Proteome of Anoplocephala perfoliata elucidate lineage-specific features of a “neglected” equine tapeworm
English
United States, Seattle
Proteome Project
数据描述
The dataset "Uncovering Systemic Biomarkers of Intervertebral Disc Degeneration through Plasma Proteomics" contains proteomic data derived from human plasma, aimed at identifying systemic biomarkers associated with intervertebral disc degeneration. Utilizing the Q Exactive mass spectrometer, the study focuses on analyzing protein profiles in plasma to uncover molecular indicators of the condition. This research contributes to understanding the pathophysiology of intervertebral disc degeneration and may aid in developing diagnostic tools or therapeutic targets. The dataset is part of a broader effort to leverage proteomics for biomarker discovery in musculoskeletal disorders, emphasizing the role of plasma proteomics in elucidating systemic changes linked to degenerative diseases.
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10.1038/S41594-023-00922-Y
ISSN:1545-9993
A non-canonical role of ATG8 in Golgi recovery from heat stress in plants
Zhou Jun•Ma Juncai•Yang Chao•Zhu Xiu•Li Jing等 19 人
Nature Plants
2023
•2023/4/20
•00 p.1-17
Above-optimal growth temperatures, usually referred to as heat stress (HS), pose a challenge to organisms’ survival as they interfere with essential physiological functions and disrupt cellular organization. Previous studies have elucidated the complex transcriptional regulatory networks involved in...
HeatProtein trafficking in plants
10.1038/S41477-023-01398-W
ISSN:2055-0278
Enantioselective OTUD7B fragment discovery through chemoproteomics screening and high-throughput optimisation
Aini Vuorinen•Cassandra R. Kennedy•Katherine A. McPhie•William McCarthy•Jonathan Pettinger等 9 人
Communications Chemistry
2025
•2025/1/15
•Vol.8 No.1 p.1-12
Deubiquitinating enzymes (DUBs) are key regulators of cellular homoeostasis, and their dysregulation is associated with several human diseases. The ovarian tumour protease (OTU) family of DUBs are biochemically well-characterised and of therapeutic interest, yet only a few tool compounds exist to st...
Chemical librariesChemical tools
10.1038/S42004-025-01410-8
ISSN:2399-3669
Quantitative single-cell proteomics as a tool to characterize cellular hierarchies
Erwin M. Schoof•Benjamin Furtwängler•Nil Üresin•Nicolas Rapin•Simonas Savickas等 10 人
Nature Communications
2021
•2021/6/7
•Vol.12 No.1 p.1-15
Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes glo...
Acute myeloid leukaemiaCancer stem cellsMass spectrometryProteome informaticsProteomics
10.1038/S41467-021-23667-Y
ISSN:2041-1723
Dependence of human cell survival and proliferation on the CASP3 prodomain
Ebrahim Eskandari•Gian Luca Negri•Susanna Tan•Margarita E. MacAldaz•Shengsen Ding等 10 人
Cell Death Discovery
2024
•2024/2/6
•Vol.10 No.1 p.1-9
Mechanisms that regulate cell survival and proliferation are important for both the development and homeostasis of normal tissue, and as well as for the emergence and expansion of malignant cell populations. Caspase-3 (CASP3) has long been recognized for its proteolytic role in orchestrating cell de...
ApoptosisCell growth
10.1038/S41420-024-01826-6
ISSN:2058-7716
Gmppb-mutant mice exhibit dystroglycanopathy symptoms that are rescued with GSK3β inhibition or AAV-mediated GMPPB gene replacement
Ziwei Fu•Tongchao Wang•Chenyang Zhang•Tianyu Qi•Yanyan Chen等 18 人
Nature Communications
2026
•2026/4/9
0Mutations in GDP-mannose pyrophosphorylase B (GMPPB) cause dystroglycanopathy, a rare neuromuscular disorder characterized by α-dystroglycan hypoglycosylation, yet the pathogenic mechanisms and therapeutic options remain poorly defined. To dissect the molecular basis of dystroglycanopathy, we genera...
DevelopmentDisease modelMutationNeuromuscular disease
10.1038/S41467-026-71524-7
ISSN:2041-1723
Nuclear N-glycosylation maintains H3K9me3 heterochromatin and genomic stability
Xiuxiao Tang•Ranran Dai•Li Qing•Zhida Zhang•Hongmei Li等 16 人
Nature Cell Biology
2026
•2026/4/28
•00 p.1-12
Polysaccharides are known to be synthesized by enzymes in the endoplasmic reticulum and Golgi apparatus and transported through the secretory pathway to the cell surface or extracellular space, where they mediate essential biological processes. While classical localization and functions of polysacch...
EpigeneticsGenomic instabilityGlycobiologyGlycosylation
10.1038/S41556-026-01941-9
ISSN:1465-7392
Proteogenomic landscape and clinical characterization of GH-producing pituitary adenomas/somatotroph pituitary neuroendocrine tumors
Yamato Azusa•Nagano Hidekazu•Gao Yue•Matsuda Tatsuma•Hashimoto Naoko等 31 人
Communications Biology
2022
•2022/11/27
•Vol.5 No.1 p.1-14
The clinical characteristics of growth hormone (GH)-producing pituitary adenomas/somatotroph pituitary neuroendocrine tumors (GHomas/somatotroph PitNETs) vary across patients. In this study, we aimed to integrate the genetic alterations, protein expression profiles, transcriptomes, and clinical char...
EndocrinologyGeneticsOncology
10.1038/S42003-022-04272-1
ISSN:2399-3642
A marine photosynthetic microbial cell factory as a platform for spider silk production
Choon Pin Foong•Mieko Higuchi-Takeuchi•Ali D. Malay•Nur Alia Oktaviani•Chonprakun Thagun等 6 人
Communications Biology
2020
•2020/7/8
•Vol.3 No.1 p.1-8
Photosynthetic microorganisms such as cyanobacteria, purple bacteria and microalgae have attracted great interest as promising platforms for economical and sustainable production of bioenergy, biochemicals, and biopolymers. Here, we demonstrate heterotrophic production of spider dragline silk protei...
Applied microbiologyBiomaterials – proteins
10.1038/S42003-020-1099-6
ISSN:2399-3642
MS CETSA deep functional proteomics uncovers DNA repair programs leading to gemcitabine resistance
Ying Yu Liang•Khalidah Khalid•Hai Van Le•Hui Min Vivian Teo•Mindaugas Raitelaitis等 13 人
Nature Communications
2025
•2025/5/7
•Vol.16 No.1 p.1-15
Mechanisms for resistance to cytotoxic cancer drugs are dependent on dynamic changes in the biochemistry of cellular pathways, information which is hard to obtain at the systems level. Here we use a deep functional proteomics implementation of the Cellular Thermal Shift Assay to reveal a range of in...
DNA damage and repairProtein–protein interaction networks
10.1038/S41467-025-59505-8
ISSN:2041-1723
ER-shaping atlastin proteins act as central hubs to promote flavivirus replication and virion assembly
Christopher J. Neufeldt•Mirko Cortese•Pietro Scaturro•Berati Cerikan•Jeremy G. Wideman等 10 人
Nature Microbiology
2019
•2019/10/21
•Vol.4 No.12 p.2416-2429
Flaviviruses, including dengue virus and Zika virus, extensively remodel the cellular endomembrane network to generate replication organelles that promote viral genome replication and virus production. However, it remains unclear how these membranes and associated cellular proteins act during the vi...
Dengue virusEndoplasmic reticulumVirologyVirus–host interactionsVirus structures
10.1038/S41564-019-0586-3
ISSN:2058-5276
Local membrane source gathering by p62 body drives autophagosome formation
Xuezhao Feng•Daxiao Sun•Yanchang Li•Jinpei Zhang•Shiyu Liu等 18 人
Nature Communications
2023
•2023/11/13
•Vol.14 No.1 p.1-14
Autophagosomes are double-membrane vesicles generated intracellularly to encapsulate substrates for lysosomal degradation during autophagy. Phase separated p62 body plays pivotal roles during autophagosome formation, however, the underlying mechanisms are still not fully understood. Here we describe...
Intrinsically disordered proteinsMacroautophagyMembrane structure and assemblyProtein–protein interaction networks
10.1038/S41467-023-42829-8
ISSN:2041-1723
P300-dependent acetylation of the FOXQ1 complex activates super-enhancers to promote colorectal cancer proliferation and metastasis
Wen-Dong Yang•Zhi-Heng Zhang•Man-Yi Zhao•Ke Shao•Yan-Feng Ma等 15 人
Communications Biology
2025
•2025/7/7
•Vol.8 No.1 p.1-14
The FOX transcription factor family plays a pivotal role in the malignant progression of tumors. We propose a hypothesis that FOXQ1 recruits p300 and BRD4 to super-enhancer regions. Our findings indicate that p300 acetylates Lys190 of FOXQ1, resulting in its recognition and binding by BRD4. Subseque...
CancerCell migration
10.1038/S42003-025-08430-Z
ISSN:2399-3642
Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency
Forny Patrick•Bonilla Ximena•Lamparter David•Shao Wenguang•Plessl Tanja等 27 人
Nature Metabolism
2023
•2023/1/26
•Vol.5 No.1 p.80-95
Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic causes and a poorly understood pathogenesis, leading to the absence of effective causal treatments. Here we employ multi-layered omics profiling combined with biochemical and clinical features of individuals with M...
Mechanisms of diseaseMetabolismPaediatric researchTranscriptomics
10.1038/S42255-022-00720-8
ISSN:2522-5812
Mdm2 requires Sprouty4 to regulate focal adhesion formation and metastasis independent of p53
Rafaela Muniz de Queiroz•Gizem Efe•Asja Guzman•Naoko Hashimoto•Yusuke Kawashima等 8 人
Nature Communications
2024
•2024/8/20
•Vol.15 No.1 p.1-20
Although the E3 ligase Mdm2 and its homologue and binding partner MdmX are the major regulators of the p53 tumor suppressor protein, it is now evident that Mdm2 and MdmX have multiple functions that do not involve p53. As one example, it is known that Mdm2 can regulate cell migration, although mecha...
Cell signallingFocal adhesionMetastasisSarcoma
10.1038/S41467-024-51488-2
ISSN:2041-1723
The Skp1-Cullin1-FBXO1 complex is a pleiotropic regulator required for the formation of gametes and motile forms in Plasmodium berghei
Rashpa Ravish•Klages Natacha•Schvartz Domitille•Pasquarello Carla•Brochet Mathieu
Nature Communications
2023
•2023/3/10
•Vol.14 No.1 p.1-18
Malaria-causing parasites of the Plasmodium genus undergo multiple developmental phases in the human and the mosquito hosts, regulated by various post-translational modifications. While ubiquitination by multi-component E3 ligases is key to regulate a wide range of cellular processes in eukaryotes, ...
Cell signallingParasite biology
10.1038/S41467-023-36999-8
ISSN:2041-1723
Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome fragment
Sara Landeras-Bueno•Chitra Hariharan•Ruben Diaz Avalos•Andrew S. Norris•Dalton T. Snyder等 14 人
Nature Communications
2025
•2025/7/15
•Vol.16 No.1 p.1-16
The nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. However, the inherent disorder of full-length N hampers its structural analysis. Here, we describe a stepwi...
Electron microscopyRNASARS-CoV-2
10.1038/S41467-025-61861-4
ISSN:2041-1723
E3 ubiquitin ligase UBR5 modulates circadian rhythm by facilitating the ubiquitination and degradation of the key clock transcription factor BMAL1
Chunyan Duan•Yue Li•Haoyu Zhi•Yao Tian•Zhengyun Huang等 18 人
Acta Pharmacologica Sinica
2024
•2024/5/13
•00 p.1-16
The circadian clock is the inner rhythm of life activities and is controlled by a self-sustained and endogenous molecular clock, which maintains a ~ 24 h internal oscillation. As the core element of the circadian clock, BMAL1 is susceptible to degradation through the ubiquitin-proteasome system (UPS...
Biomedicine, generalPharmacology/ToxicologyMedical MicrobiologyImmunologyInternal MedicineVaccine
10.1038/S41401-024-01290-Z
ISSN:1671-4083
Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2
Ken Ikeuchi•Nives Ivic•Robert Buschauer•Jingdong Cheng•Thomas Fröhlich等 10 人
Nature Communications
2023
•2023/5/12
•Vol.14 No.1 p.1-15
In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational res...
Cryoelectron microscopyRibosomal proteinsUbiquitylation
10.1038/S41467-023-38161-W
ISSN:2041-1723
Shigella effector IpaH1.4 subverts host E3 ligase RNF213 to evade antibacterial immunity
Xindi Zhou•Huijing Zhang•Yaru Wang•Danni Wang•Zhiqiao Lin等 11 人
Nature Communications
2025
•2025/4/1
•Vol.16 No.1 p.1-16
Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial immunity in mammals. Shigella flexneri, an LPS-containing pathogenic bacterium, has developed mechanisms t...
Bacterial immune evasionCryoelectron microscopyUbiquitylationX-ray crystallography
10.1038/S41467-025-58432-Y
ISSN:2041-1723
Selumetinib in adults with NF1 and inoperable plexiform neurofibroma: a phase 2 trial
Andrea M. Gross•Geraldine O’Sullivan Coyne•Eva Dombi•Cecilia Tibery•William G. Herrick等 35 人
Nature Medicine
2025
•2025/1/6
•Vol.31 No.1 p.105-115
The MEK inhibitor selumetinib induces objective responses and provides clinical benefit in children with neurofibromatosis type 1 (NF1) and inoperable plexiform neurofibromas (PNs). To evaluate whether similar outcomes were possible in adult patients, in whom PN growth is generally slower than in pe...
Cancer therapyMechanisms of diseaseMolecularly targeted therapyPhase II trialsTargeted therapies
10.1038/S41591-024-03361-4
ISSN:1078-8956
E3 ligase-inactivation rewires CBL interactome to elicit oncogenesis by hijacking RTK–CBL–CIN85 axis
Syed Feroj Ahmed•Lori Buetow•Mads Gabrielsen•Sergio Lilla•Gary J. Sibbet等 10 人
Oncogene
2021
•2021/2/24
•Vol.40 No.12 p.2149-2164
Casitas B-lineage lymphoma (CBL) is a ubiquitin ligase (E3) that becomes activated upon Tyr371-phosphorylation and targets receptor protein tyrosine kinases for ubiquitin-mediated degradation. Deregulation of CBL and its E3 activity is observed in myeloproliferative neoplasms and other cancers, incl...
OncogenesUbiquitylation
10.1038/S41388-021-01684-X
ISSN:0950-9232
Conformational plasticity of disordered regions enables sequence-diverse DNA recognition by transcription factor AflR
Shaowen Wu•Fenghua Wang•Weijie Zhou•Xinze Zhang•Lingpeng Zhan等 12 人
Nature Communications
2025
•2025/10/6
•Vol.16 No.1 p.1-18
The ability of transcription factors to recognize diverse DNA sequences while maintaining binding specificity is required for gene regulation, but the molecular mechanism enabling this flexibility remains poorly understood. Here, we show that the DNA-binding domain of transcription factor AflR emplo...
Biophysical chemistryComputational biophysicsIntrinsically disordered proteins
10.1038/S41467-025-63926-W
ISSN:2041-1723
A selective BCL-X L PROTAC degrader achieves safe and potent antitumor activity
Sajid Khan•Xuan Zhang•Dongwen Lv•Qi Zhang•Yonghan He等 25 人
Nature Medicine
2019
•2019/12/2
•Vol.25 No.12 p.1938-1947
B-cell lymphoma extra large (BCL-XL) is a well-validated cancer target. However, the on-target and dose-limiting thrombocytopenia limits the use of BCL-XL inhibitors, such as ABT263, as safe and effective anticancer agents. To reduce the toxicity of ABT263, we converted it into DT2216, a BCL-XL prot...
CancerCancer therapyDrug discoveryDrug safety
10.1038/S41591-019-0668-Z
ISSN:1078-8956
DeKinomics pulse-chases kinase functions in living cells
Yicheng Weng•Wendong Chen•Qian Kong•Ruixiang Wang•Ruxin Zeng等 15 人
Nature Chemical Biology
2024
•2024/1/2
•00 p.1-9
Cellular context is crucial for understanding the complex and dynamic kinase functions in health and disease. Systematic dissection of kinase-mediated cellular processes requires rapid and precise stimulation (‘pulse’) of a kinase of interest, as well as global and in-depth characterization (‘chase’...
KinasesProteomics
10.1038/S41589-023-01497-X
ISSN:1552-4450
Cathepsin D promotes acute myeloid leukemia progression through stabilization of the anti-apoptotic proteins
Huimin Jiang•Yongjian Wang•Churan Wang•Lu Yang•Shujuan Wang等 13 人
Cell Death & Disease
2025
•2025/8/12
•Vol.16 No.1 p.1-13
Cathepsin D (CTSD) is a lysosomal aspartic protease that plays vital roles in regulating the properties of solid tumors, including proliferation, apoptosis, migration, metastasis, and angiogenesis. However, the function of CTSD in haematological malignancies remains largely elusive. Here we show tha...
Acute myeloid leukaemiaApoptosisUbiquitylationVirtual screening
10.1038/S41419-025-07949-7
ISSN:2041-4889
Membrane organization of photosystem I complexes in the most abundant phototroph on Earth
C. MacGregor-Chatwin•P. J. Jackson•M. Sener•J. W. Chidgey•A. Hitchcock等 12 人
Nature Plants
2019
•2019/7/22
•Vol.5 No.8 p.879-889
Prochlorococcus is a major contributor to primary production, and globally the most abundant photosynthetic genus of picocyanobacteria because it can adapt to highly stratified low-nutrient conditions that are characteristic of the surface ocean. Here, we examine the structural adaptations of the ph...
Biological techniquesCell biologyOcean sciences
10.1038/S41477-019-0475-Z
ISSN:2055-0278
Elucidating the mechanisms by which disulfiram protects against obesity and metabolic syndrome
Michel Bernier•Dylan Harney•Yen Chin Koay•Antonio Diaz•Abhishek Singh等 21 人
Npj Aging And Mechanisms Of Disease
2020
•2020/7/21
•Vol.6 No.1 p.1-11
There is an unmet need and urgency to find safe and effective anti-obesity interventions. Our recent study in mice fed on obesogenic diet found that treatment with the alcohol aversive drug disulfiram reduced feeding efficiency and led to a decrease in body weight and an increase in energy expenditu...
Metabolic syndromeObesity
10.1038/S41514-020-0046-6
ISSN:2056-3973
SS18 regulates pluripotent-somatic transition through phase separation
Junqi Kuang•Ziwei Zhai•Pengli Li•Ruona Shi•Wenjing Guo等 28 人
Nature Communications
2021
•2021/7/2
•Vol.12 No.1 p.1-11
The transition from pluripotent to somatic states marks a critical event in mammalian development, but remains largely unresolved. Here we report the identification of SS18 as a regulator for pluripotent to somatic transition or PST by CRISPR-based whole genome screens. Mechanistically, SS18 forms m...
Cell biologyEmbryonic stem cellsIntrinsically disordered proteinsMolecular biology
10.1038/S41467-021-24373-5
ISSN:2041-1723
N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity
Sylvia Varland•Rui Duarte Silva•Ine Kjosås•Alexandra Faustino•Annelies Bogaert等 26 人
Nature Communications
2023
•2023/10/27
•Vol.14 No.1 p.1-27
Most eukaryotic proteins are N-terminally acetylated, but the functional impact on a global scale has remained obscure. Using genome-wide CRISPR knockout screens in human cells, we reveal a strong genetic dependency between a major N-terminal acetyltransferase and specific ubiquitin ligases. Biochem...
AcetylationAcetyltransferasesDrosophilaNeddylationProteomics
10.1038/S41467-023-42342-Y
ISSN:2041-1723
A network of chaperones prevents and detects failures in membrane protein lipid bilayer integration
João P. L. Coelho•Matthias Stahl•Nicolas Bloemeke•Kevin Meighen-Berger•Carlos Piedrafita Alvira等 8 人
Nature Communications
2019
•2019/2/8
•Vol.10 No.1 p.1-10
A fundamental step in membrane protein biogenesis is their integration into the lipid bilayer with a defined orientation of each transmembrane segment. Despite this, it remains unclear how cells detect and handle failures in this process. Here we show that single point mutations in the membrane prot...
BiochemistryCell biologyProtein folding
10.1038/S41467-019-08632-0
ISSN:2041-1723
CypA/TAF15/STAT5A/miR-514a-3p feedback loop drives ovarian cancer metastasis
Ying Li•Huiwen Yang•An Li•Buze Chen•Yue Wang等 13 人
Oncogene
2024
•2024/10/14
•00 p.1-16
Cyclophilin A (CypA) is a peptidyl-prolyl isomerase that participates in multiple cancer events, but the molecular mechanisms of abnormal expression and regulation of CypA in ovarian cancer (OC) have never been considered. This study identifies CypA as a key driver of epithelial-mesenchymal transiti...
BiomarkersCancer
10.1038/S41388-024-03188-W
ISSN:0950-9232
Identification of targets of AMPylating Fic enzymes by co-substrate-mediated covalent capture
Burak Gulen•Marie Rosselin•Joel Fauser•Michael F. Albers•Christian Pett等 10 人
Nature Chemistry
2020
•2020/7/6
•Vol.12 No.8 p.732-739
Various pathogenic bacteria use post-translational modifications to manipulate the central components of host cell functions. Many of the enzymes released by these bacteria belong to the large Fic family, which modify targets with nucleotide monophosphates. The lack of a generic method for identifyi...
Nucleotide-binding proteinsPost-translational modificationsProteomic analysis
10.1038/S41557-020-0484-6
ISSN:1755-4330
DDX1 methylation mediated MATR3 splicing regulates intervertebral disc degeneration by initiating chromatin reprogramming
Dingchao Zhu•Huaizhen Liang•Bide Tong•Zhi Du•Gaocai Li等 17 人
Nature Communications
2025
•2025/7/4
•Vol.16 No.1 p.1-20
Low back pain (LBP), primarily driven by intervertebral disc degeneration (IVDD), has become a core challenge in public health. DDX1, an RNA-binding protein, plays key roles in RNA metabolism but its function in IVDD remains unclear. We identify DDX1 as a substrate of methyltransferase EZH2, which m...
DiseasesMolecular medicineTranslational research
10.1038/S41467-025-61486-7
ISSN:2041-1723
Bacterial protoplast-derived nanovesicles carrying CRISPR-Cas9 tools re-educate tumor-associated macrophages for enhanced cancer immunotherapy
Mingming Zhao•Xiaohui Cheng•Pingwen Shao•Yao Dong•Yongjie Wu等 12 人
Nature Communications
2024
•2024/1/31
•Vol.15 No.1 p.1-18
The CRISPR-Cas9 system offers substantial potential for cancer therapy by enabling precise manipulation of key genes involved in tumorigenesis and immune response. Despite its promise, the system faces critical challenges, including the preservation of cell viability post-editing and ensuring safe i...
Applied immunologyCancer immunotherapyGene delivery
10.1038/S41467-024-44941-9
ISSN:2041-1723
Enhanced plasma half-life and efficacy of engineered human albumin-fused GLP-1 despite enzymatic cleavage of its C-terminal end
Jeannette Nilsen•Kristin Hovden Aaen•Sopisa Benjakul•Fulgencio Ruso-Julve•Thomas Uwe Greiner等 11 人
Communications Biology
2025
•2025/5/26
•Vol.8 No.1 p.1-17
Albumin has a long plasma half-life due to engagement of the neonatal Fc receptor (FcRn), which prevents intracellular degradation. However, its C-terminal end can be cleaved by carboxypeptidase A, and removal of the last leucine residue (L585) weakens receptor binding, reducing its half-life from 2...
Protein deliveryRecombinant protein therapy
10.1038/S42003-025-08249-8
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
The E3 ligase RNF5 restricts SARS-CoV-2 replication by targeting its envelope protein for degradation
Li Zhaolong•Hao Pengfei•Zhao Zhilei•Gao Wenying•Huan Chen等 12 人
Signal Transduction And Targeted Therapy
2023
•2023/2/3
•Vol.8 No.1 p.1-11
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a severe global health crisis; its structural protein envelope (E) is critical for viral entry, budding, production, and induction of pathology which makes it a potentia...
Drug developmentInfectionInfectious diseasesInnate immunity
10.1038/S41392-023-01335-5
ISSN:2059-3635
Kidney tubular epithelial cells control interstitial fibroblast fate by releasing TNFAIP8-encapsulated exosomes
Xi Liu•Zhao Liu•Cong Wang•Jinhua Miao•Shan Zhou等 9 人
Cell Death & Disease
2023
•2023/10/12
•Vol.14 No.10 p.1-15
Kidney fibrosis, characterized by the activation and expansion of the matrix-producing fibroblasts, is the common outcome of chronic kidney disease (CKD). While fibroblast proliferation is well studied in CKD, little is known about the regulation and mechanism of fibroblast depletion. Here, we show ...
Cell biologyKidney diseases
10.1038/S41419-023-06209-W
ISSN:2041-4889
Small-molecule-mediated OGG1 inhibition attenuates pulmonary inflammation and lung fibrosis in a murine lung fibrosis model
Tanner L.•Single A. B.•Bhongir R. K. V.•Heusel M.•Mohanty T.等 19 人
Nature Communications
2023
•2023/2/6
•Vol.14 No.1 p.1-16
Interstitial lung diseases such as idiopathic pulmonary fibrosis (IPF) are caused by persistent micro-injuries to alveolar epithelial tissues accompanied by aberrant repair processes. IPF is currently treated with pirfenidone and nintedanib, compounds which slow the rate of disease progression but f...
Drug developmentPreclinical researchTranslational research
10.1038/S41467-023-36314-5
ISSN:2041-1723
Identification of genotype–biochemical phenotype correlations associated with fructose 1,6-bisphosphatase deficiency
Ikki Sakuma•Hidekazu Nagano•Naoko Hashimoto•Masanori Fujimoto•Akitoshi Nakayama等 20 人
Communications Biology
2023
•2023/7/28
•Vol.6 No.1 p.1-14
Fructose-1,6-bisphosphatase (FBPase) deficiency, caused by an FBP1 mutation, is an autosomal recessive disorder characterized by hypoglycemic lactic acidosis. Due to the rarity of FBPase deficiency, the mechanism by which the mutations cause enzyme activity loss still remains unclear. Here we identi...
ChaperonesMutation
10.1038/S42003-023-05160-Y
ISSN:2399-3642
Metabolic reprogramming of proinflammatory macrophages by target delivered roburic acid effectively ameliorates rheumatoid arthritis symptoms
Na Jia•Yunzhen Gao•Min Li•Yi Liang•Yuwen Li等 14 人
Signal Transduction And Targeted Therapy
2023
•2023/7/28
•Vol.8 No.1 p.1-15
Rheumatoid arthritis (RA) is a common chronic inflammatory disorder that usually affects joints. It was found that roburic acid (RBA), an ingredient from anti-RA herb Gentiana macrophylla Pall., displayed strong anti-inflammatory activity. However, its medical application is limited by its hydrophob...
Drug developmentRheumatic diseases
10.1038/S41392-023-01499-0
ISSN:2059-3635
Photosensitizer proximity labeling captures the lipid and protein interactomes
Andrew P. Becker•Elijah Biletch•John Paul Kennelly•Soon-Gook Hong•Ashley R. Julio等 17 人
Nature Chemical Biology
2026
•2026/2/6
•00 p.1-11
The physical properties of cellular membranes are influenced by protein and lipid interactions. In situ proximity labeling interactomic methods are well suited to characterize these dynamic and often fleeting interactions. Yet, available methods require distinct chemistries for proteins and lipids. ...
Protein–protein interaction networksProteomicsSterols
10.1038/S41589-026-02140-1
ISSN:1552-4450
Maternal exercise prevents metabolic disorders in offspring mice through SERPINA3C
Yang Li•Ruo-Ying Li•Jie-Ying Zhu•Min Chen•Wang-Jing Mu等 12 人
Nature Metabolism
2025
•2025/1/31
•Vol.7 No.2 p.401-420
Maternal exercise can improve the metabolic health of the offspring. However, the molecular mechanisms underlying the beneficial effects of maternal exercise on the offspring remain unclear. Here, we show that maternal exercise during pregnancy alleviates high-fat diet (HFD)-induced adipose inflamma...
Endocrine system and metabolic diseasesEpigeneticsMetabolism
10.1038/S42255-024-01213-6
ISSN:2522-5812
Transglutaminase 3 crosslinks the secreted gel-forming mucus component Mucin-2 and stabilizes the colonic mucus layer
Sharpen Jack D. A.•Dolan Brendan•Nyström Elisabeth E. L.•Birchenough George M. H.•Arike Liisa等 9 人
Nature Communications
2022
•2022/1/11
•Vol.13 No.1 p.1-12
The colonic mucus layer is organized as a two-layered system providing a physical barrier against pathogens and simultaneously harboring the commensal flora. The factors contributing to the organization of this gel network are not well understood. In this study, the impact of transglutaminase activi...
ColonGlycobiologyIntestinal diseasesIsoenzymesTransferases
10.1038/S41467-021-27743-1
ISSN:2041-1723
TBL1X/TBL1XR1 govern β-cell identity through a PAX6-containing gene regulatory network
Alina A. Walth-Hummel•Celine Jouffe•Peter Weber•Karsten Motzler•Julia Geppert等 22 人
Nature Communications
2026
•2026/4/23
•Vol.17 No.1 p.37360
A main mechanism of β-cell dysfunction in diabetes is loss of identity, controlled by transcription factors that induce identity gene expression and disallowed gene repression. How transcription factors facilitate simultaneous expression and repression is not fully understood, representing a knowled...
DiabetesOrganogenesisTranscription
10.1038/S41467-026-72077-5
ISSN:2041-1723
FAD synthase confers ferroptosis resistance and restrains CD8+ T cell recruitment in hepatocellular carcinoma
Jiashuo Chao•Yuan Liang•Hao Wang•Ziyu Xun•Shanshan Wang等 16 人
Nature Communications
2025
•2025/10/29
•Vol.16 No.1 p.1-18
Vitamin B2 (VB2) metabolism regulates numerous cellular processes, but its role in hepatocellular carcinoma (HCC) progression remains unclear. Here we show that HCC tumors are characterized by upregulation of a VB2 metabolism signature, and VB2 metabolism promotes HCC progression. Among VB2 metaboli...
Cancer metabolismCD8-positive T cellsHepatocellular carcinomaRNA sequencing
10.1038/S41467-025-64572-Y
ISSN:2041-1723
MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells
Iris Müller•Ann Sophie Moroni•Daria Shlyueva•Sudeep Sahadevan•Erwin M. Schoof等 11 人
Nature Communications
2021
•2021/5/24
•Vol.12 No.1 p.1-17
Deciphering the mechanisms that control the pluripotent ground state is key for understanding embryonic development. Nonetheless, the epigenetic regulation of ground-state mouse embryonic stem cells (mESCs) is not fully understood. Here, we identify the epigenetic protein MPP8 as being essential for...
BiochemistryCell biologyDevelopmental biologyGeneticsMolecular biology
10.1038/S41467-021-23308-4
ISSN:2041-1723
Multi-omics analysis of human mesenchymal stem cells shows cell aging that alters immunomodulatory activity through the downregulation of PD-L1
Yuchen Gao•Ying Chi•Yunfei Chen•Wentian Wang•Huiyuan Li等 21 人
Nature Communications
2023
•2023/7/20
•Vol.14 No.1 p.1-21
Mesenchymal stem cells (MSCs) possess potent immunomodulatory activity and have been extensively investigated for their therapeutic potential in treating inflammatory disorders. However, the mechanisms underlying the immunosuppressive function of MSCs are not fully understood, hindering the developm...
Data miningImmunosuppressionMesenchymal stem cellsSenescenceTranslational immunology
10.1038/S41467-023-39958-5
ISSN:2041-1723
SpecGP as a transformer-based model for predicting energy-adaptable structural spectra of glycopeptides
Xianyong Wang•Rui Song•Zhuangzhuang Feng•Shisheng Sun
Nature Machine Intelligence
2026
•2026/5/18
•00 p.1-13
Deep learning has shown great promise for high-throughput spectral library construction in glycoproteomics. Nevertheless, precise prediction of the structural spectra of intact N-glycopeptides remains challenging due to their complex and high-dimensional information. Here we present SpecGP, a transf...
GlycosylationMachine learningMass spectrometryPolysaccharidesProteomics
10.1038/S42256-026-01246-4
ISSN:2522-5839
SPOP mutation induces replication over-firing by impairing Geminin ubiquitination and triggers replication catastrophe upon ATR inhibition
Ma Jian•Shi Qing•Cui Gaofeng•Sheng Haoyue•Botuyan Maria Victoria等 14 人
Nature Communications
2021
•2021/10/1
•Vol.12 No.1 p.1-14
Geminin and its binding partner Cdt1 are essential for the regulation of DNA replication. Here we show that the CULLIN3 E3 ubiquitin ligase adaptor protein SPOP binds Geminin at endogenous level and regulates DNA replication. SPOP promotes K27-linked non-degradative poly-ubiquitination of Geminin at...
DNA replicationOncogenesTumour-suppressor proteinsUbiquitylation
10.1038/S41467-021-26049-6
ISSN:2041-1723
Mitochondrial membrane proteins and VPS35 orchestrate selective removal of mtDNA
Sen Ayesha•Kallabis Sebastian•Gaedke Felix•Jüngst Christian•Boix Julia等 12 人
Nature Communications
2022
•2022/11/7
•Vol.13 No.1 p.1-20
Understanding the mechanisms governing selective turnover of mutation-bearing mtDNA is fundamental to design therapeutic strategies against mtDNA diseases. Here, we show that specific mtDNA damage leads to an exacerbated mtDNA turnover, independent of canonical macroautophagy, but relying on lysosom...
EndosomesMitochondriaMitophagy
10.1038/S41467-022-34205-9
ISSN:2041-1723
A short dasatinib and quercetin treatment is sufficient to reinstate potent adult neuroregenesis in the aged killifish
Jolien Van houcke•Valerie Mariën•Caroline Zandecki•Rajagopal Ayana•Elise Pepermans等 9 人
Npj Regenerative Medicine
2023
•2023/6/16
•Vol.8 No.1 p.1-13
The young African turquoise killifish has a high regenerative capacity, but loses it with advancing age, adopting several aspects of the limited form of mammalian regeneration. We deployed a proteomic strategy to identify pathways that underpin the loss of regenerative power caused by aging. Cellula...
Adult neurogenesisAgeingNeural stem cellsPreclinical researchRegeneration and repair in the nervous system
10.1038/S41536-023-00304-4
ISSN:2057-3995
StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy
Shen Jiechen•Jia Li•Dang Liuyi•Su Yuanjie•Zhang Jie等 19 人
Nature Methods
2021
•2021/8/2
•Vol.18 No.8 p.921-929
Precision mapping of glycans at structural and site-specific level is still one of the most challenging tasks in the glycobiology field. Here, we describe a modularization strategy for de novo interpretation of N-glycan structures on intact glycopeptides using tandem mass spectrometry. An algorithm ...
GlycomicsPolysaccharide sequencingProteomic analysisSoftware
10.1038/S41592-021-01209-0
ISSN:1548-7091
A distinct isoform of ZNF207 controls self-renewal and pluripotency of human embryonic stem cells
Fang Fang•Ninuo Xia•Benjamin Angulo•Joseph Carey•Zackery Cady等 9 人
Nature Communications
2018
•2018/10/22
•Vol.9 No.1 p.1-14
Self-renewal and pluripotency in human embryonic stem cells (hESCs) depends upon the function of a remarkably small number of master transcription factors (TFs) that include OCT4, SOX2, and NANOG. Endogenous factors that regulate and maintain the expression of master TFs in hESCs remain largely unkn...
Embryonic stem cellsProteomicsTranscription
10.1038/S41467-018-06908-5
ISSN:2041-1723
Quantitative analysis of phosphoproteome in necroptosis reveals a role of TRIM28 phosphorylation in promoting necroptosis-induced cytokine production
Zu Rui•Yu Zhen•Zhao Jing•Lu Xiaojuan•Liang Wei等 15 人
Cell Death & Disease
2021
•2021/10/23
•Vol.12 No.11 p.1-12
Necroptosis is a form of regulated necrotic cell death that promotes inflammation. In cells undergoing necroptosis, activated RIPK1 kinase mediates the formation of RIPK1/RIPK3/MLKL complex to promote MLKL oligomerization and execution of necroptosis. RIPK1 kinase activity also promotes cell-autonom...
Cell biologyImmunology
10.1038/S41419-021-04290-7
ISSN:2041-4889
Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome
Wan Ning•Wang Nian•Yu Siqin•Zhang Hanqing•Tang Shuo等 18 人
Nature Methods
2022
•2022/6/27
•Vol.19 No.7 p.854-864
Lactylation was initially discovered on human histones. Given its nascence, its occurrence on nonhistone proteins and downstream functional consequences remain elusive. Here we report a cyclic immonium ion of lactyllysine formed during tandem mass spectrometry that enables confident protein lactylat...
Post-translational modificationsProteomic analysisProteomics
10.1038/S41592-022-01523-1
ISSN:1548-7091
The Shigella kinase effector OspG modulates host ubiquitin signaling to escape septin-cage entrapment
Wei Xian•Jiaqi Fu•Qinxin Zhang•Chuang Li•Yan-Bo Zhao等 14 人
Nature Communications
2024
•2024/5/8
•Vol.15 No.1 p.1-15
Shigella flexneri is a Gram-negative bacterium causing severe bloody dysentery. Its pathogenesis is largely dictated by a plasmid-encoded type III secretion system (T3SS) and its associated effectors. Among these, the effector OspG has been shown to bind to the ubiquitin conjugation machinery (E2~Ub...
Cellular microbiologyPathogensProteomic analysis
10.1038/S41467-024-48205-4
ISSN:2041-1723
Extensive modulation of the circulating blood proteome by hormonal contraceptive use across two population studies
Nikola Dordevic•Clemens Dierks•Essi Hantikainen•Vadim Farztdinov•Fatma Amari等 18 人
Communications Medicine
2025
•2025/4/22
•Vol.5 No.1 p.1-12
The study of circulating blood proteins in population cohorts offers new avenues to explore lifestyle-related and genetic influences describing and shaping human health. Utilizing high-throughput mass spectrometry, we quantified 148 highly abundant proteins, functioning in the innate and adaptive im...
BiomarkersEpidemiologyHigh-throughput screeningProteomics
10.1038/S43856-025-00856-0
ISSN:2730-664X
Cell surface glycan engineering reveals that matriglycan alone can recapitulate dystroglycan binding and function
Sheikh M. Osman•Capicciotti Chantelle J.•Liu Lin•Praissman Jeremy•Ding Dahai等 12 人
Nature Communications
2022
•2022/6/24
•Vol.13 No.1 p.1-13
α-Dystroglycan (α-DG) is uniquely modified on O-mannose sites by a repeating disaccharide (-Xylα1,3-GlcAβ1,3-)n termed matriglycan, which is a receptor for laminin-G domain-containing proteins and employed by old-world arenaviruses for infection. Using chemoenzymatically synthesized matriglycans pri...
CarbohydratesExtracellular matrixGlycobiologyMolecular engineeringVirus–host interactions
10.1038/S41467-022-31205-7
ISSN:2041-1723
Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1
Jiqing Du•Marie-Kristin von Wrisberg•Burak Gulen•Matthias Stahl•Christian Pett等 9 人
Nature Communications
2021
•2021/1/19
•Vol.12 No.1 p.1-16
Legionella pneumophila infects eukaryotic cells by forming a replicative organelle – the Legionella containing vacuole. During this process, the bacterial protein DrrA/SidM is secreted and manipulates the activity and post-translational modification (PTM) states of the vesicular trafficking regulato...
Bacterial structural biologyEnzyme mechanismsPost-translational modificationsX-ray crystallography
10.1038/S41467-020-20702-2
ISSN:2041-1723
OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients
Jinhui Yuan•Boyan Sun•Murong Li•Congyi Yang•Lingqiang Zhang等 8 人
Npj Biofilms And Microbiomes
2025
•2025/4/23
•Vol.11 No.1 p.1-14
The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enriching bac...
Applied microbiologyMicrobiome
10.1038/S41522-025-00692-Z
ISSN:2055-5008
Mechanism of beta-arrestin 1 mediated Src activation via Src SH3 domain revealed by cryo-electron microscopy
Natalia Pakharukova•Brittany N. Thomas•Harsh Bansia•Linus Li•Dana K. Bassford等 16 人
Nature Communications
2026
•2026/2/20
•Vol.17 No.1 p.29730
Beta-arrestins (βarrs) are key regulators and transducers of G-protein coupled receptor signaling; however, little is known of how βarrs communicate with their downstream effectors. Here, we delineate structural mechanisms underlying βarr-mediated signal transduction. Using cryo-electron microscopy,...
Cell signallingCryoelectron microscopyKinasesMolecular conformation
10.1038/S41467-026-69884-1
ISSN:2041-1723
Enamel proteome shows that Gigantopithecus was an early diverging pongine
Frido Welker•Jazmín Ramos-Madrigal•Martin Kuhlwilm•Wei Liao•Petra Gutenbrunner等 18 人
Nature
2019
•2019/11/13
•Vol.576 No.7786 p.262-265
Gigantopithecus blacki was a giant hominid that inhabited densely forested environments of Southeast Asia during the Pleistocene epoch1. Its evolutionary relationships to other great ape species, and the divergence of these species during the Middle and Late Miocene epoch (16–5.3 million years ago),...
