascular biology. We present high-quality genome assemblies for 125 cultivated and wild accessions, capturing worldwide genetic diversity. Syntenic gene family analysis characteri...
Genetic association studyGenomicsPlant genetics
10.1038/S41588-026-02682-Z
ISSN:1061-4036
A chloroplast localized heavy metal-associated domain containing protein regulates grain calcium accumulation in rice
Huan Liu•Cun Lu•Xiang-Qian Liu•Chen-Jin Zhuo•Rong-Jian Luo等 12 人
Nature Communications
2024
•2024/10/27
•Vol.15 No.1 p.1-20
Calcium (Ca) is an essential mineral nutrient and plays a crucial signaling role in all living organisms. Increasing Ca content in staple foods such as rice is vital for improving Ca nutrition of humans. Here we map a quantitative trait locus that controls Ca concentration in rice grains and identif...
Agricultural geneticsPlant geneticsPlant molecular biology
10.1038/S41467-024-53648-W
ISSN:2041-1723
Engineered immunosuppressive dendritic cells protect against cardiac remodelling
Xiaoying Li•Jiamin Li•Guohua Li•Lisheng Zhu•Guo Cheng等 40 人
Nature
2026
•2026/4/8
•00 p.1-11
Heart failure remains a leading cause of morbidity and mortality, yet no approved therapies effectively prevent or reverse pathological cardiac fibrosis and the associated decline in cardiac function1–4. Chronic inflammation is a central driver of pathological fibrosis after ischaemic or haemodynami...
ImmunosuppressionTranslational research
10.1038/S41586-026-10346-5
ISSN:0028-0836
Integrated multi-omics analysis unravels the floral scent characteristics and regulation in “Hutou” multi-petal jasmine
Jingping Fang•Linwei Zhou•Qinchang Chen•Jinbin Wang•Ying Zhuang等 10 人
Communications Biology
2025
•2025/2/18
•Vol.8 No.1 p.1-20
The multi-petal “Hutou” jasmine (Jasminum sambac var. Trifoliatum) is highly valued for bonsai cultivation and landscape design, however, the aroma profile and mechanisms underlying floral scent formation remain elusive. In this study, we generate a nearly complete telomere-to-telomere (T2T) genome ...
Plant developmentPlant genetics
10.1038/S42003-025-07685-W
ISSN:2399-3642
Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase
Ge Weiran•Yu Cong•Li Jingjing•Yu Zhenyu•Li Xiaorong等 13 人
Nature
2023
•2023/3/29
•Vol.616 No.7955 p.176-182
Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification1–3. The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119...
Electron microscopyEpigenetics
10.1038/S41586-023-05841-Y
ISSN:0028-0836
Single-nucleus and bulk RNA sequencing reveal cellular and transcriptional mechanisms underlying lipid dynamics in high marbled pork
Liyi Wang•Xueyan Zhao•Shiqi Liu•Wenjing You•Yuqin Huang等 12 人
Npj Science Of Food
2023
•2023/6/2
•Vol.7 No.1 p.1-15
Pork is the most consumed meat in the world, and its quality is associated with human health. Intramuscular fat (IMF) deposition (also called marbling) is a key factor positively correlated with various quality traits and lipo-nutritional values of meat. However, the cell dynamics and transcriptiona...
Animal physiologyBiomaterials – cellsTranscriptomics
10.1038/S41538-023-00203-4
ISSN:2396-8370
Triticum population sequencing provides insights into wheat adaptation
Yao Zhou•Xuebo Zhao•Yiwen Li•Jun Xu•Aoyue Bi等 17 人
Nature Genetics
2020
•2020/10/26
•Vol.52 No.12 p.1412-1422
Bread wheat expanded its habitat from a core area of the Fertile Crescent to global environments within ~10,000 years. The genetic mechanisms of this remarkable evolutionary success are not well understood. By whole-genome sequencing of populations from 25 subspecies within the genera Triticum and A...
Genome informaticsGenomicsPlant geneticsPopulation genetics
10.1038/S41588-020-00722-W
ISSN:1061-4036
PAN2 maintains mRNA poly(A) tail homeostasis and regulates translation during spermiogenesis in mice
Xuan Wu•Yu-Ke Wu•Meng-Yan Jia•Zhuoyue Niu•Jingwen Liu等 11 人
Nature Communications
2026
•2026/2/19
•Vol.17 No.1 p.29250
The elongation and shortening of poly(A) tails are the most common types of post-transcriptional mRNA regulation in eukaryotic cells. PAN2-PAN3 and CCR4-NOT complexes are the main cytoplasmic enzymes that trim the poly(A) tails of mRNAs. However, the in vivo function of PAN2-PAN3 in mammals rem...
Germline developmentRNA decayTranslation
10.1038/S41467-026-69639-Y
ISSN:2041-1723
FTO-mediated m6A demethylation regulates GnRH expression in the hypothalamus via the PLCβ3/Ca2+/CAMK signalling pathway
Shaolian Zang•Xiaoqin Yin•Pin Li
Communications Biology
2023
•2023/12/21
•Vol.6 No.1 p.1-15
N6-methyladenosine (m6A) plays a crucial role in the development and functional homeostasis of the central nervous system. The fat mass and obesity-associated (FTO) gene, which is highly expressed in the hypothalamus, is closely related to female pubertal development. In this study, we found that m6...
Endocrine reproductive disordersGonadal disorders
10.1038/S42003-023-05677-2
ISSN:2399-3642
MAT2B regulates the protein level of MAT2A to preserve RNA N6-methyladenosine
Xinyi Wan•Weiwu Zeng•Haonan Fan•Chenliang Wang•Shixun Han等 15 人
Cell Death & Disease
2024
•2024/10/1
•Vol.15 No.10 p.1-16
MAT2B works together with MAT2A to synthesize S-Adenosyl methionine (SAM) as the primary methyl donor. MAT2B, despite lacking catalytic activity, exerts regulatory control over the enzymatic activity of MAT2A. In addition to the enzymatic activity regulation, we find that, in an NADP+-dependent mann...
EpigeneticsMechanisms of disease
10.1038/S41419-024-07093-8
ISSN:2041-4889
SETD5 modulates homeostasis of hematopoietic stem cells by mediating RNA Polymerase II pausing in cooperation with HCF-1
Li Mengke•Qiu Chen•Bian Yujie•Shi Deyang•Wang Bichen等 14 人
Leukemia
2021
•2021/12/1
•00 p.1-12
SETD5 mutations were identified as the genetic causes of neurodevelopmental disorders. While the whole-body knockout of Setd5 in mice leads to embryonic lethality, the role of SETD5 in adult stem cell remains unexplored. Here, a critical role of Setd5 in hematopoietic stem cells (HSCs) is identified...
Cell biologyHaematopoietic stem cells
10.1038/S41375-021-01481-1
ISSN:0887-6924
Human myelocyte and metamyelocyte-stage neutrophils suppress tumor immunity and promote cancer progression
Wei Liu•Tao Shi•Chun Lu•Keying Che•Zijian Zhang等 24 人
Cell Research
2025
•2025/7/15
•00 p.1-19
Tumor-infiltrating neutrophils (TINs) are highly heterogeneous and mostly immunosuppressive in the tumor immune microenvironment (TIME). Current biomarkers of TINs and treatment strategies targeting TINs have not yielded optimal responses in patients across cancer types. Here, we separated human and...
Cancer microenvironmentImmunosurveillanceTransdifferentiation
10.1038/S41422-025-01145-0
ISSN:1748-7838
Defective chromatin architectures in embryonic stem cells derived from somatic cell nuclear transfer impair their differentiation potentials
Wu Dan-Ya•Li Xinxin•Sun Qiao-Ran•Dou Cheng-Li•Xu Tian等 14 人
Cell Death & Disease
2021
•2021/11/16
•Vol.12 No.12 p.1-14
Nuclear transfer embryonic stem cells (ntESCs) hold enormous promise for individual-specific regenerative medicine. However, the chromatin states of ntESCs remain poorly characterized. In this study, we employed ATAC-seq and Hi-C techniques to explore the chromatin accessibility and three-dimensiona...
Embryonic stem cellsReprogrammingStem-cell differentiation
10.1038/S41419-021-04384-2
ISSN:2041-4889
A nanoparticle-based sonodynamic therapy reduces Helicobacter pylori infection in mouse without disrupting gut microbiota
Tao Liu•Shuang Chai•Mingyang Li•Xu Chen•Yutao Xie等 11 人
Nature Communications
2024
•2024/1/29
•Vol.15 No.1 p.1-19
Infection by Helicobacter pylori, a prevalent global pathogen, currently requires antibiotic-based treatments, which often lead to antimicrobial resistance and gut microbiota dysbiosis. Here, we develop a non-antibiotic approach using sonodynamic therapy mediated by a lecithin bilayer-coated poly(la...
Bacterial infectionBacterial toxinsMicrobiomeNanoparticles
10.1038/S41467-024-45156-8
ISSN:2041-1723
Mcam inhibits macrophage-mediated development of mammary gland through non-canonical Wnt signaling
Xing Yang•Haibo Xu•Xu Yang•Hui Wang•Li Zou等 14 人
Nature Communications
2024
•2024/1/2
•Vol.15 No.1 p.1-15
While canonical Wnt signaling is well recognized for its crucial regulatory functions in cell fate decisions, the role of non-canonical Wnt signaling in adult stem cells remains elusive and contradictory. Here, we identified Mcam, a potential member of the non-canonical Wnt signaling, as an importan...
Mammary stem cellsMorphogen signallingStem-cell niche
10.1038/S41467-023-44338-0
ISSN:2041-1723
DC-CD4 bispecific tolerogenic nanovesicles induce antigen-specific regulatory T cells and ameliorate collagen-induced arthritis in mice
Lei Zhao•Zhongqiang Gao•Ze Yuan•Xiaodie Yang•Duxin Li等 10 人
Nature Communications
2026
•2026/3/19
0Inducing antigen-specific regulatory T (Treg) cells is a promising strategy for treating autoimmune diseases (AID). Here, we present dendritic cells-CD4⁺ T cells (DC-CD4) bispecific tolerogenic nanovesicles (NV) co-loaded with an antigenic peptide and rapamycin. We show that these NVs bring DCs and ...
Drug deliveryImmunosuppressionRegulatory T cellsRheumatoid arthritis
10.1038/S41467-026-70898-Y
ISSN:2041-1723
IL7R remodels immunosuppression tumor microenvironment and promotes macrophage polarization by regulating NF-κB/CXCL1 axis in ovarian cancer
Yeqing Zheng•Cheng Qian•Shuyi Zhang•Meichen Wen•Xun Xu等 9 人
Cell Death & Disease
2025
•2025/12/8
0In the ovarian cancer microenvironment, the polarization of tumor-associated macrophages (TAMs) is closely associated with immunosuppressive phenotypes. Although elevated levels of circulating interleukin-7 (IL-7) have been linked to a poor prognosis, the regulatory mechanisms underlying this associ...
