Adult GTEx: WGS, RNA-Seq, and QTL data from 54 non-diseased human tissue sites
English
United States, Mountain View
QTL
数据描述
The Genotype-Tissue Expression (GTEx) dataset is a public resource for studying tissue- and cell-specific gene expression and genetic regulation across individuals, developmental stages, and species. Its core Adult GTEx component contains whole-genome sequencing, RNA-seq, and QTL data from samples collected across 54 non-diseased tissue sites from about 1,000 adult individuals. The broader resource also includes developmental human GTEx and non-human primate developmental GTEx for rhesus macaque and common marmoset, along with related histology, single-cell expression, and epigenomic data such as H3K27ac, m6A methylation, and whole-genome bisulfite sequencing. It is designed to support research on gene regulation, tissue biology, and genotype-expression relationships.
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•2021/7/6
•Vol.12 No.1 p.1-10
Despite significant clinical progress in cell and gene therapies, maximizing protein expression in order to enhance potency remains a major technical challenge. Here, we develop a high-throughput strategy to design, screen, and optimize 5′ UTRs that enhance protein expression from a strong human cyt...
Gene expression analysisHigh-throughput screeningSynthetic biologyTranslation
10.1038/S41467-021-24436-7
ISSN:2041-1723
Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation
Nighat Noureen•Shaofang Wu•Yingli Lv•Juechen Yang•W. K. Alfred Yung等 10 人
Nature Communications
2021
•2021/1/8
•Vol.12 No.1 p.1-11
Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the complex. Here we show that telomerase enzymatic activity can be robustly estimated from the...
CancerComputational biology and bioinformaticsStem cells
10.1038/S41467-020-20474-9
ISSN:2041-1723
Deciphering genetic susceptibility to clear cell renal cell carcinoma
Maria Mandelia•Philip J. Law•Charlie Mills•Molly Went•Jayaram Vijayakrishnan等 6 人
Communications Biology
2025
•2025/12/1
0Genome-wide association studies (GWAS) have identified over 60 autosomal risk loci associated with clear cell renal cell carcinoma (ccRCC), yet the functional mechanisms underlying these associations remain largely unclear. To establish connections between risk variants and their target genes, we ap...
Cancer geneticsCancer genomicsEpigeneticsGene regulatory networksRenal cell carcinoma
10.1038/S42003-025-09297-W
ISSN:2399-3642
A proteogenomic signature of age-related macular degeneration in blood
Emilsson Valur•Gudmundsson Elias F.•Jonmundsson Thorarinn•Jonsson Brynjolfur G.•Twarog Michael等 30 人
Nature Communications
2022
•2022/6/13
•Vol.13 No.1 p.1-15
Age-related macular degeneration (AMD) is one of the most common causes of visual impairment in the elderly, with a complex and still poorly understood etiology. Whole-genome association studies have discovered 34 genomic regions associated with AMD. However, the genes and cognate proteins that medi...
Computational biology and bioinformaticsEye diseasesPredictive markers
10.1038/S41467-022-31085-X
ISSN:2041-1723
Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor
Miozzo Federico•Valencia-Alarcón Eva P.•Stickley Luca•Majcin Dorcikova Michaëla•Petrelli Francesco等 10 人
Nature Communications
2022
•2022/3/17
•Vol.13 No.1 p.1-18
Progressive degeneration of dopaminergic (DA) neurons in the substantia nigra is a hallmark of Parkinson’s disease (PD). Dysregulation of developmental transcription factors is implicated in dopaminergic neurodegeneration, but the underlying molecular mechanisms remain largely unknown. Drosophila Fe...
Molecular neuroscienceParkinson's disease
10.1038/S41467-022-29075-0
ISSN:2041-1723
Elevated extracellular matrix protein 1 in circulating extracellular vesicles supports breast cancer progression under obesity conditions
Keyang Xu•Ai Fu•Zhaoyi Li•Liangbin Miao•Zhonghan Lou等 12 人
Nature Communications
2024
•2024/2/24
•Vol.15 No.1 p.1-17
The cargo content in small extracellular vesicles (sEVs) changes under pathological conditions. Our data shows that in obesity, extracellular matrix protein 1 (ECM1) protein levels are significantly increased in circulating sEVs, which is dependent on integrin-β2. Knockdown of integrin-β2 does not a...
Breast cancerMechanisms of disease
10.1038/S41467-024-45995-5
ISSN:2041-1723
Skeletal muscle transcriptional dysregulation of genes involved in senescence is associated with prognosis in severe heart failure
Eric Rullman•Alen Lovric•Michael Melin•Rodrigo Fernandez-Gonzalo•Thomas Gustafsson
Communications Medicine
2026
•2026/1/16
•Vol.6 No.1 p.970
The skeletal muscle hypothesis refers to a vicious cycle of successive deterioration of left ventricular function, skeletal muscle remodeling, and functional capacity in patients with heart failure. Despite extensive research, the regulatory mechanisms and their associations with clinical status and...
CardiologyMedical research
10.1038/S43856-025-01362-Z
ISSN:2730-664X
The cancer-testis lncRNA lnc-CTHCC promotes hepatocellular carcinogenesis by binding hnRNP K and activating YAP1 transcription
Xia Anliang•Yuan Wenwen•Wang Qiang•Xu Jianbo•Gu Yayun等 20 人
Nature Cancer
2022
•2022/1/10
•00 p.1-16
Cancer-testis (CT) genes participate in the initiation and progression of cancer, but the role of CT-associated long non-coding RNAs (CT-lncRNAs) in hepatocellular carcinoma (HCC) is still elusive. Here, we discovered a conserved CT-lncRNA, named lnc-CTHCC, which was highly expressed in the testes a...
CancerHepatocellular carcinomaLong non-coding RNAs
10.1038/S43018-021-00315-4
ISSN:2662-1347
The impact of common and rare genetic variants on bradyarrhythmia development
Lu-Chen Weng•Joel T. Rämö•Sean J. Jurgens•Shaan Khurshid•Mark Chaffin等 63 人
Nature Genetics
2025
•2025/1/2
•00 p.1-12
To broaden our understanding of bradyarrhythmias and conduction disease, we performed common variant genome-wide association analyses in up to 1.3 million individuals and rare variant burden testing in 460,000 individuals for sinus node dysfunction (SND), distal conduction disease (DCD) and pacemake...
ArrhythmiasGenome-wide association studies
10.1038/S41588-024-01978-2
ISSN:1061-4036
Adropin correlates with aging-related neuropathology in humans and improves cognitive function in aging mice
Banerjee Subhashis•Ghoshal Sarbani•Girardet Clemence•DeMars Kelly M.•Yang Changjun等 16 人
Npj Aging And Mechanisms Of Disease
2021
•2021/8/30
•Vol.7 No.1 p.1-17
The neural functions of adropin, a secreted peptide highly expressed in the brain, have not been investigated. In humans, adropin is highly expressed in astrocytes and peaks during critical postnatal periods of brain development. Gene enrichment analysis of transcripts correlating with adropin expre...