Biological anthropologyPalaeontologyPhylogeneticsProteomics
10.1038/S41586-019-1728-8
ISSN:0028-0836
Genetic properties underlying transcriptional variability across different perturbations
Saburo Tsuru•Chikara Furusawa
Nature Communications
2025
•2025/3/21
•Vol.16 No.1 p.1-16
The rate and direction of phenotypic evolution depend on the availability of phenotypic variants induced genetically or environmentally. It is widely accepted that organisms do not display uniform phenotypic variation, with certain variants arising more frequently than others in response to genetic ...
Bacterial geneticsEvolutionary geneticsGene expressionGene regulationGene regulatory networks
10.1038/S41467-025-57642-8
ISSN:2041-1723
Purification of cross-linked RNA-protein complexes by phenol-toluol extraction
Erika C. Urdaneta•Carlos H. Vieira-Vieira•Timon Hick•Hans-Herrmann Wessels•Davide Figini等 11 人
Nature Communications
2019
•2019/3/1
•Vol.10 No.1 p.1-17
Recent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRN...
High-throughput screeningProteomicsRNARNA-binding proteins
10.1038/S41467-019-08942-3
ISSN:2041-1723
Delineating cysteine-reactive compound modulation of cellular proteostasis processes
Ashley R. Julio•Flowreen Shikwana•Cindy Truong•Nikolas R. Burton•Emil R. Dominguez等 8 人
Nature Chemical Biology
2024
•2024/10/24
•00 p.1-13
Covalent modulators and covalent degrader molecules have emerged as drug modalities with tremendous therapeutic potential. Toward realizing this potential, mass spectrometry-based chemoproteomic screens have generated proteome-wide maps of potential druggable cysteine residues. However, beyond these...
Protein aggregationProteomicsSmall moleculesTarget identification
10.1038/S41589-024-01760-9
ISSN:1552-4450
Crosstalk between inovirus core gene and accessory toxin-antitoxin system mediates polylysogeny
Jiayu Gu•Yunxue Guo•Juehua Weng•Shituan Lin•Yabo Liu等 6 人
Nature Communications
2025
•2025/8/7
•Vol.16 No.1 p.1-13
Polylysogeny, the harboring of multiple prophages within a single bacterial genome, is common among bacterial pathogens and enhances virulence and genome plasticity. Inoviruses (filamentous phages) are often present in multiple copies in major pathogens, leading to polylysogeny. Two highly similar f...
BacteriologyBacteriophagesBiofilms
10.1038/S41467-025-62378-6
ISSN:2041-1723
Pyroptosis inhibition improves the symptom of acute myocardial infarction
Liu Wenju•Shen Junwei•Li Yanfei•Wu Jiawen•Luo Xiaoli等 11 人
Cell Death & Disease
2021
•2021/9/16
•Vol.12 No.10 p.1-10
Acute myocardial infarction (AMI), the leading cause of mortality worldwide, is a rapidly developing and irreversible disease. Therefore, proper prompt intervention at the early stage of AMI is crucial for its treatment. However, the molecular features in the early stage have not been clarified. Her...
Cardiovascular diseasesTranscriptomics
10.1038/S41419-021-04143-3
ISSN:2041-4889
Glucocorticoids promote breast cancer metastasis
Milan M. S. Obradović•Baptiste Hamelin•Nenad Manevski•Joana Pinto Couto•Atul Sethi等 11 人
Nature
2019
•2019/3/13
•Vol.567 No.7749 p.540-544
Diversity within or between tumours and metastases (known as intra-patient tumour heterogeneity) that develops during disease progression is a serious hurdle for therapy1–3. Metastasis is the fatal hallmark of cancer and the mechanisms of colonization, the most complex step in the metastatic cascade...
Breast cancerMetastasis
10.1038/S41586-019-1019-4
ISSN:0028-0836
Expanding the human proteome with microproteins and peptideins
Eric W. Deutsch•Leron W. Kok•Jonathan M. Mudge•Cristian F. Valls•Irwin Jungreis等 64 人
Nature
2026
•2026/5/6
•00 p.1-13
A major scientific drive is to characterize the protein-coding genome, which is a primary basis for studying human health. But the fundamental question remains of what has been missed in previous analyses. Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been o...
Evolutionary biologyGene expressionGenetic databasesOpen reading framesProtein databases
10.1038/S41586-026-10459-X
ISSN:0028-0836
Lithocholic acid binds TULP3 to activate sirtuins and AMPK to slow down ageing
Qi Qu•Yan Chen•Yu Wang•Weiche Wang•Shating Long等 35 人
Nature
2024
•2024/12/18
•00 p.1-9
Lithocholic acid (LCA) is accumulated in mammals during calorie restriction and it can activate AMP-activated protein kinase (AMPK) to slow down ageing1. However, the molecular details of how LCA activates AMPK and induces these biological effects are unclear. Here we show that LCA enhances the acti...
AcetylationAgeingNutrient signalling
10.1038/S41586-024-08348-2
ISSN:0028-0836
Maturation of human cardiac organoids enables complex disease modeling and drug discovery
Mark W. Pocock•Janice D. Reid•Harley R. Robinson•Natalie Charitakis•James R. Krycer等 38 人
Nature Cardiovascular Research
2025
•2025/6/25
•00 p.1-20
Maturation of human pluripotent stem (hPS) cell-derived cardiomyocytes is critical for their use as a model system. Here we mimic human heart maturation pathways in the setting of hPS cell-derived cardiac organoids (hCOs). Specifically, transient activation of 5′ AMP-activated protein kinase and est...
CardiomyopathiesDifferentiationTissue engineering
10.1038/S44161-025-00669-3
ISSN:2731-0590
Effects of microgravity exposure and fructo-oligosaccharide ingestion on the proteome of soleus and extensor digitorum longus muscles in developing mice
Ohira Takashi•Ino Yoko•Kimura Yayoi•Nakai Yusuke•Kimura Ayuko等 13 人
Npj Microgravity
2021
•2021/9/17
•Vol.7 No.1 p.1-11
Short-chain fatty acids produced by the gut bacterial fermentation of non-digestible carbohydrates, e.g., fructo-oligosaccharide (FOS), contribute to the maintenance of skeletal muscle mass and oxidative metabolic capacity. We evaluated the effect of FOS ingestion on protein expression of soleus (So...
Cell biologyPhysiologyPreventive medicine
10.1038/S41526-021-00164-6
ISSN:2373-8065
NPC1 controls TGFBR1 stability in a cholesterol transport-independent manner and promotes hepatocellular carcinoma progression
Shuangyan Li•Lishan Yan•Chaoying Li•Lijuan Lou•Fengjiao Cui等 8 人
Nature Communications
2025
•2025/1/7
•Vol.16 No.1 p.1-17
Niemann-Pick disease type C protein 1 (NPC1), classically associated with cholesterol transport and viral entry, has an emerging role in cancer biology. Here, we demonstrate that knockout of Npc1 in hepatocytes attenuates hepatocellular carcinoma (HCC) progression in both DEN (diethylnitrosamine)-CC...
Growth factor signallingHepatocellular carcinomaMechanisms of diseaseMetastasis
10.1038/S41467-024-55788-5
ISSN:2041-1723
Recurrent evolution of adhesive defence systems in amphibians by parallel shifts in gene expression
Shabnam Zaman•Birgit Lengerer•Joris Van Lindt•Indra Saenen•Giorgio Russo等 10 人
Nature Communications
2024
•2024/7/10
•Vol.15 No.1 p.1-13
Natural selection can drive organisms to strikingly similar adaptive solutions, but the underlying molecular mechanisms often remain unknown. Several amphibians have independently evolved highly adhesive skin secretions (glues) that support a highly effective antipredator defence mechanism. Here we ...
Animal physiologyHerpetologyMolecular evolution
10.1038/S41467-024-49917-3
ISSN:2041-1723
Exocyst dynamics during vesicle tethering and fusion
Syed Mukhtar Ahmed•Hisayo Nishida-Fukuda•Yuchong Li•W. Hayes McDonald•Claudiu C. Gradinaru等 6 人
Nature Communications
2018
•2018/12/3
•Vol.9 No.1 p.1-17
The exocyst is a conserved octameric complex that tethers exocytic vesicles to the plasma membrane prior to fusion. Exocyst assembly and delivery mechanisms remain unclear, especially in mammalian cells. Here we tagged multiple endogenous exocyst subunits with sfGFP or Halo using Cas9 gene-editing, ...
ExocytosisSingle-molecule biophysics
10.1038/S41467-018-07467-5
ISSN:2041-1723
vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics
Marica Grossegesse•Fabian Horn•Andreas Kurth•Peter Lasch•Andreas Nitsche等 6 人
Nature Communications
2025
•2025/7/31
•Vol.16 No.1 p.1-13
Viral infections are commonly diagnosed by the detection of viral genome fragments or proteins using targeted methods such as PCR and immunoassays. In contrast, metagenomics enables the untargeted identification of viral genomes, expanding its applicability across a broader spectrum. In this study, ...
Proteomic analysisViral infection
10.1038/S41467-025-62469-4
ISSN:2041-1723
Combinatorial tagging generates a multi-purpose knock-in mouse model revealing phase separation-dependent germ granules in RNA homeostasis and germline development
Lan Meng•Caoling Xu•Yuzhu Cao•Limin Wu•Yuzhang Zhu等 15 人
Cell Death & Differentiation
2025
•2025/4/23
•00 p.1-18
A large resource of epitope-tagged and Cre/CreERT2-expressing mouse models are available for studying germ granules and germline development. Germ granules are proteinaceous, membraneless organelles (MLO) involved in germ cell differentiation and maturation; however, their protein and RNA transcript...
Cell biologyDevelopment
10.1038/S41418-025-01495-7
ISSN:1350-9047
Parvimonas micra promotes oral squamous cell carcinoma metastasis through TmpC-CKAP4 axis
Houbao Qi•Haiting Gao•Meihui Li•Tianyong Sun•Xiufeng Gu等 13 人
Nature Communications
2025
•2025/3/7
•Vol.16 No.1 p.1-19
Parvimonas micra (P. micra), an opportunistic oral pathogen associated with multiple cancers, has limited research on its role in oral squamous cell carcinoma (OSCC). This study shows that P. micra is enriched in OSCC tissues and positively correlated with tumor metastasis and stages. P. micra infec...
Bacterial pathogenesisOral cancer
10.1038/S41467-025-57530-1
ISSN:2041-1723
IGF2BP1 phosphorylation in the disordered linkers regulates ribonucleoprotein condensate formation and RNA metabolism
Harald Hornegger•Aleksandra S. Anisimova•Adnan Muratovic•Benjamin Bourgeois•Elena Spinetti等 9 人
Nature Communications
2024
•2024/10/20
•Vol.15 No.1 p.1-26
The insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) is a conserved RNA-binding protein that regulates RNA stability, localization and translation. IGF2BP1 is part of various ribonucleoprotein (RNP) condensates. However, the mechanism that regulates its assembly into condensates remains...
RNA-binding proteinsSolution-state NMR
10.1038/S41467-024-53400-4
ISSN:2041-1723
The functional landscape of alternative splicing in hematopoietic lineage commitment
Xiao Hu•Jinrui Wang•Li Chen•Qin Yang•Manuel Tardaguila等 20 人
Nature Communications
2026
•2026/1/27
•Vol.17 No.1 p.20470
Alternative splicing (AS) is a ubiquitous post-transcriptional regulatory mechanism, that has greatly expanded the transcriptomic and proteomic diversity in vertebrates. While gene regulation of hematopoiesis has been extensively researched in vertebrates, the functions of species- and cell lineage-...
Alternative splicingHaematopoietic stem cellsMachine learningStem-cell differentiationSumoylation
10.1038/S41467-026-68811-8
ISSN:2041-1723
Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set
Ute Distler•Han Byul Yoo•Oliver Kardell•Dana Hein•Malte Sielaff等 39 人
Nature Communications
2025
•2025/10/2
•Vol.16 No.1 p.1-18
Human plasma is routinely collected during clinical care and constitutes a rich source of biomarkers for diagnostics and patient stratification. Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is a key method for plasma biomarker discovery, but the high dynamic range of plasma prote...
Mass spectrometryProteome informaticsProteomic analysisStandardizationTranslational research
10.1038/S41467-025-64501-Z
ISSN:2041-1723
CHAMP1 complex directs heterochromatin assembly and promotes homology-directed DNA repair
Feng Li•Tianpeng Zhang•Aleem Syed•Amira Elbakry•Noella Holmer等 9 人
Nature Communications
2025
•2025/2/17
•Vol.16 No.1 p.1-17
The CHAMP1 complex, a little-known but highly conserved protein complex consisting of CHAMP1, POGZ, and HP1α, is enriched in heterochromatin though its cellular function in these regions of the genome remain unknown. Here we show that the CHAMP complex promotes heterochromatin assembly at multiple c...
Double-strand DNA breaksHistone post-translational modificationsHomologous recombinationTelomeres
10.1038/S41467-025-56834-6
ISSN:2041-1723
Molecular mechanism underlying miR-204-5p regulation of adipose-derived stem cells differentiation into cells from three germ layers
Zhimin Wang•Meiyu Bi•Xiaoshu Zhe•Xiao Wang•Bai Dai等 9 人
Cell Death Discovery
2024
•2024/2/22
•Vol.10 No.1 p.1-14
The limited differentiation ability of adipose-derived stem cells (ADSCs) limits their application in stem cell therapy and regenerative medicine. Here, we explore the molecular mechanism by which miR-204-5p regulates ADSCs differentiation into cells derived from the three germ layers (i.e., adipocy...
Cell biologyDifferentiationEpigeneticsMesenchymal stem cellsStem-cell differentiation
10.1038/S41420-024-01852-4
ISSN:2058-7716
NUT1-Exo70A1 Regulates Xylem Vessel Development and Influences Water Use Efficiency in Maize
Tengfei Zhu•Yanyan Wang•Yijie Wang•Chen Wang•Yu Liu等 13 人
Nature Communications
2026
•2026/2/16
•Vol.17 No.1 p.28160
Efficient water uptake and transport through xylem vessels are essential for plant growth and development. The patterned secondary cell wall (SCW) structure of xylem vessels provides robust mechanical support to withstand the strong negative pressure generated by transpiration and facilitates long-d...
Agricultural geneticsCell wallDrought
10.1038/S41467-026-69436-7
ISSN:2041-1723
Identification of antiviral RNAi regulators, ILF3/DHX9, recruit at ZIKV stem loop B to protect against ZIKV induced microcephaly
Zhiwei Lei•Yu Gu•Ying Liu•Hailiang Liu•Xiaohua Lu等 17 人
Nature Communications
2025
•2025/2/26
•Vol.16 No.1 p.1-18
Zika virus (ZIKV) is a member of the Flaviviridae family and causes congenital microcephaly and Guillain–Barré syndrome. Currently, there is a lack of approved vaccines or therapies against ZIKV infection. In this study, we profile vRNA‒host protein interactomes at ZIKV stem‒loop B (SLB) and reveal ...
Viral host responseVirus–host interactions
10.1038/S41467-025-56859-X
ISSN:2041-1723
Profiling phagosome proteins identifies PD-L1 as a fungal-binding receptor
Kai Li•Avradip Chatterjee•Chen Qian•Katherine Lagree•Yang Wang等 10 人
Nature
2024
•2024/6/5
•00 p.1-8
Phagocytosis is the process by which myeloid phagocytes bind to and internalize potentially dangerous microorganisms1. During phagocytosis, innate immune receptors and associated signalling proteins are localized to the maturing phagosome compartment, forming an immune information processing hub bri...
Fungal host responsePattern recognition receptors
10.1038/S41586-024-07499-6
ISSN:0028-0836
RUVBL1 ubiquitination by DTL promotes RUVBL1/2-β-catenin-mediated transcriptional regulation of NHEJ pathway and enhances radiation resistance in breast cancer
Jie Tian•Mingxin Wen•Peng Gao•Maoxiao Feng•Guangwei Wei
Cell Death & Disease
2024
•2024/4/12
•Vol.15 No.4 p.1-15
Radiotherapy effectiveness in breast cancer is limited by radioresistance. Nevertheless, the mechanisms behind radioresistance are not yet fully understood. RUVBL1 and RUVBL2, referred to as RUVBL1/2, are crucial AAA+ ATPases that act as co-chaperones and are connected to cancer. Our research reveal...
BiomarkersBreast cancer
10.1038/S41419-024-06651-4
ISSN:2041-4889
Impaired AGO2/miR-185-3p/NRP1 axis promotes colorectal cancer metastasis
Xisheng Liu•Xiaole Meng•Xiao Peng•Qianlan Yao•Fangming Zhu等 13 人
Cell Death & Disease
2021
•2021/4/12
•Vol.12 No.4 p.1-15
Increasing evidence suggests that global downregulation of miRNA expression is a hallmark of human cancer, potentially due to defects in the miRNA processing machinery. In this study, we found that the protein expression of Argonaute 2 (AGO2), a key regulator of miRNA processing, was downregulated i...
Colorectal cancerProteomics
10.1038/S41419-021-03672-1
ISSN:2041-4889
De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation
M. Felicia Basilicata•Ange-Line Bruel•Giuseppe Semplicio•Claudia Isabelle Keller Valsecchi•Tuğçe Aktaş等 27 人
Nature Genetics
2018
•2018/9/17
•Vol.50 No.10 p.1442-1451
The etiological spectrum of ultra-rare developmental disorders remains to be fully defined. Chromatin regulatory mechanisms maintain cellular identity and function, where misregulation may lead to developmental defects. Here, we report pathogenic variations in MSL3, which encodes a member of the chr...
EpigeneticsEpigenomicsGene regulationNeurodevelopmental disorders
10.1038/S41588-018-0220-Y
ISSN:1061-4036
Vascular smooth muscle RhoA counteracts abdominal aortic aneurysm formation by modulating MAP4K4 activity
Molla Md Rasel•Shimizu Akio•Komeno Masahiro•Rahman Nor Idayu A.•Soh Joanne Ern Chi等 15 人
Communications Biology
2022
•2022/10/7
•Vol.5 No.1 p.1-17
Whether a small GTPase RhoA plays a role in the pathology of abdominal aortic aneurysm (AAA) has not been determined. We show here that RhoA expression is reduced in human AAA lesions, compared with normal areas. Furthermore, incidence of AAA formation is increased in vascular smooth muscle cell (VS...
AneurysmMechanisms of disease
10.1038/S42003-022-04042-Z
ISSN:2399-3642
Mitochondria contact lipid droplets through the mitochondrial import complex binding to lipid metabolism enzyme Ayr1
Sandra Heinen•Vitasta Tiku•Alexander Grevel•Marie Hugenroth•Lars Ellenrieder等 24 人
Nature Cell Biology
2026
•2026/2/26
•Vol.28 No.3 p.436-448
Mitochondria play central roles in the energetics and metabolism of eukaryotic cells. Their outer membrane is essential for protein transport, membrane dynamics, signalling and metabolic exchange with other cellular compartments. The mitochondrial import (MIM) complex functions as main translocase f...
Mitochondrial proteinsProtein translocation
10.1038/S41556-026-01890-3
ISSN:1465-7392
Structure-based design of potent and selective inhibitors of the HECT ligase NEDD4
Elena Maspero•Anna Cappa•Janine Weber•Paolo Trifirò•Raffaella Amici等 27 人
Communications Chemistry
2025
•2025/5/28
•Vol.8 No.1 p.1-13
Among the human E3 ubiquitin ligases, NEDD4 (Neural precursor cell expressed developmentally down-regulated 4) plays a critical role in development and cancer, making it a compelling therapeutic target. However, no specific NEDD4 inhibitors have advanced in drug development. In this study, we reveal...
Drug discovery and developmentMechanism of actionStructural biologyStructure-based drug design
10.1038/S42004-025-01557-4
ISSN:2399-3669
Low-dose metformin targets the lysosomal AMPK pathway through PEN2
Ma Teng•Tian Xiao•Zhang Baoding•Li Mengqi•Wang Yu等 35 人
Nature
2022
•2022/2/23
•00 p.1-7
Metformin, the most prescribed antidiabetic medicine, has shown other benefits such as anti-ageing and anticancer effects1–4. For clinical doses of metformin, AMP-activated protein kinase (AMPK) has a major role in its mechanism of action4,5; however, the direct molecular target of metformin remains...
Cell signallingMetabolism
10.1038/S41586-022-04431-8
ISSN:0028-0836
Primary tumors release ITGBL1-rich extracellular vesicles to promote distal metastatic tumor growth through fibroblast-niche formation
Qing Ji•Lihong Zhou•Hua Sui•Liu Yang•Xinnan Wu等 20 人
Nature Communications
2020
•2020/3/5
•Vol.11 No.1 p.1-18
Tumor metastasis is a hallmark of cancer. Metastatic cancer cells often reside in distal tissues and organs in their dormant state. Mechanisms underlying the pre-metastatic niche formation are poorly understood. Here we show that in a colorectal cancer (CRC) model, primary tumors release integrin be...
CancerGastrointestinal diseasesPrognostic markersTranslational research
10.1038/S41467-020-14869-X
ISSN:2041-1723
Autophagic extracellular vesicles (AEVs) are distinct from exosomes and play crucial roles in viral infections
Kedan Mao•Fangfang Huo•Hongqi Wei•Furong Wang•Sidong Xiong等 6 人
Nature Communications
2025
•2025/12/21
0Emerging evidence indicates important interconnections between autophagy and the secretion of small extracellular vesicles. However, our understanding of these secretory vesicles remains incomplete. Here, we identify a subtype of small extracellular vesicles, termed autophagic extracellular vesicles...
MacroautophagySecretionStress signalling
10.1038/S41467-025-67860-9
ISSN:2041-1723
Alkaloid binding to opium poppy major latex proteins triggers structural modification and functional aggregation
Ozber Natali•Carr Samuel C.•Morris Jeremy S.•Liang Siyu•Watkins Jacinta L.等 9 人
Nature Communications
2022
•2022/11/9
•Vol.13 No.1 p.1-16
Opium poppy accumulates copious amounts of several benzylisoquinoline alkaloids including morphine, noscapine, and papaverine, in the specialized cytoplasm of laticifers, which compose an internal secretory system associated with phloem throughout the plant. The contiguous latex includes an abundanc...
Plant cell biologySecondary metabolismX-ray crystallography
10.1038/S41467-022-34313-6
ISSN:2041-1723
Molecular sensing of mechano- and ligand-dependent adhesion GPCR dissociation
Scholz Nicole•Dahse Anne-Kristin•Kemkemer Marguerite•Bormann Anne•Auger Genevieve M.等 18 人
Nature
2023
•2023/3/8
•00 p.1-9
Adhesion G-protein-coupled receptors (aGPCRs) bear notable similarity to Notch proteins1, a class of surface receptors poised for mechano-proteolytic activation2–4, including an evolutionarily conserved mechanism of cleavage5–8. However, so far there is no unifying explanation for why aGPCRs are aut...
Developmental neurogenesisExtracellular signalling moleculesNeural patterningProteolysisReceptor pharmacology
10.1038/S41586-023-05802-5
ISSN:0028-0836
Brain proteomic atlas of alcohol use disorder in adult males
Pang-ning Teng•Waleed Barakat•Sophie M. Tran•Zoe M. Tran•Nicholas W. Bateman等 15 人
Translational Psychiatry
2023
•2023/10/13
•Vol.13 No.1 p.1-11
Alcohol use disorder (AUD) affects transcriptomic, epigenetic and proteomic expression in several organs, including the brain. There has not been a comprehensive analysis of altered protein abundance focusing on the multiple brain regions that undergo neuroadaptations occurring in AUD. We performed ...
AddictionMolecular neuroscience
10.1038/S41398-023-02605-0
ISSN:2158-3188
Divergent venom effectors correlate with ecological niche in neuropteran predators
Maike Laura Fischer•Henrike Schmidtberg•Olivia Tidswell•Benjamin Weiss•Ludwig Dersch等 10 人
Communications Biology
2024
•2024/8/13
•Vol.7 No.1 p.1-13
Neuropteran larvae are fierce predators that use venom to attack and feed on arthropod prey. Neuropterans have adapted to diverse and sometimes extreme habitats, suggesting their venom may have evolved accordingly, but the ecology and evolution of venom deployment in different families is poorly und...
EntomologyEvolutionary ecology
10.1038/S42003-024-06666-9
ISSN:2399-3642
Peptide-centric local stability assay (PELSA) for sensitive identification of ligand-targeting proteins and binding sites at proteome scale
Keyun Wang•Kejia Li•Jiayang Yan•Lianji Xue•Yanni Ma等 10 人
Nature Protocols
2026
•2026/4/22
•00 p.1-23
The peptide-centric local stability assay (PELSA) was developed to identify the protein targets and binding regions of diverse ligands at a proteome-wide scale. In this approach, the ligand is added to a cell lysate, and the proteins are digested for a short, defined time period using 0.5 mg ml−1 tr...
High-throughput screeningProteomic analysisTarget identification
10.1038/S41596-026-01354-W
ISSN:1754-2189
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
Two types of axonal muscarinic acetylcholine receptors mediate formation of saliva cocktail in the tick Ixodes ricinus
Cáinà Nìng•James J. Valdés•Lourdes Mateos-Hernández•Sabine Rakotobe•Lianet Abuin-Denis等 26 人
Nature Communications
2026
•2026/1/23
•Vol.17 No.1 p.28670
Hard ticks depend upon an ability to precisely and dynamically regulate their saliva to successfully evade host haemostatic and immune defences during extended blood feeding. Although pilocarpine, an exogenous muscarinic acetylcholine receptor (mAChR) agonist, can stimulate salivation experimentally...
ExcitabilityMolecular neuroscience
10.1038/S41467-026-68654-3
ISSN:2041-1723
In situ analysis of nanoparticle soft corona and dynamic evolution
Baimanov Didar•Wang Jing•Zhang Jun•Liu Ke•Cong Yalin等 14 人
Nature Communications
2022
•2022/9/14
•Vol.13 No.1 p.1-14
How soft corona, the protein corona’s outer layer, contributes to biological identity of nanomaterials is largely because capturing protein composition of the soft corona in situ remains challenging. We herein develop an in situ Fishing method that can monitor the dynamic formation of protein corona...
Cell–particle interactionsNanoparticlesProteomics
10.1038/S41467-022-33044-Y
ISSN:2041-1723
Temporal phosphoproteomics reveals circuitry of phased propagation in insulin signaling
Michael Turewicz•Christine Skagen•Sonja Hartwig•Stephan Majda•Kristina Thedinga等 18 人
Nature Communications
2025
•2025/2/12
•Vol.16 No.1 p.1-19
Insulin is a pleiotropic hormone that elicits its metabolic and mitogenic actions through numerous rapid and reversible protein phosphorylations. The temporal regulation of insulin’s intracellular signaling cascade is highly complex and insufficiently understood. We conduct a time-resolved analysis ...
BiochemistryProteomics
10.1038/S41467-025-56335-6
ISSN:2041-1723
ALKB-1-dependent tRNA methylation is required for efficient paternal mitochondrial elimination
Zhenhuan Luo•Yimin Li•Chenyang He•Dan Wu•Wenyu Dai等 13 人
Nature Communications
2026
•2026/1/29
•Vol.17 No.1 p.21440
Maternal mitochondrial inheritance is secured by mechanisms that exclude paternal mitochondrial DNA (mtDNA). While, epigenetic modifications are vital for spermatogenesis and embryo development, their roles in the paternal mitochondrial elimination (PME) remain poorly understood. Here, we identify A...
EmbryogenesisEpigenetics
10.1038/S41467-026-68813-6
ISSN:2041-1723
Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis
Isaac Park•Kwang-eun Kim•Jeesoo Kim•Ae-Kyeong Kim•Subin Bae等 18 人
Nature Chemical Biology
2023
•2023/10/26
•00 p.1-13
Targeting proximity-labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes. Here, we generated transgenic mice (MAX-Tg) expressing a mitochondrial matrix-targeted ascorbate peroxidase. Comparative analysis of matrix proteomes from the muscle tissues ...
Chemical toolsEnzyme mechanismsMass spectrometryMetabolismProteomics
10.1038/S41589-023-01452-W
ISSN:1552-4450
H2S-mediated protein S-sulfhydration modulates infectivity and autophagy in the rice blast fungus
Hong Hu•Mengyuan Qin•Jiening Zhang•Jintao Jiang•Zhiqin Su等 16 人
Nature Communications
2025
•2025/7/5
•Vol.16 No.1 p.1-18
Hydrogen sulfide (H2S) regulates cellular activities in plants and mammals through S-sulfhydration, a post-translational modification of proteins. The role of H2S and its molecular targets in fungi, however, remains unclear. Here we show that H2S, synthesized by cystathionine γ-lyase (CSE1) in the r...
Fungal pathogenesisPathogensPost-translational modifications
10.1038/S41467-025-61582-8
ISSN:2041-1723
The MFN1 and MFN2 mitofusins promote clustering between mitochondria and peroxisomes
Huo Yinbo•Sun Weiping•Shi Tiezhu•Gao Song•Zhuang Min
Communications Biology
2022
•2022/5/6
•Vol.5 No.1 p.1-11
Mitochondria and peroxisomes are two types of functionally close-related organelles, and both play essential roles in lipid and ROS metabolism. However, how they physically interact with each other is not well understood. In this study, we apply the proximity labeling method with peroxisomal protein...
MitochondriaPeroxisomes
10.1038/S42003-022-03377-X
ISSN:2399-3642
SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling
Sami T. Tuomivaara•Chin Fen Teo•Yuh Nung Jan•Arun P. Wiita•Lily Y. Jan
Communications Biology
2024
•2024/8/29
•Vol.7 No.1 p.1-16
To facilitate our understanding of proteome dynamics during signaling events, robust workflows affording fast time resolution without confounding factors are essential. We present Surface-exposed protein Labeling using PeroxidaSe, H2O2, and Tyramide-derivative (SLAPSHOT) to label extracellularly exp...
Membrane traffickingProteomic analysisProteomics
10.1038/S42003-024-06729-X
ISSN:2399-3642
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
FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer
Guneri-Sozeri Perihan Yagmur•Özden-Yılmaz Gülden•Kisim Asli•Cakiroglu Ece•Eray Aleyna等 10 人
Communications Biology
2023
•2023/2/20
•Vol.6 No.1 p.1-17
Bladder cancer is mostly present in the form of urothelium carcinoma, causing over 150,000 deaths each year. Its histopathological classification as muscle invasive (MIBC) and non-muscle invasive (NMIBC) is the most prominent aspect, affecting the prognosis and progression of this disease. In this s...
Bladder cancerEpigeneticsGene regulatory networks
10.1038/S42003-023-04561-3
ISSN:2399-3642
PTK2B promotes TBK1 and STING oligomerization and enhances the STING-TBK1 signaling
Yongfang Lin•Jing Yang•Qili Yang•Sha Zeng•Jiayu Zhang等 11 人
Nature Communications
2023
•2023/11/21
•Vol.14 No.1 p.1-17
TANK-binding kinase 1 (TBK1) is a key kinase in regulating antiviral innate immune responses. While the oligomerization of TBK1 is critical for its full activation, the molecular mechanism of how TBK1 forms oligomers remains unclear. Here, we show that protein tyrosine kinase 2 beta (PTK2B) acts as ...
Innate immunityPost-translational modifications
10.1038/S41467-023-43419-4
ISSN:2041-1723
DCAF7 recruits USP2 to facilitate hepatocellular carcinoma progression by suppressing clockophagy-induced ferroptosis
Honglv Jiang•Xiaohui Wang•Zhenhua Zhu•Cheng Song•Dan Li等 11 人
Cell Death & Disease
2025
•2025/8/28
•Vol.16 No.1 p.1-17
DDB1- and CUL4-associated factor 7 (DCAF7) has recently been identified as a critical regulator of tumorigenesis and a potential modulator of ferroptosis. However, the precise function of DCAF7 in regulating the progression of hepatocellular carcinoma (HCC) ferroptosis remains elusive. In this study...
AutophagyTumour biomarkers
10.1038/S41419-025-07977-3
ISSN:2041-4889
Zinc-dependent Zip7-MAZ-MYBL2 axis promotes prostate cancer metastasis
Qianxi Dong•Yunqiang Xiong•Situ Xiong•Ruize Yuan•Sheng Li等 12 人
Communications Biology
2026
•2026/4/20
0Zinc, an essential trace element for healthy prostate, which dramatically decreases during prostate tumorigenesis. Targeting the key zinc signaling will be a valuable strategy for PCa therapy. However, the underlying mechanisms are poorly understood. Here, we show that zinc is significantly decrease...
Cell migrationUrological cancer
10.1038/S42003-026-10074-6
ISSN:2399-3642
Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning
Jie Luo•Muge Molbay•Ying Chen•Izabela Horvath•Karoline Kadletz等 40 人
Nature Biotechnology
2025
•2025/1/14
•00 p.1-14
Efficient and accurate nanocarrier development for targeted drug delivery is hindered by a lack of methods to analyze its cell-level biodistribution across whole organisms. Here we present Single Cell Precision Nanocarrier Identification (SCP-Nano), an integrated experimental and deep learning pipel...
BiotechnologyFluorescence imaging
10.1038/S41587-024-02528-1
ISSN:1087-0156
Extracellular vesicles as structured vectors of quorum sensing signals influence aquatic microbial communities
Xueli Xu•Jingjing Lin•Li-Ting Zhu•Lu Long•Yifang Duan等 9 人
Npj Biofilms And Microbiomes
2026
•2026/1/31
•Vol.12 No.1 p.570
Quorum sensing (QS) orchestrates collective microbial behaviors and functional acclimatization through chemical communication. However, QS in natural waters is challenged by dilution, alkaline hydrolysis, and enzymatic degradation of freely dissolved autoinducers. Here, we demonstrate that extracell...
EcologyEnvironmental sciencesMicrobiology
10.1038/S41522-026-00924-W
ISSN:2055-5008
Molecular consequences of SARS-CoV-2 liver tropism
Wanner Nicola•Andrieux Geoffroy•Badia-i-Mompel Pau•Edler Carolin•Pfefferle Susanne等 37 人
Nature Metabolism
2022
•2022/3/28
•Vol.4 No.3 p.310-319
Extrapulmonary manifestations of COVID-19 have gained attention due to their links to clinical outcomes and their potential long-term sequelae1. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) displays tropism towards several organs, including the heart and kidney. Whether it also direc...
LiverMetabolismSARS-CoV-2
10.1038/S42255-022-00552-6
ISSN:2522-5812
PINX1 loss confers susceptibility to PARP inhibition in pan-cancer cells
Mei Huang•Xiaotong Zhu•Chen Wang•Liying He•Lei Li等 8 人
Cell Death & Disease
2024
•2024/8/22
•Vol.15 No.8 p.1-15
PARP1 is crucial in DNA damage repair, chromatin remodeling, and transcriptional regulation. The principle of synthetic lethality has effectively guided the application of PARP inhibitors in treating tumors carrying BRCA1/2 mutations. Meanwhile, PARP inhibitors have exhibited efficacy in BRCA-profic...
Cell biologyDNA damage and repairOncogenesTranscription
10.1038/S41419-024-07009-6
ISSN:2041-4889
Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ
Hemmerle Lucas•Maier Benjamin A.•Bortfeld-Miller Miriam•Ryback Birgitta•Gäbelein Christoph G.等 7 人
Nature Communications
2022
•2022/5/20
•Vol.13 No.1 p.1-14
Differences between species promote stable coexistence in a resource-limited environment. These differences can result from interspecies competition leading to character shifts, a process referred to as character displacement. While character displacement is often interpreted as a consequence of gen...
Microbial communitiesMicrobial ecology
10.1038/S41467-022-30469-3
ISSN:2041-1723
Seasonal variation in UVA light drives hormonal and behavioural changes in a marine annelid via a ciliary opsin
Vinoth Babu Veedin Rajan•N. Sören Häfker•Enrique Arboleda•Birgit Poehn•Thomas Gossenreiter等 15 人
Nature Ecology & Evolution
2021
•2021/1/11
•Vol.5 No.2 p.204-218
The right timing of animal physiology and behaviour ensures the stability of populations and ecosystems. To predict anthropogenic impacts on these timings, more insight is needed into the interplay between environment and molecular timing mechanisms. This is particularly true in marine environments....
Animal behaviourAnimal physiologyBehavioural ecologyMolecular ecologyNeuroscience
10.1038/S41559-020-01356-1
ISSN:2397-334X
Stellettin B renders glioblastoma vulnerable to poly (ADP-ribose) polymerase inhibitors via suppressing homology-directed repair
Peng Xin•Wang Yingying•Zhang Shaolu•Tao Zhennan•Dai Yuxiang等 10 人
Signal Transduction And Targeted Therapy
2023
•2023/3/22
•Vol.8 No.1 p.1-4
CNS cancerDrug developmentTarget identification
10.1038/S41392-023-01324-8
ISSN:2059-3635
A newly evolved small secretory peptide enhances mechanical properties of spider silk
Anqiang Jia•Yudi Mao•Tianfang Yang•Guoqing Zhang•Qingyuan Wang等 10 人
Nature Communications
2025
•2025/11/18
•Vol.16 No.1 p.100710
Spiders’ ability to spin foraging webs using silk from specialized glands represents a remarkable evolutionary innovation, yet the molecular evolution of silk glands remains unclear. Here, we investigated the evolution of silk glands in Araneoidea spiders through genomic and transcriptomic mining. A...
BiomaterialsEvolutionary developmental biologyMolecular biologyMolecular evolution
10.1038/S41467-025-65026-1
ISSN:2041-1723
High ploidy large cytoplasmic megakaryocytes are hematopoietic stem cells regulators and essential for platelet production
Heazlewood Shen Y.•Ahmad Tanveer•Cao Benjamin•Cao Huimin•Domingues Melanie等 22 人
Nature Communications
2023
•2023/4/13
•Vol.14 No.1 p.1-18
Megakaryocytes (MK) generate platelets. Recently, we and others, have reported MK also regulate hematopoietic stem cells (HSC). Here we show high ploidy large cytoplasmic megakaryocytes (LCM) are critical negative regulators of HSC and critical for platelet formation. Using a mouse knockout model (P...
Cell biologyHaematopoietic stem cellsStem cells
10.1038/S41467-023-37780-7
ISSN:2041-1723
Spatial distribution of the proteome in the human body and in cancers
Liang Yue•Wenhao Jiang•Sainan Li•Meng Luo•Ning Fan等 40 人
Nature
2026
•2026/6/17
•00 p.1-10
A detailed, spatially resolved quantitative map of the human proteome is essential for a deeper understanding of human biology and disease1–4. Here we present a comprehensive human proteomic landscape, generated by profiling more than 13,000 proteins across 2,856 samples using data-independent acqui...
ProteomicsSystems analysisTarget identificationTumour biomarkers
10.1038/S41586-026-10660-Y
ISSN:0028-0836
A glucose kinase-independent HK2 activity prevents TNF-induced cell death by phosphorylating RIPK1
Tianhao Zou•Ran Liu•Gengqiao Wang•Guoliang Wang•Zhengting Jiang等 15 人
Nature Communications
2025
•2025/11/13
•Vol.16 No.1 p.99790
Tumor necrosis factor (TNF)-induced RIPK1-mediated cell death is implicated in various human diseases. However, the mechanisms RIPK1-mediated cell death is regulated by metabolic processes remain unclear. Here, we identify hexokinase 2 (HK2), a critical regulator of glycolysis, as a suppressor of TN...
ApoptosisCell signallingPhosphorylation
10.1038/S41467-025-64939-1
ISSN:2041-1723
Enhanced validation of antibodies for research applications
Fredrik Edfors•Andreas Hober•Klas Linderbäck•Gianluca Maddalo•Alireza Azimi等 15 人
Nature Communications
2018
•2018/10/8
•Vol.9 No.1 p.1-10
There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that thes...
Assay systemsProteomics
10.1038/S41467-018-06642-Y
ISSN:2041-1723
APOE4 impairs macrophage lipophagy and promotes demyelination of spiral ganglion neurons in mouse cochleae
Junru Chen•Haibing Chen•Qinjun Wei•Yajie Lu•Tianming Wang等 10 人
Cell Death Discovery
2025
•2025/4/21
•Vol.11 No.1 p.1-10
The ApoE-ε4 gene is a well-established genetic risk factor for neurodegenerative diseases, such as Alzheimer’s disease and multiple sclerosis, which are characterized by axonal demyelination in the central nervous system. Recent studies have implicated ApoE-ε4 in age-related hearing loss (ARHL), sug...
AutophagyGene regulation
10.1038/S41420-025-02454-4
ISSN:2058-7716
Lactylation at lysine 145 fosters KAT8-TIP60 complex formation to promote p53 acetylation at lysine 120 and its pro-apoptotic function
Huashan Liu•Ze Li•Dongxu Lei•Hao Xie•Xuanhua Yang等 10 人
Nature Communications
2026
•2026/3/26
0p53 is crucial for cellular functions and disease mechanisms, yet effective clinical strategies targeting it remain challenging. Lactylation has emerged as a key factor in understanding disease pathology and offering therapeutic options. Herein, we identify lactylated KAT8 at lysine 145 (K145) as a ...