Cancer microenvironmentCancer modelsChemokinesOvarian cancer
10.1038/S41419-025-08312-6
ISSN:2041-4889
Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau
Tongrui Chen•Jinqing Xu•Lei Wang•Handong Wang•En You等 8 人
Heredity
2023
•2023/11/8
•00 p.1-11
Understanding the local adaptation of crops has long been a concern of evolutionary biologists and molecular ecologists. Identifying the adaptive genetic variability in the genome is crucial not only to provide insights into the genetic mechanism of local adaptation but also to explore the adaptatio...
Plant evolutionStructural variation
10.1038/S41437-023-00647-0
ISSN:0018-067X
Integrated analysis of GWAS and molQTLs reveals cell-specific genetic variants in the porcine immune system
Jinyan Yang•Siqian Chen•Yongjie Tang•Xini Wang•Lulu Wang等 11 人
Communications Biology
2026
•2026/2/11
•Vol.9 No.1 p.4080
Pigs are vital to global agriculture, and infectious diseases cause significant economic losses. Leukocytes provide a critical window into the genetic regulation of pig immune traits. However, understanding of these mechanisms within specific immune cell types remains insufficient. Here, we integrat...
Agricultural geneticsFunctional genomics
10.1038/S42003-026-09605-Y
ISSN:2399-3642
Impaired 2′,3′-cyclic phosphate tRNA repair causes thermo-sensitive genic male sterility in rice
Bin Yan•Chunyan Liu•Jing Sun•Yang Mao•Can Zhou等 19 人
Cell Research
2024
•2024/9/9
•00 p.1-13
Hybrid rice, widely planted in Asia, is pathogen resistant and has superior yields, making it a major contributor to global food security. The two-line hybrid rice system, which utilizes mutants exhibiting photo-/thermo-sensitive genic male sterility (P/TGMS), is the leading hybrid rice breeding tec...
Biological techniquesPlant sciences
10.1038/S41422-024-01012-4
ISSN:1748-7838
Single-cell and spatial proteo-transcriptomic profiling reveals immune infiltration heterogeneity associated with neuroendocrine features in small cell lung cancer
Ying Jin•Yuefeng Wu•Alexandre Reuben•Liang Zhu•Carl M. Gay等 18 人
Cell Discovery
2024
•2024/9/4
•Vol.10 No.1 p.1-19
Small cell lung cancer (SCLC) is an aggressive pulmonary neuroendocrine malignancy featured by cold tumor immune microenvironment (TIME), limited benefit from immunotherapy, and poor survival. The spatial heterogeneity of TIME significantly associated with anti-tumor immunity has not been systemical...
Cancer microenvironmentSmall-cell lung cancer
10.1038/S41421-024-00703-X
ISSN:2056-5968
Integrative cross-species analysis reveals conserved and unique signatures in fatty skeletal muscles
Liyi Wang•Yanbing Zhou•Yizhen Wang•Tizhong Shan
Scientific Data
2024
•2024/3/12
•Vol.11 No.1 p.1-14
Fat infiltration in skeletal muscle is now recognized as a standard feature of aging and is directly related to the decline in muscle function. However, there is still a limited systematic integration and exploration of the mechanisms underlying the occurrence of myosteatosis in aging across species...
AgeingMechanisms of diseaseTranscriptomics
10.1038/S41597-024-03114-5
ISSN:2052-4463
Metabolic reprogramming and membrane glycan remodeling as potential drivers of zebrafish heart regeneration
Spelat Renza•Ferro Federico•Contessotto Paolo•Aljaabary Amal•Martin-Saldaña Sergio等 13 人
Communications Biology
2022
•2022/12/13
•Vol.5 No.1 p.1-16
The ability of the zebrafish heart to regenerate following injury makes it a valuable model to deduce why this capability in mammals is limited to early neonatal stages. Although metabolic reprogramming and glycosylation remodeling have emerged as key aspects in many biological processes, how they m...
Developmental biologyGlycobiology
10.1038/S42003-022-04328-2
ISSN:2399-3642
A distinct neuronal ensemble of prelimbic cortex mediates spontaneous pain in rats with peripheral inflammation
Longyu Ma•Lupeng Yue•Shuting Liu•Shi Xu•Jifu Tong等 11 人
Nature Communications
2024
•2024/9/10
•Vol.15 No.1 p.1-18
The absence of a comprehensive understanding of the neural basis of spontaneous pain limits the development of therapeutic strategies targeting this primary complaint of patients with chronic pain. Here we report a distinct neuronal ensemble within the prelimbic cortex which processes signals relate...
Chronic inflammationChronic painNeural circuitsNeurophysiologySensory processing
10.1038/S41467-024-52243-3
ISSN:2041-1723
The influence of Lactobacillus johnsonii on tumor growth and lymph node metastasis in papillary thyroid carcinoma
Minghao Xie•Tingting Yang•Qiang Liu•Zhikun Ning•Lili Feng等 6 人
Communications Biology
2025
•2025/3/12
•Vol.8 No.1 p.1-12
Lymph node metastasis (LNM) is a key factor in the prognosis of papillary thyroid carcinoma (PTC). This study explores the effect of intratumoral bacteria on LNM in PTC. The intrathyroidal microbiome is analyzed in 55 PTC patients by 16S rRNA gene sequencing. The CCK8 and Transwell assays determine ...
Endocrine cancerThyroid cancer
10.1038/S42003-025-07856-9
ISSN:2399-3642
Lithium exposure causes ferroptosis to induce unexplained miscarriage through non-canonical MBOAT1 pathway
Yi Sun•Wenxin Huang•Qigang Fan•Xiaoping Yue•Yanbing Lin等 15 人
Nature Communications
2025
•2025/12/11
0High incidence of unexplained miscarriage (UM) limits global human reproduction. Lithium (Li) batteries are widely used but rarely recycled, causing Li to spread into environments and enter human body. Notably, the healthy effects of Li exposure on UM are rarely explored. Herein, higher serum Li lev...
Environmental sciencesReproductive disorders
10.1038/S41467-025-67026-7
ISSN:2041-1723
Spatial transcriptomics uncovers vasculature-centered cellular interactions driving Japanese encephalitis progression in a mouse model
Zhihua Ou•Zhaoyang Wang•Qi Chen•Peidi Ren•Xiuju He等 22 人
Nature Communications
2026
•2026/3/17
0The cellular interactions that drive the neuropathology of most neuroinvasive viruses remain elusive. We used Japanese encephalitis virus (JEV) to infect female BALB/c mice and applied Stereo-seq to simultaneously capture host and viral transcriptomes in situ, thereby constructing a comprehensive sp...
Acute inflammationViral infection
10.1038/S41467-026-70047-5
ISSN:2041-1723
Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome
Chun Wang•Li Zhang•Chuanwen Kan•Junyan He•Weijie Liang等 19 人
Npj Biofilms And Microbiomes
2025
•2025/7/7
•Vol.11 No.1 p.1-13
Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoal...
Biological techniquesMicrobial communitiesInfectious-disease diagnosticsMicrobiologyPathogensSequencing
10.1038/S41522-025-00762-2
ISSN:2055-5008
STRaM: A genetic framework for improved cell product provenance for research and clinical translations
Binglin Li•Chi Le•Wen Lei•Yingqi Zhou•Ying Zhang等 23 人
Communications Biology
2025
•2025/8/15
•Vol.8 No.1 p.1-20
Multiple assessment checks are required to handle the increasingly complex engineered-cell and cell-line provenance. To manage the biosafety and efficacy demands, we developed a bioinformatic pipeline for de novo profiling of short tandem repeats and mutations (STRaM) to identify and track homologou...
Cancer genomicsPersonalized medicine
10.1038/S42003-025-08547-1
ISSN:2399-3642
Efficacy, safety and exploratory analysis of neoadjuvant tislelizumab (a PD-1 inhibitor) plus nab-paclitaxel followed by epirubicin/cyclophosphamide for triple-negative breast cancer: a phase 2 TREND trial
Qiang Zhang•Mozhi Wang•Yumeng Li•Hengjun Zhang•Yusong Wang等 13 人
Signal Transduction And Targeted Therapy
2025
•2025/5/26
•Vol.10 No.1 p.1-13
The optimal chemotherapy backbone and specific population of triple-negative breast cancer (TNBC) patients that benefit from neoadjuvant immunotherapy are not well established. This prospective, single-arm, phase II TREND trial assessed the efficacy and safety of tislelizumab plus nab-paclitaxel and...
Breast cancerTumour immunology
10.1038/S41392-025-02254-3
ISSN:2059-3635
Spatiotemporal and single-cell atlases to dissect regional specific cell types of the developing ovary
Zheng-Hui Zhao•Tie-Gang Meng•Xue-Ying Chen•Fei Gao•Heide Schatten等 7 人
Communications Biology
2025
•2025/6/3
•Vol.8 No.1 p.1-14
Characterization of cellular heterogeneity and molecular diversity greatly enhances our understanding of the ovary differentiation process. However, regional specification remains largely unexplored during ovary development. Here, we combine spatial transcriptomics and single-cell RNA sequencing to ...
Cellular signalling networksOogenesis
10.1038/S42003-025-08277-4
ISSN:2399-3642
Antitumor efficacy and potential mechanism of FAP-targeted radioligand therapy combined with immune checkpoint blockade
Liang Zhao•Yizhen Pang•Yangfan Zhou•Jianhao Chen•Hao Fu等 16 人
Signal Transduction And Targeted Therapy
2024
•2024/6/3
•Vol.9 No.1 p.1-17
Radiotherapy combined with immune checkpoint blockade holds great promise for synergistic antitumor efficacy. Targeted radionuclide therapy delivers radiation directly to tumor sites. LNC1004 is a fibroblast activation protein (FAP)-targeting radiopharmaceutical, conjugated with the albumin binder E...
Drug developmentTranslational research
10.1038/S41392-024-01853-W
ISSN:2059-3635
EPI-SauriCas9-based mouse ovarian cancer models recapitulating pten deletion in patients
Wutao Chen•Pengju He•Ling Ding•Weihua Lou•Yishu Wang等 14 人
Communications Biology
2025
•2025/12/29
0Ovarian cancer remains a deadly gynecological malignancy, with PTEN loss and TP53 mutations frequently implicated in its progression. However, suitable models for studying ovarian cancers with PTEN and TP53 deletions are rare. Here we develop and validate the mouse ovarian epithelium with Pten and T...
Cancer modelsOvarian cancer
10.1038/S42003-025-09437-2
ISSN:2399-3642
The m6A reading protein YTHDF3 potentiates tumorigenicity of cancer stem-like cells in ocular melanoma through facilitating CTNNB1 translation
Xu Yangfan•He Xiaoyu•Wang Shanzheng•Sun Baofa•Jia Ruobing等 12 人
Oncogene
2022
•2022/2/3
•00 p.1-17
N6-methyladenosine (m6A) is the most universal internal RNA modification on messenger RNAs and regulates the fate and functions of m6A-modified transcripts through m6A-specific binding proteins. Nevertheless, the functional role and potential mechanism of the m6A reading proteins in ocular melanoma ...