Cognitive ageingRisk factors
10.1038/S41514-021-00076-5
ISSN:2056-3973
Genetic architecture of sleep in a genome wide association study of device measured sleep traits
Laura Portas•Hang Yuan•Lina Cai•Karl Smith-Byrne•Stefan van Duijvenboden等 9 人
Nature Communications
2026
•2026/4/1
0Sleep is essential for health and regulated by genetic and environmental factors. We perform genome-wide association studies of device-measured sleep duration, efficiency, and accelerometer-derived rapid eye movement (REM) and non-rapid eye movement (NREM) sleep in 80,013 UK Biobank participants. We...
Health careMedical researchRisk factors
10.1038/S41467-026-71252-Y
ISSN:2041-1723
Deciphering genetic causes for sex differences in human health through drug metabolism and transporter genes
Huang Yingbo•Shan Yuting•Zhang Weijie•Lee Adam M.•Li Feng等 7 人
Nature Communications
2023
•2023/1/12
•Vol.14 No.1 p.1-15
Sex differences have been widely observed in human health. However, little is known about the underlying mechanism behind these observed sex differences. We hypothesize that sex-differentiated genetic effects are contributors of these phenotypic differences. Focusing on a collection of drug metaboli...
Genetics researchPopulation geneticsTranslational research
10.1038/S41467-023-35808-6
ISSN:2041-1723
A PheWAS approach to identify associations of GBA1 variants with comprehensive phenotypes beyond neurological diseases
Jiaqi Yang•Yuanfeng Huang•Zheng Wang•Shiyu Zhang•Dai Wu等 16 人
Npj Parkinson's Disease
2025
•2025/3/17
•Vol.11 No.1 p.1-10
Given the established association between numerous GBA1 variants and specific neurological diseases, we extended the exploration by a phenome-wide association study to assess the impact of GBA1 variants on a wider spectrum of health-related traits. We identified 41 phenotypes associated with GBA1 va...
Computational biology and bioinformaticsDiseasesGeneticsMedical researchNeurologyNeuroscience+2
10.1038/S41531-025-00901-8
ISSN:2373-8057
Cellular retinoic acid-binding protein 1, CRABP1, in thyroid gland aging
Fatimah Najjar•Jennifer Nhieu•Natalia Calixto Mancipe•Christy Henzler•Li-Na Wei
Npj Aging
2026
•2026/4/15
0Aging differentially affects disease risks of various organs1. The endocrine organs undergo significant changes along aging. Clinical reports showed increased prevalence of thyroid disorders with age, especially hypothyroidism2. Primary hypothyroidism includes congenital, autoimmune, and iatrogenic ...
BiochemistryCell biologyDiseasesEndocrinologyPhysiology
10.1038/S41514-026-00386-6
ISSN:2731-6068
Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies
Musalula Sinkala•Panji Nkhoma•Nicola Mulder•Darren Patrick Martin
Communications Biology
2021
•2021/1/4
•Vol.4 No.1 p.1-16
The mitogen-activated protein kinase (MAPK) pathways are crucial regulators of the cellular processes that fuel the malignant transformation of normal cells. The molecular aberrations which lead to cancer involve mutations in, and transcription variations of, various MAPK pathway genes. Here, we exa...
Cancer geneticsCancer genomicsData integrationGene regulationGene regulatory networks
10.1038/S42003-020-01552-6
ISSN:2399-3642
Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X
Leitão Elsa•Schröder Christopher•Parenti Ilaria•Dalle Carine•Rastetter Agnès等 37 人
Nature Communications
2022
•2022/11/2
•Vol.13 No.1 p.1-17
Disease gene discovery on chromosome (chr) X is challenging owing to its unique modes of inheritance. We undertook a systematic analysis of human chrX genes. We observe a higher proportion of disorder-associated genes and an enrichment of genes involved in cognition, language, and seizures on chrX c...
GeneticsNeurodevelopmental disorders
10.1038/S41467-022-34264-Y
ISSN:2041-1723
Diffusion imaging genomics provides novel insight into early mechanisms of cerebral small vessel disease
Quentin Le Grand•Ami Tsuchida•Alexandra Koch•Mohammed-Aslam Imtiaz•N. Ahmad Aziz等 16 人
Molecular Psychiatry
2024
•2024/5/29
•00 p.1-13
Cerebral small vessel disease (cSVD) is a leading cause of stroke and dementia. Genetic risk loci for white matter hyperintensities (WMH), the most common MRI-marker of cSVD in older age, were recently shown to be significantly associated with white matter (WM) microstructure on diffusion tensor ima...
BiomarkersGenetics
10.1038/S41380-024-02604-7
ISSN:1359-4184
A meta-analysis of single-nucleus expression quantitative trait loci linking genetic risk to brain disorders
Beomjin Jang•Kailash BP•Alex Tokolyi•Winston H. Dredge•Ashvin Ravi等 17 人
Nature Genetics
2026
•2026/3/19
•00 p.1-11
Most genetic risk variants for neurological diseases are located in noncoding regulatory regions, where they often act as expression quantitative trait loci (eQTLs), modulating gene expression and influencing disease susceptibility. However, eQTL studies in bulk brain tissue or cell lines fail to ca...
Gene expressionTranscriptomics
10.1038/S41588-026-02541-X
ISSN:1061-4036
Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank
Jurgens Sean J.•Choi Seung Hoan•Morrill Valerie N.•Chaffin Mark•Pirruccello James P.等 18 人
Nature Genetics
2022
•2022/2/17
•00 p.1-11
Cardiometabolic diseases are the leading cause of death worldwide. Despite a known genetic component, our understanding of these diseases remains incomplete. Here, we analyzed the contribution of rare variants to 57 diseases and 26 cardiometabolic traits, using data from 200,337 UK Biobank participa...
Cardiovascular diseasesDNA sequencingGenetics researchPopulation genetics
10.1038/S41588-021-01011-W
ISSN:1061-4036
In vivo tumor immune microenvironment phenotypes correlate with inflammation and vasculature to predict immunotherapy response
Sahu Aditi•Kose Kivanc•Kraehenbuehl Lukas•Byers Candice•Holland Aliya等 35 人
Nature Communications
2022
•2022/9/9
•Vol.13 No.1 p.1-19
Response to immunotherapies can be variable and unpredictable. Pathology-based phenotyping of tumors into ‘hot’ and ‘cold’ is static, relying solely on T-cell infiltration in single-time single-site biopsies, resulting in suboptimal treatment response prediction. Dynamic vascular events (tumor angio...
Basal cell carcinomaCancer imagingCancer microenvironmentTranslational researchTumour angiogenesis
10.1038/S41467-022-32738-7
ISSN:2041-1723
Genetic effects on the timing of parturition and links to fetal birth weight
Solé-Navais Pol•Flatley Christopher•Steinthorsdottir Valgerdur•Vaudel Marc•Juodakis Julius等 85 人
Nature Genetics
2023
•2023/4/3
•00 p.1-9
The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration (n = 195,555), identifying 22 associated loci (24 independent variants) and an enrichment in genes ...