Cardiovascular biologyPost-translational modifications
10.1038/S41467-026-71108-5
ISSN:2041-1723
The parkin-γ-tubulin axis regulates epidermal homeostasis and is associated with the susceptibility to psoriasis
Yuanyuan Liu•Shaoze Yan•Jiaxuan Wang•Dan Dong•Shaodong Yan等 13 人
Cell Death & Differentiation
2026
•2026/2/27
•00 p.1-15
Psoriasis is an inflammatory skin disease marked by excessive proliferation of keratinocytes, and there is accumulating evidence indicating its association with Parkinson’s disease (PD). However, the molecular link between these two diseases remains elusive. Herein, we identify a potential role for ...
Cell biologyPathogenesis
10.1038/S41418-026-01693-X
ISSN:1350-9047
Wittig reagents for chemoselective sulfenic acid ligation enables global site stoichiometry analysis and redox-controlled mitochondrial targeting
Shi Yunlong•Fu Ling•Yang Jing•Carroll Kate S.
Nature Chemistry
2021
•2021/9/16
•00 p.1-11
Triphenylphosphonium ylides, known as Wittig reagents, are one of the most commonly used tools in synthetic chemistry. Despite their considerable versatility, Wittig reagents have not yet been explored for their utility in biological applications. Here we introduce a chemoselective ligation reaction...
Bioconjugate chemistryChemical modificationChemical toolsPost-translational modificationsProteomics
10.1038/S41557-021-00767-2
ISSN:1755-4330
Identification of structural and regulatory cell-shape determinants in Haloferax volcanii
Heather Schiller•Yirui Hong•Joshua Kouassi•Theopi Rados•Jasmin Kwak等 12 人
Nature Communications
2024
•2024/2/15
•Vol.15 No.1 p.1-15
Archaea play indispensable roles in global biogeochemical cycles, yet many crucial cellular processes, including cell-shape determination, are poorly understood. Haloferax volcanii, a model haloarchaeon, forms rods and disks, depending on growth conditions. Here, we used a combination of iterative p...
ActinArchaeal biologyCellular microbiology
10.1038/S41467-024-45196-0
ISSN:2041-1723
Cell density-dependent proteolysis by HtrA1 induces translocation of zyxin to the nucleus and increased cell survival
Fabio Sabino•Elizabeta Madzharova•Ulrich auf dem Keller
Cell Death & Disease
2020
•2020/8/21
•Vol.11 No.8 p.1-11
Proteases modulate critical processes in cutaneous tissue repair to orchestrate inflammation, cell proliferation and tissue remodeling. However, the functional consequences and implications in healing impairments of most cleavage events are not understood. Using iTRAQ-based Terminal Amine Isotopic L...
BiochemistryProteolysis
10.1038/S41419-020-02883-2
ISSN:2041-4889
Interspecies interactions drive bacterial proteome reorganization and emergent metabolism
Stephan Kamrad•Simran K. Aulakh•Simone Mozzachiodi•Sonja Blasche•David Scheidweiler等 12 人
Nature Ecology & Evolution
2026
•2026/3/31
•00 p.1-18
Species in microbial communities need to stave off competition and capitalize on new resources that become available because of metabolic activities of others. However, intra-cellular molecular changes that underpin these responses are understudied, preventing mechanistic insights into community fun...
Microbial communitiesEmergenceMicrobial ecology
10.1038/S41559-026-03030-4
ISSN:2397-334X
Lymphatic platelet thrombosis limits bone repair by precluding lymphatic transporting DAMPs
Yangkang Zheng•Lin Cong•Li Zhao•Pengyu Wang•Lianping Xing等 14 人
Nature Communications
2025
•2025/1/18
•Vol.16 No.1 p.1-25
In the musculoskeletal system, lymphatic vessels (LVs), which are interdigitated with blood vessels, travel and form an extensive transport network. Blood vessels in bone regulate osteogenesis and hematopoiesis, however, whether LVs in bone affect fracture healing is unclear. Here, we investigate th...
Acute inflammationApoptosisFracture repair
10.1038/S41467-025-56147-8
ISSN:2041-1723
SCARB2 drives hepatocellular carcinoma tumor initiating cells via enhanced MYC transcriptional activity
Feng Wang•Yang Gao•Situ Xue•Luyao Zhao•Huimin Jiang等 16 人
Nature Communications
2023
•2023/9/22
•Vol.14 No.1 p.1-20
CSCs (Cancer stem cells) with distinct metabolic features are considered to cause HCC (hepatocellular carcinoma) initiation, metastasis and therapeutic resistance. Here, we perform a metabolic gene CRISPR/Cas9 knockout library screen in tumorspheres derived from HCC cells and find that deletion of S...
AcetylationCancer stem cellsCancer therapy
10.1038/S41467-023-41593-Z
ISSN:2041-1723
The EIF3H-HAX1 axis increases RAF-MEK-ERK signaling activity to promote colorectal cancer progression
Huilin Jin•Xiaoling Huang•Qihao Pan•Ning Ma•Xiaoshan Xie等 16 人
Nature Communications
2024
•2024/3/21
•Vol.15 No.1 p.1-18
Eukaryotic initiation translation factor 3 subunit h (EIF3H) plays critical roles in regulating translational initiation and predicts poor cancer prognosis, but the mechanism underlying EIF3H tumorigenesis remains to be further elucidated. Here, we report that EIF3H is overexpressed in colorectal ca...
Cell signallingColon cancerOncogenes
10.1038/S41467-024-46521-3
ISSN:2041-1723
Oncometabolite 5-IP7 inhibits inositol 5-phosphatase to license E-cadherin endocytosis
Hongyun Zhang•Bobo Zhang•Yuebo Zhao•Yang Su•Yifan Peng等 23 人
Nature Chemical Biology
2025
•2025/8/26
•00 p.1-14
E-cadherin downregulation is an epithelial–mesenchymal transition hallmark canonically attributed to transcriptional repression. Here we delineate a metabolite-driven endocytic route of E-cadherin downregulation in inflammation-associated colorectal cancer (CRC). Specifically, IP6 kinase-2 (IP6K2), ...
CancerCell signallingKinasesMembrane traffickingPost-translational modifications
10.1038/S41589-025-02005-Z
ISSN:1552-4450
Rpl12 is a conserved ribophagy receptor
Yuting Chen•Jiaxin Hu•Pengwei Zhao•Jie Fang•Yingqi Kuang等 33 人
Nature Cell Biology
2025
•2025/2/11
•Vol.27 No.3 p.477-492
Ribophagy is a selective autophagic process that regulates ribosome turnover. Although NUFIP1 has been identified as a mammalian receptor for ribophagy, its homologues do not exist in yeast and nematodes. Here we demonstrate that Rpl12, a ribosomal large subunit protein, functions as a conserved rib...
AutophagosomesRibophagy
10.1038/S41556-024-01598-2
ISSN:1465-7392
N-terminal cysteine acetylation and oxidation patterns may define protein stability
Karen C. Heathcote•Thomas P. Keeley•Matti Myllykoski•Malin Lundekvam•Nina McTiernan等 10 人
Nature Communications
2024
•2024/6/25
•Vol.15 No.1 p.1-15
Oxygen homeostasis is maintained in plants and animals by O2-sensing enzymes initiating adaptive responses to low O2 (hypoxia). Recently, the O2-sensitive enzyme ADO was shown to initiate degradation of target proteins RGS4/5 and IL32 via the Cysteine/Arginine N-degron pathway. ADO functions by cata...
Post-translational modificationsProteolysisProteomics
10.1038/S41467-024-49489-2
ISSN:2041-1723
USP14 promotes tryptophan metabolism and immune suppression by stabilizing IDO1 in colorectal cancer
Shi Dongni•Wu Xianqiu•Jian Yunting•Wang Junye•Huang Chengmei等 18 人
Nature Communications
2022
•2022/9/26
•Vol.13 No.1 p.1-18
Indoleamine 2,3 dioxygenase 1 (IDO1) is an attractive target for cancer immunotherapy. However, IDO1 inhibitors have shown disappointing therapeutic efficacy in clinical trials, mainly because of the activation of the aryl hydrocarbon receptor (AhR). Here, we show a post-transcriptional regulatory m...
Cancer metabolismCancer microenvironmentColon cancer
10.1038/S41467-022-33285-X
ISSN:2041-1723
Cryo-EM captures early ribosome assembly in action
Qin Bo•Lauer Simon M.•Balke Annika•Vieira-Vieira Carlos H.•Bürger Jörg等 10 人
Nature Communications
2023
•2023/2/17
•Vol.14 No.1 p.1-10
Ribosome biogenesis is a fundamental multi-step cellular process in all domains of life that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. To obtain insights into the still unexplored early assembly phase of the bacterial 50S subunit...
Cryoelectron microscopyRNA
10.1038/S41467-023-36607-9
ISSN:2041-1723
SERBP1-PCIF1 complex-controlled m6Am modification in glutamatergic neurons of the primary somatosensory cortex is required for neuropathic pain in mice
Yue Huang•Gan Ma•Shan Xie•Runa Wei•Ya Liu等 18 人
Nature Communications
2025
•2025/8/5
•Vol.16 No.1 p.1-22
Nerve injury-induced changes in pain-associated genes contribute to genesis of neuropathic pain and comorbid anxiety. Phosphorylated CTD interacting factor-1 (PCIF1)-triggered N6, 2′-O-dimethyladenosine (m6Am) mRNA modification represents an additional layer of gene regulation. However, the role of ...
Epigenetics and behaviourSensory processing
10.1038/S41467-025-62565-5
ISSN:2041-1723
A single mutation in nonstructural protein 1 is critical for the adaptive evolution of influenza B virus
Pengtao Jiao•Xiaoxiao Jia•Xiaoyuan Bai•Yuna Zhao•Runshan Lin等 13 人
Nature Communications
2026
•2026/3/2
•Vol.17 No.1 p.33530
Influenza B virus (IBV) has circulated in the human population for a long time, yet the evolutionary mechanisms responsible for host adaptation remain poorly understood. Here we show that recent IBV strains exhibit an enhanced ability to evade the innate immune response and an increased replication ...
Influenza virusMicrobiology
10.1038/S41467-026-70211-X
ISSN:2041-1723
The dental proteome of Homo antecessor
Frido Welker•Jazmín Ramos-Madrigal•Petra Gutenbrunner•Meaghan Mackie•Shivani Tiwary等 26 人
Nature
2020
•2020/4/1
•Vol.580 No.7802 p.235-238
The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1–5. For the oldest remains, the molecular study of the...
Biological anthropologyEvolutionary biologyEvolutionary geneticsProteomic analysis
10.1038/S41586-020-2153-8
ISSN:0028-0836
Multi-omics elucidation of KDM5C, KDM6A, and KMT2B roles in cancer epigenetic dysregulation and transcriptional reprogramming
Tengjiao Li•Lichen Wang•Shoufeng Duan•Xinyu Cui•Chunqing Fu等 7 人
Communications Biology
2025
•2025/12/2
0Histone-modifying enzymes (HMEs) are critical regulators of tumorigenesis through epigenetic reprogramming. While mutations in HMEs are recognized drivers of cancer epigenome dysregulation, systematic comparative analyses of their mutational impacts and functional divergence across malignancies rema...
Cancer genomicsEpigenetics
10.1038/S42003-025-09305-Z
ISSN:2399-3642
Methylation-modulated PFTK1 regulates gefitinib resistance via Wnt/β-catenin signaling in EGFR mutant non-small-cell lung cancer cells
Xiaoting Jia•Jingjie Tian•Pingping Chen•Jing Dong•Lei Li等 10 人
Communications Biology
2024
•2024/12/19
•Vol.7 No.1 p.1-12
Inevitable gefitinib resistance is the biggest bottleneck in current treatment and the mechanisms are not fully understood. Here, we observe that PFTK1 (also named CDK14) is significantly enhanced in NSCLC with gefitinib resistance. And the upregulation of PFTK1 is negatively associated with progres...
Lung cancerTargeted therapies
10.1038/S42003-024-07339-3
ISSN:2399-3642
Counteracting FOX proteins epigenetically control the herpesvirus lytic-latent balance
Yuhang Xiang•Xiyuan Yang•Juncheng Zhang•Fujun Hou•Yue Deng等 18 人
Nature Communications
2026
•2026/2/2
•Vol.17 No.1 p.22560
The lytic-latent balance is a major viral persistence strategy and obstacle to curing viral diseases, yet its mechanisms remain poorly understood. Following lytic infection in non-neuronal cells, herpes simplex virus (HSV) establishes latency specifically in neurons and is reactivated by stresses. H...
Gene silencingHerpes virusViral infection
10.1038/S41467-026-68915-1
ISSN:2041-1723
Noninvasive urinary protein signatures associated with colorectal cancer diagnosis and metastasis
Sun Yulin•Guo Zhengguang•Liu Xiaoyan•Yang Lijun•Jing Zongpan等 24 人
Nature Communications
2022
•2022/5/19
•Vol.13 No.1 p.1-15
Currently, imaging, fecal immunochemical tests (FITs) and serum carcinoembryonic antigen (CEA) tests are not adequate for the early detection and evaluation of metastasis and recurrence in colorectal cancer (CRC). To comprehensively identify and validate more accurate noninvasive biomarkers in urine...
Colorectal cancerDiagnostic markersPredictive markers
10.1038/S41467-022-30391-8
ISSN:2041-1723
Regulation of the unfolded protein response through ATF4 and FAM129A in prostate cancer
Nora Pällmann•Marte Livgård•Martina Tesikova•Hatice Zeynep Nenseth•Erman Akkus等 20 人
Oncogene
2019
•2019/7/16
•Vol.38 No.35 p.6301-6318
Cancer cells exploit many of the cellular adaptive responses to support their survival needs. One such critical pathway in eukaryotic cells is the unfolded protein response (UPR) that is important in normal physiology as well as disease states, including cancer. Since UPR can serve as a lever betwee...
CancerTarget identification
10.1038/S41388-019-0879-2
ISSN:0950-9232
The role of zinc in the adaptive evolution of polar phytoplankton
Ye Naihao•Han Wentao•Toseland Andrew•Wang Yitao•Fan Xiao等 16 人
Nature Ecology & Evolution
2022
•2022/6/2
•00 p.1-14
Zinc is an essential trace metal for oceanic primary producers with the highest concentrations in polar oceans. However, its role in the biological functioning and adaptive evolution of polar phytoplankton remains enigmatic. Here, we have applied a combination of evolutionary genomics, quantitative ...
Microbial biooceanographyMolecular evolution
10.1038/S41559-022-01750-X
ISSN:2397-334X
Serine 25 phosphorylation inhibits RIPK1 kinase-dependent cell death in models of infection and inflammation
Yves Dondelinger•Tom Delanghe•Dario Priem•Meghan A. Wynosky-Dolfi•Daniel Sorobetea等 15 人
Nature Communications
2019
•2019/4/15
•Vol.10 No.1 p.1-16
RIPK1 regulates cell death and inflammation through kinase-dependent and -independent mechanisms. As a scaffold, RIPK1 inhibits caspase-8-dependent apoptosis and RIPK3/MLKL-dependent necroptosis. As a kinase, RIPK1 paradoxically induces these cell death modalities. The molecular switch between RIPK1...
ApoptosisCell death and immune responseNecroptosisPhosphorylation
10.1038/S41467-019-09690-0
ISSN:2041-1723
Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells
Kubitz Lea•Bitsch Sebastian•Zhao Xiyan•Schmitt Kerstin•Deweid Lukas等 10 人
Communications Biology
2022
•2022/7/4
•Vol.5 No.1 p.1-14
Proximity-dependent biotinylation (PDB) combined with mass spectrometry analysis has established itself as a key technology to study protein-protein interactions in living cells. A widespread approach, BioID, uses an abortive variant of the E. coli BirA biotin protein ligase, a quite bulky enzyme wi...
EnzymesProteomic analysis
10.1038/S42003-022-03604-5
ISSN:2399-3642
Multiomic analysis of stretched osteocytes reveals processes and signalling linked to bone regeneration and cancer
Lívia Santos•Aslihan Ugun-Klusek•Clare Coveney•David J. Boocock
Npj Regenerative Medicine
2021
•2021/6/7
•Vol.6 No.1 p.1-7
Exercise is a non-pharmacological intervention that can enhance bone regeneration and improve the management of bone conditions like osteoporosis or metastatic bone cancer. Therefore, it is gaining increasing importance in an emerging area of regenerative medicine—regenerative rehabilitation (RR). O...
Bone cancerFracture repairRegenerative medicine
10.1038/S41536-021-00141-3
ISSN:2057-3995
Structural and functional consequences of NEDD8 phosphorylation
Stuber Katrin•Schneider Tobias•Werner Jill•Kovermann Michael•Marx Andreas等 6 人
Nature Communications
2021
•2021/10/12
•Vol.12 No.1 p.1-15
Ubiquitin (Ub) and Ub-like proteins (Ubls) such as NEDD8 are best known for their function as covalent modifiers of other proteins but they are also themselves subject to post-translational modifications including phosphorylation. While functions of phosphorylated Ub (pUb) have been characterized, t...
NeddylationPhosphorylationProteomicsSolution-state NMR
10.1038/S41467-021-26189-9
ISSN:2041-1723
PCM1 orchestrates centrosomal and flagellar protein transport to promote sperm maturation
Zicong Huang•Runduan Yi•Xixian Cen•Hanbin Zhang•Minyu Xie等 17 人
Communications Biology
2025
•2025/6/7
•Vol.8 No.1 p.1-16
Centriolar satellites facilitate the delivery of proteins required for centrosome assembly and function, and rely on the nucleation of the scaffold protein pericentriolar material 1 (PCM1). During sperm maturation, centrosomes undergo remodeling to facilitate neckpiece formation and flagellogenesis....
Developmental biologyInfertility
10.1038/S42003-025-08319-X
ISSN:2399-3642
Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks
Müller Maik•Gräbnitz Fabienne•Barandun Niculò•Shen Yang•Wendt Fabian等 21 人
Nature Communications
2021
•2021/12/2
•Vol.12 No.1 p.1-17
The molecular nanoscale organization of the surfaceome is a fundamental regulator of cellular signaling in health and disease. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would unlock theranostic opportunities to target prot...
Chemical toolsExtracellular signalling moleculesProtein–protein interaction networksTarget identification
10.1038/S41467-021-27280-X
ISSN:2041-1723
Cpt1a Drives primed-to-naïve pluripotency transition through lipid remodeling
Zhaoyi Ma•Xingnan Huang•Junqi Kuang•Qiannan Wang•Yue Qin等 17 人
Communications Biology
2024
•2024/9/30
•Vol.7 No.1 p.1-15
Metabolism has been implicated in cell fate determination, particularly through epigenetic modifications. Similarly, lipid remodeling also plays a role in regulating cell fate. Here, we present comprehensive lipidomics analysis during BMP4-driven primed to naive pluripotency transition or BiPNT and ...
EpigenomicsLipidomicsPluripotencyReprogramming
10.1038/S42003-024-06874-3
ISSN:2399-3642
Proteomics-driven noninvasive screening of circulating serum protein panels for the early diagnosis of hepatocellular carcinoma
Xiaohua Xing•Linsheng Cai•Jiahe Ouyang•Fei Wang•Zongman Li等 13 人
Nature Communications
2023
•2023/12/18
•Vol.14 No.1 p.1-15
Early diagnosis of hepatocellular carcinoma (HCC) lacks highly sensitive and specific protein biomarkers. Here, we describe a staged mass spectrometry (MS)-based discovery-verification-validation proteomics workflow to explore serum proteomic biomarkers for HCC early diagnosis in 1002 individuals. M...
Diagnostic markersHepatocellular carcinomaTumour biomarkers
10.1038/S41467-023-44255-2
ISSN:2041-1723
Alpha-glucans from bacterial necromass indicate an intra-population loop within the marine carbon cycle
Irena Beidler•Nicola Steinke•Tim Schulze•Chandni Sidhu•Daniel Bartosik等 23 人
Nature Communications
2024
•2024/5/14
•Vol.15 No.1 p.1-15
Phytoplankton blooms provoke bacterioplankton blooms, from which bacterial biomass (necromass) is released via increased zooplankton grazing and viral lysis. While bacterial consumption of algal biomass during blooms is well-studied, little is known about the concurrent recycling of these substantia...
Carbon cycleMicrobial ecologyWater microbiology
10.1038/S41467-024-48301-5
ISSN:2041-1723
CFAP100 couples microtubule glutamylation to spindle pole integrity in keratinocytes to promote epidermal development
Shuang Sun•Zhaoying Wang•Zhaoyang Xu•Zhengfeng Wang•Jia Sun等 10 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-14
Despite the importance of keratinocytes in epidermal structure and function, the molecular mechanisms regulating the division of these cells remain poorly understood. Herein, we demonstrate an essential role for cilia and flagella associated protein 100 (CFAP100) in keratinocyte division. Cfap100-kn...
Cell proliferationMitotic spindlePost-translational modifications
10.1038/S41467-025-60677-6
ISSN:2041-1723
Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity
Joanna Cyrta•Anke Augspach•Maria Rosaria De Filippo•Davide Prandi•Phillip Thienger等 32 人
Nature Communications
2020
•2020/11/3
•Vol.11 No.1 p.1-16
Advanced prostate cancer initially responds to hormonal treatment, but ultimately becomes resistant and requires more potent therapies. One mechanism of resistance observed in around 10–20% of these patients is lineage plasticity, which manifests in a partial or complete small cell or neuroendocrine...
Cancer epigeneticsProstate cancer
10.1038/S41467-020-19328-1
ISSN:2041-1723
Leucine aminopeptidase1 controls egg deposition and hatchability in male Aedes aegypti mosquitoes
Xiaomei Sun•Xueli Wang•Kai Shi•Xiangyang Lyu•Jian Sun等 7 人
Nature Communications
2024
•2024/1/2
•Vol.15 No.1 p.1-15
Aedes aegypti are vectors for several arboviruses infecting hundreds of millions of people annually. Controlling mosquito populations by regulating their reproduction is a potential strategy to minimize viral transmission in the absence of effective antiviral therapies or vaccines. Here, we demonstr...
EmbryologyEntomologyPopulation dynamicsViral vectors
10.1038/S41467-023-44444-Z
ISSN:2041-1723
Noncanonical assembly, neddylation and chimeric cullin–RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex
Daniel Horn-Ghetko•Linus V. M. Hopf•Ishita Tripathi-Giesgen•Jiale Du•Sebastian Kostrhon等 14 人
Nature Structural & Molecular Biology
2024
•2024/4/11
•00 p.1-12
Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, ‘cullin–RING’ and ‘RBR’, are individually found in several hundred human E3 ligases, and collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex with RBX1 (also ...
Electron microscopyEnzyme mechanismsNeddylationUbiquitylation
10.1038/S41594-024-01257-Y
ISSN:1545-9993
Human ANP32A/B are SUMOylated and utilized by avian influenza virus NS2 protein to overcome species-specific restriction
Liuke Sun•Xing Guo•Mengmeng Yu•Xue-Feng Wang•Huiling Ren等 6 人
Nature Communications
2024
•2024/12/30
•Vol.15 No.1 p.1-19
Human ANP32A/B (huANP32A/B) poorly support the polymerase activity of avian influenza viruses (AIVs), thereby limiting interspecies transmission of AIVs from birds to humans. The SUMO-interacting motif (SIM) within NS2 promotes the adaptation of AIV polymerase to huANP32A/B via a yet undisclosed mec...
Influenza virusVirus–host interactions
10.1038/S41467-024-55034-Y
ISSN:2041-1723
Fluorescence imaging sheds light on the immune evasion mechanisms of hepatic stellate cells mediated by superoxide anion
Yuantao Mao•Chuanchen Wu•Xin Wang•Fanghui Zhang•Xinru Qi等 8 人
Communications Biology
2024
•2024/5/10
•Vol.7 No.1 p.1-9
Whether and how the reactive oxygen species generated by hepatic stellate cells (HSCs) promote immune evasion of hepatocellular carcinoma (HCC) remains mysterious. Therefore, investigating the function of superoxide anion (O2•−), the firstly generated reactive oxygen species, during the immune evasi...
Cancer microenvironmentChemical toolsImmune evasion
10.1038/S42003-024-06245-Y
ISSN:2399-3642
PHGDH arginine methylation by PRMT1 promotes serine synthesis and represents a therapeutic vulnerability in hepatocellular carcinoma
Wang Kui•Luo Li•Fu Shuyue•Wang Mao•Wang Zihao等 14 人
Nature Communications
2023
•2023/2/23
•Vol.14 No.1 p.1-18
Serine synthesis is crucial for tumor growth and survival, but its regulatory mechanism in cancer remains elusive. Here, using integrative metabolomics and transcriptomics analyses, we show a heterogeneity between metabolite and transcript profiles. Specifically, the level of serine in hepatocellula...
Cancer metabolismHepatocellular carcinomaMethylation
10.1038/S41467-023-36708-5
ISSN:2041-1723
Nuclear mitochondrial acetyl-CoA acetyltransferase 1 orchestrates natural killer cell-dependent antitumor immunity in colorectal cancer
Chen Wei•Kun Liao•Hao-Jie Chen•Zi-Xuan Xiao•Qi Meng等 16 人
Signal Transduction And Targeted Therapy
2025
•2025/4/28
•Vol.10 No.1 p.1-17
Tumor metabolism often interferes with the immune microenvironment. Although natural killer (NK) cells play pivotal roles in antitumor immunity, the connection between NK cells and tumor metabolism remains unclear. Our systematic analysis of multiomics data and survival data from colorectal cancer (...
Cancer metabolismCancer microenvironmentGastrointestinal cancerTumour immunology
10.1038/S41392-025-02221-Y
ISSN:2059-3635
Proteome-wide ligandability maps of drugs with diverse cysteine-reactive chemotypes
Caiping Tian•Lu Sun•Keke Liu•Ling Fu•Yi Zhang等 8 人
Nature Communications
2025
•2025/5/26
•Vol.16 No.1 p.1-16
Covalent drug discovery has experienced a revival since the 2013 approval of the first cysteine-targeting kinase inhibitors. Many drugs that were discovered by serendipity also possess the ability to react with cysteine residues, leading to interactions with multiple proteins. This widespread intera...
ProteomicsTarget identification
10.1038/S41467-025-60068-X
ISSN:2041-1723
Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes
Aditya S. Paul•Alexandra Miliu•Joao A. Paulo•Jonathan M. Goldberg•Arianna M. Bonilla等 15 人
Nature Communications
2020
•2020/7/15
•Vol.11 No.1 p.1-13
Asexual proliferation of the Plasmodium parasites that cause malaria follows a developmental program that alternates non-canonical intraerythrocytic replication with dissemination to new host cells. We carried out a functional analysis of the Plasmodium falciparum homolog of Protein Phosphatase 1 (P...
Parasite biologyParasite development
10.1038/S41467-020-17306-1
ISSN:2041-1723
The TRIM3/TLR3 axis overrides IFN-β feedback inhibition to suppress NSCLC progression
Jianyu Xu•Qianfang Hu•Ying Zhu•Qian Liu•Feng Wang等 8 人
Cell Death & Disease
2026
•2026/1/16
•Vol.17 No.1 p.440
Interferon-beta (IFN-β) has potent antitumor activity, but its clinical therapeutic potential is undermined by intrinsic negative feedback loops that suppress IFN-β production. However, the feedback mechanisms regulating IFN-β homeostasis in non-small cell lung cancer (NSCLC) remain unclear. We foun...
Non-small-cell lung cancerUbiquitylation
10.1038/S41419-025-08265-W
ISSN:2041-4889
Apical anchorage and stabilization of subpellicular microtubules by apical polar ring ensures Plasmodium ookinete infection in mosquito
Qian Pengge•Wang Xu•Guan Cuirong•Fang Xin•Cai Mengya等 12 人
Nature Communications
2022
•2022/12/3
•Vol.13 No.1 p.1-23
Morphogenesis of many protozoans depends on a polarized establishment of cortical cytoskeleton containing the subpellicular microtubules (SPMTs), which are apically nucleated and anchored by the apical polar ring (APR). In malaria parasite Plasmodium, APR emerges in the host-invading stages, includi...
Parasite biologyParasite development
10.1038/S41467-022-35270-W
ISSN:2041-1723
TGFβ-Smad3 signaling restores cell-autonomous Srsf1-mediated splicing of fibronectin in aged skeletal muscle stem cells
Yuguo Liu•Svenja C. Schüler•Simon Dumontier•Frederic Balg•Sonia Bedard等 9 人
Nature Communications
2025
•2025/11/21
0Loss of Fibronectin (FN) from the skeletal muscle stem cell (MuSC) niche represents a root cause of regenerative failure in aging. While FN has pleiotropic functions during healthy skeletal muscle regeneration, it remains unclear how aging affects its spatiotemporal specificity for MuSCs. Here, we d...
AgeingMuscle stem cellsStem-cell niche
10.1038/S41467-025-66582-2
ISSN:2041-1723
RIPK2 promotes colorectal cancer metastasis by protecting YAP degradation from ITCH-mediated ubiquitination
Chen Lu•Hongda Liu•Tianyu Liu•Sizheng Sun•Yanan Zheng等 14 人
Cell Death & Disease
2025
•2025/4/4
•Vol.16 No.1 p.1-16
Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide, making the exploration of metastatic mechanisms crucial for therapeutic advancements. In this study, we identified receptor-interacting protein kinase 2 (RIPK2) as an independent risk factor for poor CRC prognosis...
OncogenesUbiquitylation
10.1038/S41419-025-07599-9
ISSN:2041-4889
An oncopeptide regulates m 6 A recognition by the m 6 A reader IGF2BP1 and tumorigenesis
Song Zhu•Ji-Zhong Wang•De Chen•Yu-Tian He•Nan Meng等 10 人
Nature Communications
2020
•2020/4/3
•Vol.11 No.1 p.1-14
N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic RNAs. The biological importance of m6A relies on m6A readers, which control mRNA fate and function. However, it remains unexplored whether additional regulatory subunits of m6A readers are involved in the m6A recognition on RN...
EpigeneticsNon-coding RNAs
10.1038/S41467-020-15403-9
ISSN:2041-1723
Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage
Evi Goulielmaki•Anna Ioannidou•Maria Tsekrekou•Kalliopi Stratigi•Ioanna K. Poutakidou等 13 人
Nature Communications
2020
•2020/1/2
•Vol.11 No.1 p.1-18
DNA damage and metabolic disorders are intimately linked with premature disease onset but the underlying mechanisms remain poorly understood. Here, we show that persistent DNA damage accumulation in tissue-infiltrating macrophages carrying an ERCC1-XPF DNA repair defect (Er1F/−) triggers Golgi dispe...
Genomic instabilityMetabolic syndrome
10.1038/S41467-019-13894-9
ISSN:2041-1723
Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway
Yan Yan•Jun Xiao•Fengtao Huang•Wei Xian•Bingbing Yu等 18 人
Nature Microbiology
2024
•2024/4/22
•00 p.1-13
The cyclic-oligonucleotide-based anti-phage signalling system (CBASS) is a type of innate prokaryotic immune system. Composed of a cyclic GMP–AMP synthase (cGAS) and CBASS-associated proteins, CBASS uses cyclic oligonucleotides to activate antiviral immunity. One major class of CBASS contains a homo...
Enzyme mechanismsPhage biologyUbiquitylation
10.1038/S41564-024-01684-Z
ISSN:2058-5276
Hierarchical helical carbon nanotube fibre as a bone-integrating anterior cruciate ligament replacement
Wang Liyuan•Wan Fang•Xu Yifan•Xie Songlin•Zhao Tiancheng等 22 人
Nature Nanotechnology
2023
•2023/5/4
•00 p.1-9
High rates of ligament damage require replacements; however, current synthetic materials have issues with bone integration leading to implant failure. Here we introduce an artificial ligament that has the required mechanical properties and can integrate with the host bone and restore movement in ani...
BiomaterialsNanoscale materials
10.1038/S41565-023-01394-3
ISSN:1748-3387
RH3 enhances antiviral defense by facilitating small RNA loading into Argonaute 2 at endoplasmic reticulum–chloroplast membrane contact sites
Juan Huang•Juan Du•Yan Liu•Lu Lu•Yanzhuo Xu等 22 人
Nature Communications
2025
•2025/2/25
•Vol.16 No.1 p.1-17
While RNA silencing is crucial for plant resistance against viruses, the cellular connections between RNA silencing and antiviral responses in plants remain poorly understood. In this study, we aim to investigate this relationship by examining the subcellular localization of small RNA loading and vi...
Cell biologyChloroplastsPlant immunity
10.1038/S41467-025-57296-6
ISSN:2041-1723
Lactylation of NAT10 promotes N4‐acetylcytidine modification on tRNASer-CGA-1-1 to boost oncogenic DNA virus KSHV reactivation
Qin Yan•Jing Zhou•Yang Gu•Wenjing Huang•Mingpeng Ruan等 11 人
Cell Death & Differentiation
2024
•2024/6/15
•00 p.1-13
N4-acetylcytidine (ac4C), a conserved but recently rediscovered RNA modification on tRNAs, rRNAs and mRNAs, is catalyzed by N-acetyltransferase 10 (NAT10). Lysine acylation is a ubiquitous protein modification that controls protein functions. Our latest study demonstrates a NAT10-dependent ac4C modi...
Infectious diseasesMicrobiology
10.1038/S41418-024-01327-0
ISSN:1350-9047
ARIH1 signaling promotes anti-tumor immunity by targeting PD-L1 for proteasomal degradation
Youqian Wu•Chao Zhang•Xiaolan Liu•Zhengfu He•Bing Shan等 24 人
Nature Communications
2021
•2021/4/20
•Vol.12 No.1 p.1-14
Cancer expression of PD-L1 suppresses anti-tumor immunity. PD-L1 has emerged as a remarkable therapeutic target. However, the regulation of PD-L1 degradation is not understood. Here, we identify several compounds as inducers of PD-L1 degradation using a high-throughput drug screen. We find EGFR inhi...
Cell biologyMolecular biology
10.1038/S41467-021-22467-8
ISSN:2041-1723
Retinal-detachment repair and vitreous-like-body reformation via a thermogelling polymer endotamponade
Zengping Liu•Sing Shy Liow•Siew Li Lai•Asfa Alli-Shaik•Graham E. Holder等 19 人
Nature Biomedical Engineering
2019
•2019/4/8
•Vol.3 No.8 p.598-610
Internal-tamponade agents are crucial surgical adjuncts in vitreoretinal surgery. Clinically used endotamponade agents act through buoyancy forces, yet can result in prolonged post-operative positioning, temporary loss of vision, raised intra-ocular pressure, cataract formation or the need for addit...
Biomedical materialsRegenerative medicineTranslational research
10.1038/S41551-019-0382-7
ISSN:2157-846X
One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes
Zilu Ye•Pierre Sabatier•Javier Martin-Gonzalez•Akihiro Eguchi•Maico Lechner等 13 人
Nature Communications
2024
•2024/3/20
•Vol.15 No.1 p.1-10
Mass spectrometry (MS)-based proteomics workflows typically involve complex, multi-step processes, presenting challenges with sample losses, reproducibility, requiring substantial time and financial investments, and specialized skills. Here we introduce One-Tip, a proteomics methodology that seamles...
Proteomic analysisProteomics
10.1038/S41467-024-46777-9
ISSN:2041-1723
Inhibition of circulating glycocholic acid-regulated signaling potentiates immune checkpoint therapy in colorectal cancer
Senlin Zhao•Jing Zhang•Yushuai Mi•Bin Quan•Zijuan Hu等 14 人
Nature Communications
2026
•2026/4/4
0Serum bile acids (BAs) emerge as risk factors for cancer, but their roles in colorectal cancer (CRC) remain unclear. We show that glycocholic acid (GCA), a primary BA, is elevated in the serum of CRC patients. In a mouse CRC model, GCA promotes tumor programmed death-ligand 1 (PD-L1) expression in t...
Colorectal cancerImmune evasion
10.1038/S41467-026-71403-1
ISSN:2041-1723
Reduced BCL2 level in astrocytes contributes to blood-brain barrier disruption in the striatum of offspring exposed to maternal preeclampsia
Jiashuo Zhang•Mengting Zhang•Zhengyang Zhao•Min Xie•Menghan Wei等 14 人
Molecular Psychiatry
2026
•2026/6/2
•00 p.1-12
Maternal preeclampsia (PE) contributes to neurodevelopmental disorders. However, the underlying molecular mechanism remains unclear. We investigated the potential biological regulatory mechanisms by establishing an animal model and primary cell culture. Data from the Adolescent Brain Cognitive Devel...
NeurosciencePsychiatric disorders
10.1038/S41380-026-03669-2
ISSN:1359-4184
A comprehensive proteomic analysis of umbilical cord blood supports COVID-19 vaccination before pregnancy
Jianbin Guo•Xiaoyue Tang•Roujie Huang•Jiangfeng Liu•Lan Zhu
Signal Transduction And Targeted Therapy
2024
•2024/11/20
•Vol.9 No.1 p.1-3
InfectionInfectious diseasesReproductive disordersVaccines
10.1038/S41392-024-02024-7
ISSN:2059-3635
GNG5 is a novel regulator of Aβ42 production in Alzheimer’s disease
Chunyuan Li•Yan Yang•Shiqi Luo•Wenying Qiu•Xia Wang等 6 人
Cell Death & Disease
2024
•2024/11/11
•Vol.15 No.11 p.1-21
The therapeutic options for Alzheimer’s disease (AD) are limited, underscoring the critical need for finding an effective regulator of Aβ42 production. In this study, with 489 human postmortem brains, we revealed that homotrimer G protein subunit gamma 5 (GNG5) expression is upregulated in the hippo...
Cognitive neuroscienceNeurological disorders
10.1038/S41419-024-07218-Z
ISSN:2041-4889
Deep muscle-proteomic analysis of freeze-dried human muscle biopsies reveals fiber type-specific adaptations to exercise training
A. S. Deshmukh•D. E. Steenberg•M. Hostrup•J. B. Birk•J. K. Larsen等 14 人
Nature Communications
2021
•2021/1/12
•Vol.12 No.1 p.1-15
Skeletal muscle conveys several of the health-promoting effects of exercise; yet the underlying mechanisms are not fully elucidated. Studying skeletal muscle is challenging due to its different fiber types and the presence of non-muscle cells. This can be circumvented by isolation of single muscle f...
Computational biology and bioinformaticsProteomic analysisSkeletal muscle
10.1038/S41467-020-20556-8
ISSN:2041-1723
Regulation of the developmental programs in Toxoplasma by a novel SNF2L-containing chromatin remodeling complex
Yuchao Zhu•Bolin Fan•Hao Xu•Yazhou Li•Xiaohan Liang等 12 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-16
Toxoplasma gondii is an extremely successful parasite infecting one third of the human population and numerous animals. It has a complex life cycle with multiple developmental stages that are key for its transmission and pathogenesis. But how the developmental programs are regulated is largely unkno...
Parasite biologyParasite development
10.1038/S41467-025-60795-1
ISSN:2041-1723
Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility
Georg Dorn•Christoph Gmeiner•Tebbe de Vries•Emil Dedic•Mihajlo Novakovic等 18 人
Nature Communications
2023
•2023/10/13
•Vol.14 No.1 p.1-16
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due t...
Biophysical chemistryRNA-binding proteinsSolution-state NMR
10.1038/S41467-023-42012-Z
ISSN:2041-1723
CAPRI enables comparison of evolutionarily conserved RNA interacting regions
Amol Panhale•Florian M. Richter•Fidel Ramírez•Maria Shvedunova•Thomas Manke等 7 人
Nature Communications
2019
•2019/6/18
•Vol.10 No.1 p.1-22
RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. W...
ProteomicsRNARNA-binding proteins
10.1038/S41467-019-10585-3
ISSN:2041-1723
Crotonate enhances intestinal regeneration after injury via HBO1-mediated H3K14 crotonylation
Yanhui Xiao•Shicheng Yu•Mengxian Zhang•Nanshan Zhong•Shan Hua等 11 人
Nature Communications
2025
•2025/10/2
•Vol.16 No.1 p.1-18
The intestinal epithelium undergoes rapid turnover driven by Lgr5+ intestinal stem cells at the crypt base, and can recover upon damage. Histone crotonylation plays a critical role in chromatin regulation and gene expression. However, the role of histone crotonylation, specifically H3K14 crotonylati...
Intestinal stem cellsPost-translational modifications
10.1038/S41467-025-63869-2
ISSN:2041-1723
Aberrant NAD+ metabolism underlies Zika virus–induced microcephaly
Pang Huanhuan•Jiang Yisheng•Li Jie•Wang Yushen•Nie Meng等 19 人
Nature Metabolism
2021
•2021/8/12
•00 p.1-16
Zika virus (ZIKV) infection during pregnancy can cause microcephaly in newborns, yet the underlying mechanisms remain largely unexplored. Here, we reveal extensive and large-scale metabolic reprogramming events in ZIKV-infected mouse brains by performing a multi-omics study comprising transcriptomic...
Energy metabolismMetabolismVirus–host interactions
10.1038/S42255-021-00437-0
ISSN:2522-5812
Structural snapshots of human pre-60S ribosomal particles before and after nuclear export
Xiaomeng Liang•Mei-Qing Zuo•Yunyang Zhang•Ningning Li•Chengying Ma等 7 人
Nature Communications
2020
•2020/7/15
•Vol.11 No.1 p.1-14
Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly eve...