EpigeneticsHead and neck cancerPrognostic markers
10.1038/S41388-021-02146-0
ISSN:0950-9232
Oral administration of astilbin mitigates acetaminophen-induced acute liver injury in mice by modulating the gut microbiota
Qin Yang•Wen-hao He•Li Xie•Tao Chen•Ruo-fan Liu等 12 人
Acta Pharmacologica Sinica
2024
•2024/9/23
•00 p.1-14
Acetaminophen (APAP) overdose-induced acute liver injury (ALI) is characterized by extensive oxidative stress, and the clinical interventions for this adverse effect remain limited. Astilbin is an active compound found in the rhizome of Smilax glabra Roxb. with anti-inflammatory and antioxidant acti...
Biomedicine, generalPharmacology/ToxicologyMedical MicrobiologyImmunologyInternal MedicineVaccine
10.1038/S41401-024-01383-9
ISSN:1671-4083
Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo
Yang Hui•Bai Dandan•Li Yanhe•Yu Zhaowei•Wang Chenfei等 9 人
Nature Cell Biology
2022
•2022/4/28
•00 p.1-10
Parental DNA methylation and histone modifications undergo distinct global reprogramming in mammalian pre-implantation embryos, but the landscape of epigenetic crosstalk and its effects on embryogenesis are largely unknown. Here we comprehensively analyse the association between DNA methylation and ...
DNA methylationEmbryologyHistone post-translational modificationsImprinting
10.1038/S41556-022-00900-4
ISSN:1465-7392
Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica
Jiaojiao Ji•Xiaoxu Han•Lanlan Zang•Yushan Li•Liqun Lin等 11 人
Communications Biology
2025
•2025/4/23
•Vol.8 No.1 p.1-15
Furocoumarins (FCs), important natural compounds with biodefense roles and pharmacological activities, are notably abundant in medicinal plant Angelica dahurica. However, its accumulation patterns over development stages in FC-enriched tissue, biosynthetic pathways, and regulatory mechanisms in A. d...
OxidoreductasesPlant evolutionSecondary metabolism
10.1038/S42003-025-08076-X
ISSN:2399-3642
Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants
Xiao Yao•Jiao Shengbo•He Miao•Lin Da•Zuo Huanyan等 10 人
International Journal Of Oral Science
2022
•2022/8/25
•Vol.14 No.1 p.1-12
Genome-wide association studies (GWASs) are the most widely used method to identify genetic risk loci associated with orofacial clefts (OFC). However, despite the increasing size of cohort, GWASs are still insufficient to detect all the heritability, suggesting there are more associations under the ...
Functional genomicsMechanisms of disease
10.1038/S41368-022-00194-0
ISSN:1674-2818
Redesigning the tomato fruit shape for mechanized production
Qiang Zhu•Lei Deng•Jie Chen•Gustavo R. Rodríguez•Chuanlong Sun等 16 人
Nature Plants
2023
•2023/9/18
•00 p.1-16
Crop breeding for mechanized harvesting has driven modern agriculture. In tomato, machine harvesting for industrial processing varieties became the norm in the 1970s. However, fresh-market varieties whose fruits are suitable for mechanical harvesting are difficult to breed because of associated redu...
Natural variation in plantsPlant breeding
10.1038/S41477-023-01522-W
ISSN:2055-0278
Highly efficient construction of monkey blastoid capsules from aged somatic cells
Junmo Wu•Tianao Shao•Zengli Tang•Gaojing Liu•Zhuoyao Li等 14 人
Nature Communications
2025
•2025/1/28
•Vol.16 No.1 p.1-18
Blastoids—blastocyst-like structures created in vitro—emerge as a valuable model for early embryonic development research. Non-human primates stem cell-derived blastoids are an ethically viable alternative to human counterparts, yet the low formation efficiency of monkey blastoid cavities, typically...
Embryonic inductionReprogrammingStem cellsTissue engineering
10.1038/S41467-025-56447-Z
ISSN:2041-1723
Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates
Haowei Ni•Xiaoyan Jing•Xian Xiao•Na Zhang•Xiaoyue Wang等 8 人
The Isme Journal
2021
•2021/3/12
•00 p.1-13
Understanding the effects of changing climate and long-term human activities on soil organic carbon (SOC) and the mediating roles of microorganisms is critical to maintain soil C stability in agricultural ecosystem. Here, we took samples from a long-term soil transplantation experiment, in which lar...
BiodiversityMicrobial ecology
10.1038/S41396-021-00950-W
ISSN:1751-7362
Genome-wide ribosome profiling reveals a dynamic translational landscape in Arabidopsis seedling roots under simulated microgravity
Ting Zhang•Lishuang Zhang•Yilin Yang•Jinbo Hu•Huiqiong Zheng等 7 人
Communications Biology
2026
•2026/4/4
0Plants can adapt to environmental change through a variety of transcriptional and translational mechanisms. Although extensive knowledge exists about plant stress responses at the transcriptional level, understanding of these responses at the translational level is limited. This study aimed to evalu...
Plant molecular biologyTropism
10.1038/S42003-026-09991-3
ISSN:2399-3642
Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long
Jinyang Zhang•Lingling Hou•Zhenqiang Zuo•Peifeng Ji•Xiaorong Zhang等 7 人
Nature Biotechnology
2021
•2021/3/11
•00 p.1-10
Reconstructing the sequence of circular RNAs (circRNAs) from short RNA sequencing reads has proved challenging given the similarity of circRNAs and their corresponding linear messenger RNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length circRNAs. Here we...
Computational biology and bioinformaticsGene expression
10.1038/S41587-021-00842-6
ISSN:1087-0156
LKB1 inactivation promotes epigenetic remodeling-induced lineage plasticity and antiandrogen resistance in prostate cancer
Fei Li•Pengfei Dai•Huili Shi•Yajuan Zhang•Juan He等 13 人
Cell Research
2025
•2025/1/2
•00 p.1-13
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...
Cancer therapeutic resistanceProstate cancer
10.1038/S41422-024-01025-Z
ISSN:1748-7838
Histone deacetylase inhibitors promote breast cancer metastasis by elevating NEDD9 expression
Hu Zonglong•Wei Fan•Su Yi•Wang Yafang•Shen Yanyan等 8 人
Signal Transduction And Targeted Therapy
2023
•2023/1/6
•Vol.8 No.1 p.1-13
Histone deacetylase (HDAC) is a kind of protease that modifies histone to regulate gene expression, and is usually abnormally activated in tumors. The approved pan-HDAC inhibitors have demonstrated clinical benefits for patients in some hematologic malignancies. Only limited therapeutic success in b...
Drug developmentTarget identification
10.1038/S41392-022-01221-6
ISSN:2059-3635
Diet-derived galactose reprograms hepatocytes to prevent T cell exhaustion and elicit antitumour immunity
Xian Du•Wenyan Li•Guiying Li•Chenyue Guo•Xuyi Tang等 20 人
Nature Cell Biology
2025
•2025/8/8
•00 p.1-10
Dietary nutrients are inextricably linked to antitumour immune responses. However, the effect of diet-derived galactose on antitumour immunity remains unclear. Here we show that dietary galactose augments CD8+ T cell immunity to suppress tumour progression. High-galactose feeding drives hepatocyte-d...
Cancer microenvironmentT cellsTumour immunology
10.1038/S41556-025-01716-8
ISSN:1465-7392
Developmentally controlled subcellular remodeling and VND-initiated vacuole-executed PCD module shape xylem-like cells in peat moss
Ningjing Liu•Qiuqi Guo•Fangming Shi•Lei Gao•Yongqi Liu等 13 人
Communications Biology
2024
•2024/10/14
•Vol.7 No.1 p.1-12
Peat moss (Sphagnum) is a non-vascular higher plant with unique xylem-like hyaline (H) cells that are accompanied by photosynthetic chlorophyllous cells. These cellular structures play crucial roles in water storage and carbon sequestration. However, it is largely unknown how peat moss develops the ...
Cell fateProtein trafficking in plants
10.1038/S42003-024-07003-W
ISSN:2399-3642
Emergence of distinct Streptococcus pyogenes emm1 and emm12 lineages in China
Yuanhai You•Dingle Yu•Chao Yang•Xiaomin Peng•Ouli Xie等 32 人
Nature Microbiology
2026
•2026/4/23
•00 p.1-11
Cases of scarlet fever have increased since 2011 across China. However, genomic epidemiological knowledge of Streptococcus pyogenes, the causative agent, is limited. Here we present a longitudinal analysis of S. pyogenes isolates (n = 1,029) across emm1 and emm12 genotypes collected from eight provi...
Bacterial infectionBacteriology
10.1038/S41564-026-02324-4
ISSN:2058-5276
SNORA14A inhibits hepatoblastoma cell proliferation by regulating SDHB-mediated succinate metabolism
Zhu Jiabei•Mao Siwei•Zhen Ni•Zhu Guoqing•Bian Zhixuan等 13 人
Cell Death Discovery
2023
•2023/1/30
•Vol.9 No.1 p.1-14
Hepatoblastoma (HB) is the most common paediatric liver malignancy. Dysregulation of small nucleolar RNAs (snoRNAs) is a critical inducer of tumour initiation and progression. However, the association between snoRNAs and HB remains unknown. Here, we conducted snoRNA expression profiling in HB by sno...
Cancer metabolismCell signallingSmall RNAs
10.1038/S41420-023-01325-0
ISSN:2058-7716
The identification and functional analysis of CD8+PD-1+CD161+ T cells in hepatocellular carcinoma
Zhixuan Li•Bo Zheng•Xinyao Qiu•Rui Wu•Tong Wu等 14 人
Npj Precision Oncology
2020
•2020/10/30
•Vol.4 No.1 p.1-10
Immunotherapy is a powerful therapeutic strategy for end-stage hepatocellular carcinoma (HCC). It is well known that T cells, including CD8+PD-1+ T cells, play important roles involving tumor development. However, their underlying phenotypic and functional differences of T cell subsets remain unclea...
Diagnostic markersTumour immunology
10.1038/S41698-020-00133-4
ISSN:2397-768X
Natural allelic variation in SW14 determines seed weight and quality in soybean
Chunyu Zhang•Weijun Li•Cuirong Tan•Mingkun Huang•Huan Wu等 12 人
Nature Communications
2025
•2025/8/29
•Vol.16 No.1 p.1-12
Seed weight and oil/protein content are critical agronomic traits that determine soybean yield and quality. However, the key genes controlling these traits and the underlying regulatory mechanisms remain poorly understood. Here, we performed a combination of genome-wide association study and quantit...
Agricultural geneticsNatural variation in plantsPlant domesticationPlant molecular biology
10.1038/S41467-025-63582-0
ISSN:2041-1723
ppGpp accumulation reduces the expression of the global nitrogen homeostasis-modulating NtcA regulon by affecting 2-oxoglutarate levels
Ryota Hidese•Ryudo Ohbayashi•Yuichi Kato•Mami Matsuda•Kan Tanaka等 9 人
Communications Biology
2023
•2023/12/25
•Vol.6 No.1 p.1-12
The cyanobacterium Synechococcus elongatus PCC 7942 accumulates alarmone guanosine tetraphosphate (ppGpp) under stress conditions, such as darkness. A previous study observed that artificial ppGpp accumulation under photosynthetic conditions led to the downregulation of genes involved in the nitroge...