Genetics researchGenome-wide association studies
10.1038/S41588-023-01343-9
ISSN:1061-4036
Integrative transcriptome-wide analysis of atopic dermatitis for drug repositioning
Song Jaeseung•Kim Daeun•Lee Sora•Jung Junghyun•Joo Jong Wha J.等 6 人
Communications Biology
2022
•2022/6/22
•Vol.5 No.1 p.1-13
Atopic dermatitis (AD) is one of the most common inflammatory skin diseases, which significantly impact the quality of life. Transcriptome-wide association study (TWAS) was conducted to estimate both transcriptomic and genomic features of AD and detected significant associations between 31 expressio...
Data integrationDrug screeningGene expressionGenetic association studySkin diseases
10.1038/S42003-022-03564-W
ISSN:2399-3642
Genetic map of regional sulcal morphology in the human brain from UK biobank data
Sun Benjamin B.•Loomis Stephanie J.•Pizzagalli Fabrizio•Shatokhina Natalia•Painter Jodie N.等 18 人
Nature Communications
2022
•2022/10/14
•Vol.13 No.1 p.1-13
Genetic associations with macroscopic brain structure can provide insights into brain function and disease. However, specific associations with measures of local brain folding are largely under-explored. Here, we conducted large-scale genome- and exome-wide associations of regional cortical sulcal m...
Genetics of the nervous systemGenomics
10.1038/S41467-022-33829-1
ISSN:2041-1723
Genetic regulation of post-translational modification of two distinct proteins
Landini Arianna•Trbojević-Akmačić Irena•Navarro Pau•Tsepilov Yakov A.•Sharapov Sodbo Z.等 14 人
Nature Communications
2022
•2022/3/24
•Vol.13 No.1 p.1-13
Post-translational modifications diversify protein functions and dynamically coordinate their signalling networks, influencing most aspects of cell physiology. Nevertheless, their genetic regulation or influence on complex traits is not fully understood. Here, we compare the genetic regulation of th...
Genome-wide association studiesGlycosylation
10.1038/S41467-022-29189-5
ISSN:2041-1723
Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura
Gyda Bjornsdottir•Mona A. Chalmer•Lilja Stefansdottir•Astros Th. Skuladottir•Gudmundur Einarsson等 65 人
Nature Genetics
2023
•2023/10/26
•00 p.1-11
Migraine is a complex neurovascular disease with a range of severity and symptoms, yet mostly studied as one phenotype in genome-wide association studies (GWAS). Here we combine large GWAS datasets from six European populations to study the main migraine subtypes, migraine with aura (MA) and migrain...
Genome-wide association studiesNeuroscience
10.1038/S41588-023-01538-0
ISSN:1061-4036
The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer
Patel Saroor A.•Hirosue Shoko•Rodrigues Paulo•Vojtasova Erika•Richardson Emma K.等 27 人
Nature
2022
•2022/6/8
•00 p.1-8
Large-scale human genetic data1–3 have shown that cancer mutations display strong tissue-selectivity, but how this selectivity arises remains unclear. Here, using experimental models, functional genomics and analyses of patient samples, we demonstrate that the lineage transcription factor paired box...
Cancer genomicsCancer modelsFunctional genomicsGene regulationRenal cell carcinoma
10.1038/S41586-022-04809-8
ISSN:0028-0836
Spatial probabilistic mapping of metabolite ensembles in mass spectrometry imaging
Abu Sammour Denis•Cairns James L.•Boskamp Tobias•Marsching Christian•Kessler Tobias等 19 人
Nature Communications
2023
•2023/4/1
•Vol.14 No.1 p.1-15
Mass spectrometry imaging vows to enable simultaneous spatially resolved investigation of hundreds of metabolites in tissues, but it primarily relies on traditional ion images for non-data-driven metabolite visualization and analysis. The rendering and interpretation of ion images neither considers ...
Computational platforms and environmentsImage processingMass spectrometryMetabolomics
10.1038/S41467-023-37394-Z
ISSN:2041-1723
Biological process activity transformation of single cell gene expression for cross-species alignment
Hongxu Ding•Andrew Blair•Ying Yang•Joshua M. Stuart
Nature Communications
2019
•2019/10/25
•Vol.10 No.1 p.1-6
The maintenance and transition of cellular states are controlled by biological processes. Here we present a gene set-based transformation of single cell RNA-Seq data into biological process activities that provides a robust description of cellular states. Moreover, as these activities represent spec...
Computational biology and bioinformaticsSystems biology
10.1038/S41467-019-12924-W
ISSN:2041-1723
Genome-wide association study identifies five risk loci for pernicious anemia
Triin Laisk•Maarja Lepamets•Mariann Koel•Erik Abner•Reedik Mägi
Nature Communications
2021
•2021/6/18
•Vol.12 No.1 p.1-9
Pernicious anemia is a rare condition characterized by vitamin B12 deficiency anemia due to lack of intrinsic factor, often caused by autoimmune gastritis. Patients with pernicious anemia have a higher incidence of other autoimmune disorders, such as type 1 diabetes, vitiligo, and autoimmune thyroid...
Autoimmune diseasesGenetics researchGenome-wide association studies
10.1038/S41467-021-24051-6
ISSN:2041-1723
Insights into DNA repeat expansions among 900,000 biobank participants
Margaux L. A. Hujoel•Robert E. Handsaker•David Tang•Nolan Kamitaki•Ronen E. Mukamel等 9 人
Nature
2026
•2026/1/7
•Vol.650 No.8103 p.920-929
Expansions and contractions of tandem DNA repeats generate genetic variation in human populations and in human tissues. Some expanded repeats cause inherited disorders and some are also somatically unstable1,2. Here we analysed DNA sequencing data from over 900,000 participants in the UK Bioban...
Genetic association studyGenomic instabilityMutation
10.1038/S41586-025-09886-Z
ISSN:0028-0836
Multi-ancestry sleep-by-SNP interaction analysis in 126,926 individuals reveals lipid loci stratified by sleep duration
Raymond Noordam•Maxime M. Bos•Heming Wang•Thomas W. Winkler•Amy R. Bentley等 148 人
Nature Communications
2019
•2019/11/12
•Vol.10 No.1 p.1-13
Both short and long sleep are associated with an adverse lipid profile, likely through different biological pathways. To elucidate the biology of sleep-associated adverse lipid profile, we conduct multi-ancestry genome-wide sleep-SNP interaction analyses on three lipid traits (HDL-c, LDL-c and trigl...
DyslipidaemiasEpidemiologyGenome-wide association studiesSleep
10.1038/S41467-019-12958-0
ISSN:2041-1723
Identification of CD318, TSPAN8 and CD66c as target candidates for CAR T cell based immunotherapy of pancreatic adenocarcinoma
Daniel Schäfer•Stefan Tomiuk•Laura N. Küster•Wa’el Al Rawashdeh•Janina Henze等 22 人
Nature Communications
2021
•2021/3/5
•Vol.12 No.1 p.1-18
A major roadblock prohibiting effective cellular immunotherapy of pancreatic ductal adenocarcinoma (PDAC) is the lack of suitable tumor-specific antigens. To address this challenge, here we combine flow cytometry screenings, bioinformatic expression analyses and a cyclic immunofluorescence platform....