Cryoelectron microscopyRibosome
10.1038/S41467-020-17237-X
ISSN:2041-1723
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer
Hanqing Liao•Carolina Barra•Zhicheng Zhou•Xu Peng•Isaac Woodhouse等 15 人
Nature Communications
2024
•2024/1/22
•Vol.15 No.1 p.1-16
Understanding the nature and extent of non-canonical human leukocyte antigen (HLA) presentation in tumour cells is a priority for target antigen discovery for the development of next generation immunotherapies in cancer. We here employ a de novo mass spectrometric sequencing approach with a refined,...
Antigen presentationCancer immunotherapyCytotoxic T cellsImmunoeditingProteome informatics
10.1038/S41467-023-44460-Z
ISSN:2041-1723
Antibody-lectin chimeras for glyco-immune checkpoint blockade
Jessica C. Stark•Melissa A. Gray•Itziar Ibarlucea-Benitez•Marta Lustig•Annalise Bond等 21 人
Nature Biotechnology
2025
•2025/12/16
•00 p.1-15
Despite the curative potential of checkpoint blockade immunotherapy, many patients remain unresponsive to existing treatments. Glyco-immune checkpoints, which involve interactions of cell-surface glycans with lectin, or glycan-binding, immunoreceptors, have emerged as prominent mechanisms of immune ...
Applied immunologyMolecular engineering
10.1038/S41587-025-02884-6
ISSN:1087-0156
YiaC and CobB regulate lysine lactylation in Escherichia coli
Dong Hanyang•Zhang Jianji•Zhang Hui•Han Yue•Lu Congcong等 16 人
Nature Communications
2022
•2022/11/4
•Vol.13 No.1 p.1-16
Lysine lactylation (Kla) has recently been reported to participate in regulating transcription in human cells. However, the characterization, regulatory mechanism and functional consequence of Kla in prokaryotes remain unclear. Here, we report that YiaC functions as a lysine lactylase and that CobB ...
BacteriaChemical modificationPost-translational modificationsProteomics
10.1038/S41467-022-34399-Y
ISSN:2041-1723
A metabolism-chromatin axis promotes differential ribosomal RNA transcription in the human malaria parasite
Justine E. Couble•Tiziano Vignolini•Grégory Doré•Selina Mussgnug•Bérangère Lombard等 12 人
Nature Communications
2025
•2025/12/19
0The transmission of the most virulent human malaria parasite, Plasmodium falciparum, relies on its survival in the contrasting environments of the human host and mosquito vector. One of the most fascinating adaptations to this lifestyle is the specific silencing of individual rDNA genes in the human...
Parasite biologyRibosome
10.1038/S41467-025-67522-W
ISSN:2041-1723
Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry
Sven H. Giese•Ludwig R. Sinn•Fritz Wegner•Juri Rappsilber
Nature Communications
2021
•2021/5/28
•Vol.12 No.1 p.1-11
Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits the numbers of protein–protein interactions that ca...
Liquid chromatographyMachine learningMass spectrometryProtein–protein interaction networks
10.1038/S41467-021-23441-0
ISSN:2041-1723
Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription
Eui Tae Kim•Joseph M. Dybas•Katarzyna Kulej•Emigdio D. Reyes•Alexander M. Price等 10 人
Nature Microbiology
2021
•2021/1/11
•Vol.6 No.2 p.234-245
Intrinsic antiviral host factors confer cellular defence by limiting virus replication and are often counteracted by viral countermeasures. We reasoned that host factors that inhibit viral gene expression could be identified by determining proteins bound to viral DNA (vDNA) in the absence of key vir...
BiochemistryImmunologyMicrobiology
10.1038/S41564-020-00826-3
ISSN:2058-5276
K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle
Yuanyuan Yu•Qingyun Zheng•Satchal K. Erramilli•Man Pan•Seongjin Park等 11 人
Nature Chemical Biology
2021
•2021/7/8
•00 p.1-10
Protein ubiquitination shows remarkable topological and functional diversity through the polymerization of ubiquitin via different linkages. Deciphering the cellular ubiquitin code is of central importance to understand the physiology of the cell. However, our understanding of its function is rather...
Cell divisionPost-translational modificationsX-ray crystallography
10.1038/S41589-021-00823-5
ISSN:1552-4450
Algae-dominated metaproteomes uncover cellular adaptations to life on the Greenland Ice Sheet
Helen K. Feord•Anke Trautwein-Schult•Christoph Keuschnig•Anne Ostrzinski•Elisa K. Peter等 14 人
Npj Biofilms And Microbiomes
2025
•2025/9/9
•Vol.11 No.1 p.1-11
Eukaryotic algae-dominated microbiomes thrive on the Greenland Ice Sheet (GrIS) in harsh environmental conditions, including low temperatures, high light, and low nutrient availability. Chlorophyte algae bloom on snow, while streptophyte algae dominate bare ice surfaces. Empirical data about the cel...
Cellular microbiologyEnvironmental microbiologyWater microbiology
10.1038/S41522-025-00770-2
ISSN:2055-5008
A repressive H3K36me2 reader mediates Polycomb silencing
Mengting Xu•Qi Zhang•Huanbin Shi•Zhongling Wu•Wei Zhou等 8 人
Nature Communications
2024
•2024/8/24
•Vol.15 No.1 p.1-17
In animals, evolutionarily conserved Polycomb repressive complex 2 (PRC2) catalyzes histone H3 lysine 27 trimethylation (H3K27me3) and PRC1 functions in recruitment and transcriptional repression. However, the mechanisms underlying H3K27me3-mediated stable transcriptional silencing are largely unkno...
Gene silencingHistone post-translational modifications
10.1038/S41467-024-51789-6
ISSN:2041-1723
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
Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment
Rudrarup Bhattacharjee•Lachlan A. Jolly•Mark A. Corbett•Ing Chee Wee•Sushma R. Rao等 24 人
Nature Communications
2024
•2024/2/8
•Vol.15 No.1 p.1-25
We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the molecular pathology of this essential eukaryo...
Neurodevelopmental disordersNeurological disorders
10.1038/S41467-024-45121-5
ISSN:2041-1723
A bacterial YopJ-family acetyltransferase suppresses host immune response by Nε-acetylation of JAK1
Tao-Tao Chen•Si-Ru Zheng•Binbin Yang•Qiuhua Lu•Xueyan Liu等 13 人
Nature Communications
2026
•2026/2/18
•Vol.17 No.1 p.29100
A common host response to pathogen infection involves the production of robust interferons or proinflammatory cytokines to activate the JAK-STAT pathway, thereby limiting pathogen replication. The bacterial pathogen Legionella pneumophila creates an intracellular niche and evades host immunity utili...
AcetylationInfection
10.1038/S41467-026-69623-6
ISSN:2041-1723
Proteome-wide profiling of S-nitrosylated proteins using the SNOTRAP probe and mass spectrometry-based detection
Hongmei Yang•Haitham Amal•Steven R. Tannenbaum•Stuart A. Lipton
Nature Protocols
2025
•2025/11/19
•00 p.1-26
Protein S-nitrosylation (SNO) is a ubiquitous post-translational modification, which regulates a broad range of functional parameters, including protein stability; enzymatic, transcriptional and ion channel activity; and cellular signal transduction. Aberrant protein SNO is associated with diverse p...
Alzheimer's diseaseMass spectrometryProteomics
10.1038/S41596-025-01282-1
ISSN:1754-2189
Optogenetic rejuvenation of mitochondrial membrane potential extends C. elegans lifespan
Berry Brandon J.•Vodičková Anežka•Müller-Eigner Annika•Meng Chen•Ludwig Christina等 8 人
Nature Aging
2022
•2022/12/30
•Vol.3 No.2 p.157-161
Mitochondrial dysfunction plays a central role in aging but the exact biological causes are still being determined. Here, we show that optogenetically increasing mitochondrial membrane potential during adulthood using a light-activated proton pump improves age-associated phenotypes and extends lifes...
AgeingEnergy metabolismMitochondriaOptogenetics
10.1038/S43587-022-00340-7
ISSN:2662-8465
Low-input deep learning platform for citrullinated peptide identification, autoantigen discovery and rheumatoid arthritis treatment stratification
Meng Hu•Chenxi Zhu•Rui Sun•Zhiqiang Xu•Yanqiu Gong等 28 人
Nature Biomedical Engineering
2026
•2026/3/3
•00 p.1-17
Post-translationally modified proteins are crucial autoantigens in autoimmune diseases, with citrullinated proteins being key targets of autoantibodies in rheumatoid arthritis (RA). However, accurate citrullinome profiling and autoantigen identification remain limited by insufficient detection metho...
Machine learningProteomicsRheumatoid arthritis
10.1038/S41551-026-01628-4
ISSN:2157-846X
Structural basis for the asymmetric binding of coactivator SRC1 to FXR-RXRα and allosteric communication within the complex
Yanan Sheng•Yaoting Guo•Beibei Zhao•Mingze Sun•Yan Dong等 11 人
Communications Biology
2025
•2025/3/13
•Vol.8 No.1 p.1-14
Farnesoid X receptor (FXR) is a promising target for treatment of metabolic associated fatty liver disease (MAFLD). In this study, we employed an integrative approach to investigate the interaction between FXR-RXRα-DNA complex and the entire coactivator SRC1-NRID (nuclear receptor interaction domain...
Molecular modellingSupramolecular assembly
10.1038/S42003-025-07854-X
ISSN:2399-3642
Bone controls browning of white adipose tissue and protects from diet-induced obesity through Schnurri-3-regulated SLIT2 secretion
Zan Li•Baohong Shi•Na Li•Jun Sun•Xiangchen Zeng等 22 人
Nature Communications
2024
•2024/8/6
•Vol.15 No.1 p.1-15
The skeleton has been suggested to function as an endocrine organ controlling whole organism energy balance, however the mediators of this effect and their molecular links remain unclear. Here, utilizing Schnurri-3−/− (Shn3−/−) mice with augmented osteoblast activity, we show Shn3−/−mice display res...
Metabolic syndromeObesity
10.1038/S41467-024-51155-6
ISSN:2041-1723
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes
Isabell Bludau•Moritz Heusel•Max Frank•George Rosenberger•Robin Hafen等 10 人
Nature Protocols
2020
•2020/7/20
•Vol.15 No.8 p.2341-2386
Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are theref...
Protein–protein interaction networksSoftwareSystems biology
10.1038/S41596-020-0332-6
ISSN:1754-2189
ROMO1 overexpression protects the mitochondrial cysteinome from oxidations in aging
Fengli Xu•Haipeng Huang•Kun Peng•Chongshu Jian•Hao Wu等 16 人
Nature Communications
2025
•2025/6/3
•Vol.16 No.1 p.1-20
Reactive thiols of proteinaceous cysteines are vital to cell biology by serving as sensor, effector and buffer of environmental redox fluctuations. Being the major source, as well as the prime target, of reactive oxygen species (ROS), mitochondria confront great challenges in preserving their thiol ...
AgeingCell biology
10.1038/S41467-025-60503-Z
ISSN:2041-1723
Minimizing DNA trapping while maintaining activity inhibition via selective PARP1 degrader
Li Chen•Yahui Zou•Renhong Sun•Mei Huang•Xiaotong Zhu等 10 人
Cell Death & Disease
2024
•2024/12/18
•Vol.15 No.12 p.1-14
Poly (ADP-ribose) polymerase 1 (PARP1) catalyzes poly (ADP) ribosylation reaction, one of the essential post-translational modifications of proteins in eukaryotic cells. Given that PARP1 inhibition can lead to synthetic lethality in cells with compromised homologous recombination, this enzyme has be...
Drug developmentDrug safety
10.1038/S41419-024-07277-2
ISSN:2041-4889
AMPK-regulated glycerol excretion maintains metabolic crosstalk between reductive and energetic stress
Xuewei Zhai•Ronghui Yang•Qiaoyun Chu•Zihao Guo•Pengjiao Hou等 12 人
Nature Cell Biology
2025
•2025/1/2
•00 p.1-13
Glucose metabolism has been studied extensively, but the role of glucose-derived excretory glycerol remains unclear. Here we show that hypoxia induces NADH accumulation to promote glycerol excretion and this pathway consumes NADH continuously, thus attenuating its accumulation and reductive stress. ...
Cancer metabolismCell growthStress signalling
10.1038/S41556-024-01549-X
ISSN:1465-7392
Post-ischemic ubiquitination at the postsynaptic density reversibly influences the activity of ischemia-relevant kinases
Luvna Dhawka•Victoria Palfini•Emma Hambright•Ismary Blanco•Carrie Poon等 14 人
Communications Biology
2024
•2024/3/13
•Vol.7 No.1 p.1-16
Ubiquitin modifications alter protein function and stability, thereby regulating cell homeostasis and viability, particularly under stress. Ischemic stroke induces protein ubiquitination at the ischemic periphery, wherein cells remain viable, however the identity of ubiquitinated proteins is unknown...
KinasesProteomic analysisStrokeUbiquitylation
10.1038/S42003-024-06009-8
ISSN:2399-3642
Ubiquitylome study identifies increased histone 2A ubiquitylation as an evolutionarily conserved aging biomarker
Lu Yang•Zaijun Ma•Han Wang•Kongyan Niu•Ye Cao等 19 人
Nature Communications
2019
•2019/5/21
•Vol.10 No.1 p.1-11
The long-lived proteome constitutes a pool of exceptionally stable proteins with limited turnover. Previous studies on ubiquitin-mediated protein degradation primarily focused on relatively short-lived proteins; how ubiquitylation modifies the long-lived proteome and its regulatory effect on adult l...
AgeingHistone post-translational modificationsProteomicsUbiquitylation
10.1038/S41467-019-10136-W
ISSN:2041-1723
NQO1 protects obese mice through improvements in glucose and lipid metabolism
Andrea Di Francesco•Youngshim Choi•Michel Bernier•Yingchun Zhang•Alberto Diaz-Ruiz等 27 人
Npj Aging And Mechanisms Of Disease
2020
•2020/11/19
•Vol.6 No.1 p.1-18
Chronic nutrient excess leads to metabolic disorders and insulin resistance. Activation of stress-responsive pathways via Nrf2 activation contributes to energy metabolism regulation. Here, inducible activation of Nrf2 in mice and transgenesis of the Nrf2 target, NQO1, conferred protection from diet-...
DiabetesObesity
10.1038/S41514-020-00051-6
ISSN:2056-3973
Profiling the proteome-wide selectivity of diverse electrophiles
Patrick R. A. Zanon•Fengchao Yu•Patricia Z. Musacchio•Lisa Lewald•Michael Zollo等 15 人
Nature Chemistry
2025
•2025/10/30
•Vol.17 No.11 p.1712-1721
Covalent inhibitors that do not rely on hijacking enzymatic activity have mainly been limited to those targeting cysteine residues. The development of such cysteine-directed covalent inhibitors has greatly profited from the use of competitive residue-specific proteomics to determine their proteome-w...
Mass spectrometryProteomicsScreeningTarget identification
10.1038/S41557-025-01902-Z
ISSN:1755-4330
Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca2+
Ruifang Ma•Bowen Du•Chen Shi•Lei Wang•Fuxing Zeng等 9 人
Nature Communications
2025
•2025/3/28
•Vol.16 No.1 p.1-13
Phosphorylase kinase (PhK) regulates the degradation of glycogen by integrating diverse signals, providing energy to the organism. Dysfunctional mutations may directly lead to Glycogen Storage Disease type IX (GSD IX), whereas the abnormal expression of PhK is also associated with tumors. Here, we u...
Cryoelectron microscopyEnzyme mechanismsKinases
10.1038/S41467-025-58363-8
ISSN:2041-1723
c-JUN controls microbial colonization via selective phagocytosis in the sea anemone Nematostella
N. H. Kaya•M. Abukhalaf•G. Fuentes•J. Taubenheim•U. Hentschel等 7 人
Nature Communications
2026
•2026/7/10
•Vol.17 No.1 p.60870
Innate immunity is traditionally viewed as a broad defense system with limited specificity. However, increasing evidence suggests that innate immune cells can discriminate between distinct microbial partners. How such specificity arises in early-diverging animals remains unclear. Here, we identify i...
Innate immunityMicrobiome
10.1038/S41467-026-75511-W
ISSN:2041-1723
Dietary intervention improves health metrics and life expectancy of the genetically obese Titan mouse
Müller-Eigner Annika•Sanz-Moreno Adrián•de-Diego Irene•Venkatasubramani Anuroop Venkateswaran•Langhammer Martina等 29 人
Communications Biology
2022
•2022/5/3
•Vol.5 No.1 p.1-17
Suitable animal models are essential for translational research, especially in the case of complex, multifactorial conditions, such as obesity. The non-inbred mouse (Mus musculus) line Titan, also known as DU6, is one of the world’s longest selection experiments for high body mass and was previously...
BiochemistryMolecular biologyPhysiology
10.1038/S42003-022-03339-3
ISSN:2399-3642
Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation
Jonathan J. Swietlik•Stefanie Bärthel•Chiara Falcomatà•Diana Fink•Ankit Sinha等 12 人
Nature Communications
2023
•2023/5/8
•Vol.14 No.1 p.1-17
Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive...
Proteome informaticsProteomicsTumour immunology
10.1038/S41467-023-38171-8
ISSN:2041-1723
Astrocytes express aberrant immunoglobulins as putative gatekeeper of astrocytes to neuronal progenitor conversion
Capuz Alice•Osien Sylvain•Karnoub Mélodie Anne•Aboulouard Soulaimane•Laurent Estelle等 20 人
Cell Death & Disease
2023
•2023/4/4
•Vol.14 No.4 p.1-16
Using multi-omics analyses including RNAseq, RT-PCR, RACE-PCR, and shotgun proteomic with enrichment strategies, we demonstrated that newborn rat astrocytes produce neural immunoglobulin constant and variable heavy chains as well as light chains. However, their edification is different from the ones...
GliogenesisProteomicsRegeneration and repair in the nervous system
10.1038/S41419-023-05737-9
ISSN:2041-4889
CD36 mediates SARS-CoV-2-envelope-protein-induced platelet activation and thrombosis
Zihan Tang•Yanyan Xu•Yun Tan•Hui Shi•Peipei Jin等 25 人
Nature Communications
2023
•2023/8/21
•Vol.14 No.1 p.1-13
Aberrant coagulation and thrombosis are associated with severe COVID-19 post-SARS-CoV-2 infection, yet the underlying mechanism remains obscure. Here we show that serum levels of SARS-CoV-2 envelope (E) protein are associated with coagulation disorders of COVID-19 patients, and intravenous administr...
Mechanisms of diseaseResearch dataViral infection
10.1038/S41467-023-40824-7
ISSN:2041-1723
SMYD2 glutathionylation contributes to degradation of sarcomeric proteins
Dhanushka N. P. Munkanatta Godage•Garrett C. VanHecke•Kusal T. G. Samarasinghe•Han-Zhong Feng•Mark Hiske等 10 人
Nature Communications
2018
•2018/10/18
•Vol.9 No.1 p.1-14
Reactive oxygen species (ROS) contribute to the etiology of multiple muscle-related diseases. There is emerging evidence that cellular stress can lead to destabilization of sarcomeres, the contractile unit of muscle. However, it is incompletely understood how cellular stress induces structural desta...
Cardiovascular biologyPost-translational modificationsProtein quality control
10.1038/S41467-018-06786-X
ISSN:2041-1723
Chemoproteogenomic stratification of the missense variant cysteinome
Heta Desai•Katrina H. Andrews•Kristina V. Bergersen•Samuel Ofori•Fengchao Yu等 13 人
Nature Communications
2024
•2024/10/28
•Vol.15 No.1 p.1-24
Cancer genomes are rife with genetic variants; one key outcome of this variation is widespread gain-of-cysteine mutations. These acquired cysteines can be both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain unidentifi...
Chemical biologyProteome informaticsProteomics
10.1038/S41467-024-53520-X
ISSN:2041-1723
ISX-9 potentiates CaMKIIδ-mediated BMAL1 activation to enhance circadian amplitude
Li Huilin•Ou Jiali•Li Yaqun•Xu Niannian•Li Qing等 9 人
Communications Biology
2022
•2022/7/28
•Vol.5 No.1 p.1-13
Circadian dysregulation associates with numerous diseases including metabolic dysfunction, sleep disorder, depression and aging. Given that declined circadian amplitude is a trait commonly found with compromised health, interventions that design in precluding circadian amplitude from dampening will ...
Circadian rhythmsCircadian rhythms and sleep
10.1038/S42003-022-03725-X
ISSN:2399-3642
PUMILIO proteins promote colorectal cancer growth via suppressing p21
Gong Yuanyuan•Liu Zukai•Yuan Yihang•Yang Zhenzhen•Zhang Jiawei等 10 人
Nature Communications
2022
•2022/3/25
•Vol.13 No.1 p.1-17
PUMILIO (PUM) proteins belong to the highly conserved PUF family post-transcriptional regulators involved in diverse biological processes. However, their function in carcinogenesis remains under-explored. Here, we report that Pum1 and Pum2 display increased expression in human colorectal cancer (CRC...
Colon cancer
10.1038/S41467-022-29309-1
ISSN:2041-1723
Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni
Kathrin Froschauer•Sarah L. Svensson•Rick Gelhausen•Elisabetta Fiore•Philipp Kible等 14 人
Nature Communications
2025
•2025/3/30
•Vol.16 No.1 p.1-19
In contrast to transcriptome maps, bacterial small protein (≤50-100 aa) coding landscapes, including overlapping genes, are poorly characterized. However, an emerging number of small proteins have crucial roles in bacterial physiology and virulence. Here, we present a Ribo-seq-based high-resolution ...
Bacterial genesMicrobiologyNext-generation sequencingTranslation
10.1038/S41467-025-58329-W
ISSN:2041-1723
Sequestration of the phagocyte metabolite itaconate by Pseudomonas aeruginosa RpoN promotes successful pulmonary infection
Ayesha Z. Beg•Zihua Liu•Ying-Tsun Chen•Absar Talat•Griffin Gowdy等 13 人
Nature Communications
2025
•2025/12/13
0Inhaled opportunistic pathogens such as Pseudomonas aeruginosa actively modify gene expression to meet the challenges of a new environment. In the infected airway the bacteria must respond to the immunometabolite itaconate, which is abundantly produced by macrophages and has anti-inflammatory and an...
Bacterial infectionClinical microbiology
10.1038/S41467-025-67153-1
ISSN:2041-1723
Regulation of lipoprotein processing by GPNMB in foamy macrophages: potential therapeutic targets for atherosclerosis
Junqi Wang•Liming Peng•Huan Wang•Di Liu•Wenting Yang等 11 人
Nature Communications
2025
•2025/11/14
•Vol.16 No.1 p.100300
The formation of foamy macrophages is often considered a pathological hallmark of atherosclerosis, but the underlying mechanisms remain elusive. Herein, we demonstrated that the transcription factor TFEC could upregulate the expression of Glycoprotein non-metastatic melanoma protein B (GPNMB) in ath...
AtherosclerosisEndosomesFoam cellsMechanisms of diseaseMetabolic diseases
10.1038/S41467-025-65224-X
ISSN:2041-1723
Prohibitin 2 is a key regulator of T cell proliferation, differentiation, and effector functions in vivo
Johannes F. Vogt•Carsten Merkwirth•Petra Adams-Quack•Elena Zurkowski•Emmanouill Stylianakis等 19 人
Communications Biology
2026
•2026/7/20
•Vol.9 No.1 p.9890
Prohibitin 2 (PHB2) is a highly conserved protein with essential roles in cell homeostasis and survival across different cell types. Previous studies have shown that the deletion of PHB2 results in an arrest in proliferation due to impaired mitochondrial function regulated by the dynamin-like GTPase...
Cell divisionT cells
10.1038/S42003-026-10522-3
ISSN:2399-3642
Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation
Hughes Laetitia A.•Rudler Danielle L.•Siira Stefan J.•McCubbin Tim•Raven Samuel A.等 12 人
Nature Communications
2023
•2023/4/18
•Vol.14 No.1 p.1-19
The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both indivi...
DevelopmentEmbryologyRNAtRNAs
10.1038/S41467-023-37843-9
ISSN:2041-1723
The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing
Evi Goulielmaki•Maria Tsekrekou•Nikos Batsiotos•Mariana Ascensão-Ferreira•Eleftheria Ledaki等 13 人
Nature Communications
2021
•2021/5/26
•Vol.12 No.1 p.1-19
RNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to s...
Genomic instabilityRNA splicing
10.1038/S41467-021-23505-1
ISSN:2041-1723
Selective identification of epigenetic regulators at methylated genomic sites by SelectID
Wenchang Qian•Penglei Jiang•Mingming Niu•Yujuan Fu•Deyu Huang等 18 人
Nature Communications
2025
•2025/4/18
•Vol.16 No.1 p.1-14
DNA methylation is a significant component in proximal chromatin regulation and plays crucial roles in regulating gene expression and maintaining the repressive state of retrotransposon elements. However, accurate profiling of the proteomics which simultaneously identifies specific DNA sequences and...
CRISPR-Cas9 genome editingDNA methylationTranscriptional regulatory elements
10.1038/S41467-025-59002-Y
ISSN:2041-1723
A comprehensive molecular profiling approach reveals metabolic alterations that steer bone tissue regeneration
Löffler Julia•Noom Anne•Ellinghaus Agnes•Dienelt Anke•Kempa Stefan等 6 人
Communications Biology
2023
•2023/3/27
•Vol.6 No.1 p.1-17
Bone regeneration after fracture is a complex process with high and dynamic energy demands. The impact of metabolism on bone healing progression and outcome, however, is so far understudied. Our comprehensive molecular profiling reveals that central metabolic pathways, such as glycolysis and the cit...
OsteoimmunologyPreclinical research
10.1038/S42003-023-04652-1
ISSN:2399-3642
Macrophage-derived GPNMB trapped by fibrotic extracellular matrix promotes pulmonary fibrosis
Wang Jing•Zhang Xinxin•Long Min•Yuan Mengqin•Yin Juan等 10 人
Communications Biology
2023
•2023/2/2
•Vol.6 No.1 p.1-15
Pulmonary fibrosis (PF) is a form of progressive lung disease characterized by chronic inflammation and excessive extracellular matrix (ECM) deposition. However, the protein changes in fibrotic ECM during PF and their contribution to fibrosis progression are unclear. Here we show that changes in exp...
Cystic fibrosisExtracellular matrix
10.1038/S42003-022-04333-5
ISSN:2399-3642
Endoxifen downregulates AKT phosphorylation through protein kinase C beta 1 inhibition in ERα+ breast cancer
Swaathi Jayaraman•Xinyan Wu•Krishna R. Kalari•Xiaojia Tang•Mary J. Kuffel等 20 人
Npj Breast Cancer
2023
•2023/12/19
•Vol.9 No.1 p.1-16
Endoxifen, a secondary tamoxifen metabolite, is a potent antiestrogen exhibiting estrogen receptor alpha (ERα) binding at nanomolar concentrations. Phase I/II clinical trials identified clinical activity of Z-endoxifen (ENDX), in endocrine-refractory metastatic breast cancer as well as ERα+ solid tu...
Breast cancer
10.1038/S41523-023-00606-2
ISSN:2374-4677
Design of PROTACs utilizing the E3 ligase GID4 for targeted protein degradation
Yanran Li•Kaiwen Bao•Jiyue Sun•Ruixin Ge•Qiqing Zhang等 18 人
Nature Structural & Molecular Biology
2025
•2025/4/28
•00 p.1-13
Proteolysis targeting chimeras (PROTACs) hijack E3 ligases and the ubiquitin–proteasome system to achieve selective degradation of neo-substrates. Their ability to target otherwise intractable substrates has rendered them a valuable modality in drug discovery. However, only a handful of over 600 hum...
Drug discoveryUbiquitin ligasesUbiquitylationX-ray crystallography
10.1038/S41594-025-01537-1
ISSN:1545-9993
USP18 is an essential regulator of muscle cell differentiation and maturation
Olie Cyriel Sebastiaan•Pinto-Fernández Adán•Damianou Andreas•Vendrell Iolanda•Mei Hailiang等 10 人
Cell Death & Disease
2023
•2023/3/31
•Vol.14 No.3 p.1-15
The ubiquitin proteasomal system is a critical regulator of muscle physiology, and impaired UPS is key in many muscle pathologies. Yet, little is known about the function of deubiquitinating enzymes (DUBs) in the muscle cell context. We performed a genetic screen to identify DUBs as potential regula...
DifferentiationNeuroimmunology
10.1038/S41419-023-05725-Z
ISSN:2041-4889
Chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing
Jian Liu•Chunxiao Li•Jinsong Wang•Dongkui Xu•Haijuan Wang等 18 人
Nature Communications
2020
•2020/9/8
•Vol.11 No.1 p.1-17
Dysregulated alternative splicing (AS) driving carcinogenetic mitosis remains poorly understood. Here, we demonstrate that cancer metastasis-associated antigen 1 (MTA1), a well-known oncogenic chromatin modifier, broadly interacts and co-expresses with RBPs across cancers, contributing to cancerous ...
Oncogenes
10.1038/S41467-020-18259-1
ISSN:2041-1723
Epstein-Barr virus infection upregulates extracellular OLFM4 to activate YAP signaling during gastric cancer progression
Fuping Wen•Yi Han•Hui Zhang•Zhangting Zhao•Wenjia Wang等 19 人
Nature Communications
2024
•2024/12/4
•Vol.15 No.1 p.1-17
Extracellular vesicles (EVs) are known to mediate cell communications and shape tumor microenvironment. Compared to the well-studied small EVs, the function of large microvesicles (MVs) during tumorigenesis is poorly understood. Here we show the proteome of MVs in Epstein-Barr virus (EBV)-associated...
Cancer microenvironmentGastric cancer
10.1038/S41467-024-54850-6
ISSN:2041-1723
PP6 negatively modulates LUBAC-mediated M1-ubiquitination of RIPK1 and c-FLIPL to promote TNFα-mediated cell death
Wu Guowei•Li Dekang•Liang Wei•Sun Weimin•Xie Xingxing等 11 人
Cell Death & Disease
2022
•2022/9/7
•Vol.13 No.9 p.1-14
Activation of TNFR1 by TNFα induces the formation of a membrane-associated, intracellular complex termed complex I. Complex I orchestrates a complex pattern of modifications on key regulators of TNF signaling that collectively determines the cell fate by activating pro-survival or executing cell dea...
ApoptosisNecroptosis
10.1038/S41419-022-05206-9
ISSN:2041-4889
Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
Enrico Cappellini•Frido Welker•Luca Pandolfi•Jazmín Ramos-Madrigal•Diana Samodova等 43 人
Nature
2019
•2019/9/11
•Vol.574 No.7776 p.103-107
The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately ...
Evolutionary biologyEvolutionary geneticsPalaeontologyProteomics
10.1038/S41586-019-1555-Y
ISSN:0028-0836
Nitrous oxide respiring bacteria in biogas digestates for reduced agricultural emissions
Jonassen Kjell Rune•Hagen Live H.•Vick Silas H. W.•Arntzen Magnus Ø.•Eijsink Vincent G. H.等 10 人
The Isme Journal
2021
•2021/9/6
•00 p.1-11
Inoculating agricultural soils with nitrous oxide respiring bacteria (NRB) can reduce N2O-emission, but would be impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production are suitable substrates and vectors for NRB. We show that indigenous NRB in dig...
Environmental microbiologyEnvironmental sciences
10.1038/S41396-021-01101-X
ISSN:1751-7362
Targeting astrocytic CLC2(CLCN2) restores myelin regeneration through inhibition of SPP1/CD44 signaling pathway in leukoencephalopathy
Lu Yang•Yubao Lu•Jia Liu•Fan Zhu•Ying Jiang等 10 人
Molecular Psychiatry
2025
•2025/8/21
•00 p.1-21
Accumulating myelin damage and impaired remyelination are central pathological features of leukoencephalopathies, including Multiple Sclerosis and Alexander Disease, where astrocytes play essential roles in maintaining central nervous system homeostasis and mediating astrocyte-oligodendrocyte intera...
NeuroscienceStem cells
10.1038/S41380-025-03159-X
ISSN:1359-4184
A covalent peptide-based lysosome-targeting protein degradation platform for cancer immunotherapy
Youmei Xiao•Zhuoying He•Wanqiong Li•Danhong Chen•Xiaoshuang Niu等 16 人
Nature Communications
2025
•2025/2/6
•Vol.16 No.1 p.1-16
The lysosome-targeting chimera (LYTAC) strategy provided a very powerful tool for the degradation of membrane proteins. However, the synthesis of LYTACs, antibody-small molecule conjugates, is challenging. The ability of antibody-based LYTACs to penetrate solid tumor is limited as well, especially t...
Cancer therapyPeptidesStructure-based drug design
10.1038/S41467-025-56648-6
ISSN:2041-1723
SARS-CoV-2 infection in the mouse olfactory system
Qing Ye•Jia Zhou•Qi He•Rui-Ting Li•Guan Yang等 19 人
Cell Discovery
2021
•2021/7/6
•Vol.7 No.1 p.1-13
SARS-CoV-2 infection causes a wide spectrum of clinical manifestations in humans, and olfactory dysfunction is one of the most predictive and common symptoms in COVID-19 patients. However, the underlying mechanism by which SARS-CoV-2 infection leads to olfactory disorders remains elusive. Herein, we...
Cell signallingMechanisms of disease
10.1038/S41421-021-00290-1
ISSN:2056-5968
A naturally occurring variant of SHLP2 is a protective factor in Parkinson’s disease
Su-Jeong Kim•Brendan Miller•Nicolas G. Hartel•Ricardo Ramirez•Regina Gonzalez Braniff等 19 人
Molecular Psychiatry
2024
•2024/1/3
•00 p.1-13
Mitochondrial DNA single nucleotide polymorphisms (mtSNPs) have been associated with a reduced risk of developing Parkinson’s disease (PD), yet the underlying mechanisms remain elusive. In this study, we investigate the functional role of a PD-associated mtSNP that impacts the mitochondrial-derived ...
Cell biologyNeuroscience
10.1038/S41380-023-02344-0
ISSN:1359-4184
RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets
Luisa Hemm•Dominik Rabsch•Halie Rae Ropp•Viktoria Reimann•Philip Gerth等 11 人
Nature Communications
2025
•2025/9/26
•Vol.16 No.1 p.1-21
The computational analysis of large proteomics datasets from gradient profiling or spatially resolved proteomics is often as crucial as experimental design. We present RAPDOR, a tool for intuitive analyzing and visualizing such datasets, based on the Jensen-Shannon distance and analysis of similarit...
Bacterial genesBioinformatics
10.1038/S41467-025-64086-7
ISSN:2041-1723
KMT5A-methylated SNIP1 promotes triple-negative breast cancer metastasis by activating YAP signaling
Yu Bo•Su Jun•Shi Qiqi•Liu Qing•Ma Jun等 10 人
Nature Communications
2022
•2022/4/21
•Vol.13 No.1 p.1-18
Smad nuclear-interacting protein 1 (SNIP1) is a transcription repressor related to the TGF-β signaling pathway and associates with c-MYC, a key regulator of cell proliferation and tumor development. Currently, the mechanism by which SNIP1 regulates tumorigenesis and cancer metastasis is unknown. Her...
Breast cancerMethylation
10.1038/S41467-022-29899-W
ISSN:2041-1723
Abnormal glycosylation of MUC20 mediates TAM polarization and promotes immune escape in colorectal cancer
Yingru Zhi•Yifeng Zhang•Huanhuan Fei•Jie Yuan•Xiaobei Liu等 6 人
Communications Biology
2026
•2026/4/11
0Immune evasion is one of the critical factors contributing to the advanced progression of colorectal cancer (CRC). Our research identified that CRC cells exhibit high expression of the zinc finger protein ZNF30, which transcriptionally activates the expression of the glycosyltransferase B4GALT2. B4G...
CancerCell biologyColorectal cancer
10.1038/S42003-026-10017-1
ISSN:2399-3642
The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination
Mühlenbruch Lena•Abou-Kors Tsima•Dubbelaar Marissa L.•Bichmann Leon•Kohlbacher Oliver等 23 人
British Journal Of Cancer
2023
•2023/2/23
•00 p.1-11
The immune peptidome of OPSCC has not previously been studied. Cancer-antigen specific vaccination may improve clinical outcome and efficacy of immune checkpoint inhibitors such as PD1/PD-L1 antibodies. Mapping of the OPSCC HLA ligandome was performed by mass spectrometry (MS) based analysis of natu...
Translational researchTumour immunology
10.1038/S41416-023-02197-Y
ISSN:0007-0920
Wdr47, Camsaps, and Katanin cooperate to generate ciliary central microtubules
Liu Hao•Zheng Jianqun•Zhu Lei•Xie Lele•Chen Yawen等 12 人
Nature Communications
2021
•2021/10/4
•Vol.12 No.1 p.1-15
The axonemal central pair (CP) are non-centrosomal microtubules critical for planar ciliary beat. How they form, however, is poorly understood. Here, we show that mammalian CP formation requires Wdr47, Camsaps, and microtubule-severing activity of Katanin. Katanin severs peripheral microtubules to p...
CiliaCiliogenesisMicrotubules
10.1038/S41467-021-26058-5
ISSN:2041-1723
Cardiomyocyte mitochondrial mono-ADP-ribosylation dictates cardiac tolerance to sepsis by configuring bioenergetic reserve in male mice
Xiaoqiang Chen•Tianyou Yuan•Danchuan Zheng•Fangfang Li•Hao Xu等 8 人
Nature Communications
2025
•2025/8/30
•Vol.16 No.1 p.1-20
The metabolic flexibility of tissues determines the degree and reversibility of organ damage during inflammatory challenges. However, effective treatments for myocardial metabolic dysfunction in septic cardiomyopathy (SCM) are unavailable. Nicotinamide adenine dinucleotide-dependent signaling is fun...
Heart failureMechanisms of diseasePost-translational modifications
10.1038/S41467-025-62384-8
ISSN:2041-1723
Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma
Yan Zhou•Yingrui Wang•Xiao Shi•Jiatong Wang•Zelin Zang等 26 人
Nature Communications
2026
•2026/1/14
•Vol.17 No.1 p.4320
Medullary thyroid carcinoma (MTC) is a rare, aggressive neuroendocrine tumor with limited treatment options and frequent recurrence. Comprehensive recurrence risk stratification remains lacking. Here, we profile 482 MTC samples from 452 patients across ten Chinese clinical centers, identifying 10,09...
Prognostic markersProteomicsThyroid cancerThyroid diseasesTumour biomarkers
10.1038/S41467-025-67533-7
ISSN:2041-1723
Two KaiABC systems control circadian oscillations in one cyanobacterium
Christin Köbler•Nicolas M. Schmelling•Anika Wiegard•Alice Pawlowski•Gopal K. Pattanayak等 15 人
Nature Communications
2024
•2024/9/3
•Vol.15 No.1 p.1-20
The circadian clock of cyanobacteria, which predicts daily environmental changes, typically includes a standard oscillator consisting of proteins KaiA, KaiB, and KaiC. However, several cyanobacteria have diverse Kai protein homologs of unclear function. In particular, Synechocystis sp. PCC 6803 harb...
Bacterial geneticsBacterial physiologyCircadian rhythmsPhosphorylation
10.1038/S41467-024-51914-5
ISSN:2041-1723
Electrostatic and steric effects underlie acetylation-induced changes in ubiquitin structure and function
Kienle Simon Maria•Schneider Tobias•Stuber Katrin•Globisch Christoph•Jansen Jasmin等 10 人
Nature Communications
2022
•2022/9/16
•Vol.13 No.1 p.1-16
Covalent attachment of ubiquitin (Ub) to proteins is a highly versatile posttranslational modification. Moreover, Ub is not only a modifier but itself is modified by phosphorylation and lysine acetylation. However, the functional consequences of Ub acetylation are poorly understood. By generation an...
Protein–protein interaction networksSolution-state NMRUbiquitins
10.1038/S41467-022-33087-1
ISSN:2041-1723
A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex
Hong-Wei Zhang•Kun Huang•Zhan-Xi Gu•Xiao-Xian Wu•Jia-Wei Wang等 6 人
Nature Communications
2023
•2023/5/30
•Vol.14 No.1 p.1-11
De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. Th...
Cryoelectron microscopyDNA methylation
10.1038/S41467-023-38619-X
ISSN:2041-1723
A circular RNA activated by TGFβ promotes tumor metastasis through enhancing IGF2BP3-mediated PDPN mRNA stability
Ke Li•Jiawei Guo•Yue Ming•Shuang Chen•Tingting Zhang等 10 人
Nature Communications
2023
•2023/10/28
•Vol.14 No.1 p.1-18
Metastasis is the leading cause of cancer-related death, where TGFβ-induced epithelial-mesenchymal transition (EMT) process confers on cancer cells increased metastatic potential. However, the involvement of circRNAs in this process is still obscure. Here, we identify a TGFβ-induced circRNA called c...
Epithelial–mesenchymal transitionMetastasisNon-coding RNAs
10.1038/S41467-023-42571-1
ISSN:2041-1723
Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona
John E. Blume•William C. Manning•Gregory Troiano•Daniel Hornburg•Michael Figa等 25 人
Nature Communications
2020
•2020/7/22
•Vol.11 No.1 p.1-14
Large-scale, unbiased proteomics studies are constrained by the complexity of the plasma proteome. Here we report a highly parallel protein quantitation platform integrating nanoparticle (NP) protein coronas with liquid chromatography-mass spectrometry for efficient proteomic profiling. A protein co...