Plant physiologyPlant stress responses
10.1038/S42003-023-05632-1
ISSN:2399-3642
Gut microbial-derived phenylacetylglutamine accelerates host cellular senescence
Hao Yang•Tongyao Wang•Chenglang Qian•Huijing Wang•Dong Yu等 27 人
Nature Aging
2025
•2025/1/10
•00 p.1-18
Gut microbiota plays a crucial role in the host health in the aging process. However, the mechanisms for how gut microbiota triggers cellular senescence and the consequent impact on human aging remain enigmatic. Here we show that phenylacetylglutamine (PAGln), a metabolite linked to gut microbiota, ...
AgeingMedical researchMicrobiologySenescence
10.1038/S43587-024-00795-W
ISSN:2662-8465
Single cell profiling of female breast fibroadenoma reveals distinct epithelial cell compositions and therapeutic targets
Zhigang Chen•Yi Zhang•Wenlu Li•Chenyi Gao•Fengbo Huang等 9 人
Nature Communications
2023
•2023/6/16
•Vol.14 No.1 p.1-12
Fibroadenomas (FAs) are the most common breast tumors in women. No pharmacological agents are currently approved for FA intervention owing to its unclear mechanisms and a shortage of reproducible human models. Here, using single-cell RNA sequencing of human FAs and normal breast tissues, we observe ...
CancerCancer therapyTranslational research
10.1038/S41467-023-39059-3
ISSN:2041-1723
The consensus molecular subtypes of esophageal squamous cell carcinoma
Heyang Cui•Zhongxu Zhu•Enwei Xu•Lin Qi•Yikun Cheng等 34 人
Signal Transduction And Targeted Therapy
2026
•2026/2/19
•Vol.11 No.1 p.650
Esophageal squamous cell carcinoma (ESCC) lacks a standardized classification system, resulting in inconsistent clinical management and a suboptimal prognosis. This study addresses the urgent need for a robust consensus taxonomy to facilitate precision treatment for ESCC. We employed a network-based...
Genome informaticsTumour heterogeneity
10.1038/S41392-026-02577-9
ISSN:2059-3635
An E3 ligase TRIM1 promotes colorectal cancer progression via K63-linked ubiquitination and activation of HIF1α
Liuliu Shi•Xianglan Fang•Lijie Du•Jin Yang•Juan Xue等 9 人
Oncogenesis
2024
•2024/5/20
•Vol.13 No.1 p.1-15
Accumulating studies have shown that E3 ligases play crucial roles in regulating cellular biological processes and signaling pathways during carcinogenesis via ubiquitination. Tripartite-motif (TRIM) ubiquitin E3 ligases consist of over 70 members. However, the clinical significance and their contri...
Innate immunityTumour biomarkersUbiquitylation
10.1038/S41389-024-00517-2
ISSN:2157-9024
Pangenome analysis provides insights into legume evolution and breeding
Longfei Wang•Xinyu Jiang•Wu Jiao•Junrong Mao•Wenxue Ye等 8 人
Nature Genetics
2025
•2025/7/30
•00 p.1-10
Grain legumes hold great promise for advancing sustainable agriculture. Although the evolutionary history of legume species has been investigated, the conserved mechanisms that drive adaptive evolution and govern agronomic improvement remain elusive. Here we present high-quality genome assemblies fo...
MetagenomicsPlant genetics
10.1038/S41588-025-02280-5
ISSN:1061-4036
A longitudinal pilot study in pre-menopausal women links cervicovaginal microbiome to CIN3 progression and recovery
Cristiana Banila•Efthymios Ladoukakis•Dorota Scibior-Bentkowska•Leandro Rodrigues Santiago•Caroline Reuter等 7 人
Communications Biology
2025
•2025/6/6
•Vol.8 No.1 p.1-10
Increasing evidence suggests vaginal dysbiosis is associated with persistent high-risk human papillomavirus (hrHPV) infection and cervical intraepithelial neoplasia (CIN) development. In this pilot longitudinal study, we investigate the potential of vaginal microbiome biomarkers to predict CIN3 deve...
Cervical cancerMicrobiome
10.1038/S42003-025-08328-W
ISSN:2399-3642
SERPINA3 predicts long-term neurological outcomes and mortality in patients with intracerebral hemorrhage
Pei Zheng•Zhihui Qi•Bin Gao•Yang Yao•Jingshan Chen等 8 人
Cell Death & Disease
2025
•2025/3/29
•Vol.16 No.1 p.1-12
Intracerebral hemorrhage (ICH) is a severe stroke subtype with high mortality and disability rates, and long-term outcomes among survivors remain unpredictable due to the lack of reliable biomarkers. In this study, spatial transcriptomics was used to analyze molecular profiles in autopsy brain tissu...
Brain injuriesPredictive markersStroke
10.1038/S41419-025-07551-X
ISSN:2041-4889
Genome Assembly and Characterization of the Endangered Long-armed Scarab Beetle, Cheirotonus jansoni
Liwei Liu•Rui Guo•Qian Lei•Qiao Li•Yi Zhu等 11 人
Scientific Data
2026
•2026/2/10
•Vol.13 No.1 p.4090
Cheirotonus jansoni is a nationally protected and ornamental beetle species endemic to southern China, northern Burma, and Vietnam. Due to habitat degradation and illegal collection, its populations have declined significantly, prompting urgent conservation efforts. Here, we present a high-quality, ...
EntomologyGenome
10.1038/S41597-026-06814-2
ISSN:2052-4463
Loss of colonic fidelity enables multilineage plasticity and metastasis
Patrizia Cammareri•Michela Raponi•Yourae Hong•Caroline V. Billard•Nat Peckett等 27 人
Nature
2025
•2025/6/4
•00 p.1-10
Cancer cell plasticity enables the acquisition of new phenotypic features and is implicated as a major driver of metastatic progression1,2. Metastasis occurs mostly in the absence of additional genetic alterations3–5, which suggests that epigenetic mechanisms are important6. However, they remai...
Cancer geneticsCancer modelsColon cancerMetastasis
10.1038/S41586-025-09125-5
ISSN:0028-0836
Genomic locus of lncRNA-Gm26793 forms an inter-chromosomal interaction with Cubn to ensure proper stem cell differentiation in vitro and in vivo
Zhiwen Liu•Xin Wan•Jiehui Chen•Yongjian Ma•Yonggao Fu等 14 人
Cell Discovery
2025
•2025/6/3
•Vol.11 No.1 p.530
Inter-chromosomal interactions play a crucial role in 3D genome organization, yet the organizational principles and functional significances remain elusive. In general, lncRNA loci and transcripts are frequently associated with transcriptional programs modulated by long-range chromatin interactions....
Chromatin structureEmbryonic stem cellsLong non-coding RNAs
10.1038/S41421-025-00805-0
ISSN:2056-5968
Glis1 facilitates induction of pluripotency via an epigenome–metabolome–epigenome signalling cascade
Linpeng Li•Keshi Chen•Tianyu Wang•Yi Wu•Guangsuo Xing等 23 人
Nature Metabolism
2020
•2020/8/24
•Vol.2 No.9 p.882-892
Somatic cell reprogramming provides insight into basic principles of cell fate determination, which remain poorly understood. Here we show that the transcription factor Glis1 induces multi-level epigenetic and metabolic remodelling in stem cells that facilitates the induction of pluripotency. We fin...
Cell biologyHistone post-translational modificationsMetabolismStem-cell differentiation
10.1038/S42255-020-0267-9
ISSN:2522-5812
Ginger genome reveals the SMPED1 gene causing sex-phase synchrony and outcrossing in a flowering plant
Jian-Li Zhao•Yang Dong•Ao-Dan Huang•Sheng-Chang Duan•Xiao-Chang Peng等 20 人
Nature Plants
2025
•2025/10/7
•00 p.1-14
In many flowering plants, male and female reproductive organs mature at different times to avoid self-pollination, a phenomenon termed dichogamy. Most dichogamous species are either protandrous or protogynous, making this strategy difficult to study genetically. However, in the ginger Alpinia mutica...
Plant evolutionPlant molecular biologyPlant reproduction
10.1038/S41477-025-02125-3
ISSN:2055-0278
Heterogeneous plasma cells and long-lived subsets in response to immunization, autoantigen and microbiota
Liu Xin•Yao Jiacheng•Zhao Yongshan•Wang Jianbin•Qi Hai
Nature Immunology
2022
•2022/10/31
•Vol.23 No.11 p.1564-1576
Durable antibody immunity depends on long-lived plasma cells (LLPCs) that primarily reside in the bone marrow (BM). However, due to LLPC rarity, it has not been possible to define their phenotypes or determine their heterogeneity. By single-cell mRNA sequencing, cytometry and a genetic pulse–chase m...
AntibodiesImmunological memory
10.1038/S41590-022-01345-5
ISSN:1529-2908
FGF9 alleviates diabetic cardiomyopathy by activating Nrf2 via SQSTM1/p62-Keap1 in mice
Ning An•Yunjie Chen•Lin Li•Bingyu Wang•Xuan Zhou等 6 人
Communications Biology
2025
•2025/11/25
•Vol.8 No.1 p.16810
Fibroblast growth factor 9 (FGF9) plays a key role in development and cardioprotection, yet its function in diabetic cardiomyopathy (DCM) remains unclear. In a high-fat diet/streptozotocin (HFD/STZ)-induced DCM model, FGF9 attenuated cardiac hypertrophy, fibrosis, and systolic dysfunction, effects a...
Diabetes complicationsHeart failure
10.1038/S42003-025-09077-6
ISSN:2399-3642
Generation and characterization of stable pig pregastrulation epiblast stem cell lines
Zhi Minglei•Zhang Jinying•Tang Qianzi•Yu Dawei•Gao Shuai等 47 人
Cell Research
2021
•2021/11/30
•00 p.1-18
Pig epiblast-derived pluripotent stem cells are considered to have great potential and broad prospects for human therapeutic model development and livestock breeding. Despite ongoing attempts since the 1990s, no stably defined pig epiblast-derived stem cell line has been established. Here, guided by...
Developmental biologyPluripotent stem cells
10.1038/S41422-021-00592-9
ISSN:1001-0602
Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics–gut microbiome–immunity axis
Haonan Sha•Jiaqi Lu•Jiong Chen•Jinbo Xiong
Npj Biofilms And Microbiomes
2024
•2024/4/11
•Vol.10 No.1 p.1-15
Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to el...
Applied microbiologyMicrobiome
10.1038/S41522-024-00509-5
ISSN:2055-5008
Extensive variation within the pan-genome of cultivated and wild sorghum
Yongfu Tao•Hong Luo•Jiabao Xu•Alan Cruickshank•Xianrong Zhao等 13 人
Nature Plants
2021
•2021/5/20
•00 p.1-8
Sorghum is a drought-tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its inter-fertile wild relatives constitute the primary gene pool for sorghum. Underst...