Gastrointestinal cancerImmunotherapyPreclinical researchTarget identificationTarget validation
10.1038/S41467-021-21774-4
ISSN:2041-1723
Genetically proxied HTRA1 protease activity and circulating levels independently predict risk of ischemic stroke and coronary artery disease
Rainer Malik•Nathalie Beaufort•Jiang Li•Koki Tanaka•Marios K. Georgakis等 13 人
Nature Cardiovascular Research
2024
•2024/5/20
•00 p.1-13
Genetic variants in HTRA1 are associated with stroke risk. However, the mechanisms mediating this remain largely unknown, as does the full spectrum of phenotypes associated with genetic variation in HTRA1. Here we show that rare HTRA1 variants are linked to ischemic stroke in the UK Biobank and BioB...
Genetics researchMyocardial infarctionStroke
10.1038/S44161-024-00475-3
ISSN:2731-0590
Shared genetic risk factors and causal association between psoriasis and coronary artery disease
Patrick Matthew T.•Li Qinmengge•Wasikowski Rachael•Mehta Nehal•Gudjonsson Johann E.等 8 人
Nature Communications
2022
•2022/11/2
•Vol.13 No.1 p.1-12
Psoriasis and coronary artery disease (CAD) are related comorbidities that are well established, but whether a genetic basis underlies this is not well studied. We apply trans-disease meta-analysis to 11,024 psoriasis and 60,801 CAD cases, along with their associated controls, identifying one opposi...
Genome-wide association studiesRisk factorsSkin diseases
10.1038/S41467-022-34323-4
ISSN:2041-1723
A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study
Hui Chen•Zeyang Wang•Lihai Gong•Qixuan Wang•Wenyan Chen等 17 人
Nature Communications
2024
•2024/2/26
•Vol.15 No.1 p.1-16
Alternative polyadenylation plays an important role in cancer initiation and progression; however, current transcriptome-wide association studies mostly ignore alternative polyadenylation when identifying putative cancer susceptibility genes. Here, we perform a pan-cancer 3′ untranslated region alte...
Cancer geneticsData miningNon-coding RNAs
10.1038/S41467-024-46064-7
ISSN:2041-1723
Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets
Audrey A. Omidsalar•Carmel G. McCullough•Lili Xu•Stanley Boedijono•Daniel Gerke等 15 人
Communications Biology
2024
•2024/2/17
•Vol.7 No.1 p.1-20
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA de...
Computational biology and bioinformaticsGenomicsMetabolic disordersNeural ageingNeurological disorders
10.1038/S42003-024-05877-4
ISSN:2399-3642
The DNA virome varies with human genes and environments
Nolan Kamitaki•David Tang•Steven A. McCarroll•Po-Ru Loh
Nature
2026
•2026/3/25
•00 p.1-11
Many viruses have adapted to persist in infected humans for life1,2. Variable host control of their ongoing abundance (viral load) can lead to clearance or disease3–5. Here we analysed the viral DNA load of 31 common viruses in human blood and saliva using whole-genome sequencing data from UK Bioban...
Genome-wide association studiesRisk factorsTumour virus infectionsVirus–host interactions
10.1038/S41586-026-10288-Y
ISSN:0028-0836
A phenome-wide comparative analysis of genetic discordance between obesity and type 2 diabetes
Coral Daniel E.•Fernandez-Tajes Juan•Tsereteli Neli•Pomares-Millan Hugo•Fitipaldi Hugo等 15 人
Nature Metabolism
2023
•2023/1/26
•Vol.5 No.2 p.237-247
Obesity and type 2 diabetes are causally related, yet there is considerable heterogeneity in the consequences of both conditions and the mechanisms of action are poorly defined. Here we show a genetic-driven approach defining two obesity profiles that convey highly concordant and discordant diabetog...
Genetic variationMachine learningMetabolismObesityType 2 diabetes
10.1038/S42255-022-00731-5
ISSN:2522-5812
Comprehensive genetic analysis of the human lipidome identifies loci associated with lipid homeostasis with links to coronary artery disease
Cadby Gemma•Giles Corey•Melton Phillip E.•Huynh Kevin•Mellett Natalie A.等 44 人
Nature Communications
2022
•2022/6/6
•Vol.13 No.1 p.1-17
We integrated lipidomics and genomics to unravel the genetic architecture of lipid metabolism and identify genetic variants associated with lipid species putatively in the mechanistic pathway for coronary artery disease (CAD). We quantified 596 lipid species in serum from 4,492 individuals from the ...
Cardiovascular diseasesGenome-wide association studiesLipidomicsMass spectrometry
10.1038/S41467-022-30875-7
ISSN:2041-1723
The pancancer overexpressed NFYC Antisense 1 controls cell cycle mitotic progression through in cis and in trans modes of action
Cecilia Pandini•Giulia Pagani•Martina Tassinari•Emanuele Vitale•Eugenia Bezzecchi等 12 人
Cell Death & Disease
2024
•2024/3/11
•Vol.15 No.3 p.1-14
Antisense RNAs (asRNAs) represent an underappreciated yet crucial layer of gene expression regulation. Generally thought to modulate their sense genes in cis through sequence complementarity or their act of transcription, asRNAs can also regulate different molecular targets in trans, in the nucleus ...
Long non-coding RNAsNon-small-cell lung cancerSmall-cell lung cancer
10.1038/S41419-024-06576-Y
ISSN:2041-4889
Multi-tissue transcriptome analyses identify genetic mechanisms underlying neuropsychiatric traits
Eric R. Gamazon•Aeilko H. Zwinderman•Nancy J. Cox•Damiaan Denys•Eske M. Derks
Nature Genetics
2019
•2019/5/13
•Vol.51 No.6 p.933-940
The genetic architecture of psychiatric disorders is characterized by a large number of small-effect variants1 located primarily in non-coding regions, suggesting that the underlying causal effects may influence disease risk by modulating gene expression2–4. We provide comprehensive analyses using t...
Gene expressionGenomicsSchizophreniaTranscriptomics
10.1038/S41588-019-0409-8
ISSN:1061-4036
The proteogenomic landscape of the human kidney and implications for cardio-kidney-metabolic health
Daigoro Hirohama•João Fadista•Eunji Ha•Hongbo Liu•Amin Abedini等 18 人
Nature Medicine
2025
•2025/8/12
•00 p.1-13
Nearly one-third of the global population is affected by cardio-kidney-metabolic (CKM) diseases; however, the molecular mechanisms underlying CKM diseases are poorly understood. Here we show that tissue proteomics provide critical insights not captured by tissue gene expression or blood proteomics i...
Chronic kidney diseaseGenetics researchProteome informaticsQuantitative trait
10.1038/S41591-025-03872-8
ISSN:1078-8956
DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood
Prachand Issarapu•Manisha Arumalla•Hannah R. Elliott•Suraj S. Nongmaithem•Alagu Sankareswaran等 25 人
Nature Communications
2023
•2023/8/25
•Vol.14 No.1 p.1-16
Human height is strongly influenced by genetics but the contribution of modifiable epigenetic factors is under-explored, particularly in low and middle-income countries (LMIC). We investigate links between blood DNA methylation and child height in four LMIC cohorts (n = 1927) and identify a robust a...