Blood proteinsMass spectrometryNanoparticlesNon-small-cell lung cancerProteomics
10.1038/S41467-020-17033-7
ISSN:2041-1723
iJAZ-based approach to engineer lepidopteran pest resistance in multiple crop species
Huijuan Mo•Huimin Chang•Ge Zhao•Guanjing Hu•Xiumei Luo等 13 人
Nature Plants
2024
•2024/4/29
•00 p.1-14
The fall armyworm (FAW) poses a significant threat to global crop production. Here we showed that overexpression of jasmonate ZIM-domain (JAZ) protein GhJAZ24 confers resistance to cotton bollworm and FAW, while also causing sterility in transgenic cotton by recruiting TOPLESS and histone deacetylas...
Molecular engineering in plantsPlant molecular biology
10.1038/S41477-024-01682-3
ISSN:2055-0278
Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness
Schiavoni Federica•Zuazua-Villar Pedro•Roumeliotis Theodoros I.•Benstead-Hume Graeme•Pardo Mercedes等 8 人
Nature Communications
2022
•2022/4/1
•Vol.13 No.1 p.1-15
Aneuploidy results in decreased cellular fitness in many species and model systems. However, aneuploidy is commonly found in cancer cells and often correlates with aggressive growth, suggesting that the impact of aneuploidy on cellular fitness is context dependent. The BRG1 (SMARCA4) subunit of the ...
BiochemistryCell biologyMolecular biology
10.1038/S41467-022-29420-3
ISSN:2041-1723
Brain neuron-derived WDFY1 induces bone loss
Chun-Yuan Chen•Zun Wang•Chun-Gu Hong•Yi-Juan Tan•Yan-Xin Duan等 23 人
Nature Aging
2026
•2026/1/5
•Vol.6 No.2 p.329-348
Brain health is closely linked to bone homeostasis. Skeletal aging is characterized by inadequate bone formation and marrow adiposity, but whether the brain contributes to this imbalance remains unknown. This study shows that aged brain neurons, mainly those in the hippocampus and cerebral cortex, p...
AgeingMetabolic disordersNeuroendocrine diseases
10.1038/S43587-025-01032-8
ISSN:2662-8465
Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber
Live H. Hagen•Charles G. Brooke•Claire A. Shaw•Angela D. Norbeck•Hailan Piao等 20 人
The Isme Journal
2020
•2020/9/14
•Vol.15 No.2 p.421-434
The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. Whil...
FungiMicrobial ecologyMicrobiome
10.1038/S41396-020-00769-X
ISSN:1751-7362
Dual-site molecular glues for enhancing protein-protein interactions of the CDK12-DDB1 complex
Zemin Zhang•Yuanqing Li•Jie Yang•Jiacheng Li•Xiongqiang Lin等 20 人
Nature Communications
2024
•2024/8/1
•Vol.15 No.1 p.1-13
Protein-protein interactions (PPIs) stabilization with molecular glues plays a crucial role in drug discovery, albeit with significant challenges. In this study, we propose a dual-site approach, targeting the PPI region and its dynamic surroundings. We conduct molecular dynamics simulations to ident...
Chemical modificationProteinsSmall molecules
10.1038/S41467-024-50642-0
ISSN:2041-1723
ULK1-dependent phosphorylation of PKM2 antagonizes O-GlcNAcylation and regulates the Warburg effect in breast cancer
Zibin Zhou•Xiyuan Zheng•Jianxin Zhao•Aiyun Yuan•Zhuan Lv等 11 人
Oncogene
2024
•2024/4/17
•00 p.1-10
Pyruvate kinase M2 (PKM2) is a central metabolic enzyme driving the Warburg effect in tumor growth. Previous investigations have demonstrated that PKM2 is subject to O-linked β-N-acetylglucosamine (O-GlcNAc) modification, which is a nutrient-sensitive post-translational modification. Here we found t...
GlycobiologyPhosphorylation
10.1038/S41388-024-03035-Y
ISSN:0950-9232
Gefitinib and fostamatinib target EGFR and SYK to attenuate silicosis: a multi-omics study with drug exploration
Wang Mingyao•Zhang Zhe•Liu Jiangfeng•Song Meiyue•Zhang Tiantian等 18 人
Signal Transduction And Targeted Therapy
2022
•2022/5/13
•Vol.7 No.1 p.1-13
Silicosis is the most prevalent and fatal occupational disease with no effective therapeutics, and currently used drugs cannot reverse the disease progress. Worse still, there are still challenges to be addressed to fully decipher the intricated pathogenesis. Thus, specifying the essential mechanism...
Molecular medicineRespiratory tract diseasesTranslational research
10.1038/S41392-022-00959-3
ISSN:2059-3635
Diurnal oscillations of endogenous H 2 O 2 sustained by p66 Shc regulate circadian clocks
Jian-Fei Pei•Xun-Kai Li•Wen-Qi Li•Qian Gao•Yang Zhang等 19 人
Nature Cell Biology
2019
•2019/11/25
•Vol.21 No.12 p.1553-1564
Redox balance, an essential feature of healthy physiological steady states, is regulated by circadian clocks, but whether or how endogenous redox signalling conversely regulates clockworks in mammals remains unknown. Here, we report circadian rhythms in the levels of endogenous H2O2 in mammalian cel...
Circadian rhythm signalling peptides and proteinsCircadian rhythmsPost-translational modifications
10.1038/S41556-019-0420-4
ISSN:1465-7392
Nucleophilic covalent ligand discovery for the cysteine redoxome
Ling Fu•Youngeun Jung•Caiping Tian•Renan B. Ferreira•Ruifeng Cheng等 8 人
Nature Chemical Biology
2023
•2023/5/29
•00 p.1-11
With an eye toward expanding chemistries used for covalent ligand discovery, we elaborated an umpolung strategy that exploits the ‘polarity reversal’ of sulfur when cysteine is oxidized to sulfenic acid, a widespread post-translational modification, for selective bioconjugation with C-nucleophiles. ...
Cell signallingDNA damage and repairPost-translational modificationsProteomicsSmall molecules
10.1038/S41589-023-01330-5
ISSN:1552-4450
Coagulation factor IX analysis in bioreactor cell culture supernatant predicts quality of the purified product
Lucia F. Zacchi•Dinora Roche-Recinos•Cassandra L. Pegg•Toan K. Phung•Mark Napoli等 11 人
Communications Biology
2021
•2021/3/23
•Vol.4 No.1 p.1-19
Coagulation factor IX (FIX) is a complex post-translationally modified human serum glycoprotein and high-value biopharmaceutical. The quality of recombinant FIX (rFIX), especially complete γ-carboxylation, is critical for rFIX clinical efficacy. Bioreactor operating conditions can impact rFIX produc...
BiologicsProteomics
10.1038/S42003-021-01903-X
ISSN:2399-3642
Receptor discovery for nanomaterial soft and hard coronas via a biosensor-based Fishing strategy
Didar Baimanov•Jing Wang•Chunying Chen•Liming Wang
Nature Protocols
2026
•2026/5/7
•00 p.1-46
Upon exposure to biological fluids, nanomaterials rapidly acquire dynamic layers of adsorbed proteins called the protein corona, redefining the biological identity of nanomaterials and governing their in vivo fate. While corona composition has been extensively profiled, two aspects remain poorly und...
Blood proteinsDrug deliveryNanoparticlesProteomic analysis
10.1038/S41596-026-01358-6
ISSN:1754-2189
TcrXY is an acid-sensing two-component transcriptional regulator of Mycobacterium tuberculosis required for persistent infection
Miljan Stupar•Lendl Tan•Edward D. Kerr•Christopher J. De Voss•Brian M. Forde等 7 人
Nature Communications
2024
•2024/2/22
•Vol.15 No.1 p.1-14
The ability of Mycobacterium tuberculosis (Mtb) to persist in the host complicates and prolongs tuberculosis (TB) patient chemotherapy. Here we demonstrate that a neglected two-component system (TCS) of Mtb, TcrXY, is an autoregulated acid-sensing TCS that controls a functionally diverse 70-gene reg...
Bacterial geneticsCellular microbiologyPathogensTuberculosis
10.1038/S41467-024-45343-7
ISSN:2041-1723
Allergen protease-activated stress granule assembly and gasdermin D fragmentation control interleukin-33 secretion
Chen Wen•Chen Shuangfeng•Yan Chenghua•Zhang Yaguang•Zhang Ronghua等 26 人
Nature Immunology
2022
•2022/7/6
•Vol.23 No.7 p.1021-1030
Interleukin-33 (IL-33), an epithelial cell-derived cytokine that responds rapidly to environmental insult, has a critical role in initiating airway inflammatory diseases. However, the molecular mechanism underlying IL-33 secretion following allergen exposure is not clear. Here, we found that two cel...
Innate lymphoid cellsInterleukins
10.1038/S41590-022-01255-6
ISSN:1529-2908
Global detection of human variants and isoforms by deep proteome sequencing
Sinitcyn Pavel•Richards Alicia L.•Weatheritt Robert J.•Brademan Dain R.•Marx Harald等 12 人
Nature Biotechnology
2023
•2023/3/23
•00 p.1-11
An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically identified by peptide sequences representing a small fraction of their total amino acids. Hence, an average shotgun experiment fails to distinguish di...
Data integrationProteome informaticsProteomics
10.1038/S41587-023-01714-X
ISSN:1087-0156
SIRT2 regulates extracellular vesicle-mediated liver–bone communication
Longshuai Lin•Zengya Guo•Enjun He•Xidai Long•Difei Wang等 16 人
Nature Metabolism
2023
•2023/5/15
•00 p.1-21
The interplay between liver and bone metabolism remains largely uncharacterized. Here, we uncover a mechanism of liver-bone crosstalk regulated by hepatocyte SIRT2. We demonstrate that hepatocyte SIRT2 expression is increased in aged mice and elderly humans. Liver-specific SIRT2 deficiency inhibits ...
AgeingBoneMetabolismOsteoporosis
10.1038/S42255-023-00803-0
ISSN:2522-5812
USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation
Na Shao•Lei Xi•Yangfan Lv•Muhammad Idris•Lin Zhang等 14 人
Nature Communications
2025
•2025/2/3
•Vol.16 No.1 p.1-18
The N6-methyladenosine binding protein YTHDF1, often upregulated in cancer, promotes tumor growth and hinders immune checkpoint blockade treatment. A comprehensive understanding of the molecular mechanisms governing YTHDF1 protein stability is pivotal for enhancing clinical response rates and the ef...
Targeted therapiesUbiquitylation
10.1038/S41467-025-56564-9
ISSN:2041-1723
Insulin signalling regulates Pink1 mRNA localization via modulation of AMPK activity to support PINK1 function in neurons
J. Tabitha Hees•Simone Wanderoy•Jana Lindner•Marlena Helms•Hariharan Murali Mahadevan等 6 人
Nature Metabolism
2024
•2024/3/19
•Vol.6 No.3 p.514-530
Mitochondrial quality control failure is frequently observed in neurodegenerative diseases. The detection of damaged mitochondria by stabilization of PTEN-induced kinase 1 (PINK1) requires transport of Pink1 messenger RNA (mRNA) by tethering it to the mitochondrial surface. Here, we report that inhi...
Alzheimer's diseaseCellular neuroscienceInsulin signallingMetabolismMitophagy
10.1038/S42255-024-01007-W
ISSN:2522-5812
Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis
Chen Wang•Cheng Ma•Yuanyou Xu•Shenghai Chang•Hangjun Wu等 17 人
Nature Communications
2025
•2025/1/22
•Vol.16 No.1 p.1-15
The multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all components have been individually characterized, the intact PDHc structure remains unclear, hampering our unde...
BiocatalysisComputational biophysicsCryoelectron tomographySupramolecular assembly
10.1038/S41467-025-56171-8
ISSN:2041-1723
Semaphorin 3C (Sema3C) reshapes stromal microenvironment to promote hepatocellular carcinoma progression
Hao Peng•Meng Yang•Kun Feng•Qingpeng Lv•Yewei Zhang
Signal Transduction And Targeted Therapy
2024
•2024/7/3
•Vol.9 No.1 p.1-20
More than 90% of hepatocellular carcinoma (HCC) cases develop in the presence of fibrosis or cirrhosis, making the tumor microenvironment (TME) of HCC distinctive due to the intricate interplay between cancer-associated fibroblasts (CAFs) and cancer stem cells (CSCs), which collectively regulate HCC...
Cancer microenvironmentCancer stem cells
10.1038/S41392-024-01887-0
ISSN:2059-3635
Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer
Xiaocui Lu•Xiuyun Wang•Zheng Yang•Xusheng Wang•Lin Wang等 21 人
Nature
2026
•2026/6/10
•00 p.1-10
BRAF gain-of-function mutations, particularly BRAF(V600E), affect roughly 10% of all patients with colorectal cancer (CRC), and portend poor prognosis with limited therapeutic interventions. BRAF inhibitors such as encorafenib are ineffective due to MAPK pathway reactivation driven by BRAF dimerizat...
Targeted therapies
10.1038/S41586-026-10613-5
ISSN:0028-0836
Chemoproteomic mapping of the glycolytic targetome in cancer cells
Yang Tian•Ning Wan•Hanqing Zhang•Chang Shao•Ming Ding等 14 人
Nature Chemical Biology
2023
•2023/6/15
•00 p.1-12
Hyperactivated glycolysis is a metabolic hallmark of most cancer cells. Although sporadic information has revealed that glycolytic metabolites possess nonmetabolic functions as signaling molecules, how these metabolites interact with and functionally regulate their binding targets remains largely el...
CancerMetabolismProteomicsTarget identification
10.1038/S41589-023-01355-W
ISSN:1552-4450
A Cullin 5-based complex serves as an essential modulator of ORF9b stability in SARS-CoV-2 replication
Yuzheng Zhou•Zongpeng Chen•Sijie Liu•Sixu Liu•Yujie Liao等 25 人
Signal Transduction And Targeted Therapy
2024
•2024/6/28
•Vol.9 No.1 p.1-18
The ORF9b protein, derived from the nucleocapsid’s open-reading frame in both SARS-CoV and SARS-CoV-2, serves as an accessory protein crucial for viral immune evasion by inhibiting the innate immune response. Despite its significance, the precise regulatory mechanisms underlying its function remain ...
InfectionMicrobiologyMolecular biology
10.1038/S41392-024-01874-5
ISSN:2059-3635
MTH1 protects platelet mitochondria from oxidative damage and regulates platelet function and thrombosis
Yangyang Ding•Xiang Gui•Xiang Chu•Yueyue Sun•Sixuan Zhang等 16 人
Nature Communications
2023
•2023/8/10
•Vol.14 No.1 p.1-15
Human MutT Homolog 1 (MTH1) is a nucleotide pool sanitization enzyme that hydrolyzes oxidized nucleotides to prevent their mis-incorporation into DNA under oxidative stress. Expression and functional roles of MTH1 in platelets are not known. Here, we show MTH1 expression in platelets and its deficie...
Cell signallingPlateletsThrombosis
10.1038/S41467-023-40600-7
ISSN:2041-1723
Systematic detection of functional proteoform groups from bottom-up proteomic datasets
Isabell Bludau•Max Frank•Christian Dörig•Yujia Cai•Moritz Heusel等 10 人
Nature Communications
2021
•2021/6/21
•Vol.12 No.1 p.1-18
To a large extent functional diversity in cells is achieved by the expansion of molecular complexity beyond that of the coding genome. Various processes create multiple distinct but related proteins per coding gene – so-called proteoforms – that expand the functional capacity of a cell. Evaluating p...
Mass spectrometryPost-translational modificationsProtein–protein interaction networksProteome informatics
10.1038/S41467-021-24030-X
ISSN:2041-1723
The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells
Vipat Sameera•Gupta Dipika•Jonchhe Sagun•Anderspuk Hele•Rothenberg Eli等 6 人
Nature Communications
2022
•2022/11/19
•Vol.13 No.1 p.1-15
DNA polymerase epsilon (PolE) in an enzyme essential for DNA replication. Deficiencies and mutations in PolE cause severe developmental abnormalities and cancers. Paradoxically, the catalytic domain of yeast PolE catalytic subunit is dispensable for survival, and its non-catalytic essential function...
Origin firingReplisome
10.1038/S41467-022-34911-4
ISSN:2041-1723
IDH1-mutant metabolite D-2-hydroxyglutarate inhibits proliferation and sensitizes glioma to temozolomide via down-regulating ITGB4/PI3K/AKT
Shuangmei Tong•Jian Wu•Yun Song•Wenhuan Fu•Yifan Yuan等 8 人
Cell Death Discovery
2024
•2024/7/9
•Vol.10 No.1 p.1-17
The heterogeneous molecular subtypes of gliomas demonstrate varied responses to chemotherapy and distinct prognostic outcomes. Gliomas with Isocitrate dehydrogenase 1 (IDH1) mutation are associated with better outcomes and are more responsive to temozolomide (TMZ) compared to those without IDH1 muta...
Cancer therapyCNS cancer
10.1038/S41420-024-02088-Y
ISSN:2058-7716
Spermidine mediates acetylhypusination of RIPK1 to suppress diabetes onset and progression
Tian Zhang•Weixin Fu•Haosong Zhang•Jianlong Li•Beizi Xing等 32 人
Nature Cell Biology
2024
•2024/11/7
•00 p.1-16
It has been established that N-acetyltransferase (murine NAT1 (mNAT1) and human NAT2 (hNAT2)) mediates insulin sensitivity in type 2 diabetes. Here we show that mNAT1 deficiency leads to a decrease in cellular spermidine—a natural polyamine exhibiting health-protective and anti-ageing effects—but un...
Cell deathMetabolic disorders
10.1038/S41556-024-01540-6
ISSN:1465-7392
Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral
Fränze Müller•Micha J. Birklbauer•Julia Bubis•Karel Stejskal•Viktoria Dorfer等 6 人
Nature Communications
2025
•2025/11/10
•Vol.16 No.1 p.98770
Crosslinking mass spectrometry is an essential tool for probing protein-protein interactions and structural organization. We here compare Orbitrap Astral and Orbitrap Eclipse instruments using Cas9 crosslinked with PhoX and DSSO under standardized chromatographic and acquisition conditions. The Astr...
Protein–protein interaction networksProteomics
10.1038/S41467-025-64844-7
ISSN:2041-1723
AQP7 deficiency drives adipose tissue remodeling and disrupts homeostasis
Ines PD Costa•Guglielmo Schiano•Juan Manuel Sacnun•Rebecca Herzog•Alastair Kerr等 9 人
Npj Metabolic Health And Disease
2025
•2025/11/7
•Vol.3 No.1 p.1-13
The aquaporin-7 (AQP7) channel mediates glycerol release from adipocytes. Genetic variants decreasing AQP7 expression are associated with adiposity and metabolic complications in humans. Using human data, mouse models, and cellular systems, we investigated how AQP7 influences adipose tissue maturati...
Endocrine system and metabolic diseasesMetabolic disordersMetabolic syndromeMetabolismObesity
10.1038/S44324-025-00085-Y
ISSN:2948-2828
Photoproximity labeling of endogenous receptors in the live mouse brain in minutes
Mikiko Takato•Seiji Sakamoto•Hiroshi Nonaka•Fátima Yuri Tanimura Valor•Tomonori Tamura等 6 人
Nature Chemical Biology
2024
•2024/8/1
•00 p.1-11
Understanding how protein–protein interaction networks in the brain give rise to cognitive functions necessitates their characterization in live animals. However, tools available for this purpose require potentially disruptive genetic modifications and lack the temporal resolution necessary to track...
Chemical toolsMolecular neuroscienceProtein–protein interaction networks
10.1038/S41589-024-01692-4
ISSN:1552-4450
Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate
Yu-Qing Wu•Chen-Song Zhang•Jinye Xiong•Dong-Qi Cai•Chen-Zhe Wang等 31 人
Cell Research
2023
•2023/9/19
•00 p.1-16
Glycolytic intermediary metabolites such as fructose-1,6-bisphosphate can serve as signals, controlling metabolic states beyond energy metabolism. However, whether glycolytic metabolites also play a role in controlling cell fate remains unexplored. Here, we find that low levels of glycolytic metabol...
ApoptosisCancerNutrient signalling
10.1038/S41422-023-00874-4
ISSN:1748-7838
Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators
Pennemann Friederike L.•Mussabekova Assel•Urban Christian•Stukalov Alexey•Andersen Line Lykke等 18 人
Nature Communications
2021
•2021/12/1
•Vol.12 No.1 p.1-22
The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins t...
InterferonsPattern recognition receptorsVirology
10.1038/S41467-021-27192-W
ISSN:2041-1723
Disruption of TEX38 impairs sperm morphogenesis and the migration of sperm into the oviduct
Lu Yuan•Tingting Ge•Ling Yang•Wenhua Xu•Guanghua Li等 14 人
Communications Biology
2025
•2025/8/9
•Vol.8 No.1 p.1-20
In male reproduction, spermatogenesis and sperm maturation are critical for the production of normal sperm and offspring, yet the underlying molecular mechanisms remain largely elusive. Tex38 is a testis-enriched gene, and its deficiency results in oligoasthenoteratospermia (OAT) with aberrant epidi...
CiliogenesisDevelopmentProtein–protein interaction networks
10.1038/S42003-025-08644-1
ISSN:2399-3642
DTX3L-mediated TIRR nuclear export and degradation regulates DNA repair pathway choice and PARP inhibitor sensitivity
Qi Ye•Jian Ma•Zixi Wang•Lei Li•Tianjie Liu等 17 人
Nature Communications
2024
•2024/12/5
•Vol.15 No.1 p.1-15
53BP1 plays an important role in DNA double-strand break (DSB) repair and this activity is negatively regulated by its interaction with Tudor interacting repair regulator (TIRR). However, how the TIRR-53BP1 repair axis is regulated in response to DNA damage remains elusive. Here, we demonstrate that...
DNA damage responseProtein translocation
10.1038/S41467-024-54978-5
ISSN:2041-1723
Preserving ester-linked modifications reveals glutamate and aspartate mono-ADP-ribosylation by PARP1 and its reversal by PARG
Edoardo José Longarini•Ivan Matić
Nature Communications
2024
•2024/5/18
•Vol.15 No.1 p.1-17
Ester-linked post-translational modifications, including serine and threonine ubiquitination, have gained recognition as important cellular signals. However, their detection remains a significant challenge due to the chemical lability of the ester bond. This is the case even for long-known modificat...
Enzyme mechanismsPolyADP-ribosylationProteomics
10.1038/S41467-024-48314-0
ISSN:2041-1723
Integrated proteogenomic characterization across major histological types of pituitary neuroendocrine tumors
Zhang Fan•Zhang Qilin•Zhu Jiajun•Yao Boyuan•Ma Chi等 24 人
Cell Research
2022
•2022/10/28
•Vol.32 No.12 p.1047-1067
Pituitary neuroendocrine tumor (PitNET) is one of the most common intracranial tumors. Due to its extensive tumor heterogeneity and the lack of high-quality tissues for biomarker discovery, the causative molecular mechanisms are far from being fully defined. Therefore, more studies are needed to imp...
Pituitary tumoursProteomic analysis
10.1038/S41422-022-00736-5
ISSN:1748-7838
Distinct proteostasis circuits cooperate in nuclear and cytoplasmic protein quality control
Rahul S. Samant•Christine M. Livingston•Emily M. Sontag•Judith Frydman
Nature
2018
•2018/10/31
•Vol.563 No.7731 p.407-411
Protein misfolding is linked to a wide array of human disorders, including Alzheimer’s disease, Parkinson’s disease and type II diabetes1,2. Protective cellular protein quality control (PQC) mechanisms have evolved to selectively recognize misfolded proteins and limit their toxic effects3–9, thus co...
ChaperonesProtein quality controlUbiquitin ligasesUbiquitylation
10.1038/S41586-018-0678-X
ISSN:0028-0836
FBXO7 ubiquitinates PRMT1 to suppress serine synthesis and tumor growth in hepatocellular carcinoma
Li Luo•Xingyun Wu•Jiawu Fan•Lixia Dong•Mao Wang等 10 人
Nature Communications
2024
•2024/6/5
•Vol.15 No.1 p.1-15
Cancer cells are often addicted to serine synthesis to support growth. How serine synthesis is regulated in cancer is not well understood. We recently demonstrated protein arginine methyltransferase 1 (PRMT1) is upregulated in hepatocellular carcinoma (HCC) to methylate and activate phosphoglycerate...
Cancer metabolismHepatocellular carcinomaUbiquitylation
10.1038/S41467-024-49087-2
ISSN:2041-1723
High-throughput chemical proteomics workflow for profiling protein citrullination dynamics
Rebecca Meelker González•Sophia Laposchan•Erik Riedel•Anna Fürst•Naomi O’Sullivan等 11 人
Nature Communications
2026
•2026/2/21
•Vol.17 No.1 p.19820
Citrullination is a post-translational modification implicated in autoimmune and inflammatory diseases, yet its low abundance and lack of effective enrichment tools have limited proteome-wide analysis. Here, we develop a robust chemical proteomics workflow with improved specificity and throughput. T...
Post-translational modificationsProteomic analysis
10.1038/S41467-026-69490-1
ISSN:2041-1723
dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts
Demichev Vadim•Szyrwiel Lukasz•Yu Fengchao•Teo Guo Ci•Rosenberger George等 13 人
Nature Communications
2022
•2022/7/8
•Vol.13 No.1 p.1-8
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and increase sensitivity in proteomic experiments. Here we present a two-dimensional peak-picking algorithm and generation of optimized spectral libraries, as well as take advantage of neural network-based processin...
ProteinsProteomic analysisSoftware
10.1038/S41467-022-31492-0
ISSN:2041-1723
Signature-driven repurposing of Midostaurin for combination with MEK1/2 and KRASG12C inhibitors in lung cancer
Irati Macaya•Marta Roman•Connor Welch•Rodrigo Entrialgo-Cadierno•Marina Salmon等 32 人
Nature Communications
2023
•2023/10/10
•Vol.14 No.1 p.1-19
Drug combinations are key to circumvent resistance mechanisms compromising response to single anti-cancer targeted therapies. The implementation of combinatorial approaches involving MEK1/2 or KRASG12C inhibitors in the context of KRAS-mutated lung cancers focuses fundamentally on targeting KRAS pro...
CancerLung cancerTargeted therapies
10.1038/S41467-023-41828-Z
ISSN:2041-1723
TANGO2 binds crystallin alpha B and its loss causes desminopathy
Maike Stentenbach•Laetitia A. Hughes•Samuel V. Fagan•Blake Payne•Danielle L. Rudler等 20 人
Nature Communications
2025
•2025/6/6
•Vol.16 No.1 p.1-17
Mutations in the TANGO2 gene cause an autosomal recessive disorder characterised by developmental delay, stress-induced episodic rhabdomyolysis, and cardiac arrhythmias along with severe metabolic crises. Although TANGO2 mutations result in a well characterised disease pathology, the function of TAN...
CardiologyGeneticsIntermediate filaments
10.1038/S41467-025-60563-1
ISSN:2041-1723
Circular RNA circBNC2 inhibits epithelial cell G2-M arrest to prevent fibrotic maladaptive repair
Wang Peng•Huang Zhitao•Peng Yili•Li Hongwei•Lin Tong等 11 人
Nature Communications
2022
•2022/10/31
•Vol.13 No.1 p.1-19
The mechanisms underlying fibrogenic responses after injury are not well understood. Epithelial cell cycle arrest in G2/M after injury is a key checkpoint for determining wound-healing leading to either normal cell proliferation or fibrosis. Here, we identify a kidney- and liver-enriched circular RN...
Acute kidney injuryMechanisms of diseaseMolecular medicineRenal fibrosis
10.1038/S41467-022-34287-5
ISSN:2041-1723
Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale
Steger Martin•Demichev Vadim•Backman Mattias•Ohmayer Uli•Ihmor Phillip等 8 人
Nature Communications
2021
•2021/9/13
•Vol.12 No.1 p.1-13
Mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with data-independent acquisition (DIA)-MS and neural netw...
Mass spectrometryProteomicsTime seriesUbiquitylation
10.1038/S41467-021-25454-1
ISSN:2041-1723
Chimeric exosomes-derived immunomodulator restoring lymph nodes microenvironment for sensitizing TNBC immunotherapy
Mengchi Sun•Yuxia Wu•Zhichao Chen•Boyan Zhang•Xiaoyang Liu等 14 人
Nature Communications
2025
•2025/8/2
•Vol.16 No.1 p.1-16
Immunotherapy is a breakthrough in the treatment of triple-negative breast cancer (TNBC), although it is only effective in a portion of patients. Our clinical studies find that pathological elevated level of reactive oxygen species (ROS) and lipid homeostasis imbalance are closely associated with dy...
Breast cancerCancer immunotherapyDrug delivery
10.1038/S41467-025-62543-X
ISSN:2041-1723
Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance
Ying Xiang•Kunpeng Zhu•Kaiyuan Min•Yaowen Zhang•Jiangfeng Liu等 32 人
Nature Communications
2024
•2024/7/20
•Vol.15 No.1 p.1-15
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-g...
BacteriaBacterial infection
10.1038/S41467-024-50331-Y
ISSN:2041-1723
OTUB1 promotes osteoblastic bone formation through stabilizing FGFR2
Zhu Qiong•Fu Yesheng•Cui Chun-Ping•Ding Yi•Deng Zhikang等 15 人
Signal Transduction And Targeted Therapy
2023
•2023/4/7
•Vol.8 No.1 p.1-13
Bone homeostasis is maintained by the balance between osteoblastic bone formation and osteoclastic bone resorption. Dysregulation of this process leads to multiple diseases, including osteoporosis. However, the underlying molecular mechanisms are not fully understood. Here, we show that the global a...
AgeingBone development
10.1038/S41392-023-01354-2
ISSN:2059-3635
Lithocholic acid phenocopies anti-ageing effects of calorie restriction
Qi Qu•Yan Chen•Yu Wang•Shating Long•Weiche Wang等 27 人
Nature
2024
•2024/12/18
•00 p.1-9
Calorie restriction (CR) is a dietary intervention used to promote health and longevity1,2. CR causes various metabolic changes in both the production and the circulation of metabolites1; however, it remains unclear which altered metabolites account for the physiological benefits of CR. Here we...
AgeingMetabolismMetabolomicsNutrient signalling
10.1038/S41586-024-08329-5
ISSN:0028-0836
PARylation of 14-3-3 proteins controls the virulence of Magnaporthe oryzae
Xiuqin Gao•Gaigai Gao•Weifeng Zheng•Haibing Liu•Wenbo Pan等 10 人
Nature Communications
2024
•2024/9/14
•Vol.15 No.1 p.1-18
Magnaporthe oryzae is a devastating fungal pathogen that causes the rice blast disease worldwide. The post-translational modification of ADP-ribosylation holds significant importance in various fundamental biological processes. However, the specific function of this modification in M. oryzae remains...
CheckpointsPathogensPolyADP-ribosylation
10.1038/S41467-024-51955-W
ISSN:2041-1723
A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription
Ekaterini Platanitis•Duygu Demiroz•Anja Schneller•Katrin Fischer•Christophe Capelle等 10 人
Nature Communications
2019
•2019/7/2
•Vol.10 No.1 p.1-17
Cells maintain the balance between homeostasis and inflammation by adapting and integrating the activity of intracellular signaling cascades, including the JAK-STAT pathway. Our understanding of how a tailored switch from homeostasis to a strong receptor-dependent response is coordinated remains lim...
Gene regulation in immune cellsInnate immunityInterferonsProteomicsTranscriptomics
10.1038/S41467-019-10970-Y
ISSN:2041-1723
TREX reveals proteins that bind to specific RNA regions in living cells
Martin Dodel•Giulia Guiducci•Maria Dermit•Sneha Krishnamurthy•Emilie L. Alard等 9 人
Nature Methods
2024
•2024/2/19
•Vol.21 No.3 p.423-434
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA region...
Mass spectrometryRNA
10.1038/S41592-024-02181-1
ISSN:1548-7091
Identification of pimavanserin tartrate as a potent Ca2+-calcineurin-NFAT pathway inhibitor for glioblastoma therapy
Liu Zhen-zhen•Liu Xiao-ning•Fan Rui-cheng•Jia Yu-ping•Zhang Qing-ke等 13 人
Acta Pharmacologica Sinica
2021
•2021/8/6
•00 p.1-15
Glioblastoma multiforme (GBM) is the most common and malignant type of primary brain tumor, and 95% of patients die within 2 years after diagnosis. In this study, aiming to overcome chemoresistance to the first-line drug temozolomide (TMZ), we carried out research to discover a novel alternative dru...
Biomedicine, generalPharmacology/ToxicologyMedical MicrobiologyImmunologyInternal MedicineVaccine
10.1038/S41401-021-00724-2
ISSN:1671-4083
Tumor-agnostic cancer therapy using antibodies targeting oncofetal chondroitin sulfate
Elena Ethel Vidal-Calvo•Anne Martin-Salazar•Swati Choudhary•Robert Dagil•Sai Sundar Rajan Raghavan等 41 人
Nature Communications
2024
•2024/8/30
•Vol.15 No.1 p.1-20
Molecular similarities between embryonic and malignant cells can be exploited to target tumors through specific signatures absent in healthy adult tissues. One such embryonic signature tumors express is oncofetal chondroitin sulfate (ofCS), which supports disease progression and dissemination in can...
Cancer imagingCancer microenvironmentMolecular medicineTargeted therapiesTumour biomarkers
10.1038/S41467-024-51781-0
ISSN:2041-1723
tRF-Gln-CTG-026 ameliorates liver injury by alleviating global protein synthesis
Ying Sunyang•Li Pengcheng•Wang Jiaqiang•Chen Kaiqiong•Zou Yu等 13 人
Signal Transduction And Targeted Therapy
2023
•2023/4/3
•Vol.8 No.1 p.1-15
tsRNAs (tRNA-derived small RNAs), as products of the stress response, exert considerable influence on stress response and injury regulation. However, it remains largely unclear whether tsRNAs can ameliorate liver injury. Here, we demonstrate the roles of tsRNAs in alleviating liver injury by utilizi...
Cell biologyNon-coding RNAs
10.1038/S41392-023-01351-5
ISSN:2059-3635
A novel bystander effect in tamoxifen treatment: PPIB derived from ER+ cells attenuates ER− cells via endoplasmic reticulum stress-induced apoptosis
Tinglin Yang•Wenhui Li•Jun Zhou•Ming Xu•Ziwei Huang等 7 人
Cell Death & Disease
2024
•2024/2/15
•Vol.15 No.2 p.1-14
Tamoxifen (TAM) is the frontline therapy for estrogen receptor-positive (ER+) breast cancer in premenopausal women that interrupts ER signaling. As tumors with elevated heterogeneity, amounts of ER-negative (ER−) cells are present in ER+ breast cancer that cannot be directly killed by TAM. Despite c...
Breast cancerCancer therapy
10.1038/S41419-024-06539-3
ISSN:2041-4889
Cytoplasmic TRIM24 promotes colorectal cancer cell proliferation by activating Wnt/β-catenin signaling
Ya Wang•Yuanbing Yao•Zehong Liu•Shichao Long•Feng Yi等 12 人
Nature Communications
2025
•2025/9/29
•Vol.16 No.1 p.1-15
Aberrant activation of Wnt/β-catenin signaling is proposed as a major molecular mechanism underlying the occurrence and progression of colorectal cancer (CRC). However, the precise mechanisms controlling the accumulation of β-catenin protein in CRC cells remain incompletely understood. Here, we show...
Colon cancerOncogenes
10.1038/S41467-025-63685-8
ISSN:2041-1723
Modulation of virus-induced neuroinflammation by the autophagy receptor SHISA9 in mice
Zheng Yanyan•Wang Liqiu•Liu Qingxiang•Xian Huifang•Zhang Chenqiu等 9 人
Nature Microbiology
2023
•2023/4/20
•00 p.1-15
Microglia and astrocytes are subgroups of brain glia cells that support and protect neurons within the central nervous system (CNS). At early stages of viral infection in the CNS, they are predominant responding cells and lead to recruitment of peripheral immune cells for viral clearance. Inhibitor ...
AutophagyChronic inflammationUbiquitylationViral infection
10.1038/S41564-023-01357-3
ISSN:2058-5276
A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis
Tadasuke Tsukiyama•Juqi Zou•Jihoon Kim•Shohei Ogamino•Yuki Shino等 17 人
Nature Communications
2020
•2020/9/15
•Vol.11 No.1 p.1-16
Frequent mutation of the tumour suppressor RNF43 is observed in many cancers, particularly colon malignancies. RNF43, an E3 ubiquitin ligase, negatively regulates Wnt signalling by inducing degradation of the Wnt receptor Frizzled. In this study, we discover that RNF43 activity requires phosphorylat...
Cancer geneticsCancer modelsGrowth factor signallingTumour-suppressor proteinsUbiquitin ligases
10.1038/S41467-020-18257-3
ISSN:2041-1723
Calcium-mediated calreticulin-IRE1α interaction drives dynamic fluctuation of IRE1α activity under chronic endoplasmic reticulum stress
Jianwei Cao•Xudong Zhao•Yunxin Xu•Chen Yang•Yazhen Huo等 10 人
Nature Communications
2026
•2026/3/17
0The unfolded protein response (UPR) triggered by endoplasmic reticulum (ER) stress can be both pro-survival or pro-apoptotic, depending on the duration and intensity of the stress. ER stress under (patho)physiological conditions can last for long time, yet the dynamic regulation of the UPR under pro...
Calcium signallingEndoplasmic reticulumStress signalling
10.1038/S41467-026-70679-7
ISSN:2041-1723
Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction
Haofan Sun•Bin Fu•Xiaohong Qian•Ping Xu•Weijie Qin
Nature Communications
2024
•2024/1/29
•Vol.15 No.1 p.1-16
The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221...
Mass spectrometryNucleusProteomic analysisProteomicsRNA
10.1038/S41467-024-44987-9
ISSN:2041-1723
ST6Gal1 targets the ectodomain of ErbB2 in a site-specific manner and regulates gastric cancer cell sensitivity to trastuzumab
Henrique O. Duarte•Joana G. Rodrigues•Catarina Gomes•Paul J. Hensbergen•Agnes L. Hipgrave Ederveen等 15 人
Oncogene
2021
•2021/5/4
•Vol.40 No.21 p.3719-3733
The clinical performance of the therapeutic monoclonal antibody trastuzumab in the treatment of ErbB2-positive unresectable gastric cancer (GC) is severely hampered by the emergence of molecular resistance. Trastuzumab’s target epitope is localized within the extracellular domain of the oncogenic ce...
Gastric cancerGlycobiologyGlycosylationPrognostic markersProteomics
10.1038/S41388-021-01801-W
ISSN:0950-9232
Phosphoglycerate dehydrogenase stabilizes protein kinase C delta type mRNA to promote hepatocellular carcinoma progression
Bin Cheng•Pai Peng•Shi Chen•Rui Liu•Xiaosong Li等 10 人
Signal Transduction And Targeted Therapy
2025
•2025/7/18
•Vol.10 No.1 p.1-15
Metabolic reprogramming not only reshapes cellular bioenergetics but also profoundly influences RNA metabolism through metabolite signaling and the RNA-binding activities of metabolic enzymes. Emerging evidence highlights that certain metabolic enzymes act as RNA-binding proteins (RBPs) to regulate ...
Cell biologyMolecular biology
10.1038/S41392-025-02304-W
ISSN:2059-3635
Unveiling the impact of cGMP-dependent protein kinase of Neospora caninum on calcium fluxes and egress functions through quantitative phosphoproteome analysis
Xianmei Wang•Kun Guo•Zhili Shan•Zhu Ying•Zifu Zhu等 10 人
Communications Biology
2025
•2025/5/13
•Vol.8 No.1 p.1-15
Neospora caninum, a pathogen associated with abortion in pregnant cattle and motor nerve disorders in dogs, poses a substantial threat. Cyclic GMP-dependent protein kinase (PKG) functions as a central signal transduction hub in apicomplexan parasites. However, PKG has not been characterized in N. ca...
Cellular microbiologyPathogens
10.1038/S42003-025-08173-X
ISSN:2399-3642
Phosphorylation of caspases by a bacterial kinase inhibits host programmed cell death
Jinli Ge•Ying Wang•Xueyu Li•Qian Lu•Hangqian Yu等 11 人
Nature Communications
2024
•2024/9/30
•Vol.15 No.1 p.1-14
The intracellular bacterial pathogen Legionella pneumophila utilizes the Dot/Icm system to translocate over 330 effectors into the host cytosol. These virulence factors modify a variety of cell processes, including pathways involved in cell death and survival, to promote bacterial proliferation. Her...
ApoptosisBacterial infectionKinases
10.1038/S41467-024-52817-1
ISSN:2041-1723
Sensing of mitochondrial DNA by ZBP1 promotes RIPK3-mediated necroptosis and ferroptosis in response to diquat poisoning
Kunmei Lai•Junjie Wang•Siyi Lin•Zhimin Chen•Guo Lin等 12 人
Cell Death & Differentiation
2024
•2024/3/16
•00 p.1-16
Diquat (DQ) poisoning is a severe medical condition associated with life-threatening implications and multiorgan dysfunction. Despite its clinical significance, the precise underlying mechanism remains inadequately understood. This study elucidates that DQ induces instability in the mitochondrial ge...