Plant breedingPlant genetics
10.1038/S41477-021-00925-X
ISSN:2055-0278
Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat
Duo Su•Tingting Jiang•Yulong Song•Die Li•Siyuan Zhan等 10 人
Communications Biology
2025
•2025/1/9
•Vol.8 No.1 p.1-15
Uncoupling protein 1 (UCP1) is a crucial protein located in the mitochondrial inner membrane that mediates nonshivering thermogenesis. However, the molecular mechanisms by which enhancer–promoter chromatin interactions control Ucp1 transcriptional regulation in brown adipose tissue (BAT) are unclear...
Gene expressionGene regulation
10.1038/S42003-025-07468-3
ISSN:2399-3642
Age mosaic of gut epithelial cells prevents aging
Peizhong Qin•Qi Wang•You Wu•Qiqi You•Mingyu Li等 6 人
Nature Communications
2025
•2025/7/22
•Vol.16 No.1 p.1-20
Improving gut health by altering the activity of intestinal stem cells is thought to have the potential to reverse aging. The aged Drosophila midgut undergoes hyperplasia and barrier dysfunction. However, it is still unclear how to limit hyperplasia to extend lifespan. Here, we show that early midgu...
EndodermIntestinal stem cellsStress signalling
10.1038/S41467-025-62043-Y
ISSN:2041-1723
Heterogeneous distribution of toxic arsenic modulates the mutualistic interaction between Pteris vittata and soil microbiota
Xiaoming Wan•Yuluo Wang•Weibin Zeng•Yanru Zhou•Mei Lei等 6 人
Communications Biology
2025
•2025/11/23
0While soil nutrient heterogeneity is known to influence plant fitness and ecosystem diversity, the ecological effects of heterogeneous arsenic (As) contamination on plant–microbe interactions remain unclear. Using multi-omics, we demonstrate that the As-hyperaccumulator Pteris vittata restores dimin...
BiodiversityEnvironmental biotechnology
10.1038/S42003-025-09233-Y
ISSN:2399-3642
Accurate quantification of circular RNAs identifies extensive circular isoform switching events
Jinyang Zhang•Shuai Chen•Jingwen Yang•Fangqing Zhao
Nature Communications
2020
•2020/1/3
•Vol.11 No.1 p.1-14
Detection and quantification of circular RNAs (circRNAs) face several significant challenges, including high false discovery rate, uneven rRNA depletion and RNase R treatment efficiency, and underestimation of back-spliced junction reads. Here, we propose a novel algorithm, CIRIquant, for accurate c...
Computational biology and bioinformaticsGene expression
10.1038/S41467-019-13840-9
ISSN:2041-1723
Quasi Fe MIL-53 nanozyme inducing ferroptosis and immunogenic cell death for cancer immunotherapy
Zihui Yan•Yang Bai•Songtao Zhang•Lingyi Kong•Yu Wang等 15 人
Nature Communications
2025
•2025/3/7
•Vol.16 No.1 p.1-19
Nanozymes offer diverse therapeutic potentials for cancer treatment which is dependent on the development of nanomaterials. Quasi-metal-organic framework is a class of metal-organic framework-derived nanomaterials with a transition state from metal-organic frameworks towards metal oxide featuring po...
Bioinorganic chemistryBiomedical materials
10.1038/S41467-025-57542-X
ISSN:2041-1723
Single-cell profiling unveils a geroprotective role of Procyanidin C1 in hematopoietic immune system via senolytic and senomorphic effects
Xiuxing Liu•Yidan Liu•Yuehan Gao•Chun Zhang•Chenyang Gu等 8 人
Npj Aging
2025
•2025/5/2
•Vol.11 No.1 p.1-16
Aging of hematopoietic and immune system (HIS) leads to cellular senescence and immune dysregulation, contributing to age-related diseases. Here, we show that Procyanidin C1 (PCC1), a compound with both senolytic and senomorphic properties, can counteract aging-related changes in HIS. Using single-c...
AgeingBiomarkersInflammationModel vertebratesSenescence
10.1038/S41514-025-00222-3
ISSN:2731-6068
Grapevine pangenome facilitates trait genetics and genomic breeding
Zhongjie Liu•Nan Wang•Ying Su•Qiming Long•Yanling Peng等 41 人
Nature Genetics
2024
•2024/11/4
•00 p.1-11
Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we bu...
Plant breeding
10.1038/S41588-024-01967-5
ISSN:1061-4036
MAP2K6 remodels chromatin and facilitates reprogramming by activating Gatad2b-phosphorylation dependent heterochromatin loosening
Xing Guangsuo•Liu Zichao•Huang Luyuan•Zhao Danyun•Wang Tao等 22 人
Cell Death & Differentiation
2021
•2021/11/24
•00 p.1-13
Somatic cell reprogramming is an ideal model for studying epigenetic regulation as it undergoes dramatic chromatin remodeling. However, a role for phosphorylation signaling in chromatin protein modifications for reprogramming remains unclear. Here, we identified mitogen-activated protein kinase kina...
Chromatin remodellingEpigenetics
10.1038/S41418-021-00902-Z
ISSN:1350-9047
Stress-induced red nucleus attenuation induces anxiety-like behavior and lymph node CCL5 secretion
Dong-Dong Shi•Ying-Dan Zhang•Sen Zhang•Bing-Bing Liao•Min-Yi Chu等 10 人
Nature Communications
2023
•2023/10/30
•Vol.14 No.1 p.1-17
Previous studies have speculated that brain activity directly controls immune responses in lymphoid organs. However, the upstream brain regions that control lymphoid organs and how they interface with lymphoid organs to produce stress-induced anxiety-like behavior remain elusive. Using stressed huma...
Neurological disordersStress and resilience
10.1038/S41467-023-42814-1
ISSN:2041-1723
Phased chromosome-level genome provides insights into the molecular adaptation for migratory lifestyle and population diversity for Pacific saury, Cololabis saira
Yang Liu•Yanping Luo•Penghao Wang•Wenjia Li•Hao Tian等 14 人
Communications Biology
2024
•2024/11/15
•Vol.7 No.1 p.1-13
The Pacific saury (Cololabis saira) is a pelagic fish commonly found in the North Pacific Ocean. Its population diversity and migratory lifestyle have long captured global attention. Despite the inherent complexity of the C. saira genome, characterized by extremely high heterozygosity, we successful...
Comparative genomicsEcological genetics
10.1038/S42003-024-07126-0
ISSN:2399-3642
De novo genome assembly depicts the immune genomic characteristics of cattle
Ting-Ting Li•Tian Xia•Jia-Qi Wu•Hao Hong•Zhao-Lin Sun等 17 人
Nature Communications
2023
•2023/10/19
•Vol.14 No.1 p.1-14
Immunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb). In contrast to the current referen...
Functional genomicsGenome informaticsImmunogeneticsSequence annotation
10.1038/S41467-023-42161-1
ISSN:2041-1723
Multi-dimensional single-cell characterization revealed suppressive immune microenvironment in AFP-positive hepatocellular carcinoma
Huisi He•Shuzhen Chen•Zhecai Fan•Yaping Dong•Ying Wang等 14 人
Cell Discovery
2023
•2023/6/19
•Vol.9 No.1 p.1-21
Alpha-fetoprotein (AFP)-secreting hepatocellular carcinoma (HCC), which accounts for ~75% of HCCs, is more aggressive with a worse prognosis than those without AFP production. The mechanism through which the interaction between tumors and the microenvironment leads to distinct phenotypes is not yet ...
Cancer microenvironmentLiver cancer
10.1038/S41421-023-00563-X
ISSN:2056-5968
Comprehensive profiling of smoke-induced T cells in mice implicates clonal γδT17 cells as a hallmark of COPD
Xinyue Mei•Junxiang Wang•Yuan Wang•Li Cheng•Xiaoyu Wang等 27 人
Nature Communications
2025
•2025/12/8
0The mechanisms of the chronic inflammatory response in smoking-induced chronic obstructive pulmonary disease (COPD) remain unclear, with limited understanding of T cell responses to smoke exposure in lung tissue and circulation. We characterized the alterations in T cells associated with smoke expos...
Chronic inflammationChronic obstructive pulmonary diseaseGammadelta T cellsMucosal immunologyT-cell receptor
10.1038/S41467-025-67120-W
ISSN:2041-1723
Neoadjuvant pyrotinib and trastuzumab in HER2-positive breast cancer with no early response (NeoPaTHer): efficacy, safety and biomarker analysis of a prospective, multicentre, response-adapted study
Fei Wang•Yongjiu Wang•Bin Xiong•Zhenlin Yang•Jingfen Wang等 18 人
Signal Transduction And Targeted Therapy
2025
•2025/1/29
•Vol.10 No.1 p.1-9
The potential benefits of pyrotinib for patients with trastuzumab-insensitive, HER2-positive early-stage breast cancer remain unclear. This prospective, multicentre, response-adapted study evaluated the efficacy and safety of adding pyrotinib to the neoadjuvant treatment of HER2-positive breast canc...
Breast cancerDrug regulation
10.1038/S41392-025-02138-6
ISSN:2059-3635
P38α MAPK-induced senescence in cranial suture progenitor cells promotes craniosynostosis
Zong Chen•Zhiyou Chen•Xinyan Chen•Yingying Yue•Yu Wang等 10 人
Communications Biology
2025
•2025/12/13
0Craniosynostosis is a congenital cranial developmental disorder that frequently leads to craniofacial deformities and even neurological dysfunction. The abnormalities in cranial suture progenitor cells (SPC) are considered a key event in craniosynostosis; however, the specific mechanism remains uncl...
Mechanisms of diseaseSenescence
10.1038/S42003-025-09350-8
ISSN:2399-3642
SNORD11B-mediated 2′-O-methylation of primary let-7a in colorectal carcinogenesis
Zhixuan Bian•Chang Xu•Yi Xie•Xiaoying Wang•Yan Chen等 13 人
Oncogene
2023
•2023/8/24
•00 p.1-12
Evidence indicates that small nucleolar RNAs (snoRNAs) participate in tumorigenesis and development and could be promising biomarkers for colorectal cancer (CRC). Here, we examine the profile of snoRNAs in CRC and find that expression of SNORD11B is increased in CRC tumor tissues and cell lines, wit...
Colorectal cancerRNA splicing
10.1038/S41388-023-02808-1
ISSN:0950-9232
The secretory protein, CLCF1, improves cholestatic liver disease by inhibiting hepatic bile acid synthesis and promoting bile acid excretion
Man Liu•Yingxi Su•Yujie Hu•Meng Shen•Suriguge Bao等 13 人
Communications Biology
2026
•2026/3/16
•Vol.9 No.1 p.3700
Cholestatic liver disease (CLD) is characterized by disrupted bile acid (BA) homeostasis and excessive accumulation of toxic bile acids in the liver. While both genetic and acquired factors are known to contribute to its pathogenesis, the full spectrum of underlying pathological mechanisms remains i...