DevelopmentDNA methylationEpigenomics
10.1038/S41467-023-40607-0
ISSN:2041-1723
Tumour-targeted interleukin-12 and entinostat combination therapy improves cancer survival by reprogramming the tumour immune cell landscape
Hicks Kristin C.•Chariou Paul L.•Ozawa Yohei•Minnar Christine M.•Knudson Karin M.等 10 人
Nature Communications
2021
•2021/8/26
•Vol.12 No.1 p.1-18
Poorly inflamed carcinomas do not respond well to immune checkpoint blockade. Converting the tumour microenvironment into a functionally inflamed immune hub would extend the clinical benefit of immune therapy to a larger proportion of cancer patients. Here we show, by using comprehensive single-cell...
Cancer microenvironmentImmunoeditingImmunotherapyTumour vaccines
10.1038/S41467-021-25393-X
ISSN:2041-1723
Impact of rare non-coding variants on human diseases through alternative polyadenylation outliers
Xudong Zou•Zhaozhao Zhao•Yu Chen•Kewei Xiong•Zeyang Wang等 12 人
Nature Communications
2025
•2025/1/16
•Vol.16 No.1 p.1-17
Although rare non-coding variants (RVs) play crucial roles in complex traits and diseases, understanding their mechanisms and identifying disease-associated RVs continue to be major challenges. Here we constructed a comprehensive atlas of alternative polyadenylation (APA) outliers (aOutliers), inclu...
Data miningGene regulation
10.1038/S41467-024-55407-3
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
Multi-tissue transcriptome-wide association study identifies eight candidate genes and tissue-specific gene expression underlying endometrial cancer susceptibility
Kho Pik Fang•Wang Xuemin•Cuéllar-Partida Gabriel•Dörk Thilo•Goode Ellen L.等 10 人
Communications Biology
2021
•2021/10/21
•Vol.4 No.1 p.1-8
Genome-wide association studies (GWAS) have revealed sixteen risk loci for endoemtrial cancer but the identification of candidate susceptibility genes remains challenging. Here, we perform transcriptome-wide association study (TWAS) analyses using the largest endometrial cancer GWAS and gene express...
Cancer geneticsEndometrial cancer
10.1038/S42003-021-02745-3
ISSN:2399-3642
Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes
Akbari Parsa•Sosina Olukayode A.•Bovijn Jonas•Landheer Karl•Nielsen Jonas B.等 60 人
Nature Communications
2022
•2022/8/23
•Vol.13 No.1 p.1-17
Body fat distribution is a major, heritable risk factor for cardiometabolic disease, independent of overall adiposity. Using exome-sequencing in 618,375 individuals (including 160,058 non-Europeans) from the UK, Sweden and Mexico, we identify 16 genes associated with fat distribution at exome-wide s...
Genetic association studyObesityPersonalized medicine
10.1038/S41467-022-32398-7
ISSN:2041-1723
Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification
Celina Tretter•Niklas de Andrade Krätzig•Matteo Pecoraro•Sebastian Lange•Philipp Seifert等 39 人
Nature Communications
2023
•2023/8/2
•Vol.14 No.1 p.1-22
Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized com...
Cancer immunotherapyTranslational researchTumour immunology
10.1038/S41467-023-39570-7
ISSN:2041-1723
Multi-ancestry genome-wide association meta-analysis of Parkinson’s disease
Jonggeol Jeffrey Kim•Dan Vitale•Diego Véliz Otani•Michelle Mulan Lian•Karl Heilbron等 18 人
Nature Genetics
2023
•2023/12/28
•00 p.1-10
Although over 90 independent risk variants have been identified for Parkinson’s disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson’s disease with 49,049 cases, 18,...
GenomicsParkinson's disease
10.1038/S41588-023-01584-8
ISSN:1061-4036
Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies
Zhang Jingning•Dutta Diptavo•Köttgen Anna•Tin Adrienne•Schlosser Pascal等 11 人
Nature Genetics
2022
•2022/5/2
•00 p.1-10
Improved understanding of genetic regulation of the proteome can facilitate identification of the causal mechanisms for complex traits. We analyzed data on 4,657 plasma proteins from 7,213 European American (EA) and 1,871 African American (AA) individuals from the Atherosclerosis Risk in Communities...
EpidemiologyGene regulation
10.1038/S41588-022-01051-W
ISSN:1061-4036
A spectrum of nonsense-mediated mRNA decay efficiency along the degree of mutational constraint
Young-gon Kim•Hyunju Kang•Beomki Lee•Hyeok-Jae Jang•Jong-ho Park等 8 人
Communications Biology
2024
•2024/11/7
•Vol.7 No.1 p.1-9
Despite its importance for regulating gene expression, nonsense-mediated mRNA decay (NMD) remains poorly understood. Here, we extend the findings of a previous landmark study that proposed several factors associated with NMD efficiency using matched genome and transcriptome data from The Cancer Geno...
Gene regulationMolecular medicine
10.1038/S42003-024-07136-Y
ISSN:2399-3642
Multi-ancestry GWAS meta-analyses of lung cancer reveal susceptibility loci and elucidate smoking-independent genetic risk
Bryan R. Gorman•Sun-Gou Ji•Michael Francis•Anoop K. Sendamarai•Yunling Shi等 23 人
Nature Communications
2024
•2024/10/4
•Vol.15 No.1 p.1-13
Lung cancer remains the leading cause of cancer mortality, despite declining smoking rates. Previous lung cancer GWAS have identified numerous loci, but separating the genetic risks of lung cancer and smoking behavioral susceptibility remains challenging. Here, we perform multi-ancestry GWAS meta-an...
Cancer geneticsGenome-wide association studiesLung cancer
10.1038/S41467-024-52129-4
ISSN:2041-1723
The HAPSTR2 retrogene buffers stress signaling and resilience in mammals
Amici David R.•Cingoz Harun•Alasady Milad J.•Alhayek Sammy•Phoumyvong Claire M.等 8 人
Nature Communications
2023
•2023/1/11
•Vol.14 No.1 p.1-12
We recently identified HAPSTR1 (C16orf72) as a key component in a novel pathway which regulates the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding. Here, we identify a functional paralog to HAPSTR1: HAPSTR2. HAPSTR2 formed early in mammalian e...
Evolutionary geneticsStress signalling
10.1038/S41467-022-35697-1
ISSN:2041-1723
Genetic architecture of heart failure with preserved versus reduced ejection fraction
Joseph Jacob•Liu Chang•Hui Qin•Aragam Krishna•Wang Zeyuan等 18 人
Nature Communications
2022
•2022/12/14
•Vol.13 No.1 p.1-14
Pharmacologic clinical trials for heart failure with preserved ejection fraction have been largely unsuccessful as compared to those for heart failure with reduced ejection fraction. Whether differences in the genetic underpinnings of these major heart failure subtypes may provide insights into the ...