Cell biologyDiseases
10.1038/S41418-024-01279-5
ISSN:1350-9047
Determinants of genome-wide distribution and evolution of uORFs in eukaryotes
Hong Zhang•Yirong Wang•Xinkai Wu•Xiaolu Tang•Changcheng Wu等 6 人
Nature Communications
2021
•2021/2/17
•Vol.12 No.1 p.1-17
Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic spec...
Functional genomicsGene regulationMolecular evolutionPopulation genetics
10.1038/S41467-021-21394-Y
ISSN:2041-1723
Leveraging pretrained deep protein language model to predict peptide collision cross section
Ayano Nakai-Kasai•Kosuke Ogata•Yasushi Ishihama•Toshiyuki Tanaka
Communications Chemistry
2025
•2025/5/6
•Vol.8 No.1 p.1-9
Collision cross section (CCS) of peptide ions provides an important separation dimension in liquid chromatography/tandem mass spectrometry-based proteomics that incorporates ion mobility spectrometry (IMS), and its accurate prediction is the basis for advanced proteomics workflows. This paper descri...
CheminformaticsComputational chemistryMass spectrometryProteomics
10.1038/S42004-025-01540-Z
ISSN:2399-3669
Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities
Sejin Oh•Jeonghun Yeom•Hee Jin Cho•Ju-Hwa Kim•Seon-Jin Yoon等 25 人
Nature Communications
2020
•2020/7/3
•Vol.11 No.1 p.1-16
The prognostic and therapeutic relevance of molecular subtypes for the most aggressive isocitrate dehydrogenase 1/2 (IDH) wild-type glioblastoma (GBM) is currently limited due to high molecular heterogeneity of the tumors that impedes patient stratification. Here, we describe a distinct binary class...
CNS cancerProteomic analysis
10.1038/S41467-020-17139-Y
ISSN:2041-1723
Thermal proteome profiling reveals fructose-1,6-bisphosphate as a phosphate donor to activate phosphoglycerate mutase 1
Yanling Zhang•Yafei Cao•Xia Wu•Zhenghui Chen•Bowen Chen等 21 人
Nature Communications
2024
•2024/10/16
•Vol.15 No.1 p.1-17
Deep understanding of sugar metabolite-protein interactions should provide implications on sugar metabolic reprogramming in human physiopathology. Although tremendous efforts have been made for determining individual event, global profiling of such interactome remains challenging. Here we describe t...
GlycobiologyMetabolic pathwaysProteomicsSugar phosphates
10.1038/S41467-024-53238-W
ISSN:2041-1723
Tumor-secreted factors induce aberrant accumulation of vitamin A–enriched lipid droplets in the liver
Xiangjie Huang•Wenyu Zhou•Wenkui Hou•Yihui Zhou•Meixin Li等 10 人
Communications Biology
2025
•2025/12/27
0Cancer is increasingly recognized as a systemic disease, extending beyond local alterations to systemic alterations in distant organs through the release of various factors that promote tumor progression and metastasis. Here, we applied hyperspectral stimulated Raman scattering (hSRS) microscopy to ...
Cancer metabolismCancer microenvironment
10.1038/S42003-025-09404-X
ISSN:2399-3642
Bacteriophage protein Dap1 regulates evasion of antiphage immunity and Pseudomonas aeruginosa virulence impacting phage therapy in mice
Shuai Le•Leilei Wei•Jing Wang•Fang Tian•Qian Yang等 12 人
Nature Microbiology
2024
•2024/6/17
•00 p.1-14
Bacteriophages have evolved diverse strategies to overcome host defence mechanisms and to redirect host metabolism to ensure successful propagation. Here we identify a phage protein named Dap1 from Pseudomonas aeruginosa phage PaoP5 that both modulates bacterial host behaviour and contributes to pha...
GeneticsMicrobiology
10.1038/S41564-024-01719-5
ISSN:2058-5276
Methylation of ESCRT-III components regulates the timing of cytokinetic abscission
Aurélie Richard•Jérémy Berthelet•Delphine Judith•Tamara Advedissian•Javier Espadas等 16 人
Nature Communications
2024
•2024/5/13
•Vol.15 No.1 p.1-17
Abscission is the final stage of cytokinesis, which cleaves the intercellular bridge (ICB) connecting two daughter cells. Abscission requires tight control of the recruitment and polymerization of the Endosomal Protein Complex Required for Transport-III (ESCRT-III) components. We explore the role of...
CancerCytokinesisMethylation
10.1038/S41467-024-47717-3
ISSN:2041-1723
Simulated closed-loop magnetic stimulation promotes function recovery and axonal regeneration in spinal cord injury
Lechi Zhang•Zhihang Xiao•Chunya Xia•Tingting Li•Zelin Su等 9 人
Communications Biology
2026
•2026/3/18
0Spinal cord injury (SCI) represents significant central nervous system trauma and has consistently been a focal point of research in the domain of neural regeneration and repair. Currently, there is no effective treatment available. Various modalities of magnetic stimulation have emerged for recover...
Neural circuitsNeurophysiologySpinal cord injury
10.1038/S42003-026-09848-9
ISSN:2399-3642
Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes
Yuanchun Luo•Jianglong Yu•Zhuofan Li•Wanning Li•Le Jiang等 15 人
Nature Cell Biology
2026
•2026/7/20
•00 p.1-14
Lysosomes are central degradative organelles essential for cellular homeostasis, yet the mechanisms that maintain their integrity and function under stress remain incompletely understood. Here we identify a previously unrecognized lysosomal renewal process, termed budding-type fission (B-fission), w...
LysosomesMitochondria
10.1038/S41556-026-02010-X
ISSN:1465-7392
Developing a new cleavable crosslinker reagent for in-cell crosslinking
Fränze Müller•Bogdan R. Brutiu•Iakovos Saridakis•Thomas Leischner•Micha J. Birklbauer等 12 人
Communications Chemistry
2025
•2025/6/23
•Vol.8 No.1 p.1-15
Crosslinking mass spectrometry (XL-MS) is a powerful technology that recently emerged as an essential complementary tool for elucidating protein structures and mapping interactions within a protein network. Crosslinkers which are amenable to post-linking backbone cleavage simplify peptide identifica...
Mass spectrometryProtein–protein interaction networksStructural biology
10.1038/S42004-025-01568-1
ISSN:2399-3669
Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut
Leszek Michalak•John Christian Gaby•Leidy Lagos•Sabina Leanti La Rosa•Torgeir R. Hvidsten等 16 人
Nature Communications
2020
•2020/11/13
•Vol.11 No.1 p.1-15
Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecali...
BioinformaticsMetagenomicsMicrobiome
10.1038/S41467-020-19585-0
ISSN:2041-1723
Matrix Gla Protein drives stemness and tumor initiation in ovarian cancer
Nieddu V.•Melocchi V.•Battistini C.•Franciosa G.•Lupia M.等 11 人
Cell Death & Disease
2023
•2023/3/28
•Vol.14 No.3 p.1-16
Ovarian cancer (OC) displays the highest mortality among gynecological tumors, mainly due to early peritoneal dissemination, the high frequency of tumor relapse following primary debulking, and the development of chemoresistance. All these events are thought to be initiated and sustained by a subpop...
Cancer stem cellsOvarian cancer
10.1038/S41419-023-05760-W
ISSN:2041-4889
THEMIS is a substrate and allosteric activator of SHP1, playing dual roles during T cell development
Jiali Zhang•Zhenzhou Jiang•Xueyuan Zhang•Ziqun Yang•Jinjiao Wang等 22 人
Nature Structural & Molecular Biology
2024
•2024/1/4
•00 p.1-14
THEMIS plays an indispensable role in T cells, but its mechanism of action has remained highly controversial. Using the systematic proximity labeling methodology PEPSI, we identify THEMIS as an uncharacterized substrate for the phosphatase SHP1. Saturated mutagenesis assays and mass spectrometry ana...
Cell biologyCell signallingImmunologyPhosphorylation
10.1038/S41594-023-01131-3
ISSN:1545-9993
How paired PSII–LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by structural mass-spectrometry
Pascal Albanese•Sem Tamara•Guido Saracco•Richard A. Scheltema•Cristina Pagliano
Nature Communications
2020
•2020/3/13
•Vol.11 No.1 p.1-14
Grana are a characteristic feature of higher plants’ thylakoid membranes, consisting of stacks of appressed membranes enriched in Photosystem II (PSII) and associated light-harvesting complex II (LHCII) proteins, together forming the PSII-LHCII supercomplex. Grana stacks undergo light-dependent stru...
Light responsesMass spectrometryPhotosystem IIProteomics
10.1038/S41467-020-15184-1
ISSN:2041-1723
In vivo endosomal escape assay identifies mechanisms for efficient hepatic LNP delivery
Antony Jozić•Chloé Le Roux•Jeonghwan Kim•Mathieu Berchel•Deepak Kumar Sahel等 15 人
Nature Biotechnology
2026
•2026/3/11
•00 p.1-11
Endosomal escape is a central barrier to efficient nucleic acid delivery by lipid nanoparticles (LNPs) and remains challenging to quantify in vivo. We report a library of branched ionizable phospholipids that markedly enhance messenger RNA delivery to the liver. The lead candidate BiP-20 outperforme...
Gene therapyNanoparticlesProteomics
10.1038/S41587-026-03022-6
ISSN:1087-0156
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
Reconstitution of pluripotency from mouse fibroblast through Sall4 overexpression
Lizhan Xiao•Zifen Huang•Zixuan Wu•Yongzheng Yang•Zhen Zhang等 19 人
Nature Communications
2024
•2024/12/30
•Vol.15 No.1 p.1-18
Somatic cells can be reprogrammed into pluripotent stem cells (iPSCs) by overexpressing defined transcription factors. Specifically, overexpression of OCT4 alone has been demonstrated to reprogram mouse fibroblasts into iPSCs. However, it remains unclear whether any other single factor can induce iP...
EpigenomicsInduced pluripotent stem cellsReprogramming
10.1038/S41467-024-54924-5
ISSN:2041-1723
Plasma proteomic and metabolomic characterization of COVID-19 survivors 6 months after discharge
Li Hongwei•Li Xue•Wu Qian•Wang Xing•Qin Zhonghua等 10 人
Cell Death & Disease
2022
•2022/3/14
•Vol.13 No.3 p.1-12
Coronavirus disease 2019 (COVID-19) has gained prominence as a global pandemic. Studies have suggested that systemic alterations persist in a considerable proportion of COVID-19 patients after hospital discharge. We used proteomic and metabolomic approaches to analyze plasma samples obtained from 30...
Predictive markersViral infection
10.1038/S41419-022-04674-3
ISSN:2041-4889
A UFD1 variant encoding a microprotein modulates UFD1f and IPMK ubiquitination to play pivotal roles in anti-stress responses
Xiuzhi Li•Xiaolin Wang•Xu Liu•Ge Shan•Liang Chen
Nature Communications
2025
•2025/7/21
•Vol.16 No.1 p.1-24
Eukaryotic cells make multiple efforts to cope with internal and external stresses; such mechanisms include metabolic responses and the generation of stress-responsive mRNA isoforms (SR-mRNAisos), such as the classical XBP1s. Here, we identified a mammalian conserved SR-mRNAiso, UFD1s, which encodes...
PeptidesUbiquitylation
10.1038/S41467-025-62073-6
ISSN:2041-1723
A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research
Christian M. Beusch•Ken Braesch-Andersen•Ulrika Felldin•Pierre Sabatier•Anna Widgren等 8 人
Communications Biology
2025
•2025/1/17
•Vol.8 No.1 p.1-10
Recent developments in mass spectrometry-based proteomics have established it as a robust tool for system-wide analyses essential for pathophysiological research. While post-mortem samples are a critical source for these studies, our understanding of how body decomposition influences the proteome re...
Proteomic analysisProteomics
10.1038/S42003-025-07515-Z
ISSN:2399-3642
LincRNA-EPS alleviates osteoclastogenesis under inflammatory microenvironment through preventing excessive iron metabolism
Jin Wang•Yabing Wang•Zhanwei Zhang•Xin Wang•Jiansheng Su
Cell Death & Disease
2026
•2026/4/3
0The precise regulation of bone homeostasis and the balance between bone resorption and formation in periodontitis remain unclear. This study explores the role of long intergenic noncoding RNA-erythroid prosurvival (lincRNA-EPS) in inflammatory osteoclastogenesis and bone resorption. LincRNA-EPS knoc...
Cell biologyLong non-coding RNAsOsteoimmunology
10.1038/S41419-026-08716-Y
ISSN:2041-4889
Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry
Alexander Reim•Roland Ackermann•Jofre Font-Mateu•Robert Kammel•Miguel Beato等 9 人
Nature Communications
2020
•2020/6/15
•Vol.11 No.1 p.1-14
Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the struc...
DNA-binding proteinsMass spectrometryProteomicsStructural biologyTranscription
10.1038/S41467-020-16837-X
ISSN:2041-1723
Deep and fast label-free Dynamic Organellar Mapping
Julia P. Schessner•Vincent Albrecht•Alexandra K. Davies•Pavel Sinitcyn•Georg H. H. Borner
Nature Communications
2023
•2023/8/29
•Vol.14 No.1 p.1-19
The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics for global profiling analysis of protein subcellular localization. Here, we enhance the performance of DOMs through data-independent acquisition (DIA) mass spectrometry. DIA-DOMs achieve twice the depth of...
GolgiProteomicsSoftware
10.1038/S41467-023-41000-7
ISSN:2041-1723
A positive feedback loop between TNS1 and ZEB1 promotes TGFβ-induced epithelial-to-mesenchymal transition in lung cancer
Tingting Zhang•Zhang Li•Yue Ming•Jiao Li•Zixia Ye等 10 人
Communications Biology
2025
•2025/11/26
•Vol.8 No.1 p.16860
Epithelial-mesenchymal transition (EMT) plays a pivotal role in tumor metastasis initiation. Although emerging evidence suggests that Tensin-1 (TNS1) contributes to tumor metastasis, its precise function in EMT during lung cancer progression and the underlying mechanisms remain unclear. Here, we ide...
Epithelial–mesenchymal transitionNon-small-cell lung cancer
10.1038/S42003-025-09079-4
ISSN:2399-3642
Total synthesis and target identification of marine cyclopiane diterpenes
Tian Li•Shan Jiang•Yuanhao Dai•Xia Wu•Huihui Guo等 13 人
Nature Communications
2024
•2024/12/30
•Vol.15 No.1 p.1-14
Marine cyclopianes are a family of diterpenoid with novel carbon skeleton and diverse biological activities. Herein, we report our synthetic and chemical proteomics studies of cyclopiane diterpenes which culminate in the asymmetric total synthesis of conidiogenones C, K and 12β-hydroxy conidiogenone...
Natural product synthesis
10.1038/S41467-024-55189-8
ISSN:2041-1723
AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells
Shuai Wang•Zongyang Qiu•Yingnan Hou•Xiya Deng•Wei Xu等 20 人
Cell Research
2021
•2021/1/8
•Vol.31 No.2 p.126-140
The current coronavirus disease 2019 (COVID-19) pandemic presents a global public health challenge. The viral pathogen responsible, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to the host receptor ACE2 through its spike (S) glycoprotein, which mediates membrane fusion and vir...
Cell biologyMolecular biology
10.1038/S41422-020-00460-Y
ISSN:1001-0602
AMPK targets PDZD8 to trigger carbon source shift from glucose to glutamine
Mengqi Li•Yu Wang•Xiaoyan Wei•Wei-Feng Cai•Jianfeng Wu等 33 人
Cell Research
2024
•2024/6/19
•00 p.1-24
The shift of carbon utilization from primarily glucose to other nutrients is a fundamental metabolic adaptation to cope with decreased blood glucose levels and the consequent decline in glucose oxidation. AMP-activated protein kinase (AMPK) plays crucial roles in this metabolic adaptation. However, ...
Nutrient signallingStress signalling
10.1038/S41422-024-00985-6
ISSN:1748-7838
Integrated landscape of plasma metabolism and proteome of patients with post-traumatic deep vein thrombosis
Kun Zhang•Pengfei Wang•Wei Huang•Shi-Hao Tang•Hanzhong Xue等 19 人
Nature Communications
2024
•2024/9/7
•Vol.15 No.1 p.1-14
Deep vein thrombosis (DVT) is a leading cause of morbidity and mortality after trauma. Here, we integrate plasma metabolomics and proteomics to evaluate the metabolic alterations and their function in up to 680 individuals with and without DVT after trauma (pt-DVT). We identify 28 metabolites and 2 ...
MetabolomicsProteomicsThrombosis
10.1038/S41467-024-52262-0
ISSN:2041-1723
Airway epithelial CD47 plays a critical role in inducing influenza virus-mediated bacterial super-infection
Sungmin Moon•Seunghan Han•In-Hwan Jang•Jaechan Ryu•Min-Seok Rha等 15 人
Nature Communications
2024
•2024/4/30
•Vol.15 No.1 p.1-16
Respiratory viral infection increases host susceptibility to secondary bacterial infections, yet the precise dynamics within airway epithelia remain elusive. Here, we elucidate the pivotal role of CD47 in the airway epithelium during bacterial super-infection. We demonstrated that upon influenza vir...
Bacterial infectionBacterial pathogenesisInfluenza virusViral infection
10.1038/S41467-024-47963-5
ISSN:2041-1723
Recoding multiple rare codons enables the simultaneous incorporation of up to five distinct noncanonical amino acids
Yu Fang•Wei Yu•Junjie Li•Lihui Lao•Ying Yuan等 8 人
Nature Chemistry
2026
•2026/3/13
•Vol.18 No.4 p.695-706
Expanding the genetic code has revolutionized our ability to study and manipulate biological systems through site-specific incorporation of noncanonical amino acids (ncAAs). However, current methods are primarily limited to single-type ncAA incorporation in mammalian cells owing to translation ineff...
BiosynthesisChemical biologySynthetic biology
10.1038/S41557-026-02084-Y
ISSN:1755-4330
Med13 is involved in the radial migration and contralateral projection of cortical neurons via PlxnA4
Ze-Xuan Li•Si-Xin Tu•Yi-Wei Li•Zhi-Bin Hu•Wei-Tang Liu等 14 人
Communications Biology
2026
•2026/2/9
•Vol.9 No.1 p.3940
Mediator complex (MED) is an important auxiliary factor in the RNA polymerase II transcription apparatus, and MED13 is a subunit in the CDK8-kinase module of the complex. Currently, extensive clinical evidence has implicated its involvement in the pathogenesis of neurodevelopmental disorders (NDDs)....
Disease geneticsNeurogenesis
10.1038/S42003-026-09704-W
ISSN:2399-3642
AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A
Alexandra K. Davies•Daniel N. Itzhak•James R. Edgar•Tara L. Archuleta•Jennifer Hirst等 8 人
Nature Communications
2018
•2018/9/27
•Vol.9 No.1 p.1-21
Adaptor protein 4 (AP-4) is an ancient membrane trafficking complex, whose function has largely remained elusive. In humans, AP-4 deficiency causes a severe neurological disorder of unknown aetiology. We apply unbiased proteomic methods, including ‘Dynamic Organellar Maps’, to find proteins whose su...
AutophagyMechanisms of diseaseMembrane traffickingProteomicsSystems biology
10.1038/S41467-018-06172-7
ISSN:2041-1723
Arabidopsis thaliana myosin XIK is recruited to the Golgi through interaction with a MyoB receptor
Perico Chiara•Gao Hongbo•Heesom Kate J.•Botchway Stanley W.•Sparkes Imogen A.
Communications Biology
2021
•2021/10/13
•Vol.4 No.1 p.1-15
Plant cell organelles are highly mobile and their positioning play key roles in plant growth, development and responses to changing environmental conditions. Movement is acto-myosin dependent. Despite controlling the dynamics of several organelles, myosin and myosin receptors identified so far in Ar...
Cell biologyMyosinPlant cell biologyPlant cytoskeletonPlant sciences
10.1038/S42003-021-02700-2
ISSN:2399-3642
Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells
Xi Chen•Elisa Saccon•K. Sofia Appelberg•Flora Mikaeloff•Jimmy Esneider Rodriguez等 11 人
Cell Death Discovery
2021
•2021/5/18
•Vol.7 No.1 p.1-15
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) has caused a global health emergency. A key feature of COVID-19 is dysregulated interferon-response. Type-I interferon (IFN-I) is one of the earliest antiviral innate immune responses followi...
Cell biologyImmunologyMicrobiology
10.1038/S41420-021-00487-Z
ISSN:2058-7716
Pyruvate kinase M2 -mediated histone lactylation alters three-dimensional genomic architecture in polycystic ovary syndrome
Chuanjin Yu•Tingting Liu•Yishu Wang•Xinghui Guo•Yujie Chen等 20 人
Signal Transduction And Targeted Therapy
2025
•2025/11/19
•Vol.10 No.1 p.3760
Polycystic ovary syndrome (PCOS) is a frequent endocrine and metabolic imbalance that typically occurs in women of reproductive age. Its molecular pathophysiology is yet unknown, especially the ovarian cellular metabolic inefficiency that causes the transcriptional dysregulation of key genes linked ...
Endocrine system and metabolic diseasesEpigenetics
10.1038/S41392-025-02468-5
ISSN:2059-3635
METTL3-mediated m6A RNA methylation promotes the anti-tumour immunity of natural killer cells
Song Hao•Song Jiaxi•Cheng Ming•Zheng Meijuan•Wang Tian等 14 人
Nature Communications
2021
•2021/9/17
•Vol.12 No.1 p.1-15
Natural killer (NK) cells exert critical roles in anti-tumor immunity but how their functions are regulated by epitranscriptional modification (e.g., N6-methyladenosine (m6A) methylation) is unclear. Here we report decreased expression of the m6A “writer” METTL3 in tumor-infiltrating NK cells, and a...
ImmunosurveillanceInterleukinsNK cells
10.1038/S41467-021-25803-0
ISSN:2041-1723
Elevated FBXL6 expression in hepatocytes activates VRK2-transketolase-ROS-mTOR-mediated immune evasion and liver cancer metastasis in mice
Jie Zhang•Xiao-Tong Lin•Hong-Qiang Yu•Lei Fang•Di Wu等 8 人
Experimental & Molecular Medicine
2023
•2023/9/1
•00 p.1-15
Metastatic hepatocellular carcinoma (HCC) is the most lethal malignancy and lacks effective treatment. FBXL6 is overexpressed in human hepatocellular carcinoma (HCC), but whether this change drives liver tumorigenesis and lung metastasis in vivo remains unknown. In this study, we aimed to identify F...
Liver cancerPhosphorylationProtein–protein interaction networksUbiquitylation
10.1038/S12276-023-01060-7
ISSN:2092-6413
Unveiling the role of transgelin as a prognostic and therapeutic target in kidney fibrosis via a proteomic approach
Soie Kwon•Seongmin Cheon•Kyu-Hong Kim•Areum Seo•Eunjin Bae等 13 人
Experimental & Molecular Medicine
2024
•2024/10/7
•00 p.1-13
Chronic kidney disease (CKD) progression involves tubulointerstitial fibrosis, a process characterized by excessive extracellular matrix accumulation. To identify potential biomarkers for kidney fibrosis, we performed mass spectrometry-based proteomic profiling of human kidney tubular epithelial cel...
End-stage renal diseasePredictive markers
10.1038/S12276-024-01319-7
ISSN:2092-6413
Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice
Siqi Ji•Yuanhui Liu•Yuejie Xu•Junzhao Gao•Jingzheng Jin等 14 人
Nature Microbiology
2026
•2026/4/17
•00 p.1-18
Microbiome–host interactions can influence colorectal cancer (CRC) outcomes and the effectiveness of immunotherapy treatment, but the precise mechanisms underlying this are poorly understood. Here we analyse CRC patient cohort data and observe that Facalibacterium prausnitzii abundance in faecal sam...
Cellular microbiologyImmunotherapyTumour-suppressor proteins
10.1038/S41564-026-02326-2
ISSN:2058-5276
The protein kinase DYRK1B is a p53 target gene and functions as a negative feedback regulator of the transcription factor RFX7
Gerrit Wilms•Katharina Schwandt•Stefan Düsterhöft•Philip Helmich•Justyna Wozniak等 9 人
Cell Death & Disease
2026
•2026/3/26
•Vol.17 No.1 p.3860
The tumor suppressor protein p53 orchestrates cellular responses to stress by regulating the transcription of target genes involved in processes such as cell cycle control, DNA damage repair and apoptosis. The protein kinase DYRK1B, known to promote cancer cell survival and contribute to DNA damage ...
DNA damage and repairLung cancerTarget identification
10.1038/S41419-026-08660-X
ISSN:2041-4889
A male steroid controls female sexual behaviour in the malaria mosquito
Peng Duo•Kakani Evdoxia G.•Mameli Enzo•Vidoudez Charles•Mitchell Sara N.等 11 人
Nature
2022
•2022/7/6
•Vol.608 No.7921 p.93-97
Insects, unlike vertebrates, are widely believed to lack male-biased sex steroid hormones1. In the malaria mosquito Anopheles gambiae, the ecdysteroid 20-hydroxyecdysone (20E) appears to have evolved to both control egg development when synthesized by females2 and to induce mating refractoriness whe...
EntomologyInsect hormonesReproductive biology
10.1038/S41586-022-04908-6
ISSN:0028-0836
Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid resolution
Jong Woo Bae•S. Chul Kwon•Yongwoo Na•V. Narry Kim•Jong-Seo Kim
Nature Structural & Molecular Biology
2020
•2020/6/8
•Vol.27 No.7 p.678-682
RNA-binding sites (RBSs) can be identified by liquid chromatography and tandem mass spectrometry analyses of the protein–RNA conjugates created by crosslinking, but RBS mapping remains highly challenging due to the complexity of the formed RNA adducts. Here, we introduce RBS-ID, a method that uses h...
Mass spectrometryProteomicsRNARNA-binding proteins
10.1038/S41594-020-0436-2
ISSN:1545-9993
EatA mediated degradation of intestinal mucus is species-specific and driven by MUC2 structural features
Sergio Trillo-Muyo•Brendan Dolan•Frida Svensson•Tim J. Vickers•Liisa Arike等 12 人
Nature Communications
2025
•2025/12/31
0Enterotoxigenic Escherichia coli (ETEC) infections are a leading cause of diarrheal illness, responsible for an estimated 100,000 deaths annually. ETEC pathogenesis is driven by various virulence factors, including toxins, adhesins, and noncanonical factors such as the protease EatA. The first line ...
Molecular modellingPathogensProteases
10.1038/S41467-025-68037-0
ISSN:2041-1723
Aberrant amino acid-sensing promotes immunotherapy resistance via the inflammatory cytokine–ZBTB5–mTORC1 axis
Junyu Xiang•Tao Wang•Shuoran Tian•Jinyang Li•Mengyun Luo等 26 人
Nature Cell Biology
2026
•2026/4/3
•00 p.1-15
Acute activation of mTORC1 by amino acids (AAs) is pivotal for growth regulation, yet it remains unclear how the intracellular nutrient-sensing machinery might be rewired by environmental cues to execute distinct functions. Here we report that, despite nutrient insufficiency, cancer-intrinsic AA-sen...
Cancer metabolismCancer microenvironmentTOR signallingTumour immunology
10.1038/S41556-026-01926-8
ISSN:1465-7392
Targeting CD37 promotes macrophage-dependent phagocytosis of multiple cancer cell types and facilitates tumor clearance in mice
Xinya Gao•Jing Zhang•Hui Zhang•Xin Liu•Bo Zeng等 11 人
Nature Communications
2025
•2025/7/18
•Vol.16 No.1 p.1-15
Macrophages play vital roles in innate and adaptive immunity, and their functions are mediated via phagocytosis and antigen presentation. Despite the effort to identify phagocytic checkpoints and explore their mechanism of action, current checkpoint-scanning strategies cannot provide a complete and ...
ImmunoeditingPhagocytes
10.1038/S41467-025-61348-2
ISSN:2041-1723
Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling
Lisa Bertrand•Annika Nelde•Bertha Cecilia Ramirez•Isabelle Hatin•Hugo Arbes等 33 人
Nature Communications
2025
•2025/2/18
•Vol.16 No.1 p.1-18
The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open read...
Gene expressionHIV infectionsMHC
10.1038/S41467-025-56773-2
ISSN:2041-1723
NSD2 promotes tumor angiogenesis through methylating and activating STAT3 protein
Da Song•Jingqin Lan•Yaqi Chen•Anyi Liu•Qi Wu等 13 人
Oncogene
2021
•2021/3/19
•00 p.1-16
Tumor angiogenesis plays vital roles in tumorigenesis and development; regulatory mechanism of angiogenesis is still not been fully elucidated. NSD2, a histone methyltransferase catalyzing di-methylation of histone H3 at lysine 36, has been proved a critical molecule in proliferation, metastasis, an...
MethylationTumour angiogenesis
10.1038/S41388-021-01747-Z
ISSN:0950-9232
Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer
Carolina Moretto Carnielli•Carolina Carneiro Soares Macedo•Tatiane De Rossi•Daniela Campos Granato•César Rivera等 33 人
Nature Communications
2018
•2018/9/5
•Vol.9 No.1 p.1-17
Different regions of oral squamous cell carcinoma (OSCC) have particular histopathological and molecular characteristics limiting the standard tumor−node−metastasis prognosis classification. Therefore, defining biological signatures that allow assessing the prognostic outcomes for OSCC patients woul...
ImmunohistochemistryOral cancerProteomic analysisTumour biomarkers
10.1038/S41467-018-05696-2
ISSN:2041-1723
High-throughput proteomic sample preparation using pressure cycling technology
Cai Xue•Xue Zhangzhi•Wu Chunlong•Sun Rui•Qian Liujia等 15 人
Nature Protocols
2022
•2022/8/5
•00 p.1-19
High-throughput lysis and proteolytic digestion of biopsy-level tissue specimens is a major bottleneck for clinical proteomics. Here we describe a detailed protocol of pressure cycling technology (PCT)-assisted sample preparation for proteomic analysis of biopsy tissues. A piece of fresh frozen or f...
Mass spectrometryProteomic analysis
10.1038/S41596-022-00727-1
ISSN:1754-2189
EGFR orchestrates neutrophil activation and NETosis via CEBPβ-dependent PGLYRP1 induction
Xiaolei Liu•Yue Lu•Yuanbo Guo•Guorong Huang•Jiahui Li等 11 人
Cell Death & Differentiation
2026
•2026/1/15
•00 p.1-15
Excessive neutrophil activation and neutrophil extracellular trap (NET) release drive systemic inflammation and organ injury in sepsis, yet the upstream regulatory pathways remain incompletely defined. Here, we identify epidermal growth factor receptor (EGFR) as a critical neutrophil-intrinsic regul...
Autocrine motility factorImmune cell deathProtein–protein interaction networks
10.1038/S41418-026-01660-6
ISSN:1350-9047
Comprehensive Human Red Blood Cell Membrane and Cytoplasmic Proteome Analyses
Xue Zhang•Huiru Liu•Qiuhong Zhang•Ting Liu•Shanyu Qi等 18 人
Scientific Data
2026
•2026/2/7
•Vol.13 No.1 p.3830
Red blood cells (RBCs) are essential to human and involved in many clinical disorders. Many proteomics studies have been done on human RBCs, but the coverages are insufficient, limiting full understanding of protein profiles in RBCs and the mechanisms of their involved diseases. With major advances ...
AnaemiaBlood flow
10.1038/S41597-026-06792-5
ISSN:2052-4463
DDX39B K63-linked ubiquitination mediated by TRIM28 promotes NSCLC metastasis by enhancing ECAD lysosomal degradation
Hang Yuan•Qin Li•Liang Li•Gang Zhao•Jie Zhang等 19 人
Signal Transduction And Targeted Therapy
2025
•2025/7/16
•Vol.10 No.1 p.1-17
Metastasis is a leading cause of treatment failure and high mortality in non-small cell lung cancer (NSCLC). Recently, we demonstrated that DEAD box helicase 39B (DDX39B) was upregulated and activated metabolic reprogramming in colorectal cancer and hepatocellular carcinoma. However, the function of...
Cancer therapyCell biologyLung cancerMetastasisOncogenes
10.1038/S41392-025-02305-9
ISSN:2059-3635
Autophagy induction promoted by m6A reader YTHDF3 through translation upregulation of FOXO3 mRNA
Hao WeiChao•Dian MeiJuan•Zhou Ying•Zhong QiuLing•Pang WenQian等 18 人
Nature Communications
2022
•2022/10/4
•Vol.13 No.1 p.1-23
Autophagy is crucial for maintaining cellular energy homeostasis and for cells to adapt to nutrient deficiency, and nutrient sensors regulating autophagy have been reported previously. However, the role of eiptranscriptomic modifications such as m6A in the regulation of starvation-induced autophagy ...
AutophagyEpigenomicsNutrient signallingRNA modification
10.1038/S41467-022-32963-0
ISSN:2041-1723
PfPPM2 signalling regulates asexual division and sexual conversion of human malaria parasite Plasmodium falciparum
Akanksha Rawat•Neelam Antil•Meenakshi•Bhagyashree Deshmukh•Akhila Balakrishna Rai等 10 人
Nature Communications
2025
•2025/5/23
•Vol.16 No.1 p.1-16
Malaria parasite undergoes interesting developmental transition in human and mosquito host. While it divides asynchronously in the erythrocytes, it switches to sexual forms, which is critical for disease transmission. We report a novel signalling pathway involving Protein Phosphatase PfPPM2, which r...
Infectious diseasesParasite biology
10.1038/S41467-025-59476-W
ISSN:2041-1723
ANP32E drives lung adenocarcinoma progression via GSK3β-mediated glycolytic reprogramming
Zhongliang Wang•Qianxia Li•Zeguang Ye•Xi Wu•Can Fang等 7 人
Cell Death & Disease
2026
•2026/4/14
0Lung adenocarcinoma (LUAD), a leading cause of cancer mortality, involves incompletely understood epigenetic-metabolic crosstalk. We identified ANP32E as a key regulator through multi-omics (TCGA, scRNA-seq) and clinical analyses, finding its overexpression correlates with poor prognosis. Functional...
GlycobiologyLung cancerTranscriptional regulatory elements
10.1038/S41419-026-08712-2
ISSN:2041-4889
Phosphorylated Toll-like receptor 3 nuclear translocation in cancer cell promotes metastasis and chemoresistance
Zixin Wang•Yan Gu•Yanfang Liu•Ziqiao Wang•Xinyuan Chen等 9 人
Signal Transduction And Targeted Therapy
2025
•2025/7/18
•Vol.10 No.1 p.1-15
Aberrant expression and subcellular location of innate sensors in cancer cells, such as Toll-like receptors (TLRs), correlates with pro-tumoral inflammation and cancer progression, but the mechanism is still largely unknown. Deciphering the proinflammatory mediators in tumor microenvironment will co...
Molecular medicineTumour immunology
10.1038/S41392-025-02307-7
ISSN:2059-3635
Nuclear ANLN regulates transcription initiation related Pol II clustering and target gene expression
Yu-Fei Cao•Hui Wang•Yong Sun•Bei-Bei Tong•Wen-Qi Shi等 13 人
Nature Communications
2025
•2025/2/2
•Vol.16 No.1 p.1-19
Anillin (ANLN), a mitotic protein that regulates contractile ring assembly, has been reported as an oncoprotein. However, the function of ANLN in cancer cells, especially in the nucleus, has not been fully understood. Here, we report a role of nuclear ANLN in gene transcriptional regulation. We find...
Mechanisms of diseaseOncogenesTranscription
10.1038/S41467-025-56645-9
ISSN:2041-1723
Establishment of fetomaternal tolerance through glycan-mediated B cell suppression
Rizzuto G.•Brooks J. F.•Tuomivaara S. T.•McIntyre T. I.•Ma S.等 9 人
Nature
2022
•2022/3/2
•Vol.603 No.7901 p.497-502
Discrimination of self from non-self is fundamental to a wide range of immunological processes1. During pregnancy, the mother does not recognize the placenta as immunologically foreign because antigens expressed by trophoblasts, the placental cells that interface with the maternal immune system, do ...
Follicular B cellsGlycobiologyPeripheral tolerance
10.1038/S41586-022-04471-0
ISSN:0028-0836
Small leucine-rich proteoglycans inhibit CNS regeneration by modifying the structural and mechanical properties of the lesion environment
Julia Kolb•Vasiliki Tsata•Nora John•Kyoohyun Kim•Conrad Möckel等 27 人
Nature Communications
2023
•2023/10/26
•Vol.14 No.1 p.1-23
Extracellular matrix (ECM) deposition after central nervous system (CNS) injury leads to inhibitory scarring in humans and other mammals, whereas it facilitates axon regeneration in the zebrafish. However, the molecular basis of these different fates is not understood. Here, we identify small leucin...
BiophysicsMechanisms of diseaseSpinal cord injury
10.1038/S41467-023-42339-7
ISSN:2041-1723
Human blood microRNA hsa-miR-21-5p induces vitellogenin in the mosquito Aedes aegypti
Hugo D. Perdomo•Mazhar Hussain•Rhys Parry•Kayvan Etebari•Lauren M. Hedges等 8 人
Communications Biology
2021
•2021/7/9
•Vol.4 No.1 p.1-10
Mosquito vectors transmit various diseases through blood feeding, required for their egg development. Hence, blood feeding is a major physiological event in their life cycle, during which hundreds of genes are tightly regulated. Blood is a rich source of proteins for mosquitoes, but also contains ma...
EntomologymiRNAs
10.1038/S42003-021-02385-7
ISSN:2399-3642
Discovery of metal-binding proteins by thermal proteome profiling
Xin Zeng•Tiantian Wei•Xianghe Wang•Yuan Liu•Zhenshu Tan等 14 人
Nature Chemical Biology
2024
•2024/2/26
•00 p.1-9
Metal-binding proteins (MBPs) have various and important biological roles in all living species and many human diseases are intricately linked to dysfunctional MBPs. Here, we report a chemoproteomic method named ‘metal extraction-triggered agitation logged by thermal proteome profiling’ (METAL-TPP) ...
Mass spectrometryMetalsProteomics
10.1038/S41589-024-01563-Y
ISSN:1552-4450
Speg interactions that regulate the stability of excitation-contraction coupling protein complexes in triads and dyads
Chang Seok Lee•Sung Yun Jung•Rachel Sue Zhen Yee•Nadia H. Agha•Jin Hong等 18 人
Communications Biology
2023
•2023/9/14
•Vol.6 No.1 p.1-19
Here we show that striated muscle preferentially expressed protein kinase α (Spegα) maintains cardiac function in hearts with Spegβ deficiency. Speg is required for stability of excitation-contraction coupling (ECC) complexes and interacts with esterase D (Esd), Cardiomyopathy-Associated Protei...
Cardiovascular diseasesProtein–protein interaction networks
10.1038/S42003-023-05330-Y
ISSN:2399-3642
Quantitative SUMO proteomics identifies PIAS1 substrates involved in cell migration and motility
Chongyang Li•Francis P. McManus•Cédric Plutoni•Cristina Mirela Pascariu•Trent Nelson等 8 人
Nature Communications
2020
•2020/2/11
•Vol.11 No.1 p.1-14
The protein inhibitor of activated STAT1 (PIAS1) is an E3 SUMO ligase that plays important roles in various cellular pathways. Increasing evidence shows that PIAS1 is overexpressed in various human malignancies, including prostate and lung cancers. Here we used quantitative SUMO proteomics to identi...
Cytoskeletal proteinsIntermediate filamentsProteomicsSumoylation
10.1038/S41467-020-14581-W
ISSN:2041-1723
Lipid droplets sequester palmitic acid to disrupt endothelial ciliation and exacerbate atherosclerosis in male mice
Yanjie Tan•Zhenzhou Huang•Yi Jin•Jiaying Wang•Hongjun Fan等 16 人
Nature Communications
2024
•2024/9/27
•Vol.15 No.1 p.1-19
Disruption of ciliary homeostasis in vascular endothelial cells has been implicated in the development of atherosclerosis. However, the molecular basis for the regulation of endothelial cilia during atherosclerosis remains poorly understood. Herein, we provide evidence in male mice that the accumula...
Cell biologyCilia
10.1038/S41467-024-52621-X
ISSN:2041-1723
Porphyromonas gingivalis aggravates atherosclerotic plaque instability by promoting lipid-laden macrophage necroptosis
Xiaofei Huang•Mengru Xie•Yixuan Wang•Xiaofeng Lu•Feng Mei等 15 人
Signal Transduction And Targeted Therapy
2025
•2025/5/23
•Vol.10 No.1 p.1-18
At advanced phases of atherosclerosis, the rupture and thrombogenesis of vulnerable plaques emerge as primary triggers for acute cardiovascular events and fatalities. Pathogenic infection such as periodontitis-associated Porphyromonas gingivalis (Pg) has been suspected of increasing the risks of ath...