Liver fibrosisPrimary biliary cirrhosisPrimary sclerosing cholangitis
10.1038/S42003-026-09847-W
ISSN:2399-3642
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
MT1G induces lipid droplet accumulation through modulation of H3K14 trimethylation accelerating clear cell renal cell carcinoma progression
Sen Wang•Kexin Wang•Dong Yue•Xiaxia Yang•Xiaozao Pan等 12 人
British Journal Of Cancer
2024
•2024/6/21
•00 p.1-14
Lipid droplet formation is a prominent histological feature in clear cell renal cell carcinoma (ccRCC), but the significance and mechanisms underlying lipid droplet accumulation remain unclear. Expression and clinical significance of MT1G in ccRCC were analyzed by using TCGA data, GEO data and scRNA...
Renal cell carcinomaSurgical oncology
10.1038/S41416-024-02747-Y
ISSN:0007-0920
A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation
Guanjing Hu•Zhenyu Wang•Zunzhe Tian•Kai Wang•Gaoxiang Ji等 30 人
Nature Genetics
2025
•2025/3/17
•00 p.1-13
Cotton (Gossypium hirsutum L.) is a key allopolyploid crop with global economic importance. Here we present a telomere-to-telomere assembly of the elite variety Zhongmian 113. Leveraging technologies including PacBio HiFi, Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C, our asse...
DNA sequencingPlant breeding
10.1038/S41588-025-02130-4
ISSN:1061-4036
STK40 inhibits profibrotic Arg1+ macrophage differentiation and renal fibrosis by regulating poly-ubiquitination of STAT3
Jun Ni•Jia Li•Si-ying Sun•Jia-min Liu•Zhen-yan Jiang等 16 人
Acta Pharmacologica Sinica
2026
•2026/8/4
•00 p.1-17
Monocyte-derived macrophages are central drivers of chronic renal inflammation and fibrosis, yet the regulatory mechanisms that restrain their profibrotic differentiation remain poorly defined. Here, we identified serine/threonine kinase 40 (STK40) as a suppressor of profibrotic macrophage different...
Biomedicine, generalPharmacology/ToxicologyMedical MicrobiologyImmunologyInternal MedicineVaccine
10.1038/S41401-026-01893-8
ISSN:1671-4083
Impact of SARS-CoV-2 infection on respiratory and gut microbiome stability: a metagenomic investigation in long-term-hospitalized COVID-19 patients
Zhengtu Li•Jing Chen•Yinhu Li•Linghua Li•Yangqing Zhan等 18 人
Npj Biofilms And Microbiomes
2024
•2024/11/13
•Vol.10 No.1 p.1-11
During the coronavirus disease 2019 (COVID-19) pandemic, the exploration of microecology has been essential for elucidating the intricacies of infection mechanisms and the recovery of afflicted individuals. To decipher the interplay of microorganisms between the intestinal and respiratory tracts, we...
Infectious-disease diagnosticsMicrobial ecology
10.1038/S41522-024-00596-4
ISSN:2055-5008
The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence
Huang Xiong•Wang Wenling•Gong Ting•Wickell David•Kuo Li-Yaung等 32 人
Nature Plants
2022
•2022/5/9
•00 p.1-12
To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny,...
Genetic variationGenome evolutionPhylogeneticsPlant morphogenesisSecondary metabolism
10.1038/S41477-022-01146-6
ISSN:2055-0278
Comparing acute versus AIDS ART initiation on HIV-1 integration sites and clonal expansion
Jun Wang•Nan Xiao•Zhengnong Zhu•Haiyan Qiao•Fang Zhao等 11 人
Signal Transduction And Targeted Therapy
2025
•2025/1/10
•Vol.10 No.1 p.1-15
Early antiretroviral therapy (ART) initiation is known to limit the establishment of the HIV reservoir, with studies suggesting benefits such as a reduced number of infected cells and a smaller latent reservoir. However, the long-term impact of early ART initiation on the dynamics of the infected ce...
InfectionInfectious diseases
10.1038/S41392-024-02113-7
ISSN:2059-3635
Lactobacillus acidophilus potentiates oncolytic virotherapy through modulating gut microbiota homeostasis in hepatocellular carcinoma
Jiayu Zhang•Jinneng Yang•Jinyan Luo•Weili Wu•Haidan Luo等 21 人
Nature Communications
2025
•2025/4/7
•Vol.16 No.1 p.1-20
Oncolytic viruses (OVs) hold promise for cancer treatment. However, the antitumor efficacy is limited. Microbiota plays a pivotal role in cancer treatment and its impact on oncolytic virotherapy is unknown. Here, we show that VSVΔ51 has higher antitumor efficacy for hepatocellular carcinoma in the a...
MicrobiomeMolecular medicineTargeted therapies
10.1038/S41467-025-58407-Z
ISSN:2041-1723
Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation
Liu Xuemei•Bie Xiao Min•Lin Xuelei•Li Menglu•Wang Hongzhe等 10 人
Nature Plants
2023
•2023/5/4
•00 p.1-18
Genetic transformation is important for gene functional study and crop improvement. However, it is less effective in wheat. Here we employed a multi-omic analysis strategy to uncover the transcriptional regulatory network (TRN) responsible for wheat regeneration. RNA-seq, ATAC-seq and CUT&Tag te...
Molecular engineering in plantsPlant regeneration
10.1038/S41477-023-01406-Z
ISSN:2055-0278
Nucleic acid spheres for treating capillarisation of liver sinusoidal endothelial cells in liver fibrosis
Wenjia Liu•Yuting Liu•Liqiang Zhang•Liya Li•Wenguang Yang等 7 人
Nature Communications
2025
•2025/5/15
•Vol.16 No.1 p.1-15
Liver sinusoidal endothelial cells (LSECs) lose their characteristic fenestrations and become capillarized during the progression of liver fibrosis. Mesenchymal stem cell (MSC) transplantation can reverse this capillarization and reduce fibrosis, but MSC therapy has practical limitations that hinder...
Cell biologyDrug deliveryLiver fibrosisNanoparticlesRNAi therapy
10.1038/S41467-025-59885-X
ISSN:2041-1723
Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis
Xingtan Zhang•Shuai Chen•Longqing Shi•Daping Gong•Shengcheng Zhang等 33 人
Nature Genetics
2021
•2021/7/15
•00 p.1-10
Tea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expr...
GenomicsPlant geneticsPopulation genetics
10.1038/S41588-021-00895-Y
ISSN:1061-4036
Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression
Guohe Song•Yang Shi•Meiying Zhang•Shyamal Goswami•Saifullah Afridi等 23 人
Cell Discovery
2020
•2020/12/8
•Vol.6 No.1 p.1-15
Diverse immune cells in the tumor microenvironment form a complex ecosystem, but our knowledge of their heterogeneity and dynamics within hepatocellular carcinoma (HCC) still remains limited. To assess the plasticity and phenotypes of immune cells within HBV/HCV-related HCC microenvironment at singl...
Liver cancerTumour immunology
10.1038/S41421-020-00214-5
ISSN:2056-5968
Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11
Dan Xu•Mengyao Guo•Xin Xu•Gan Luo•Yaxin Liu等 21 人
Nature Microbiology
2025
•2025/2/3
•Vol.10 No.2 p.509-526
Human enteric α-defensin 5 (HD5) is an immune system peptide that acts as an important antimicrobial factor but is also known to promote pathogen infections by enhancing adhesion of the pathogens. The mechanistic basis of these conflicting functions is unknown. Here we show that HD5 induces abundant...
Cellular microbiologyInfectionPathogens
10.1038/S41564-024-01901-9
ISSN:2058-5276
The landscape of tissue-resident microbiota across normal, polyp, and colorectal cancer tissues
Haoyi Xiang•Baining Shen•Weifeng Lao•Bingjun Bai•Min Chen等 12 人
Nature Communications
2026
•2026/2/24
•Vol.17 No.1 p.30990
Emerging evidence suggests that tissue-resident microbiota (TRM) is associated with tumor biology; however, their distribution and compositional characteristics across different colorectal tissue types remain incompletely defined. Here, we conducted a comprehensive cross-sectional analysis of TRM di...
Predictive markersSurgical oncologyTumour biomarkers
10.1038/S41467-026-69705-5
ISSN:2041-1723
GSK-3 regulates CD4-CD8 cooperation for super-armed CD8+ cytolytic T cells in immunotherapy against tumors
Bastien Moës•Janna Krueger•Chen Liu•Nikhil Ponnoor Anto•Atena Nemati等 14 人
Signal Transduction And Targeted Therapy
2026
•2026/5/20
•Vol.11 No.1 p.1880
Although the efficacy of immune checkpoint blockade (ICB) depends on coordinated activity across progenitor and terminal effector CD4⁺ and CD8⁺ T-cell compartments, the cell-intrinsic pathways that enable this cooperation remain incompletely defined. Here, we identify glycogen synthase kinase-3 (GSK...
Tumour immunology
10.1038/S41392-026-02663-Y
ISSN:2059-3635
Intestinal bacteria trigger a hibernation-like state in homotherms via the gut-brain axis
Ziqiang Bao•Cheng Guo•Yi Chen•Tao Lei•Hua Peng等 11 人
Npj Biofilms And Microbiomes
2025
•2025/12/17
•Vol.11 No.1 p.2290
The adaptation to low temperature has research value in the fields of spaceflight, disease treatment, and ecological evolution. However, continuous exposure to cold leads to hypothermia and death in homothermic animals. Interestingly, heterothermic animals can easily overcome this challenge. We tran...
EvolutionMicrobiology
10.1038/S41522-025-00856-X
ISSN:2055-5008
Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization
Lu Jing•Zhang Li•Zhai Qixiao•Zhao Jianxin•Zhang Hao等 9 人
Npj Biofilms And Microbiomes
2021
•2021/9/6
•Vol.7 No.1 p.1-12
The gut microbiota could affect human health and disease. Although disease-associated microbiota alteration has been extensively investigated in the Chinese population, a nationwide Chinese gut microbiota baseline is still lacking. Here we performed 16 S rRNA gene sequencing on fecal samples from 26...
Clinical microbiologyMicrobiome
10.1038/S41522-021-00245-0
ISSN:2055-5008
p16High senescence restricts cellular plasticity during somatic cell reprogramming
Bogdan B. Grigorash•Dominic van Essen•Guixian Liang•Laurent Grosse•Alexander Emelyanov等 15 人
Nature Cell Biology
2023
•2023/8/31
•00 p.1-14
Despite advances in four-factor (4F)-induced reprogramming (4FR) in vitro and in vivo, how 4FR interconnects with senescence remains largely under investigated. Here, using genetic and chemical approaches to manipulate senescent cells, we show that removal of p16High cells resulted in the 4FR of som...
ReprogrammingSenescence
10.1038/S41556-023-01214-9
ISSN:1465-7392
A synergetic effect of BARD1 mutations on tumorigenesis
Wenjing Li•Xiaoyang Gu•Chunhong Liu•Yanyan Shi•Pan Wang等 11 人
Nature Communications
2021
•2021/2/23
•Vol.12 No.1 p.1-13
To date, a large number of mutations have been screened from breast and ovarian cancer patients. However, most of them are classified into benign or unidentified alterations due to their undetectable phenotypes. Whether and how they could cause tumors remains unknown, and this significantly limits d...