Cardiovascular geneticsGenome-wide association studiesMedical genomics
10.1038/S41467-022-35323-0
ISSN:2041-1723
Tissue-specific and interferon-inducible expression of nonfunctional ACE2 through endogenous retroelement co-option
Kevin W. Ng•Jan Attig•William Bolland•George R. Young•Jack Major等 9 人
Nature Genetics
2020
•2020/10/19
•Vol.52 No.12 p.1294-1302
Angiotensin-converting enzyme 2 (ACE2) is an entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and a regulator of several physiological processes. ACE2 has recently been proposed to be interferon (IFN) inducible, suggesting that SARS-CoV-2 may exploit this phenomenon to...
Gene expressionGene regulationSARS-CoV-2
10.1038/S41588-020-00732-8
ISSN:1061-4036
A genome-wide association meta-analysis implicates Hedgehog and Notch signaling in Dupuytren’s disease
Sophie A. Riesmeijer•Zoha Kamali•Michael Ng•Dmitriy Drichel•Bram Piersma等 14 人
Nature Communications
2024
•2024/1/3
•Vol.15 No.1 p.1-11
Dupuytren’s disease (DD) is a highly heritable fibrotic disorder of the hand with incompletely understood etiology. A number of genetic loci, including Wnt signaling members, have been previously identified. Our overall aim was to identify novel genetic loci, to prioritize genes within the loci for ...
Connective tissue diseasesGenetic association studyPopulation genetics
10.1038/S41467-023-44451-0
ISSN:2041-1723
Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease
Young William J.•Haessler Jeffrey•Benjamins Jan-Walter•Repetto Linda•Yao Jie等 94 人
Nature Communications
2023
•2023/3/14
•Vol.14 No.1 p.1-16
The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) ...
Genome-wide association studiesGenotype
10.1038/S41467-023-36997-W
ISSN:2041-1723
CCorGsDB: a database for clock correlated genes in the mouse and human central nervous systems
José Luiz Araújo Santos•Vinícius Tenório Braga Cavalcante Pinto•Thales Eduardo da Silva Santos•Daniel Gomes Coimbra•Tiago Gomes de Andrade
Npj Biological Timing And Sleep
2026
•2026/1/9
•Vol.3 No.1 p.30
We developed CCorGsDB, a web-based resource integrating mouse and human CNS co-expression networks filtered by circadian biomarkers. We validated the networks using time-series data from sixteen mouse regions and identified a conserved set of 251 orthologs enriched for RNA processing, chromatin regu...
BiomarkersComputational biology and bioinformaticsNeuroscience
10.1038/S44323-025-00064-Y
ISSN:2948-281X
Environmental and genetic predictors of human cardiovascular ageing
Mit Shah•Marco H. de A. Inácio•Chang Lu•Pierre-Raphaël Schiratti•Sean L. Zheng等 18 人
Nature Communications
2023
•2023/8/21
•Vol.14 No.1 p.1-15
Cardiovascular ageing is a process that begins early in life and leads to a progressive change in structure and decline in function due to accumulated damage across diverse cell types, tissues and organs contributing to multi-morbidity. Damaging biophysical, metabolic and immunological factors excee...
Cardiovascular diseasesCardiovascular geneticsGenome-wide association studies
10.1038/S41467-023-40566-6
ISSN:2041-1723
Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation
Elizabeth J. Radford•Hong-Kee Tan•Malin H. L. Andersson•James D. Stephenson•Eugene J. Gardner等 19 人
Nature Communications
2023
•2023/12/6
•Vol.14 No.1 p.1-17
Loss-of-function of DDX3X is a leading cause of neurodevelopmental disorders (NDD) in females. DDX3X is also a somatically mutated cancer driver gene proposed to have tumour promoting and suppressing effects. We perform saturation genome editing of DDX3X, testing in vitro the functional impact of 12...
Cancer geneticsMutagenesisMutationNeurodevelopmental disorders
10.1038/S41467-023-43041-4
ISSN:2041-1723
The genetic architecture of sporadic and multiple consecutive miscarriage
Triin Laisk•Ana Luiza G. Soares•Teresa Ferreira•Jodie N. Painter•Jenny C. Censin等 55 人
Nature Communications
2020
•2020/11/25
•Vol.11 No.1 p.1-12
Miscarriage is a common, complex trait affecting ~15% of clinically confirmed pregnancies. Here we present the results of large-scale genetic association analyses with 69,054 cases from five different ancestries for sporadic miscarriage, 750 cases of European ancestry for multiple (≥3) consecutive m...
Genome-wide association studiesInfertility
10.1038/S41467-020-19742-5
ISSN:2041-1723
Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways
Young William J.•Lahrouchi Najim•Isaacs Aaron•Duong ThuyVy•Foco Luisa等 166 人
Nature Communications
2022
•2022/9/1
•Vol.13 No.1 p.1-18
The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry ...
Genetic markersGenome-wide association studies
10.1038/S41467-022-32821-Z
ISSN:2041-1723
Genetically personalised organ-specific metabolic models in health and disease
Foguet Carles•Xu Yu•Ritchie Scott C.•Lambert Samuel A.•Persyn Elodie等 14 人
Nature Communications
2022
•2022/11/29
•Vol.13 No.1 p.1-15
Understanding how genetic variants influence disease risk and complex traits (variant-to-function) is one of the major challenges in human genetics. Here we present a model-driven framework to leverage human genome-scale metabolic networks to define how genetic variants affect biochemical reaction f...
Biochemical networksCardiovascular diseasesMetabolomics
10.1038/S41467-022-35017-7
ISSN:2041-1723
Associations between antagonistic SNPs for neuropsychiatric disorders and human brain structure
Lydia M. Federmann•Friederike S. David•Christiane Jockwitz•Thomas W. Mühleisen•Dominique I. Pelzer等 17 人
Translational Psychiatry
2024
•2024/10/2
•Vol.14 No.1 p.1-10
A previously published genome-wide association study (GWAS) meta-analysis across eight neuropsychiatric disorders identified antagonistic single-nucleotide polymorphisms (SNPs) at eleven genomic loci where the same allele was protective against one neuropsychiatric disorder and increased the risk fo...
Molecular neurosciencePsychiatric disorders
10.1038/S41398-024-03098-1
ISSN:2158-3188
A regulatory variant at 19p13.3 is associated with primary biliary cholangitis risk and ARID3A expression
Li You•Li Zhiqiang•Chen Ruiling•Lian Min•Wang Hanxiao等 25 人
Nature Communications
2023
•2023/3/28
•Vol.14 No.1 p.1-14
Genome-wide association studies have identified 19p13.3 locus associated with primary biliary cholangitis (PBC). Here we aim to identify causative variant(s) and initiate efforts to define the mechanism by which the 19p13.3 locus variant(s) contributes to the pathogenesis of PBC. A genome-wide meta-...
Gene regulationGenome-wide association studiesPrimary biliary cirrhosis
10.1038/S41467-023-37213-5
ISSN:2041-1723
Male-specific lethal 1 (MSL1) promotes Erastin-induced ferroptosis in colon cancer cells by regulating the KCTD12-SLC7A11 axis
Lifu Luo•Qingzhi Zhao•Xueli Cui•Shijiao Dong•Yong Wang等 9 人
Cell Death & Disease
2025
•2025/4/12
•Vol.16 No.1 p.1-12
MSL1, a scaffold protein of the MSL histone acetyltransferase complex, is crucial for its structural integrity and enzymatic activity. While MSL1 is highly expressed in various tumors, its role in tumor progression and cell death remains unclear. Here, we provide evidence of a negative regulatory re...