Cardiovascular diseasesInfectious diseases
10.1038/S41392-025-02251-6
ISSN:2059-3635
Discovery of a NAPE-PLD inhibitor that modulates emotional behavior in mice
Elliot D. Mock•Mohammed Mustafa•Ozge Gunduz-Cinar•Resat Cinar•Gavin N. Petrie等 39 人
Nature Chemical Biology
2020
•2020/5/11
•Vol.16 No.6 p.667-675
N-acylethanolamines (NAEs), which include the endocannabinoid anandamide, represent an important family of signaling lipids in the brain. The lack of chemical probes that modulate NAE biosynthesis in living systems hamper the understanding of the biological role of these lipids. Using a high-through...
Chemical toolsDrug discoveryEnzymesLipidsNeuroscience
10.1038/S41589-020-0528-7
ISSN:1552-4450
Targeting lipid raft-related stomatin to ameliorate osteoporosis in preclinical models
Huaqiang Tao•Kai Chen•Qiufei Wang•Pengfei Zhu•Miao Chu等 12 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-20
Osteoporosis is a metabolic bone disease characterized by a disruption in the balance between bone resorption and formation. The specific role and mechanism of stomatin (STOM), a major component of lipid rafts, in regulating bone physiology remain unclear. This research identifies increased STOM exp...
Mechanisms of diseaseProtein translocationStress signalling
10.1038/S41467-025-60032-9
ISSN:2041-1723
Quantitative profiling of posttranslational modifications of pathological tau via sarkosyl fractionation and mass spectrometry
Kathrin Wenger•Arthur Viode•Mukesh Kumar•Hanno Steen•Judith A. Steen
Nature Protocols
2024
•2024/1/30
•00 p.1-17
Tau protein aggregation is associated with posttranslational modifications (PTMs) in 75% of all dementia cases. The distribution of tau pathology and the presence of specific tau phosphorylation sites of interest are typically visualized and measured using antibodies. However, previous knowledge of ...
Alzheimer's diseaseMolecular neuroscience
10.1038/S41596-023-00939-Z
ISSN:1754-2189
A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response
Advait Subramanian•Lan Wang•Tom Moss•Mark Voorhies•Smriti Sangwan等 17 人
Nature Cell Biology
2023
•2023/10/19
•00 p.1-16
A widespread strategy employed by pathogens to establish infection is to inhibit host-cell protein synthesis. Legionella pneumophila, an intracellular bacterial pathogen and the causative organism of Legionnaires’ disease, secretes a subset of protein effectors into host cells that inhibit translati...
Cryoelectron microscopyMicrobiologyStress signallingTranslation
10.1038/S41556-023-01248-Z
ISSN:1465-7392
The cryo-EM structure of intraflagellar transport trains reveals how dynein is inactivated to ensure unidirectional anterograde movement in cilia
Mareike A. Jordan•Dennis R. Diener•Ludek Stepanek•Gaia Pigino
Nature Cell Biology
2018
•2018/10/15
•Vol.20 No.11 p.1250-1255
Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the assembly site is essential for the assembly and disassembly of the structure itself1. This bidirectio...
CiliaCryoelectron tomographyDyneinMotor proteins
10.1038/S41556-018-0213-1
ISSN:1465-7392
PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair
Andrew Craxton•Deeksha Munnur•Rebekah Jukes-Jones•George Skalka•Claudia Langlais等 7 人
Nature Communications
2018
•2018/9/24
•Vol.9 No.1 p.1-16
PAXX is a recently identified component of the nonhomologous end joining (NHEJ) DNA repair pathway. The molecular mechanisms of PAXX action remain largely unclear. Here we characterise the interactomes of PAXX and its paralogs, XLF and XRCC4, to show that these factors share the ability to interact ...
DNADNA-binding proteinsDouble-strand DNA breaksNon-homologous-end joining
10.1038/S41467-018-06127-Y
ISSN:2041-1723
Nuclear lactate dehydrogenase A senses ROS to produce α-hydroxybutyrate for HPV-induced cervical tumor growth
Yuan Liu•Ji-Zheng Guo•Ying Liu•Kui Wang•Wencheng Ding等 18 人
Nature Communications
2018
•2018/10/24
•Vol.9 No.1 p.1-16
It is well known that high-risk human papilloma virus (HR-HPV) infection is strongly associated with cervical cancer and E7 was identified as one of the key initiators in HPV-mediated carcinogenesis. Here we show that lactate dehydrogenase A (LDHA) preferably locates in the nucleus in HPV16-positive...
Cancer metabolismCervical cancer
10.1038/S41467-018-06841-7
ISSN:2041-1723
Specific deletion of protein phosphatase 6 catalytic subunit in Sertoli cells leads to disruption of spermatogenesis
Lei Wen-Long•Li Yuan-Yuan•Meng Tie-Gang•Ning Yan•Sun Si-Min等 10 人
Cell Death & Disease
2021
•2021/9/27
•Vol.12 No.10 p.1-13
Protein phosphatase 6 (PP6) is a member of the PP2A-like subfamily, which plays significant roles in numerous fundamental biological activities. We found that PPP6C plays important roles in male germ cells recently. Spermatogenesis is supported by the Sertoli cells in the seminiferous epithelium. In...
InfertilitySpermatogenesis
10.1038/S41419-021-04172-Y
ISSN:2041-4889
Abundance of bacterial Type VI secretion system components measured by targeted proteomics
Lin Lin•Emmanuelle Lezan•Alexander Schmidt•Marek Basler
Nature Communications
2019
•2019/6/13
•Vol.10 No.1 p.1-11
The Type VI secretion system (T6SS) is important for bacterial competition as well as virulence in many Gram-negative bacteria and its dynamics and regulation varies significantly between species. To gain insights into the mechanisms regulating T6SS assembly, we apply targeted proteomics to determin...
Bacterial secretionMass spectrometryMembrane proteinsProteomics
10.1038/S41467-019-10466-9
ISSN:2041-1723
Multi-omics characterization of the monkeypox virus infection
Yiqi Huang•Valter Bergant•Vincent Grass•Quirin Emslander•M. Sabri Hamad等 22 人
Nature Communications
2024
•2024/8/8
•Vol.15 No.1 p.1-19
Multiple omics analyzes of Vaccinia virus (VACV) infection have defined molecular characteristics of poxvirus biology. However, little is known about the monkeypox (mpox) virus (MPXV) in humans, which has a different disease manifestation despite its high sequence similarity to VACV. Here, we perfor...
Cell signallingPhosphorylationPox virusProteomics
10.1038/S41467-024-51074-6
ISSN:2041-1723
Selenium-based metabolic oligosaccharide engineering strategy for quantitative glycan detection
Xiao Tian•Lingna Zheng•Changjiang Wang•Yida Han•Yujie Li等 17 人
Nature Communications
2023
•2023/12/13
•Vol.14 No.1 p.1-18
Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and the background signal readout makes it challenging to achieve glycan quantification. Here w...
GlycobiologyMass spectrometryProteomics
10.1038/S41467-023-44118-W
ISSN:2041-1723
Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection
Pekayvaz Kami•Leunig Alexander•Kaiser Rainer•Joppich Markus•Brambs Sophia等 44 人
Nature Communications
2022
•2022/2/23
•Vol.13 No.1 p.1-21
The antiviral immune response to SARS-CoV-2 infection can limit viral spread and prevent development of pneumonic COVID-19. However, the protective immunological response associated with successful viral containment in the upper airways remains unclear. Here, we combine a multi-omics approach with l...
InfectionInflammatory diseasesSARS-CoV-2Viral infection
10.1038/S41467-022-28508-0
ISSN:2041-1723
Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics
Zilu Ye•Pierre Sabatier•Leander van der Hoeven•Maico Y. Lechner•Teeradon Phlairaharn等 20 人
Nature Methods
2025
•2025/1/16
•00 p.1-11
Single-cell proteomics (SCP) promises to revolutionize biomedicine by providing an unparalleled view of the proteome in individual cells. Here, we present a high-sensitivity SCP workflow named Chip-Tip, identifying >5,000 proteins in individual HeLa cells. It also facilitated direct detection of ...
Mass spectrometryProteomic analysis
10.1038/S41592-024-02558-2
ISSN:1548-7091
A Pseudomonas aeruginosa quorum-sensing metabolite manipulates macrophage ferroptosis through a methylation pathway
Tianyuan Jia•Fengming Li•Tianzhen Li•Anmin Ren•Peiyi Lu等 13 人
Nature Communications
2025
•2025/11/13
•Vol.16 No.1 p.99920
Ferroptosis is a type of iron- and lipid peroxidation–dependent programmed cell death that is involved in various diseases. Some pathogens manipulate host ferroptosis for pathogenesis; however, the potential mechanisms of action remain unclear. Pseudomonas aeruginosa is an opportunistic pathogen tha...
ApoptosisBacterial host responseCell death and immune response
10.1038/S41467-025-65142-Y
ISSN:2041-1723
Bi-directional signaling by membrane-bound KitL induces proliferation and coordinates thymic endothelial cell and thymocyte expansion
Mario Buono•Marie-Laëtitia Thézénas•Alessandro Ceroni•Roman Fischer•Claus Nerlov
Nature Communications
2018
•2018/11/8
•Vol.9 No.1 p.1-10
The ligand for the c-Kit receptor, KitL, exists as a membrane-associated (mKitL) and a soluble form (sKitL). KitL functions outside c-Kit activation have not been identified. We show that co-culture of c-Kit– and mKitL–expressing NIH3T3 cells results in signaling through mKitL: c-Kit–bound mKitL rec...
Cell proliferationGrowth factor signallingLymphopoiesis
10.1038/S41467-018-07024-0
ISSN:2041-1723
Variant-divergent death: Omicron intensifies bystander T-cell apoptosis via GDF15–BCL2L13
Chao Gao•Hanbing Chen•Ying Chi•Xinxing Lu•Jiahuang Li等 13 人
Cell Death Discovery
2026
•2026/3/28
0Severe Omicron cases present profound lymphocytopenia, suggesting variant-specific immune injury. We identify CD63 as a conserved T-cell host factor supporting ACE2-independent SARS-CoV-2 entry. Despite lower intracellular viral loads than the ancestral strain, Omicron elicits enhanced T-cell apopto...
InfectionViral infection
10.1038/S41420-026-03079-X
ISSN:2058-7716
CD4 + T h immunogenicity of the Ascaris spp . secreted products
Friederike Ebner•Eliot Morrison•Miriam Bertazzon•Ankur Midha•Susanne Hartmann等 7 人
Npj Vaccines
2020
•2020/3/20
•Vol.5 No.1 p.1-8
Ascaris spp. is a major health problem of humans and animals alike, and understanding the immunogenicity of its antigens is required for developing urgently needed vaccines. The parasite-secreted products represent the most relevant, yet complex (>250 proteins) antigens of Ascaris spp. as defining t...
DiseasesImmunology
10.1038/S41541-020-0171-Z
ISSN:2059-0105
A soybean cyst nematode suppresses microbial plant symbionts using a lipochitooligosaccharide-hydrolysing enzyme
Wei Chen•Di Wang•Shaoyong Ke•Yangrong Cao•Wensheng Xiang等 7 人
Nature Microbiology
2024
•2024/6/17
•00 p.1-13
Cyst nematodes are the most damaging species of plant-parasitic nematodes. They antagonize the colonization of beneficial microbial symbionts that are important for nutrient acquisition of plants. The molecular mechanism of the antagonism, however, remains elusive. Here, through biochemical combined...
Arbuscular mycorrhizaParasitismRhizobial symbiosis
10.1038/S41564-024-01727-5
ISSN:2058-5276
Mesothelin-directed protein-drug conjugates for mesothelin-low solid tumor therapy
Ying Wang•Jiayao Yan•Lin Li•Tianran Chen•Jingyi Guo等 10 人
Nature Communications
2025
•2025/8/23
•Vol.16 No.1 p.1-20
Mesothelin (MSLN) is an attractive therapeutic target for precision cancer treatments. However, MSLN can be cleaved and shed from tumor cells, resulting in the presence of soluble MSLN (sMSLN), which significantly hinders the efficacy of MSLN-targeted therapies. Here, we identify a MSLN-targeting de...
Neuroendocrine cancerPreclinical researchTargeted therapies
10.1038/S41467-025-63269-6
ISSN:2041-1723
SARS-CoV-2 hijacks cellular kinase CDK2 to promote viral RNA synthesis
Guo Saisai•Lei Xiaobo•Chang Yan•Zhao Jianyuan•Wang Jing等 19 人
Signal Transduction And Targeted Therapy
2022
•2022/12/27
•Vol.7 No.1 p.1-12
The coronavirus disease 2019 (COVID-19) pandemic has devastated global health. Identifying key host factors essential for SARS-CoV-2 RNA replication is expected to unravel cellular targets for the development of broad-spectrum antiviral drugs which have been quested for the preparedness of future vi...
Drug screeningInfectionInfectious diseasesMicrobiology
10.1038/S41392-022-01239-W
ISSN:2059-3635
Long-term effects of Omicron BA.2 breakthrough infection on immunity-metabolism balance: a 6-month prospective study
Yanhua Li•Shijie Qin•Lei Dong•Shitong Qiao•Xiao Wang等 14 人
Nature Communications
2024
•2024/3/19
•Vol.15 No.1 p.1-18
There have been reports of long coronavirus disease (long COVID) and breakthrough infections (BTIs); however, the mechanisms and pathological features of long COVID after Omicron BTIs remain unclear. Assessing long-term effects of COVID-19 and immune recovery after Omicron BTIs is crucial for unders...
Molecular medicineOutcomes researchSARS-CoV-2Viral infection
10.1038/S41467-024-46692-Z
ISSN:2041-1723
A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1
Ling Hai•Dirk C. Hoffmann•Robin J. Wagener•Daniel D. Azorin•David Hausmann等 31 人
Nature Communications
2024
•2024/2/6
•Vol.15 No.1 p.1-29
Tumor microtubes (TMs) connect glioma cells to a network with considerable relevance for tumor progression and therapy resistance. However, the determination of TM-interconnectivity in individual tumors is challenging and the impact on patient survival unresolved. Here, we establish a connectivity s...
Cancer genomicsCNS cancerGenetics researchMolecular neuroscienceTumour biomarkers
10.1038/S41467-024-45067-8
ISSN:2041-1723
Proteomic comparison of intact and fetoscopy-induced fetal membrane defect sites
Lukas Moser•Katharina Gegenschatz-Schmid•Eva Avilla-Royo•Ladina Rüegg•Bernd Roschitzki等 8 人
Pediatric Research
2025
•2025/12/26
•00 p.1-9
Iatrogenic preterm premature rupture of fetal membranes (iPPROM) following fetoscopic interventions remains a major barrier to the advancement of fetal therapies. The mechanisms underlying iPPROM are poorly understood, but the inability of fetal membrane (FM) defects to heal spontaneously likely pla...
Medicine/Public Health, generalPediatricsPediatric Surgery
10.1038/S41390-025-04692-9
ISSN:0031-3998
Molecular insights into mRNA export regulation by the human TREX-2 complex
Xing Gong•Ran Tao•Xiaofei Ge•Huihui Zhu•Mengqi Li等 9 人
Nature Communications
2026
•2026/2/26
•Vol.17 No.1 p.32440
The nuclear export of mRNA represents a critical regulatory node in eukaryotic gene expression. This process is orchestrated by two conserved multi-subunit assemblies: the transcription-and-export complex (TREX) and TREX-2. While TREX facilitates mRNP packaging through multivalent RNA-protein intera...
Cryoelectron microscopyRNA
10.1038/S41467-026-70088-W
ISSN:2041-1723
Development of nucleus-targeted histone-tail-based photoaffinity probes to profile the epigenetic interactome in native cells
Yu Wang•Jian Fan•Xianbin Meng•Qingyao Shu•Yincui Wu等 13 人
Nature Communications
2025
•2025/1/6
•Vol.16 No.1 p.1-13
Dissection of the physiological interactomes of histone post-translational modifications (hPTMs) is crucial for understanding epigenetic regulatory pathways. Peptide- or protein-based histone photoaffinity tools expanded the ability to probe the epigenetic interactome, but in situ profiling in nativ...
Chemical modificationChemical toolsEpigeneticsHistone post-translational modificationsProteomics
10.1038/S41467-024-55046-8
ISSN:2041-1723
Acevaltrate as a novel ferroptosis inducer with dual targets of PCBP1/2 and GPX4 in colorectal cancer
Dianping Yu•Hongmei Hu•Qing Zhang•Chengji Wang•Mengting Xu等 19 人
Signal Transduction And Targeted Therapy
2025
•2025/7/7
•Vol.10 No.1 p.1-18
Ferroptosis induced by ferrous ions (Fe2+) and lipid peroxidation accumulation is a novel form of regulated cell death that has become a hot topic in tumor therapy research. Identifying small-molecule drugs that can induce ferroptosis in tumor cells is a very attractive therapeutic strategy. Here, w...
Gastrointestinal cancer
10.1038/S41392-025-02296-7
ISSN:2059-3635
BAHCC1 binds H3K27me3 via a conserved BAH module to mediate gene silencing and oncogenesis
Huitao Fan•Jiuwei Lu•Yiran Guo•Dongxu Li•Zhi-Min Zhang等 19 人
Nature Genetics
2020
•2020/11/2
•Vol.52 No.12 p.1384-1396
Trimethylated histone H3 lysine 27 (H3K27me3) regulates gene repression, cell-fate determination and differentiation. We report that a conserved bromo-adjacent homology (BAH) module of BAHCC1 (BAHCC1BAH) ‘recognizes’ H3K27me3 specifically and enforces silencing of H3K27me3-demarcated genes in mammal...
EpigeneticsLeukaemiaX-ray crystallography
10.1038/S41588-020-00729-3
ISSN:1061-4036
SUMOylation disassembles the tetrameric pyruvate kinase M2 to block myeloid differentiation of leukemia cells
Li Xia•Yue Jiang•Xue-Hong Zhang•Xin-Ran Wang•Ran Wei等 7 人
Cell Death & Disease
2021
•2021/1/20
•Vol.12 No.1 p.1-13
Leukemia arises from blockage of the differentiation/maturation of hematopoietic progenitor cells at different stages with uncontrolled proliferation of leukemic cells. However, the signal pathways that block cell differentiation remain unclear. Herein we found that SUMOylation of the M2 isoform of ...
Haematological cancerLeukaemia
10.1038/S41419-021-03400-9
ISSN:2041-4889
Cancer-cell-secreted DDAH1 induces TGF-β1/Smad3 signaling pathway to promote fibrosis and aging in lung
Liu Liu•Qianyue Wang•Meng Chen•Haifeng Zhou•Xu Li等 15 人
Nature Aging
2025
•2025/12/24
•Vol.6 No.1 p.143-161
Lung aging is a multifactorial series of molecular alterations that leads to gradual deterioration of lung function and increased vulnerability to cancer. Tumor communicates with host organs partially through extracellular vesicles; however, the mechanistic drivers and consequences of lung aging in ...
AgeingCancerSenescence
10.1038/S43587-025-01024-8
ISSN:2662-8465
Immunoregulatory role of the gut microbiota in inflammatory depression
Penghong Liu•Zhifen Liu•Jizhi Wang•Junyan Wang•Mingxue Gao等 14 人
Nature Communications
2024
•2024/4/8
•Vol.15 No.1 p.1-17
Inflammatory depression is a treatment-resistant subtype of depression. A causal role of the gut microbiota as a source of low-grade inflammation remains unclear. Here, as part of an observational trial, we first analyze the gut microbiota composition in the stool, inflammatory factors and short-cha...
DepressionDiagnostic markers
10.1038/S41467-024-47273-W
ISSN:2041-1723
Uncovering injury-specific proteomic signatures and neurodegenerative risks in single and repetitive traumatic brain injury
Sarah Mantash•Soulaimane Aboulouard•Hassan Dakik•Yanis Zirem•Lydia Ziane-Chaouche等 13 人
Signal Transduction And Targeted Therapy
2025
•2025/6/23
•Vol.10 No.1 p.1-23
Traumatic brain injury (TBI) is a major public health concern associated with an increased risk of neurodegenerative diseases including Alzheimer’s disease (AD), Parkinson’s disease (PD), and chronic traumatic encephalopathy, yet the underlying molecular mechanisms in repetitive TBI remain poorly de...
BioinformaticsMolecular engineeringPredictive markersRegeneration and repair in the nervous system
10.1038/S41392-025-02286-9
ISSN:2059-3635
Degron models: a toolbox for rapid in vivo depletion of essential proteins regulating mRNA metabolism
Wiktor Antczak•Marcin Szpila•Katarzyna Sałas•Patrycja Daszczuk•Vanessa Linke等 8 人
Communications Biology
2026
•2026/3/18
0Due to their essentiality, studying proteins involved in fundamental processes in vivo is challenging. PROTAC-based systems offer time-controlled protein depletion, but their characterization in vivo remains limited. Here, with an efficient direct zygote editing protocol, we generate degron-tag mode...
CRISPR-Cas9 genome editingGene regulationRNA metabolismUbiquitylation
10.1038/S42003-026-09828-Z
ISSN:2399-3642
Schwann cell plasticity regulates neuroblastic tumor cell differentiation via epidermal growth factor-like protein 8
Tamara Weiss•Sabine Taschner-Mandl•Lukas Janker•Andrea Bileck•Fikret Rifatbegovic等 13 人
Nature Communications
2021
•2021/3/12
•Vol.12 No.1 p.1-19
Adult Schwann cells (SCs) possess an inherent plastic potential. This plasticity allows SCs to acquire repair-specific functions essential for peripheral nerve regeneration. Here, we investigate whether stromal SCs in benign-behaving peripheral neuroblastic tumors adopt a similar cellular state. We ...
Cancer in the nervous systemEmbryonal neoplasmsMechanisms of diseaseSchwann cell
10.1038/S41467-021-21859-0
ISSN:2041-1723
ERK and USP5 govern PD-1 homeostasis via deubiquitination to modulate tumor immunotherapy
Xiangling Xiao•Jie Shi•Chuan He•Xia Bu•Yishuang Sun等 24 人
Nature Communications
2023
•2023/5/19
•Vol.14 No.1 p.1-19
The programmed cell death protein 1 (PD-1) is an inhibitory receptor on T cells and plays an important role in promoting cancer immune evasion. While ubiquitin E3 ligases regulating PD-1 stability have been reported, deubiquitinases governing PD-1 homeostasis to modulate tumor immunotherapy remain u...
Cancer therapyTumour immunology
10.1038/S41467-023-38605-3
ISSN:2041-1723
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia
Minjun Yang•Mattias Vesterlund•Ioannis Siavelis•Larissa H. Moura-Castro•Anders Castor等 15 人
Nature Communications
2019
•2019/4/3
•Vol.10 No.1 p.1-15
Hyperdiploidy, i.e. gain of whole chromosomes, is one of the most common genetic features of childhood acute lymphoblastic leukemia (ALL), but its pathogenetic impact is poorly understood. Here, we report a proteogenomic analysis on matched datasets from genomic profiling, RNA-sequencing, and mass s...
Acute lymphocytic leukaemiaCancer genomicsGenetics research
10.1038/S41467-019-09469-3
ISSN:2041-1723
The NuRD complex cooperates with SALL4 to orchestrate reprogramming
Bo Wang•Chen Li•Jin Ming•Linlin Wu•Shicai Fang等 20 人
Nature Communications
2023
•2023/5/18
•Vol.14 No.1 p.1-14
Cell fate decision involves rewiring of the genome, but remains poorly understood at the chromatin level. Here, we report that chromatin remodeling complex NuRD participates in closing open chromatin in the early phase of somatic reprogramming. Sall4, Jdp2, Glis1 and Esrrb can reprogram MEFs to iPSC...
Chromatin remodellingPluripotent stem cellsReprogramming
10.1038/S41467-023-38543-0
ISSN:2041-1723
The pathogenicity and multi-organ proteomic profiles of Mpox virus infection in SIVmac239-infected rhesus macaques
Dong Zhang•Jiangfeng Liu•Lin Zhu•Baoying Huang•Zhe Cong等 17 人
Nature Communications
2025
•2025/8/17
•Vol.16 No.1 p.1-15
Mpox poses a heightened risk of severe disease and mortality among individuals with HIV, yet the molecular mechanisms and immunopathology underlying multi-organ damage caused by the mpox virus (MPXV), particularly in the context of HIV co-infection, remain poorly understood. Here, we observe increas...
HIV infectionsPox virusProteome informaticsViral infection
10.1038/S41467-025-62919-Z
ISSN:2041-1723
Zinc is a master-regulator of sperm function associated with binding, motility, and metabolic modulation during porcine sperm capacitation
Zigo Michal•Kerns Karl•Sen Sidharth•Essien Clement•Oko Richard等 7 人
Communications Biology
2022
•2022/6/3
•Vol.5 No.1 p.1-12
Sperm capacitation is a post-testicular maturation step endowing spermatozoa with fertilizing capacity within the female reproductive tract, significant for fertility, reproductive health, and contraception. Recently discovered mammalian sperm zinc signatures and their changes during sperm in vitro ...
ProteomicsReproductive biology
10.1038/S42003-022-03485-8
ISSN:2399-3642
Biofunctionalized dissolvable hydrogel microbeads enable efficient characterization of native protein complexes
Xinyang Shao•Meng Tian•Junlong Yin•Haifeng Duan•Ye Tian等 16 人
Nature Communications
2024
•2024/10/5
•Vol.15 No.1 p.1-18
The characterization of protein complex is vital for unraveling biological mechanisms in various life processes. Despite advancements in biophysical tools, the capture of non-covalent complexes and deciphering of their biochemical composition continue to present challenges for low-input samples. Her...
Biophysical methodsMass spectrometryProtein enrichmentStructural biology
10.1038/S41467-024-52948-5
ISSN:2041-1723
Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins
Van Leene Jelle•Eeckhout Dominique•Gadeyne Astrid•Matthijs Caroline•Han Chao等 17 人
Nature Plants
2022
•2022/11/14
•Vol.8 No.11 p.1245-1261
The central metabolic regulator SnRK1 controls plant growth and survival upon activation by energy depletion, but detailed molecular insight into its regulation and downstream targets is limited. Here we used phosphoproteomics to infer the sucrose-dependent processes targeted upon starvation by kina...
Nutrient signallingPlant signallingPlant stress responses
10.1038/S41477-022-01269-W
ISSN:2055-0278
Phosphorylation-coupled autoregulation of TANGO1 and Sec16A maintains functional ER exit sites
Miharu Maeda•Masashi Arakawa•Masaki Wakabayashi•Yukie Komatsu•Kota Saito
Nature Communications
2025
•2025/11/25
•Vol.16 No.1 p.104340
Secretory proteins are synthesized in the endoplasmic reticulum (ER) and begin their transport from specialized domains on the ER called ER exit sites (ERES), where COPII proteins assemble. We previously demonstrated that the interaction between TANGO1 and Sec16A is critical for ERES formation. In t...
Endoplasmic reticulumKinasesSecretion
10.1038/S41467-025-65409-4
ISSN:2041-1723
DJ-1 protects proteins from acylation by catalyzing the hydrolysis of highly reactive cyclic 3-phosphoglyceric anhydride
Aizhan Akhmadi•Adilkhan Yeskendir•Nelly Dey•Arman Mussakhmetov•Zariat Shatkenova等 8 人
Nature Communications
2024
•2024/3/5
•Vol.15 No.1 p.1-12
Mutations in the human PARK7 gene that encodes protein DJ-1 lead to familial Parkinsonism due to loss of dopaminergic neurons. However, the molecular function of DJ-1 underpinning its cytoprotective effects are unclear. Recently, DJ-1 has been shown to prevent acylation of amino groups of proteins a...
AcetylationEnzyme mechanismsEnzymesMechanisms of diseaseMetabolic pathways
10.1038/S41467-024-46391-9
ISSN:2041-1723
A microprotein encoded by LINC00263 promotes breast cancer osteolytic bone metastasis by inducing osteoclastogenesis and inhibiting osteoclast ferroptosis
Suwen Chen•Miaoling Tang•Xuexin Yu•Wanying Qian•Yingru Xu等 8 人
Oncogene
2025
•2025/4/12
•00 p.1-16
Currently, there are no effective prevention or therapeutic methods for breast cancer bone metastasis (BC-BM), which leading to severe skeletal complications and increased mortality. Understanding the mechanisms underlying BC-BM could provide potential strategies for its prevention and treatment. In...
Bone metastasesCell biology
10.1038/S41388-025-03400-5
ISSN:0950-9232
The mitotic STAG3–cohesin complex shapes male germline nucleome
Masahiro Nagano•Bo Hu•Kosuke Ogata•Fumiya Umemura•Yukiko Ishikura等 31 人
Nature Structural & Molecular Biology
2025
•2025/8/25
•00 p.1-16
Germ cells are unique in that they tailor chromatin toward generating totipotency. Accordingly, mammalian spermatogonia, including spermatogonial stem cells that constitute the source for male gametes, acquire distinctive chromatin organization with weak insulation, but the underlying mechanism rema...
Nuclear organizationReprogrammingStem cells
10.1038/S41594-025-01647-W
ISSN:1545-9993
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
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
Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection
Mikaeloff Flora•Svensson Akusjärvi Sara•Ikomey George Mondinde•Krishnan Shuba•Sperk Maike等 21 人
Communications Biology
2022
•2022/1/11
•Vol.5 No.1 p.1-12
Despite successful combination antiretroviral therapy (cART), persistent low-grade immune activation together with inflammation and toxic antiretroviral drugs can lead to long-lasting metabolic flexibility and adaptation in people living with HIV (PLWH). Our study investigated alterations in the pla...
MetabolomicsSystems analysis
10.1038/S42003-021-02985-3
ISSN:2399-3642
A synthetic antibiotic class with a deeply-optimized design for overcoming bacterial resistance
Jin Feng•Youle Zheng•Wanqing Ma•Defeng Weng•Dapeng Peng等 8 人
Nature Communications
2024
•2024/7/18
•Vol.15 No.1 p.1-16
The lack of new drugs that are effective against antibiotic-resistant bacteria has caused increasing concern in global public health. Based on this study, we report development of a modified antimicrobial drug through structure-based drug design (SBDD) and modular synthesis. The optimal modified com...
AntibioticsAntimicrobial resistanceStructure-based drug design
10.1038/S41467-024-50453-3
ISSN:2041-1723
Ubiquitin-dependent mitochondrial protein degradation ensures seedling emergence by regulating ER–mitochondrial interaction and mitophagy
Zhen Tian•Yawen Huo•Chengyang Li•Qiwei Zheng•Fan Hu等 12 人
Nature Plants
2026
•2026/5/28
•00 p.1-12
Seedling emergence is a pivotal step of plant survival, requiring rapid hypocotyl elongation for soil penetration1,2. This energy-demanding process necessitates active mitochondrial respiration, which inevitably induces oxidative damage3–6. Plants have therefore evolved a quality-control mechanism t...
Cell biologyPlant cell biologyPlant development
10.1038/S41477-026-02306-8
ISSN:2055-0278
Excessive copper impairs intrahepatocyte trafficking and secretion of selenoprotein P
Maria Schwarz•Caroline E. Meyer•Alina Löser•Kristina Lossow•Julian Hackler等 25 人
Nature Communications
2023
•2023/6/13
•Vol.14 No.1 p.1-15
Selenium homeostasis depends on hepatic biosynthesis of selenoprotein P (SELENOP) and SELENOP-mediated transport from the liver to e.g. the brain. In addition, the liver maintains copper homeostasis. Selenium and copper metabolism are inversely regulated, as increasing copper and decreasing selenium...
HomeostasisMetalsProtein translocation
10.1038/S41467-023-39245-3
ISSN:2041-1723
EBV miRNAs BART11 and BART17-3p promote immune escape through the enhancer-mediated transcription of PD-L1
Wang Jie•Ge Junshang•Wang Yian•Xiong Fang•Guo Jiayue等 22 人
Nature Communications
2022
•2022/2/14
•Vol.13 No.1 p.1-21
Epstein-Barr virus (EBV) is reportedly the first identified human tumor virus, and is closely related to the occurrence and development of nasopharyngeal carcinoma (NPC), gastric carcinoma (GC), and several lymphomas. PD-L1 expression is elevated in EBV-positive NPC and GC tissues; however, the spec...
Cancer epigeneticsImmunoeditingTumour virus infections
10.1038/S41467-022-28479-2
ISSN:2041-1723
Skeletal muscle-secreted DLPC orchestrates systemic energy homeostasis by enhancing adipose browning
Xiaodi Hu•Mingwei Sun•Qian Chen•Yixia Zhao•Na Liang等 23 人
Nature Communications
2023
•2023/11/30
•Vol.14 No.1 p.1-18
MyoD is a skeletal muscle-specifically expressed transcription factor and plays a critical role in regulating myogenesis during muscle development and regeneration. However, whether myofibers-expressed MyoD exerts its metabolic function in regulating whole body energy homeostasis in vivo remains lar...
MetabolismObesityPhospholipids
10.1038/S41467-023-43402-Z
ISSN:2041-1723
Proteomic analysis reveals key differences between squamous cell carcinomas and adenocarcinomas across multiple tissues
Song Qi•Yang Ye•Jiang Dongxian•Qin Zhaoyu•Xu Chen等 25 人
Nature Communications
2022
•2022/7/18
•Vol.13 No.1 p.1-20
Squamous cell carcinoma (SCC) and adenocarcinoma (AC) are two main histological subtypes of solid cancer; however, SCCs are derived from different organs with similar morphologies, and it is challenging to distinguish the origin of metastatic SCCs. Here we report a deep proteomic analysis of 333 SCC...
Cancer microenvironmentProteomicsSquamous cell carcinomaTumour biomarkersTumour virus infections
10.1038/S41467-022-31719-0
ISSN:2041-1723
CB1R-stabilized NLRP3 inflammasome drives antipsychotics cardiotoxicity
Li Liliang•Gao Pan•Tang Xinru•Liu Zheng•Cao Mengying等 16 人
Signal Transduction And Targeted Therapy
2022
•2022/6/24
•Vol.7 No.1 p.1-15
Long-term use of antipsychotics is a common cause of myocardial injury and even sudden cardiac deaths that often lead to drug withdrawn or discontinuation. Mechanisms underlying antipsychotics cardiotoxicity remain largely unknown. Herein we performed RNA sequencing and found that NLRP3 inflammasome...
CardiologyDrug safety
10.1038/S41392-022-01018-7
ISSN:2059-3635
N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation
Jeremy Monroe•Daniel E. Eyler•Lili Mitchell•Indrajit Deb•Abigail Bojanowski等 10 人
Nature Communications
2024
•2024/9/16
•Vol.15 No.1 p.1-11
The ribosome utilizes hydrogen bonding between mRNA codons and aminoacyl-tRNAs to ensure rapid and accurate protein production. Chemical modification of mRNA nucleobases can adjust the strength and pattern of this hydrogen bonding to alter protein synthesis. We investigate how the N1-methylpseudouri...
RibosomeRNAtRNAs
10.1038/S41467-024-51301-0
ISSN:2041-1723
Microbiota-derived succinate promotes enterohaemorrhagic Escherichia coli virulence via lysine succinylation
Linxing Li•Yutao Liu•Dan Liu•Jing Wang•Min Wang等 27 人
Nature Microbiology
2025
•2025/1/31
•Vol.10 No.3 p.749-764
Succinate upregulates enterohaemorrhagic Escherichia coli (EHEC) virulence. Lysine succinylation, a post-translational modification, regulates cellular function in eukaryotes but is less characterized in bacteria. We hypothesized that lysine succinylation regulates EHEC virulence. Here we used SILAC...
InfectionInfectious diseasesPathogens
10.1038/S41564-025-01931-X
ISSN:2058-5276
UBR4/POE facilitates secretory trafficking to maintain circadian clock synchrony
Hegazi Sara•Cheng Arthur H.•Krupp Joshua J.•Tasaki Takafumi•Liu Jiashu等 19 人
Nature Communications
2022
•2022/3/24
•Vol.13 No.1 p.1-21
Ubiquitin ligases control the degradation of core clock proteins to govern the speed and resetting properties of the circadian pacemaker. However, few studies have addressed their potential to regulate other cellular events within clock neurons beyond clock protein turnover. Here, we report that the...
Circadian mechanismsGolgiProtein transportUbiquitin ligases
10.1038/S41467-022-29244-1
ISSN:2041-1723
Knockdown of METTL16 disrupts learning and memory by reducing the stability of MAT2A mRNA
Zhang Runjiao•Zhang Yizhou•Guo Fangzhen•Huang Guannan•Zhao Yan等 11 人
Cell Death Discovery
2022
•2022/10/28
•Vol.8 No.1 p.1-14
N6-methyladenosine (m6A) is abundant in the mammalian brain and is considered to have a wide range of effects on learning and memory. Here, we found that the upregulated methyltransferase-like protein 16 (METTL16) in the hippocampal tissues of Morris water maze (MWM)-trained mice contributed to impr...
Cellular neuroscienceHippocampus
10.1038/S41420-022-01220-0
ISSN:2058-7716
Targeting IRF1-TRIM21 axis enhances anti-tumor immunity by promoting ubiquitin-mediated degradation of FGL1 in non-small cell lung cancer
Yuchen Zhang•Pingjing Zhou•Yifan Guo•Hongyu Zhang•Guangyin Zhao等 10 人
Communications Biology
2026
•2026/4/22
0Immunotherapy has emerged as a first-line treatment for patients with advanced non-small cell lung cancer (NSCLC), but over half of patients fail to benefit, largely due to tumor heterogeneity and a complex tumor microenvironment. Here, we demonstrate that fibrinogen-like protein 1 (FGL1), a recentl...
Non-small-cell lung cancerUbiquitylation
10.1038/S42003-026-10070-W
ISSN:2399-3642
Nicotinamide mononucleotide treatment improves spermatogenesis in obese mice by reducing lysine acetylation of lactate dehydrogenase C
Ke Liu•Weihua Nong•Hua Huang•Yanhong Wei•Jinyuan Wang等 14 人
Communications Biology
2025
•2025/11/26
0Obesity is associated with impaired spermatogenesis and decreased sperm quality, in part through reducing Sertoli cells (SCs) lactate and nicotinamide adenine dinucleotide (NAD+) production. It is not known whether nicotinamide mononucleotide (NMN) treatment improves spermatogenesis. In the present ...
Molecular medicineObesity
10.1038/S42003-025-09094-5
ISSN:2399-3642
Targeting USP18 overcomes acquired resistance in hepatocellular carcinoma by regulating NCOA4 deISGylation and ferroptosis
Shengtao Ye•Junxin Chen•Ying Zheng•Mengmeng He•Yanqiu Zhang等 10 人
Cell Death & Disease
2025
•2025/6/13
•Vol.16 No.1 p.1-15
Targeted therapy resistance has become a major challenge for hepatocellular carcinoma (HCC) treatment. Triggering ferroptosis emerges as a promising strategy to overcome therapeutic resistance. Here, we have identified ubiquitin-specific protease 18 (USP18), a member of the deubiquitinating enzyme f...
Cancer therapeutic resistancePost-translational modifications
10.1038/S41419-025-07772-0
ISSN:2041-4889
CRISPR screening reveals that RNA helicase DDX41 triggers ribosome biogenesis and cancer progression through R-loop-mediated RPL/RPS transcription
Hongquan Li•Yifei He•Jiawen Jiang•Zhen Liu•Yizhe Liu等 12 人
Nature Communications
2025
•2025/8/11
•Vol.16 No.1 p.1-18
The RNA helicase DDX41 is a DEAD-box helicase that is well known as a virus sensor in dendritic cells and a tumor suppressor that is frequently mutated in myeloid neoplasms. However, the functions and relevance of DDX41 in solid tumors remain largely unexplored. In this study, through in vivo CRISPR...
Cancer epigeneticsCRISPR-Cas9 genome editingCell growthTranscriptional regulatory elements
10.1038/S41467-025-62743-5
ISSN:2041-1723
Integrated plasma and vegetation proteomic characterization of infective endocarditis for early diagnosis and treatment
Shiman He•Xuejiao Hu•Jiajun Zhu•Weiteng Wang•Chi Ma等 21 人
Nature Communications
2025
•2025/5/30
•Vol.16 No.1 p.1-21
Infective endocarditis, a life-threatening condition, poses challenges for early diagnosis and personalized treatment due to insufficient biomarkers and limited understanding of its pathophysiology. Here, we performed proteomic profiling of plasma and vegetation samples from 238 patients with infect...
Diagnostic markersProteomicsValvular disease
10.1038/S41467-025-60184-8
ISSN:2041-1723
A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape
Philipp Hubel•Christian Urban•Valter Bergant•William M. Schneider•Barbara Knauer等 15 人
Nature Immunology
2019
•2019/3/4
•Vol.20 No.4 p.493-502
Interferon-stimulated genes (ISGs) form the backbone of the innate immune system and are important for limiting intra- and intercellular viral replication and spread. We conducted a mass-spectrometry-based survey to understand the fundamental organization of the innate immune system and to explore t...
Innate immunityVirology
10.1038/S41590-019-0323-3
ISSN:1529-2908
Integrative multi-omics analysis reveals the translational landscape of the plant-parasitic nematode Meloidogyne incognita
Zhaolu Zhu•Dexin Bo•Chuanshuai Xie•Dadong Dai•Donghai Peng等 7 人
Communications Biology
2025
•2025/1/28
•Vol.8 No.1 p.1-12
Root-knot nematodes (RKNs) of the genus Meloidogyne pose the most significant threats to global food security due to their destructive nature as plant-parasitic nematodes. Although significant attention has been devoted to investigating the gene transcription profiling of RKNs, our understanding of ...