Breast cancerDNA damage response
10.1038/S41467-021-21519-3
ISSN:2041-1723
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid
Wenchao Wei•Chi Chun Wong•Zhongjun Jia•Weixin Liu•Changan Liu等 14 人
Nature Microbiology
2023
•2023/6/29
•00 p.1-15
Non-alcoholic steatohepatitis (NASH) is the severe form of non-alcoholic fatty liver disease, and is characterized by liver inflammation and fat accumulation. Dietary interventions, such as fibre, have been shown to alleviate this metabolic disorder in mice via the gut microbiota. Here, we investiga...
Bacterial systems biologyMetagenomics
10.1038/S41564-023-01418-7
ISSN:2058-5276
K88 acetylation of FTO increases its RNA m6A demethylation and promotes tumorigenesis
Jing Li•Xinxin Zhang•Si-Yi Zhao•Ling Ran•Minmin Zhang等 8 人
Oncogene
2025
•2025/6/19
•00 p.1-11
N6-Methyladenosine (m6A) is the most abundant modification in mRNAs and regulates RNA splicing, stabilization, translation and export. FTO was the first discovered RNA m6A demethylase, and it is frequently dysregulated in cancers and plays important roles in tumorigenesis, cancer cell stemness, immu...
AcetylationRNA metabolism
10.1038/S41388-025-03473-2
ISSN:0950-9232
Transposon proliferation drives genome architecture and regulatory evolution in wild and domesticated peppers
Kang Zhang•Hailong Yu•Lingkui Zhang•Yacong Cao•Xing Li等 18 人
Nature Plants
2025
•2025/1/28
•Vol.11 No.2 p.359-375
Pepper (Capsicum spp.) is a widely consumed vegetable with exceptionally large genomes in Solanaceae, yet its genomic evolutionary history remains largely unknown. Here we present 11 high-quality Capsicum genome assemblies, including two gap-free genomes, covering four wild and all five domesticated...
PhylogeneticsPlant evolutionPlant genetics
10.1038/S41477-025-01905-1
ISSN:2055-0278
Protein-level mutant p53 reporters identify druggable rare precancerous clones in noncancerous tissues
Pengle Yao•Peng Xiao•Zongyao Huang•Min Tang•Xiwen Tang等 23 人
Nature Cancer
2023
•2023/8/3
•00 p.1-17
Detecting and targeting precancerous cells in noncancerous tissues is a major challenge for cancer prevention. Massive stabilization of mutant p53 (mutp53) proteins is a cancer-specific event that could potentially mark precancerous cells, yet in vivo protein-level mutp53 reporters are lacking. Here...
CancerCancer geneticsCancer modelsCancer prevention
10.1038/S43018-023-00608-W
ISSN:2662-1347
High-fat diet disrupts a septal control on feeding to promote obesity in male mice
Shaolei Jiang•Shishi Lai•Haiyang Jing•Xiaocong Wu•Fengling Li等 10 人
Nature Communications
2025
•2025/12/27
0The global epidemic of diet-induced obesity poses a significant health challenge. Among brain regions regulating energy homeostasis, the lateral septum has emerged as a critical brake on feeding behavior to prevent overeating. However, the neural adaptations within the septal area under high-fat die...
Neural circuitsNeurotransmittersObesitySynaptic plasticity
10.1038/S41467-025-68010-X
ISSN:2041-1723
VDR–SOX2 signaling promotes colorectal cancer stemness and malignancy in an acidic microenvironment
Pei-Shan Hu•Ting Li•Jin-Fei Lin•Miao-Zhen Qiu•De-Shen Wang等 19 人
Signal Transduction And Targeted Therapy
2020
•2020/9/9
•Vol.5 No.1 p.1-13
The acidic tumor microenvironment provides an energy source driving malignant tumor progression. Adaptation of cells to an acidic environment leads to the emergence of cancer stem cells. The expression of the vitamin D receptor (VDR) is closely related to the initiation and development of colorectal...
Cancer stem cellsEpigeneticsGastrointestinal cancer
10.1038/S41392-020-00230-7
ISSN:2059-3635
Multi-omics analysis of canine aging markers and evaluation of stem cell intervention
Balun Li•Yanheng Ding•Miao Han•Zengyu Zhang•Zixi Ling等 12 人
Communications Biology
2025
•2025/6/10
•Vol.8 No.1 p.1-18
Dogs serve as ideal research subjects for aging studies. In this study, 9 aging-related cell populations are identified through single-cell RNA sequencing of dogs of different ages. Additionally, 9 CD8+ T cell senescence-specific markers conserved across species are identified. Furthermore, multi-om...
AgeingAnimal physiologyPredictive markers
10.1038/S42003-025-08333-Z
ISSN:2399-3642
AKT-mediated regulation of chromatin ubiquitylation and tumorigenesis through Mel18 phosphorylation
Jia Mai•Xiao-Dan Peng•Jun Tang•Tian Du•Yu-Hong Chen等 15 人
Oncogene
2021
•2021/3/4
•Vol.40 No.13 p.2422-2436
Polycomb repressor complex 1 (PRC1) is linked to the regulation of gene expression and histone ubiquitylation conformation, which contributes to carcinogenesis. However, the upstream regulators of PRC1 biogenesis machinery remain obscure. Here, we report that the polycomb group-related mammalian gen...
CancerCell biology
10.1038/S41388-020-01602-7
ISSN:0950-9232
ADNP promotes neural differentiation by modulating Wnt/β-catenin signaling
Xiaoyun Sun•Xixia Peng•Yuqin Cao•Yan Zhou•Yuhua Sun
Nature Communications
2020
•2020/6/12
•Vol.11 No.1 p.1-16
ADNP (Activity Dependent Neuroprotective Protein) is a neuroprotective protein whose aberrant expression has been frequently linked to neural developmental disorders, including the Helsmoortel-Van der Aa syndrome (also called the ADNP syndrome). However, its role in neural development and pathology ...
Cell signallingDevelopmental neurogenesisStem-cell differentiation
10.1038/S41467-020-16799-0
ISSN:2041-1723
Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis
Weipeng Mo•Yi Shu•Bo Liu•Yanping Long•Tong Li等 8 人
Nature Plants
2023
•2023/8/20
•00 p.1-12
The short read-length of next-generation sequencing makes it challenging to characterize highly repetitive regions (HRRs) such as centromeres, telomeres and ribosomal DNAs. Based on recent strategies that combined long-read sequencing and exogenous enzymatic labelling of open chromatin, we developed...
EpigeneticsSequencing
10.1038/S41477-023-01498-7
ISSN:2055-0278
Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences
Xinkai Tong•Dong Chen•Jianchao Hu•Shiyao Lin•Ziqi Ling等 8 人
Nature Communications
2023
•2023/8/23
•Vol.14 No.1 p.1-11
High-quality whole-genome resequencing in large-scale pig populations with pedigree structure and multiple breeds would enable accurate construction of haplotype and robust selection-signature detection. Here, we sequence 740 pigs, combine with 149 of our previously published resequencing data, retr...
Agricultural geneticsAnimal breedingGenetic variationGenome-wide association studiesHaplotypes
10.1038/S41467-023-40434-3
ISSN:2041-1723
Natural variation in GmSW17 controls seed size in soybean
Shan Liang•Zongbiao Duan•Xuemei He•Xia Yang•Yaqin Yuan等 11 人
Nature Communications
2024
•2024/8/28
•Vol.15 No.1 p.1-14
Seed size/weight plays an important role in determining crop yield, yet only few genes controlling seed size have been characterized in soybean. Here, we perform a genome-wide association study and identify a major quantitative trait locus (QTL), named GmSW17 (Seed Width 17), on chromosome 17 that d...
Agricultural geneticsPlant breedingPlant geneticsPlant molecular biology
10.1038/S41467-024-51798-5
ISSN:2041-1723
Time-course swRNA-seq uncovers a hierarchical gene regulatory network in controlling the response-repair-remodeling after wounding
Xinghai Yu•Jinghua Zhou•Wenkai Ye•Jingxiu Xu•Rui Li等 10 人
Communications Biology
2024
•2024/6/6
•Vol.7 No.1 p.1-16
Wounding initiates intricate responses crucial for tissue repair and regeneration. Yet, the gene regulatory networks governing wound healing remain poorly understood. Here, employing single-worm RNA sequencing (swRNA-seq) across 12 time-points, we delineated a three-stage wound repair process in C. ...
Disease modelGene regulationGenome-wide analysis of gene expression
10.1038/S42003-024-06352-W
ISSN:2399-3642
Population-level variation in gut bifidobacterial composition and association with geography, age, ethnicity, and staple food
Jing Lu•Li Zhang•Hao Zhang•Yutao Chen•Jianxin Zhao等 8 人
Npj Biofilms And Microbiomes
2023
•2023/12/12
•Vol.9 No.1 p.1-12
Bifidobacteria are key gut commensals that confer various health benefits and are commonly used as probiotics. However, little is known about the population-level variation in gut bifidobacterial composition and its affecting factors. Therefore, we analyzed Bifidobacterium species with amplicon sequ...
Microbial ecologyMicrobiome
10.1038/S41522-023-00467-4
ISSN:2055-5008
Chromosome-level genomes of two Bracteacoccaceae highlight adaptations to biocrusts
Hongping Liang•Yan Xu•Sunil Kumar Sahu•Hongli Wang•Linzhou Li等 14 人
Nature Communications
2025
•2025/2/10
•Vol.16 No.1 p.1-18
Biological soil crusts (biocrusts) cover the majority of the world’s dryland ground and are a significant component of the vegetation-free surface of the planet. They consist of an intimate association of microbial organisms, lichens, bryophytes and fungi. Biocrusts are severely endangered by anthro...
AbioticEvolutionary geneticsGenome evolution
10.1038/S41467-025-56614-2
ISSN:2041-1723
Treatment with perampanel alleviates depression-like behavior in mice via modulating GluN2B expression to improve excitatory synaptic transmission
Jin-Ming Liu•Yan-Lin Zhang•Fang Guo•Bin-Wu Li•Hu Chen等 10 人
Translational Psychiatry
2026
•2026/2/11
•Vol.16 No.1 p.900
Antidepressants that target the glutamatergic system, such as ketamine, have shown promising results. However, the contribution of other potential medications targeting the glutamate system to depression is unclear. Our research found that perampanel can exert a rapid and long-lasting antidepressant...
Clinical pharmacologyDepressionMolecular neuroscience
10.1038/S41398-026-03874-1
ISSN:2158-3188
High-throughput cultivation and identification of bacteria from the plant root microbiota
Jingying Zhang•Yong-Xin Liu•Xiaoxuan Guo•Yuan Qin•Ruben Garrido-Oter等 7 人
Nature Protocols
2021
•2021/1/13
•Vol.16 No.2 p.988-1012
Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation...