Colon cancerPreclinical research
10.1038/S41419-025-07555-7
ISSN:2041-4889
Structural variation of the coding and non-coding human pharmacogenome
Roman Tremmel•Yitian Zhou•Matthias Schwab•Volker M. Lauschke
Npj Genomic Medicine
2023
•2023/9/8
•Vol.8 No.1 p.1-11
Genetic variants in drug targets and genes encoding factors involved in drug absorption, distribution, metabolism and excretion (ADME) can have pronounced impacts on drug pharmacokinetics, response, and toxicity. While the landscape of genetic variability at the level of single nucleotide variants (...
Functional genomicsMolecular medicinePredictive markers
10.1038/S41525-023-00371-Y
ISSN:2056-7944
Associated transcriptional, brain and clinical variations in schizophrenia
Long-Biao Cui•Shu-Wan Zhao•Ya-Hong Zhang•Kun Chen•Yu-Fei Fu等 18 人
Nature Mental Health
2024
•2024/9/9
•00 p.1-11
Understanding the relationship between genetic variations and brain abnormalities is crucial for uncovering the cross-scale pathophysiological mechanisms underlying schizophrenia. This cross-sectional study identifies brain structural correlates of individual variation in gene expression in schizoph...
Computational neuroscienceSchizophrenia
10.1038/S44220-024-00306-1
ISSN:2731-6076
Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans
Hsieh PingHsun•Dang Vy•Vollger Mitchell R.•Mao Yafei•Huang Tzu-Hsueh等 14 人
Nature Communications
2021
•2021/8/25
•Vol.12 No.1 p.1-14
TRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read s...
Evolutionary biologyGenome informatics
10.1038/S41467-021-25435-4
ISSN:2041-1723
Genome-wide meta-analysis of muscle weakness identifies 15 susceptibility loci in older men and women
Garan Jones•Katerina Trajanoska•Adam J. Santanasto•Najada Stringa•Chia-Ling Kuo等 66 人
Nature Communications
2021
•2021/1/28
•Vol.12 No.1 p.1-11
Low muscle strength is an important heritable indicator of poor health linked to morbidity and mortality in older people. In a genome-wide association study meta-analysis of 256,523 Europeans aged 60 years and over from 22 cohorts we identify 15 loci associated with muscle weakness (European Working...
Genetic association studyGenetics researchGenomicsPredictive markers
10.1038/S41467-021-20918-W
ISSN:2041-1723
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
Võsa Urmo•Claringbould Annique•Westra Harm-Jan•Bonder Marc Jan•Deelen Patrick等 108 人
Nature Genetics
2021
•2021/9/2
•Vol.53 No.9 p.1300-1310
Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms on the transcriptome. To investigate the genetics of gene expression, we performed cis- and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals...
Gene expressionGene regulationGenome-wide association studies
10.1038/S41588-021-00913-Z
ISSN:1061-4036
Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19
Liam Gaziano•Claudia Giambartolomei•Alexandre C. Pereira•Anna Gaulton•Daniel C. Posner等 56 人
Nature Medicine
2021
•2021/4/9
•Vol.27 No.4 p.668-676
Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable p...
EpidemiologyGenetics research
10.1038/S41591-021-01310-Z
ISSN:1078-8956
Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits
Tiago Azevedo•Giovanna Maria Dimitri•Pietro Lió•Eric R. Gamazon
Npj Systems Biology And Applications
2021
•2021/5/27
•Vol.7 No.1 p.1-13
Here, we performed a comprehensive intra-tissue and inter-tissue multilayer network analysis of the human transcriptome. We generated an atlas of communities in gene co-expression networks in 49 tissues (GTEx v8), evaluated their tissue specificity, and investigated their methodological implications...
Computational biology and bioinformaticsGenetics
10.1038/S41540-021-00186-6
ISSN:2056-7189
Large-scale genome-wide association analyses identify novel genetic loci and mechanisms in hypertrophic cardiomyopathy
Rafik Tadros•Sean L. Zheng•Christopher Grace•Paloma Jordà•Catherine Francis等 62 人
Nature Genetics
2025
•2025/2/18
•Vol.57 No.3 p.530-538
Hypertrophic cardiomyopathy (HCM) is an important cause of morbidity and mortality with both monogenic and polygenic components. Here, we report results from a large genome-wide association study and multitrait analysis including 5,900 HCM cases, 68,359 controls and 36,083 UK Biobank participants wi...
CardiomyopathiesGenome-wide association studies
10.1038/S41588-025-02087-4
ISSN:1061-4036
Palmitoylation of GPX4 via the targetable ZDHHC8 determines ferroptosis sensitivity and antitumor immunity
Liang Zhou•Guangyu Lian•Tao Zhou•Zhe Cai•Shuai Yang等 16 人
Nature Cancer
2025
•2025/3/19
•00 p.1-18
Ferroptosis is closely linked with various pathophysiological processes, including aging, neurodegeneration, ischemia-reperfusion injury, viral infection and, notably, cancer progression; however, its post-translational regulatory mechanisms remain incompletely understood. Here we revealed a crucial...
CancerCell death and immune responsePost-translational modifications
10.1038/S43018-025-00937-Y
ISSN:2662-1347
The NUCKS1-SKP2-p21/p27 axis controls S phase entry
Hume Samuel•Grou Claudia P.•Lascaux Pauline•D’Angiolella Vincenzo•Legrand Arnaud J.等 7 人
Nature Communications
2021
•2021/11/29
•Vol.12 No.1 p.1-14
Efficient entry into S phase of the cell cycle is necessary for embryonic development and tissue homoeostasis. However, unscheduled S phase entry triggers DNA damage and promotes oncogenesis, underlining the requirement for strict control. Here, we identify the NUCKS1-SKP2-p21/p27 axis as a checkpoi...
BiochemistryCell-cycle exitCheckpointsGene expression analysisUbiquitin ligases
10.1038/S41467-021-27124-8
ISSN:2041-1723
Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure
Danielle Rasooly•Gina M. Peloso•Alexandre C. Pereira•Hesam Dashti•Claudia Giambartolomei等 34 人
Nature Communications
2023
•2023/7/10
•Vol.14 No.1 p.1-15
We conduct a large-scale meta-analysis of heart failure genome-wide association studies (GWAS) consisting of over 90,000 heart failure cases and more than 1 million control individuals of European ancestry to uncover novel genetic determinants for heart failure. Using the GWAS results and blood prot...
Cardiovascular geneticsGenome-wide association studiesHeart failureStatistical methods
10.1038/S41467-023-39253-3
ISSN:2041-1723
Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers
He Jingni•Wen Wanqing•Beeghly Alicia•Chen Zhishan•Cao Chen等 9 人
Nature Communications
2022
•2022/11/19
•Vol.13 No.1 p.1-15
Transcriptome-wide association studies (TWAS) have successfully discovered many putative disease susceptibility genes. However, TWAS may suffer from inaccuracy of gene expression predictions due to inclusion of non-regulatory variants. By integrating prior knowledge of susceptible transcription fact...