Gene regulationGenome-wide analysis of gene expressionParasite geneticsRibosome
10.1038/S42003-025-07533-X
ISSN:2399-3642
Elevated SFXN2 limits mitochondrial autophagy and increases iron-mediated energy production to promote multiple myeloma cell proliferation
Chen Ying•Qian Jinjun•Ding Pinggang•Wang Wang•Li Xinying等 9 人
Cell Death & Disease
2022
•2022/9/26
•Vol.13 No.9 p.1-14
Human sideroflexin 2 (SFXN2) belongs to the SFXN protein family, which is a mitochondrial outer membrane protein involved in mitochondrial iron metabolism. Mitochondria are indispensable for cellular energy production and iron metabolism. However, it remains elusive how SFXN2 modulates mitochondrial...
Myeloma
10.1038/S41419-022-05272-Z
ISSN:2041-4889
Proteogenomic discovery of sORF-encoded peptides associated with bacterial virulence in Yersinia pestis
Cao Shiyang•Liu Xinyue•Huang Yin•Yan Yanfeng•Zhou Congli等 10 人
Communications Biology
2021
•2021/11/2
•Vol.4 No.1 p.1-12
Plague caused by Yersinia pestis is one of the deadliest diseases. However, many molecular mechanisms of bacterial virulence remain unclear. This study engaged in the discovery of small open reading frame (sORF)-encoded peptides (SEPs) in Y. pestis. An integrated proteogenomic pipeline was establish...
PathogensPeptidesProteomic analysisProteomics
10.1038/S42003-021-02759-X
ISSN:2399-3642
Rapid metabolic reprogramming mediated by the AMP-activated protein kinase during the lytic cycle of Toxoplasma gondii
Li Yaqiong•Niu Zhipeng•Yang Jichao•Yang Xuke•Chen Yukun等 12 人
Nature Communications
2023
•2023/1/26
•Vol.14 No.1 p.1-15
The ubiquitous pathogen Toxoplasma gondii has a complex lifestyle with different metabolic activities at different stages that are intimately linked to the parasitic environments. Here we identified the eukaryotic regulator of cellular homeostasis AMP-activated protein kinase (AMPK) in Toxoplasma an...
Cellular microbiologyParasite biology
10.1038/S41467-023-36084-0
ISSN:2041-1723
Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu
Chi-Min Ho•Xiaorun Li•Mason Lai•Thomas C. Terwilliger•Josh R. Beck等 9 人
Nature Methods
2019
•2019/11/25
•Vol.17 No.1 p.79-85
X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cry...
Cryoelectron microscopyMass spectrometryProteinsProteomic analysisSoftware
10.1038/S41592-019-0637-Y
ISSN:1548-7091
Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis
Mise Shintaro•Matsumoto Akinobu•Shimada Keisuke•Hosaka Toshiaki•Takahashi Masatomo等 19 人
Nature Communications
2022
•2022/2/28
•Vol.13 No.1 p.1-17
Although several long noncoding RNAs (lncRNAs) have recently been shown to encode small polypeptides, those in testis remain largely uncharacterized. Here we identify two sperm-specific polypeptides, Kastor and Polluks, encoded by a single mouse locus (Gm9999) previously annotated as encoding a lncR...
Gene expressionLong non-coding RNAsReproductive biologySpermatogenesis
10.1038/S41467-022-28677-Y
ISSN:2041-1723
Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase
Jelle Van Leene•Chao Han•Astrid Gadeyne•Dominique Eeckhout•Caroline Matthijs等 18 人
Nature Plants
2019
•2019/3/4
•Vol.5 No.3 p.316-327
The target of rapamycin (TOR) kinase is a conserved regulatory hub that translates environmental and nutritional information into permissive or restrictive growth decisions. Despite the increased appreciation of the essential role of the TOR complex in plants, no large-scale phosphoproteomics or int...
Mass spectrometryNutrient signallingPlant molecular biologyProtein purificationProteomic analysis
10.1038/S41477-019-0378-Z
ISSN:2055-0278
Selective depletion of tumor-associated SAMHD1 enhances chemotherapeutic efficacy and antitumor immune responses
Jing Sun•Wenwen Zheng•Zheng-Guo Zhang•Hongkun Zhou•Songdi Wang等 30 人
Signal Transduction And Targeted Therapy
2025
•2025/12/15
•Vol.10 No.1 p.4060
SAMHD1 is a human deoxyribonucleoside triphosphatase (dNTPase) known for its role as a restriction factor that targets a wide spectrum of viruses, its involvement in autoimmune disease Aicardi–Goutières syndrome (AGS), and its participation in innate immune regulation. The role of SAMHD1 in cancer, ...
Drug developmentHaematological cancerMolecular medicine
10.1038/S41392-025-02523-1
ISSN:2059-3635
High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation
Shen Shichen•Wang Xue•Zhu Xiaoyu•Rasam Sailee•Ma Min等 17 人
Nature Protocols
2022
•2022/12/9
•Vol.18 No.3 p.700-731
Robust, reliable quantification of large sample cohorts is often essential for meaningful clinical or pharmaceutical proteomics investigations, but it is technically challenging. When analyzing very large numbers of samples, isotope labeling approaches may suffer from substantial batch effects, and ...
BiomarkersProteomic analysisTranslational research
10.1038/S41596-022-00780-W
ISSN:1754-2189
Multi-hierarchical profiling the structure-activity relationships of engineered nanomaterials at nano-bio interfaces
Xiaoming Cai•Jun Dong•Jing Liu•Huizhen Zheng•Chitrada Kaweeteerawat等 8 人
Nature Communications
2018
•2018/10/24
•Vol.9 No.1 p.1-12
Increasing concerns over the possible risks of nanotechnology necessitates breakthroughs in structure–activity relationship (SAR) analyses of engineered nanomaterials (ENMs) at nano-bio interfaces. However, current nano-SARs are often based on univariate assessments and fail to provide tiered views ...
InflammationMetabolomicsNanotoxicologyProteomics
10.1038/S41467-018-06869-9
ISSN:2041-1723
Exosomal circEZH2_005, an intestinal injury biomarker, alleviates intestinal ischemia/reperfusion injury by mediating Gprc5a signaling
Wenjuan Zhang•Bowei Zhou•Xiao Yang•Jin Zhao•Jingjuan Hu等 19 人
Nature Communications
2023
•2023/9/6
•Vol.14 No.1 p.1-17
Intestinal ischemia/reperfusion (I/R) injury is a severe clinical condition without optimal diagnostic markers nor clear molecular etiological insights. Plasma exosomal circular RNAs (circRNAs) are valuable biomarkers and therapeutic targets for various diseases, but their role in intestinal I/R inj...
Diagnostic markersStem-cell research
10.1038/S41467-023-41147-3
ISSN:2041-1723
Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera
Zhouchen Ye•Jing Yu•Wuping Yan•Junfeng Zhang•Dongmei Yang等 9 人
Horticulture Research
2021
•2021/7/1
•Vol.8 No.1 p.1-26
Camellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation...
Plant molecular biologyTranscriptomics
10.1038/S41438-021-00591-2
ISSN:2662-6810
Marrow leptin-LEPR signaling rewires mitochondrial oxidative metabolism to confer chemoresistance in acute myeloid leukemia
Xinai Liao•Wei Dai•Xiaolin Xu•Danni Cai•Maoqing Tan等 15 人
Cell Death & Disease
2026
•2026/2/23
•Vol.17 No.1 p.2490
Leptin is abundant within marrow adipose tissue, yet its impact on acute myeloid leukemia (AML) therapy response is undefined. Here, we report that elevated bone-marrow leptin and blast-cell leptin-receptor (LEPR) levels strongly associate with poor cytarabine (Ara-C) clearance and reduced survival ...
Cancer therapyPrognostic markers
10.1038/S41419-026-08528-0
ISSN:2041-4889
TmcA functions as a lysine 2-hydroxyisobutyryltransferase to regulate transcription
Dong Hanyang•Zhao Yujie•Bi Changfen•Han Yue•Zhang Jianji等 12 人
Nature Chemical Biology
2021
•2021/12/13
•00 p.1-10
Protein lysine 2-hydroxyisobutyrylation (Khib) has recently been shown to play a critical role in the regulation of cellular processes. However, the mechanism and functional consequence of Khib in prokaryotes remain unclear. Here we report that TmcA, an RNA acetyltransferase, functions as a lysine 2...
Post-translational modificationsProtein–protein interaction networksTranscription
10.1038/S41589-021-00906-3
ISSN:1552-4450
Unusual zymogen activation patterns in the protein corona of Ca-zeolites
Xiaoqiang Shang•Hao Chen•Valentina Castagnola•Kai Liu•Luca Boselli等 12 人
Nature Catalysis
2021
•2021/7/22
•Vol.4 No.7 p.607-614
Zymogen (prothrombin) activation is central to the process of haemostasis (blood clotting) in the body, preventing serious blood loss and death from haemorrhagic shock. Zeolites comprise a family of crystalline microporous aluminosilicates that show increasing promise for use in massive bleeding con...
Coagulation systemEnzymesProteomicsSurface assemblyTrauma
10.1038/S41929-021-00654-6
ISSN:2520-1158
Dihydroartemisinin regulates immune cell heterogeneity by triggering a cascade reaction of CDK and MAPK phosphorylation
Li Qilong•Yuan Quan•Jiang Ning•Zhang Yiwei•Su Ziwei等 10 人
Signal Transduction And Targeted Therapy
2022
•2022/7/11
•Vol.7 No.1 p.1-11
Artemisinin (ART) and dihydroartemisinin (DHA), apart from their profound anti-malaria effect, can also beneficially modulate the host immune system; however, the underlying molecular mechanisms remain unclear. Here, we report that DHA selectively induced T-cell activation, with an increased proport...
ImmunotherapyMolecular medicine
10.1038/S41392-022-01028-5
ISSN:2059-3635
Kinetic proofreading through the multi-step activation of the ZAP70 kinase underlies early T cell ligand discrimination
Voisinne Guillaume•Locard-Paulet Marie•Froment Carine•Maturin Emilie•Menoita Marisa Goncalves等 11 人
Nature Immunology
2022
•2022/8/31
•Vol.23 No.9 p.1355-1364
T cells recognize a few high-affinity antigens among a vast array of lower affinity antigens. According to the kinetic proofreading model, antigen discrimination properties could be explained by the gradual amplification of small differences in binding affinities as the signal is transduced downstre...
KinasesT-cell receptor
10.1038/S41590-022-01288-X
ISSN:1529-2908
Tipping the immunostimulatory and inhibitory DAMP balance to harness immunogenic cell death
K. Hayashi•F. Nikolos•Y. C. Lee•A. Jain•E. Tsouko等 12 人
Nature Communications
2020
•2020/12/7
•Vol.11 No.1 p.1-13
Induction of tumor cell death is the therapeutic goal for most anticancer drugs. Yet, a mode of drug-induced cell death, known as immunogenic cell death (ICD), can propagate antitumoral immunity to augment therapeutic efficacy. Currently, the molecular hallmark of ICD features the release of damage-...
Bladder cancerCell death and immune responseChemotherapyPancreatic cancerTumour immunology
10.1038/S41467-020-19970-9
ISSN:2041-1723
Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel
Alberto J. Taurozzi•Patrick L. Rüther•Ioannis Patramanis•Claire Koenig•Ryan Sinclair Paterson等 12 人
Nature Protocols
2024
•2024/4/26
•00 p.1-32
In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursu...
Biological anthropologyEvolutionary biologyMass spectrometryPalaeontologyProteomics
10.1038/S41596-024-00975-3
ISSN:1754-2189
VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC
Mikulski Pawel•Wolff Philip•Lu Tiancong•Nielsen Mathias•Echevarria Elsa Franco等 10 人
Nature Communications
2022
•2022/9/21
•Vol.13 No.1 p.1-12
Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of...
ChromatinGene silencingPlant molecular biologyTranscriptional regulatory elements
10.1038/S41467-022-32897-7
ISSN:2041-1723
Functional optic tract rewiring via subtype- and target-specific axonal regeneration and presynaptic activity enhancement
Xin Zhang•Chao Yang•Chengle Zhang•Junqiang Wu•Xiang Zhang等 18 人
Nature Communications
2025
•2025/3/4
•Vol.16 No.1 p.1-20
Mechanisms underlying functional axonal rewiring after adult mammalian central nervous system (CNS) injuries remain unclear partially due to limited models. Here we develop a mouse intracranial pre–olivary pretectal nucleus (OPN) optic tract injury model and demonstrate that Pten/Socs3 knockout and ...
Molecular neuroscienceRegeneration and repair in the nervous systemVisual system
10.1038/S41467-025-57445-X
ISSN:2041-1723
Metabolic characterization of hypertrophic cardiomyopathy in human heart
Wang Wenmin•Wang Jizheng•Yao Ke•Wang Shuiyun•Nie Meng等 24 人
Nature Cardiovascular Research
2022
•2022/5/9
•00 p.1-17
Hypertrophic cardiomyopathy (HCM) is a common inherited cardiovascular disease with heterogeneous clinical presentations, governed by multiple molecular mechanisms. Metabolic perturbations underlie most cardiovascular diseases; however, the metabolic alterations and their function in HCM are unknown...
Cardiac hypertrophyMetabolomics
10.1038/S44161-022-00057-1
ISSN:2731-0590
Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
Annabelle Hoegl•Matthew B. Nodwell•Volker C. Kirsch•Nina C. Bach•Martin Pfanzelt等 8 人
Nature Chemistry
2018
•2018/10/8
•Vol.10 No.12 p.1234-1245
Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in many central cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging. Here we pre...
Chemical modificationChemical toolsEnzymesProteomics
10.1038/S41557-018-0144-2
ISSN:1755-4330
Merging PROTAC and molecular glue for degrading BTK and GSPT1 proteins concurrently
Yang Zimo•Sun Yonghui•Ni Zhihao•Yang Celi•Tong Yan等 8 人
Cell Research
2021
•2021/8/20
•00 p.1-4
Drug developmentTargeted therapies
10.1038/S41422-021-00533-6
ISSN:1001-0602
Periplasmic crowding and peptidoglycan hydrolase activity as drivers of outer membrane vesiculation in Acinetobacter baumannii
Bitnara Kim•Yongjun Son•Reagan Lee•Jihyeon Min•Woojun Park
Communications Biology
2026
•2026/3/18
0Acinetobacter baumannii produces outer membrane vesicles (OMVs) to alleviate envelope stress, though the mechanisms remain poorly understood. To induce periplasmic accumulation of misfolded proteins and trigger stress, a degP mutant is exposed to elevated temperatures. Periplasmic crowding-induced O...
Cellular microbiologyPathogens
10.1038/S42003-026-09876-5
ISSN:2399-3642
Conformational cycle of human polyamine transporter ATP13A2
Mu Jianqiang•Xue Chenyang•Fu Lei•Yu Zongjun•Nie Minhan等 19 人
Nature Communications
2023
•2023/4/8
•Vol.14 No.1 p.1-12
Dysregulation of polyamine homeostasis strongly associates with human diseases. ATP13A2, which is mutated in juvenile-onset Parkinson’s disease and autosomal recessive spastic paraplegia 78, is a transporter with a critical role in balancing the polyamine concentration between the lysosome and the c...
Cryoelectron microscopyLysosomesMembrane proteinsPermeation and transport
10.1038/S41467-023-37741-0
ISSN:2041-1723
MaxDIA enables library-based and library-free data-independent acquisition proteomics
Pavel Sinitcyn•Hamid Hamzeiy•Favio Salinas Soto•Daniel Itzhak•Frank McCarthy等 18 人
Nature Biotechnology
2021
•2021/7/8
•00 p.1-11
MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software....
Proteome informaticsProteomics
10.1038/S41587-021-00968-7
ISSN:1087-0156
Serum Proteomics Reveals Diagnostic Biomarkers and Molecular Pathways in Cerebral Palsy
Yiran Xu•Chi Ma•Yanyan Sun•Jiajun Zhu•Shiman He等 22 人
Nature Communications
2025
•2025/11/21
•Vol.16 No.1 p.102530
Cerebral palsy (CP), a prevalent non-progressive neurological disorder in children, lacks reliable biomarkers for early diagnosis, and its molecular mechanisms remain poorly understood. In this study, we conducted serum proteomic profiling of 346 CP patients and 190 healthy controls and developed a ...
Diagnostic markersDiseases of the nervous systemProteomics
10.1038/S41467-025-65110-6
ISSN:2041-1723
LipidII interaction with specific residues of Mycobacterium tuberculosis PknB extracytoplasmic domain governs its optimal activation
Prabhjot Kaur•Marvin Rausch•Basanti Malakar•Uchenna Watson•Nikhil P. Damle等 14 人
Nature Communications
2019
•2019/3/15
•Vol.10 No.1 p.1-17
The Mycobacterium tuberculosis kinase PknB is essential for growth and survival of the pathogen in vitro and in vivo. Here we report the results of our efforts to elucidate the mechanism of regulation of PknB activity. The specific residues in the PknB extracytoplasmic domain that are essential for ...
Cell biologyMicrobiologyMolecular biology
10.1038/S41467-019-09223-9
ISSN:2041-1723
α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation
Mariana Pavel•So Jung Park•Rebecca A. Frake•Sung Min Son•Marco M. Manni等 11 人
Nature Communications
2021
•2021/3/17
•Vol.12 No.1 p.1-21
The factors regulating cellular identity are critical for understanding the transition from health to disease and responses to therapies. Recent literature suggests that autophagy compromise may cause opposite effects in different contexts by either activating or inhibiting YAP/TAZ co-transcriptiona...
AutophagyCell biologyMacroautophagy
10.1038/S41467-021-21882-1
ISSN:2041-1723
Nucleoporin Nup155 is part of the p53 network in liver cancer
Kerstin Holzer•Alessandro Ori•Amy Cooke•Daniel Dauch•Elisabeth Drucker等 19 人
Nature Communications
2019
•2019/5/14
•Vol.10 No.1 p.1-13
Cancer-relevant signalling pathways rely on bidirectional nucleocytoplasmic transport events through the nuclear pore complex (NPC). However, mechanisms by which individual NPC components (Nups) participate in the regulation of these pathways remain poorly understood. We discover by integrating larg...
Hepatocellular carcinomaNuclear pore complexOncogene proteinsTranslation
10.1038/S41467-019-10133-Z
ISSN:2041-1723
Covalent penicillin-protein conjugates elicit anti-drug antibodies that are clonally and functionally restricted
Lachlan P. Deimel•Lucile Moynié•Guoxuan Sun•Viliyana Lewis•Abigail Turner等 17 人
Nature Communications
2024
•2024/8/10
•Vol.15 No.1 p.1-12
Many archetypal and emerging classes of small-molecule therapeutics form covalent protein adducts. In vivo, both the resulting conjugates and their off-target side-conjugates have the potential to elicit antibodies, with implications for allergy and drug sequestration. Although β-lactam antibiotics ...
AntibodiesChemical biologyImmunologyNMR spectroscopyStructural biology
10.1038/S41467-024-51138-7
ISSN:2041-1723
Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization
Fátima C. Pereira•Kenneth Wasmund•Iva Cobankovic•Nico Jehmlich•Craig W. Herbold等 14 人
Nature Communications
2020
•2020/10/9
•Vol.11 No.1 p.1-15
Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevert...
MetagenomicsMicrobial ecologyMicrobiomePathogens
10.1038/S41467-020-18928-1
ISSN:2041-1723
Co-regulation map of the human proteome enables identification of protein functions
Georg Kustatscher•Piotr Grabowski•Tina A. Schrader•Josiah B. Passmore•Michael Schrader等 6 人
Nature Biotechnology
2019
•2019/11/4
•Vol.37 No.11 p.1361-1371
Assigning functions to the vast array of proteins present in eukaryotic cells remains challenging. To identify relationships between proteins, and thereby enable functional annotation of proteins, we determined changes in abundance of 10,323 human proteins in response to 294 biological perturbations...
Machine learningProtein–protein interaction networksProteomic analysisSystems biology
10.1038/S41587-019-0298-5
ISSN:1087-0156
An Alveolata secretory machinery adapted to parasite host cell invasion
Eleonora Aquilini•Marta Mendonça Cova•Shrawan Kumar Mageswaran•Nicolas Dos Santos Pacheco•Daniela Sparvoli等 19 人
Nature Microbiology
2021
•2021/1/25
•Vol.6 No.4 p.425-434
Apicomplexa are unicellular eukaryotes and obligate intracellular parasites, including Plasmodium (the causative agent of malaria) and Toxoplasma (one of the most widespread zoonotic pathogens). Rhoptries, one of their specialized secretory organelles, undergo regulated exocytosis during invasion1. ...
MalariaParasite biology
10.1038/S41564-020-00854-Z
ISSN:2058-5276
Proteogenomic characterization of skull-base chordoma
Qilin Zhang•Ziyan Xu•Rui Han•Yunzhi Wang•Zhen Ye等 19 人
Nature Communications
2024
•2024/9/27
•Vol.15 No.1 p.1-32
Skull-base chordoma is a rare, aggressive bone cancer with a high recurrence rate. Despite advances in genomic studies, its molecular characteristics and effective therapies remain unknown. Here, we conduct integrative genomics, transcriptomics, proteomics, and phosphoproteomics analyses of 187 skul...
Bone cancerCancer genomicsCancer microenvironmentTumour heterogeneity
10.1038/S41467-024-52285-7
ISSN:2041-1723
A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs
Ulrike Kusebauch•Zhi Sun•Mukul K. Midha•Charu Kapil•Michal Maes等 13 人
Scientific Data
2026
•2026/4/2
•Vol.13 No.1 p.5240
The domestic dog, Canis lupus familiaris, plays a vital role as companion or service animal, and the well-being and healthy aging of dogs is gaining importance. Proteins are key actors in cells, tissues and body fluids, and the ability to measure their composition and abundance is crucial to underst...
ProteomicsSystems biology
10.1038/S41597-026-06647-Z
ISSN:2052-4463
A phosphorylation-dependent ubiquitination switch orchestrates nuclear immune reprogramming upon chitin perception
Chongyang Zhang•Pavinee Suttiviriya•Ruyi Wang•Feng He•Hui Tao等 13 人
Nature Communications
2026
•2026/2/21
•Vol.17 No.1 p.29980
The 14-3-3 proteins, a highly conserved class in all eukaryotes, are widely associated with plant growth and stress responses. However, their role in plant immunity and its regulatory mechanisms remains elusive. Here, we show that two homologous rice 14-3-3 proteins, OsGF14f and OsGF14c, function re...
BioticPattern recognition receptors in plantsUbiquitylation
10.1038/S41467-026-69627-2
ISSN:2041-1723
CK2-mediated phosphorylation of SUZ12 promotes PRC2 function by stabilizing enzyme active site
Gong Lihu•Liu Xiuli•Jiao Lianying•Yang Xin•Lemoff Andrew等 6 人
Nature Communications
2022
•2022/11/9
•Vol.13 No.1 p.1-15
Polycomb repressive complex 2 (PRC2) plays a key role in maintaining cell identity during differentiation. Methyltransferase activity of PRC2 on histone H3 lysine 27 is regulated by diverse cellular mechanisms, including posttranslational modification. Here, we report a unique phosphorylation-depend...
Embryonic stem cellsEnzyme mechanismsGene silencingPhosphorylationX-ray crystallography
10.1038/S41467-022-34431-1
ISSN:2041-1723
Proteogenomic insights into the biology and treatment of pan-melanoma
Hang Xiang•Rongkui Luo•Yunzhi Wang•Bing Yang•Sha Xu等 19 人
Cell Discovery
2024
•2024/7/23
•Vol.10 No.1 p.1-35
Melanoma is one of the most prevalent skin cancers, with high metastatic rates and poor prognosis. Understanding its molecular pathogenesis is crucial for improving its diagnosis and treatment. Integrated analysis of multi-omics data from 207 treatment-naïve melanomas (primary-cutaneous-melanomas (C...
MelanomaProteomics
10.1038/S41421-024-00688-7
ISSN:2056-5968
Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene
Wan Li•Hu Peilei•Zhang Lili•Wang Zhao-Xi•Fleming Joy等 20 人
Communications Biology
2023
•2023/2/7
•Vol.6 No.1 p.1-14
Global control of the tuberculosis epidemic is threatened by increasing prevalence of drug resistant M. tuberculosis isolates. Many genome-wide studies focus on SNP-associated drug resistance mechanisms, but drug resistance in 5–30% of M. tuberculosis isolates (varying with antibiotic) appears unrel...
Antimicrobial resistanceClinical microbiologyPathogens
10.1038/S42003-023-04433-W
ISSN:2399-3642
Nanoparticle elasticity affects systemic circulation lifetime by modulating adsorption of apolipoprotein A-I in corona formation
Li Mingyang•Jin Xinyang•Liu Tao•Fan Feng•Gao Feng等 7 人
Nature Communications
2022
•2022/7/16
•Vol.13 No.1 p.1-16
Nanoparticle elasticity is crucial in nanoparticles’ physiological fate, but how this occurs is largely unknown. Using core-shell nanoparticles with a same PEGylated lipid bilayer shell yet cores differing in elasticity (45 kPa – 760 MPa) as models, we isolate the effects of nanoparticle elasticity ...
Biomaterials – proteinsBiosurfacesNanoparticles
10.1038/S41467-022-31882-4
ISSN:2041-1723
Structure of the Methanosarcina mazei Mtr complex bound to the oxygen-stress responsive small protein MtrI
Tristan Reif-Trauttmansdorff•Eva Herdering•Stefan Bohn•Tomas Pascoa•Jörg Kahnt等 9 人
Nature Communications
2025
•2025/12/23
0Methanogenic archaea emit ~1 Gt of methane annually, impacting global carbon cycling and climate. Central to their energy metabolism is a membrane-bound, sodium-translocating methyltransferase complex: the N⁵-tetrahydromethanopterin:CoM-S-methyltransferase (Mtr). It couples methyl transfer between t...
BioenergeticsCryoelectron microscopyMembrane proteins
10.1038/S41467-025-67705-5
ISSN:2041-1723
Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network
Richard G. Lee•Danielle L. Rudler•Samuel A. Raven•Liuyu Peng•Anaëlle Chopin等 21 人
Nature Cell Biology
2023
•2023/12/21
•00 p.1-15
The structures and functions of organelles in cells depend on each other but have not been systematically explored. We established stable knockout cell lines of peroxisomal, Golgi and endoplasmic reticulum genes identified in a whole-genome CRISPR knockout screen for inducers of mitochondrial biogen...
Energy metabolismMechanisms of diseaseSuper-resolution microscopy
10.1038/S41556-023-01297-4
ISSN:1465-7392
SIRT5 safeguards against primate skeletal muscle ageing via desuccinylation of TBK1
Qian Zhao•Ying Jing•Xiaoyu Jiang•Xin Zhang•Feifei Liu等 17 人
Nature Metabolism
2025
•2025/3/14
•00 p.1-18
Ageing-induced skeletal muscle deterioration contributes to sarcopenia and frailty, adversely impacting the quality of life in the elderly. However, the molecular mechanisms behind primate skeletal muscle ageing remain largely unexplored. Here, we show that SIRT5 expression is reduced in aged primat...
MetabolismSenescenceSkeletal muscle
10.1038/S42255-025-01235-8
ISSN:2522-5812
The NSL complex maintains nuclear architecture stability via lamin A/C acetylation
Adam Karoutas•Witold Szymanski•Tobias Rausch•Sukanya Guhathakurta•Eva A. Rog-Zielinska等 16 人
Nature Cell Biology
2019
•2019/10/1
•Vol.21 No.10 p.1248-1260
While nuclear lamina abnormalities are hallmarks of human diseases, their interplay with epigenetic regulators and precise epigenetic landscape remain poorly understood. Here, we show that loss of the lysine acetyltransferase MOF or its associated NSL-complex members KANSL2 or KANSL3 leads to a stoc...
AcetylationHistone post-translational modificationsNuclear envelope
10.1038/S41556-019-0397-Z
ISSN:1465-7392
Glucose depletion enables Candida albicans mating independently of the epigenetic white-opaque switch
Guan Guobo•Tao Li•Li Chao•Xu Ming•Liu Ling等 7 人
Nature Communications
2023
•2023/4/12
•Vol.14 No.1 p.1-12
The human fungal pathogen Candida albicans can switch stochastically and heritably between a “white” phase and an “opaque” phase. Opaque cells are the mating-competent form of the species, whereas white cells are thought to be essentially “sterile”. Here, we report that glucose depletion, a common n...
Cellular microbiologyFungal biologyPathogens
10.1038/S41467-023-37755-8
ISSN:2041-1723
The pan-cancer lncRNA PLANE regulates an alternative splicing program to promote cancer pathogenesis
Liu Teng•Yu Chen Feng•Su Tang Guo•Pei Lin Wang•Teng Fei Qi等 25 人
Nature Communications
2021
•2021/6/18
•Vol.12 No.1 p.1-17
Genomic amplification of the distal portion of chromosome 3q, which encodes a number of oncogenic proteins, is one of the most frequent chromosomal abnormalities in malignancy. Here we functionally characterise a non-protein product of the 3q region, the long noncoding RNA (lncRNA) PLANE, which is u...
CancerCell growthLong non-coding RNAsRNA
10.1038/S41467-021-24099-4
ISSN:2041-1723
Branched-chain amino acids alleviate sepsis-induced myocardial dysfunction via inhibition of protein tyrosine phosphatase-6
Shu-Rui Pang•Yu-Tong Zhu•Hou-Zao Chen•Jian-Fei Pei•De-Pei Liu
Signal Transduction And Targeted Therapy
2025
•2025/4/30
•Vol.10 No.1 p.1-3
CardiologyCardiovascular diseases
10.1038/S41392-025-02224-9
ISSN:2059-3635
MamF-like proteins are distant Tic20 homologs involved in organelle assembly in bacteria
Anja Paulus•Frederik Ahrens•Annika Schraut•Hannah Hofmann•Tim Schiller等 8 人
Nature Communications
2024
•2024/12/9
•Vol.15 No.1 p.1-16
Organelle-specific protein translocation systems are essential for organelle biogenesis and maintenance in eukaryotes but thought to be absent from prokaryotic organelles. Here, we demonstrate that MamF-like proteins are crucial for the formation and functionality of bacterial magnetosome organelles...
BacteriaCellular microbiologyMolecular evolutionOrganelles
10.1038/S41467-024-55121-0
ISSN:2041-1723
Steric hindrance-mediated extracellular vesicle size fractionation for rapid prehospital diagnosis of intracerebral hemorrhage
Xingjie Wu•Shasha Xiong•Litao Zhang•Yueyue Zhao•Zhilu Sun等 15 人
Nature Communications
2026
•2026/4/9
0Diagnosing intracerebral hemorrhage (ICH) in prehospital settings remains challenging due to unavailability of immediate neuroimaging, clinical overlap with ischemic stroke, and absence of validated circulating biomarkers for time-critical settings. Extracellular vesicles (EVs), subcellular structur...
BiosensorsDiagnostic markersNanobiotechnology
10.1038/S41467-026-71751-Y
ISSN:2041-1723
Structural basis of ubiquitin ligase Nedd4-2 autoinhibition and regulation by calcium and 14-3-3 proteins
Masa Janosev•Dalibor Kosek•Andrej Tekel•Rohit Joshi•Karolina Honzejkova等 8 人
Nature Communications
2025
•2025/5/26
•Vol.16 No.1 p.1-18
Nedd4-2 E3 ligase regulates Na+ homeostasis by ubiquitinating various channels and membrane transporters, including the epithelial sodium channel ENaC. In turn, Nedd4-2 dysregulation leads to various conditions, including electrolytic imbalance, respiratory distress, hypertension, and kidney disease...
Cryoelectron microscopyLigasesSAXS
10.1038/S41467-025-60207-4
ISSN:2041-1723
Marine bacteroidetes use a conserved enzymatic cascade to digest diatom β-mannan
Beidler Irena•Robb Craig S.•Vidal-Melgosa Silvia•Zühlke Marie-Katherin•Bartosik Daniel等 10 人
The Isme Journal
2022
•2022/11/21
•Vol.17 No.2 p.276-285
The polysaccharide β-mannan, which is common in terrestrial plants but unknown in microalgae, was recently detected during diatom blooms. We identified a β-mannan polysaccharide utilization locus (PUL) in the genome of the marine flavobacterium Muricauda sp. MAR_2010_75. Proteomics showed β-mannan i...
Microbial ecologyProteomicsWater microbiology
10.1038/S41396-022-01342-4
ISSN:1751-7362
Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association
Amar R. Bhagwat•Valerie Le Sage•Eric Nturibi•Katarzyna Kulej•Jennifer Jones等 11 人
Nature Communications
2020
•2020/1/7
•Vol.11 No.1 p.1-14
Assembly of infectious influenza A viruses (IAV) is a complex process involving transport from the nucleus to the plasma membrane. Rab11A-containing recycling endosomes have been identified as a platform for intracellular transport of viral RNA (vRNA). Here, using high spatiotemporal resolution ligh...
Cellular imagingEndosomesLight-sheet microscopyMembrane traffickingVirology
10.1038/S41467-019-13838-3
ISSN:2041-1723
Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C
Lena Reimann•Anja N. Schwäble•Anna L. Fricke•Wignand W. D. Mühlhäuser•Yvonne Leber等 21 人
Communications Biology
2020
•2020/5/22
•Vol.3 No.1 p.1-19
The PI3K/Akt pathway promotes skeletal muscle growth and myogenic differentiation. Although its importance in skeletal muscle biology is well documented, many of its substrates remain to be identified. We here studied PI3K/Akt signaling in contracting skeletal muscle cells by quantitative phosphopro...
Mass spectrometryPhosphorylationProteome
10.1038/S42003-020-0982-5
ISSN:2399-3642
Dual chemical probes enable quantitative system-wide analysis of protein prenylation and prenylation dynamics
Elisabeth M. Storck•Julia Morales-Sanfrutos•Remigiusz A. Serwa•Nattawadee Panyain•Thomas Lanyon-Hogg等 11 人
Nature Chemistry
2019
•2019/4/1
•Vol.11 No.6 p.552-561
Post-translational farnesylation or geranylgeranylation at a C-terminal cysteine residue regulates the localization and function of over 100 proteins, including the Ras isoforms, and is a therapeutic target in diseases including cancer and infection. Here, we report global and selective profiling of...
Chemical modificationChemical toolsLipidsPost-translational modificationsProteomics
10.1038/S41557-019-0237-6
ISSN:1755-4330
Digital microfluidic isolation of single cells for -Omics
Julian Lamanna•Erica Y. Scott•Harrison S. Edwards•M. Dean Chamberlain•Michael D. M. Dryden等 16 人
Nature Communications
2020
•2020/11/11
•Vol.11 No.1 p.1-13
We introduce Digital microfluidic Isolation of Single Cells for -Omics (DISCO), a platform that allows users to select particular cells of interest from a limited initial sample size and connects single-cell sequencing data to their immunofluorescence-based phenotypes. Specifically, DISCO combines d...
Biomedical engineeringLab-on-a-chipMicrofluidicsProteomicsTranscriptomics
10.1038/S41467-020-19394-5
ISSN:2041-1723
Lon protease 1-mediated metabolic reprogramming promotes the progression of prostate cancer
Mengfei Yao•Xingming Zhang•Tianqi Wu•Tao Feng•Xiaojie Bian等 14 人
Cell Death & Disease
2025
•2025/2/19
•Vol.16 No.1 p.1-15
Lon protease 1 (LONP1) is an ATP-dependent protease located in the mitochondrial matrix and plays a crucial role in regulating mitochondrial proteostasis, metabolism, and cellular stress responses et al. Aberrant LONP1 expression has been found in the progression of various tumors; however, the role...
Cancer metabolismProstate cancer
10.1038/S41419-025-07449-8
ISSN:2041-4889
Human cytomegalovirus induces neuronal gene expression through IE1 for viral maturation
Laurel E. Kelnhofer-Millevolte•Julian R. Smith•Daniel H. Nguyen•Lea S. Wilson•Hannah C. Lewis等 14 人
Nature Communications
2025
•2025/8/8
•Vol.16 No.1 p.1-16
Viral invasion of the host cell causes some of the most dramatic changes in biology. Human cytomegalovirus (HCMV) extensively remodels host cells, altering nuclear shape and generating a cytoplasmic viral-induced assembly compartment (vIAC). How these striking morphology changes occur in the context...
Herpes virusHistone variants
10.1038/S41467-025-61915-7
ISSN:2041-1723
In vitro reconstitution of meiotic DNA double-strand-break formation
Xinzhe Tang•Zetao Hu•Jian Ding•Meixia Wu•Pin Guan等 11 人
Nature
2025
•2025/2/19
•Vol.639 No.8055 p.800-807
The Spo11 complex catalyses the formation of DNA double-strand breaks (DSBs), initiating meiotic recombination—a process that is essential for fertility and genetic diversity1,2. Although the function of Spo11 has been known for 27 years, previous efforts to reconstitute DSB formation in vitro have ...
Double-strand DNA breaksEnzyme mechanismsMeiosis
10.1038/S41586-024-08551-1
ISSN:0028-0836
Integrating multi-omics to reveal the molecular mechanism of lipid metabolism regulated by a splice variant of Lysyl-oxidase like-2, LOXL2Δ13
Yang Chen•Liu Peng•Jian-Zhong He•Xiao-Dong Wu•Xing Xu等 8 人
Communications Biology
2025
•2025/11/21
0LOXL2Δ13, a splice variant of Lysyl-oxidase like-2 (LOXL2), enhances glucose metabolism and induces adipose depletion in mice. The precise role of LOXL2Δ13 in lipid metabolism is unclear. Through multi-omics integration, we analyzed the transcriptome, metabolome, proteome, and protein modifications ...
Data integrationObesity
10.1038/S42003-025-09199-X
ISSN:2399-3642
Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves
Wu Chenhao•Mori Matteo•Abele Miriam•Banaei-Esfahani Amir•Zhang Zhongge等 9 人
Nature Microbiology
2023
•2023/2/3
•Vol.8 No.2 p.347-359
Bacterial fitness depends on adaptability to changing environments. In rich growth medium, which is replete with amino acids, Escherichia coli primarily expresses protein synthesis machineries, which comprise ~40% of cellular proteins and are required for rapid growth. Upon transition to minimal med...
MicrobiologySystems analysis
10.1038/S41564-022-01310-W
ISSN:2058-5276
OTUD6A promotes prostate tumorigenesis via deubiquitinating Brg1 and AR
Fu Xuhong•Zhao Junjie•Yu Guopeng•Zhang Xiaomin•Sun Jie等 12 人
Communications Biology
2022
•2022/3/1
•Vol.5 No.1 p.1-13
Ovarian tumor (OTU) subfamily deubiquitinases are involved in various cellular processes, such as inflammation, ferroptosis and tumorigenesis; however, their pathological roles in prostate cancer (PCa) remain largely unexplored. In this study, we observed that several OTU members displayed genomic a...
Cell signallingProstate cancer
10.1038/S42003-022-03133-1
ISSN:2399-3642
An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation
Sabatier Pierre•Beusch Christian M.•Saei Amir A.•Aoun Mike•Moruzzi Noah等 23 人
Nature Communications
2021
•2021/11/12
•Vol.12 No.1 p.1-16
Detailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine. To systematically study such transitions, we introduce a method that simultaneously measures protein expression and ...
Proteome informaticsProteomicsStem-cell differentiationTranslation
10.1038/S41467-021-26879-4
ISSN:2041-1723
HK1 from hepatic stellate cell–derived extracellular vesicles promotes progression of hepatocellular carcinoma
Chen Qi-tao•Zhang Zhi-yuan•Huang Qiao-ling•Chen Hang-zi•Hong Wen-bin等 16 人
Nature Metabolism
2022
•2022/10/3
•Vol.4 No.10 p.1306-1321
Extracellular vesicles play crucial roles in intercellular communication in the tumor microenvironment. Here we demonstrate that in hepatic fibrosis, TGF-β stimulates the palmitoylation of hexokinase 1 (HK1) in hepatic stellate cells (HSCs), which facilitates the secretion of HK1 via large extracell...
Cancer metabolismCancer microenvironmentMetabolismProtein translocation
10.1038/S42255-022-00642-5
ISSN:2522-5812
Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors
Maria Reinecke•Paul Brear•Larsen Vornholz•Benedict-Tilmann Berger•Florian Seefried等 15 人
Nature Chemical Biology
2023
•2023/10/30
•00 p.1-9
Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover s...
KinasesProteomicsSmall moleculesTarget identification
10.1038/S41589-023-01459-3
ISSN:1552-4450
Multidisciplinary analyses and ancient DNA reveal social inequality and mobility in the Central Plains during the Eastern Zhou period in China
Baoshuai Zhang•Jiajing Zheng•Lei Sun•Yuanyuan Zhang•Zhenlong Gao等 23 人
Nature Human Behaviour
2025
•2025/12/30
•00 p.1-17
The Eastern Zhou period (771–221 BC), characterized by social stratification, was marked by important inequality. Here the authors analyse 32 skeletons from Songzhuang Cemetery in Henan Province using sex-specific peptides, ancient DNA and isotopes to explore multidimensional inequality in sexes, di...
ArchaeologyBiological anthropologyGenetic variation
10.1038/S41562-025-02356-6
ISSN:2397-3374