Microbiology techniquesMicrobiome
10.1038/S41596-020-00444-7
ISSN:1754-2189
Loss of KDM5A-mediated H3K4me3 demethylation promotes aberrant neural development by Wnt/β-catenin pathway activation
Jianting Li•Yuxiang Liang•Zhihua Cao•Qi Xie•Xiaolong Gu等 15 人
Cell Death & Disease
2025
•2025/11/20
0Neural tube defects (NTDs) are common and severe birth defects. Folate supplementation can prevent NTDs, but the underlying molecular mechanisms are unclear. Aberrant wnt/β-catenin pathway activation leads to defective anteroposterior patterning, resulting in NTDs, but little is known about whether ...
Developmental neurogenesisNeural tube defects
10.1038/S41419-025-08208-5
ISSN:2041-4889
Multiomics profiling reveals VDR as a central regulator of mesenchymal stem cell senescence with a known association with osteoporosis after high-fat diet exposure
Jiayao Chen•Shuhong Kuang•Jietao Cen•Yong Zhang•Zongshan Shen等 11 人
International Journal Of Oral Science
2024
•2024/5/22
•Vol.16 No.1 p.1-16
The consumption of a high-fat diet (HFD) has been linked to osteoporosis and an increased risk of fragility fractures. However, the specific mechanisms of HFD-induced osteoporosis are not fully understood. Our study shows that exposure to an HFD induces premature senescence in bone marrow mesenchyma...
Dental diseasesObesityOsteoporosisStem-cell therapies
10.1038/S41368-024-00309-9
ISSN:2049-3169
CHD8 mutations increase gliogenesis to enlarge brain size in the nonhuman primate
Li Bang•Zhao Hui•Tu Zhuchi•Yang Weili•Han Rui等 27 人
Cell Discovery
2023
•2023/3/7
•Vol.9 No.1 p.1-23
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition that affects social interaction and behavior. Mutations in the gene encoding chromodomain helicase DNA-binding protein 8 (CHD8) lead to autism symptoms and macrocephaly by a haploinsufficiency mechanism. However, studies of sma...
Developmental biologyMechanisms of disease
10.1038/S41421-023-00525-3
ISSN:2056-5968
Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet
Chen Zhang•Yang Yu•Ling Yue•Yi Chen•Yixin Chen等 9 人
Communications Biology
2025
•2025/1/20
•Vol.8 No.1 p.1-13
The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatr...
MicrobiologyZoology
10.1038/S42003-025-07538-6
ISSN:2399-3642
mTOR-driven integrin β4-enriched extracellular vesicles from lenvatinib-resistant hepatocellular carcinoma fuel lung metastasis via fibroblast-niche formation
Tiantian Zou•Xufeng Wang•Haoting Sun•Beiyuan Hu•Jianhua Li等 16 人
Signal Transduction And Targeted Therapy
2026
•2026/4/16
•Vol.11 No.1 p.1380
Tumor-derived extracellular vesicles (EVs) play crucial roles in facilitating the colonization and growth of metastatic cancer cells in distant organs. Nevertheless, the precise mechanisms by which EVs contribute to therapy-resistant cancer dissemination remain poorly understood. In the present stud...
Gastrointestinal cancerMetastasis
10.1038/S41392-026-02625-4
ISSN:2059-3635
Population genomics unravels the Holocene history of bread wheat and its relatives
Zhao Xuebo•Guo Yafei•Kang Lipeng•Yin Changbin•Bi Aoyue等 19 人
Nature Plants
2023
•2023/3/16
•Vol.9 No.3 p.403-419
Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accession...
GenomicsPopulation genetics
10.1038/S41477-023-01367-3
ISSN:2055-0278
The Anna Karenina principle in the assembly of plant microbiome under pathogen stress
Da Li•Zi-Shuo Qu•Cong Wang•Zi-Heng Peng•Xin Zhou等 6 人
Npj Biofilms And Microbiomes
2026
•2026/3/15
0The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to wheth...
MicrobiologyPlant sciences
10.1038/S41522-026-00964-2
ISSN:2055-5008
Single-cell transcriptomic and cross-species comparison analyses reveal distinct molecular changes of porcine testes during puberty
Xiaoyan Wang•Yang Wang•Yu Wang•Yifei Guo•Ruojun Zong等 11 人
Communications Biology
2024
•2024/11/9
•Vol.7 No.1 p.1-14
The pig is an important model for studying human diseases and is also a significant livestock species, yet its testicular development remains underexplored. Here, we employ single-cell RNA sequencing to characterize the transcriptomic landscapes across multiple developmental stages of Bama pig teste...
Self-renewalSpermatogenesis
10.1038/S42003-024-07163-9
ISSN:2399-3642
Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest
Marie Buysse•Rachid Koual•Florian Binetruy•Benoit de Thoisy•Xavier Baudrimont等 12 人
Nature Communications
2024
•2024/5/11
•Vol.15 No.1 p.1-12
Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenom...
Bacterial genomicsInfectious-disease epidemiologyPathogens
10.1038/S41467-024-48459-Y
ISSN:2041-1723
A wheat CC-NBS-LRR protein Ym1 confers WYMV resistance by recognizing viral coat protein
Yiming Chen•Dehui Kong•Zongkuan Wang•Jiaqian Liu•Linghan Wang等 23 人
Nature Communications
2025
•2025/4/16
•Vol.16 No.1 p.1-16
Ym1 is the most widely utilized gene for wheat yellow mosaic virus (WYMV) disease control in worldwide wheat breeding. Here, we successfully isolated the responsible gene for Ym1. It encodes a typical CC-NBS-LRR type R protein, which is specifically expressed in root and induced upon WYMV infection....
Plant breedingVirologyVirulence
10.1038/S41467-025-58816-0
ISSN:2041-1723
CSF1R inhibitors mitigate CDK4/6 inhibitor-induced immunosuppression to increase antitumor immunity in HR+/HER2− breast cancer
Siwei Li•Yajie Gong•Hui Li•Siyu Liu•Yanling Yin等 17 人
Oncogene
2026
•2026/4/15
•00 p.1-18
Hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR + /HER2 − ) breast cancer, the most common subtype, shows a low pathological complete response (pCR) rate and limited benefit from immunotherapy, highlighting the need for more effective strategies. Although immunothera...
Breast cancerCancer immunotherapyCancer microenvironmentImmunotherapy
10.1038/S41388-026-03786-W
ISSN:0950-9232
Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage
Yanchun Deng•Hongxia Zhao•Li Zhang•Sa Yang•Dexin Zou等 7 人
Npj Biofilms And Microbiomes
2025
•2025/11/20
•Vol.11 No.1 p.2150
Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the l...
EvolutionMicrobiology
10.1038/S41522-025-00843-2
ISSN:2055-5008
L-citrulline protects testicular Sertoli cell function by mitigating DNA damage via the gut-testis axis of sheep fed a high-concentrate diet
Liying Shan•Xinru Guo•Yanting Hu•Heyang Zhou•Xiangyue Meng等 11 人
Npj Biofilms And Microbiomes
2025
•2025/10/30
•Vol.11 No.1 p.1-13
Mounting evidence underscores that high-concentrate diets (HCD) significantly impair male reproductive health, leading to infertility, and are closely associated with dysregulation of the gut microbiome and metabolome. However, effective therapeutic strategies targeting these alterations remain elus...
Health careMicrobiology
10.1038/S41522-025-00832-5
ISSN:2055-5008
The gut microbiota-bile acid axis links the positive association between chronic insomnia and cardiometabolic diseases
Jiang Zengliang•Zhuo Lai-bao•He Yan•Fu Yuanqing•Shen Luqi等 19 人
Nature Communications
2022
•2022/5/30
•Vol.13 No.1 p.1-13
Evidence from human cohorts indicates that chronic insomnia is associated with higher risk of cardiometabolic diseases (CMD), yet whether gut microbiota plays a role is unclear. Here, in a longitudinal cohort (n = 1809), we find that the gut microbiota-bile acid axis may link the positive associatio...
Cardiovascular diseasesEndocrine system and metabolic diseasesSleep disorders
10.1038/S41467-022-30712-X
ISSN:2041-1723
Correction of eIF4E overactivation rescues translatome imbalance and core ASD-like behaviors in valproic acid-induced offspring mice
Miaoqi Huang•Han Ye•Yong Xu•Jiaoyan Xie•Xinyu Wang等 13 人
Molecular Psychiatry
2026
•2026/3/7
•00 p.1-19
Perturbed protein synthesis plays a crucial role in the pathogenesis of autism spectrum disorder (ASD), but the altered translational pattern and underlying mechanism remain poorly understood. Here, we identified an exaggeration of global protein synthesis in the cerebral cortex of offspring mice fo...
Autism spectrum disordersNeuroscience
10.1038/S41380-026-03517-3
ISSN:1359-4184
Foraging strategies and geographic factors jointly shape gut microbiota of spiders in the Sichuan and Guizhou regions of China
Jiao Wang•Shuqiao Wang•Qian Chen•Chuang Zhou•Zhenxin Fan等 6 人
Communications Biology
2025
•2025/12/13
0Spiders, a keystone predatory group for terrestrial ecosystem balance, have underexplored gut microbiotas. We collected 1090 spiders from 34 families in southwestern China, performing 16S rRNA sequencing to investigate their gut microbiota. Wandering and ambushing spiders exhibited higher α-diversit...
Microbial ecology
10.1038/S42003-025-09358-0
ISSN:2399-3642
Cyclic guanosine monophosphate-protein kinase G signaling attenuates aortic valve calcification through ULK1-mediated autophagy
Yan Wang•Fei Xu•Chengxiang Song•Xi Wang•Hao Zhou等 12 人
Signal Transduction And Targeted Therapy
2026
•2026/3/12
•Vol.11 No.1 p.900
Calcific aortic valve disease (CAVD) is a prevalent age-related valvulopathy characterized by high morbidity and mortality. CAVD pathogenesis involves maladaptive differentiation of valvular interstitial cells (VICs) into profibrotic and osteogenic phenotypes, yet the underlying mechanisms remain un...
Cardiology
10.1038/S41392-026-02624-5
ISSN:2059-3635
Virome characteristics of small mammals and their associated environments in pastoral areas on the Qinghai-Tibet Plateau
Xiang Lu•Qing Zhang•Haisheng Wu•Likai Ji•Yongshun Wang等 19 人
Npj Biofilms And Microbiomes
2025
•2025/8/22
•Vol.11 No.1 p.1-15
The Qinghai-Tibet Plateau (QTP), known for its rich biodiversity and unique ecological niche, harbors numerous endemic species and serves as a reservoir for both established human pathogens and numerous poorly characterized pathogens. Despite certain advances, virological research on small mammals i...
Microbial communitiesEnvironmental microbiologyVirology
10.1038/S41522-025-00814-7
ISSN:2055-5008
Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D
Ying Chen•Zhuo-Bin Lin•Shao-Kai Wang•Bo Wu•Longjian Niu等 17 人
Nature Structural & Molecular Biology
2025
•2025/3/4
•00 p.1-13
Differential high-order chromatin interactions between homologous chromosomes affect many biological processes. Traditional chromatin conformation capture genome analysis methods mainly identify two-way interactions and cannot provide comprehensive haplotype information, especially for low-heterozyg...
EpigenomicsGenomic analysisGenomicsHigh-throughput screening
10.1038/S41594-025-01512-W
ISSN:1545-9993