Cancer geneticsGenetic association studyStatistical methods
10.1038/S41467-022-34888-0
ISSN:2041-1723
Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits
Nora Scherer•Daniel Fässler•Oleg Borisov•Yurong Cheng•Pascal Schlosser等 29 人
Nature Genetics
2025
•2025/1/2
•00 p.1-13
Genetic studies of the metabolome can uncover enzymatic and transport processes shaping human metabolism. Using rare variant aggregation testing based on whole-exome sequencing data to detect genes associated with levels of 1,294 plasma and 1,396 urine metabolites, we discovered 235 gene–metabolite ...
EpidemiologyGenetic association studyGenetics researchMetabolomicsPopulation genetics
10.1038/S41588-024-01965-7
ISSN:1061-4036
Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure
Marios Arvanitis•Emmanouil Tampakakis•Yanxiao Zhang•Wei Wang•Adam Auton等 13 人
Nature Communications
2020
•2020/2/28
•Vol.11 No.1 p.1-12
Heart failure is a major public health problem affecting over 23 million people worldwide. In this study, we present the results of a large scale meta-analysis of heart failure GWAS and replication in a comparable sized cohort to identify one known and two novel loci associated with heart failure. H...
Clinical geneticsFunctional genomicsGenome-wide association studiesHeart failure
10.1038/S41467-020-14843-7
ISSN:2041-1723
Activated MAFB in ovarian cancer promotes cytoskeletal remodeling and immune microenvironment suppression by interfering with m6A modifications through WTAP competition
Qinke Li•Siying Zhang•Min Wang•Qiang Yi•Hang Xu等 7 人
Oncogene
2025
•2025/8/12
•00 p.1-17
The tumor microenvironment (TME) coordinates cancer progression through complex transcriptional networks, but the molecular mechanisms controlling immune evasion in ovarian cancer remain elusive. Here, by integrating immune dysfunction characteristics across multiple clinical cohorts and single-cell...
Cancer microenvironmentOncogenesOvarian cancer
10.1038/S41388-025-03522-W
ISSN:0950-9232
Pan-cancer transcriptomic analysis identified six classes of immunosenescence genes revealed molecular links between aging, immune system and cancer
Wang Xinyue•Guo Shuang•Zhou Hanxiao•Sun Yue•Gan Jing等 13 人
Genes & Immunity
2023
•2023/2/17
•00 p.1-11
Aging is a complex process that significantly impacts the immune system. The aging-related decline of the immune system, termed immunosenescence, can lead to disease development, including cancer. The perturbation of immunosenescence genes may characterize the associations between cancer and aging. ...
Gene expressionImmunotherapy
10.1038/S41435-023-00197-9
ISSN:1476-5470
PTPN2 copper-sensing relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression
Matthew O. Ross•Yuan Xie•Ryan C. Owyang•Chang Ye•Olivia N. P. Zbihley等 12 人
Nature Communications
2024
•2024/8/13
•Vol.15 No.1 p.1-15
Fluxes in human copper levels recently garnered attention for roles in cellular signaling, including affecting levels of the signaling molecule cyclic adenosine monophosphate. We herein apply an unbiased temporal evaluation of the signaling and whole genome transcriptional activities modulated ...
Cell signallingMetalloproteinsMolecular biology
10.1038/S41467-024-50524-5
ISSN:2041-1723
AI-guided multi-omics analysis identifies NPC1-modulated susceptibility to SARS-CoV-2 infection under PM2.5 exposure
Guoqing Feng•Zheng Dong•Limei Ke•Weilai Zhou•Yu Tian等 19 人
Nature Communications
2026
•2026/3/30
0Exposure to airborne fine particulate matter (PM2.5) has been linked to increased risk of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, yet the underlying mechanisms remain unclear. Here, by leveraging a fine-tuned foundation model of single-cell transcriptomics, we unc...
Environmental sciencesEpidemiologyGenetics researchRisk factorsViral infection
10.1038/S41467-026-71196-3
ISSN:2041-1723
Stroke genetics informs drug discovery and risk prediction across ancestries
Mishra Aniket•Malik Rainer•Hachiya Tsuyoshi•Jürgenson Tuuli•Namba Shinichi等 187 人
Nature
2022
•2022/9/30
•Vol.611 No.7934 p.115-123
Previous genome-wide association studies (GWASs) of stroke — the second leading cause of death worldwide — were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 3...
Genetic markersGenome-wide association studiesPredictive markersStroke
10.1038/S41586-022-05165-3
ISSN:0028-0836
Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance
Cui Miao•Atmanli Ayhan•Morales Maria Gabriela•Tan Wei•Chen Kenian等 10 人
Nature Communications
2021
•2021/9/6
•Vol.12 No.1 p.1-15
Following injury, cells in regenerative tissues have the ability to regrow. The mechanisms whereby regenerating cells adapt to injury-induced stress conditions and activate the regenerative program remain to be defined. Here, using the mammalian neonatal heart regeneration model, we show that Nrf1, ...
Cardiac regenerationTranscriptomics
10.1038/S41467-021-25653-W
ISSN:2041-1723
Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications
Rosalie B. T. M. Sterenborg•Inga Steinbrenner•Yong Li•Melissa N. Bujnis•Tatsuhiko Naito等 141 人
Nature Communications
2024
•2024/1/30
•Vol.15 No.1 p.1-18
To date only a fraction of the genetic footprint of thyroid function has been clarified. We report a genome-wide association study meta-analysis of thyroid function in up to 271,040 individuals of European ancestry, including reference range thyrotropin (TSH), free thyroxine (FT4), free and total tr...
Genome-wide association studiesThyroid diseases
10.1038/S41467-024-44701-9
ISSN:2041-1723
Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation
Nicoletta Cieri•Nidhi Hookeri•Kari Stromhaug•Liang Li•Julia Keating等 37 人
Nature Biotechnology
2024
•2024/8/21
•00 p.1-12
T cell alloreactivity against minor histocompatibility antigens (mHAgs)—polymorphic peptides resulting from donor–recipient (D–R) disparity at sites of genetic polymorphisms—is at the core of the therapeutic effect of allogeneic hematopoietic cell transplantation (allo-HCT). Despite the crucial role...
ImmunogeneticsImmunotherapyPrognostic markersTranslational research
10.1038/S41587-024-02348-3
ISSN:1087-0156
SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801
Angela Wahl•Lisa E. Gralinski•Claire E. Johnson•Wenbo Yao•Martina Kovarova等 26 人
Nature
2021
•2021/2/9
•Vol.591 No.7850 p.451-457
All coronaviruses known to have recently emerged as human pathogens probably originated in bats1. Here we use a single experimental platform based on immunodeficient mice implanted with human lung tissue (hereafter, human lung-only mice (LoM)) to demonstrate the efficient in vivo replication of seve...
SARS-CoV-2Viral pathogenesis
10.1038/S41586-021-03312-W
ISSN:0028-0836
A second update on mapping the human genetic architecture of COVID-19
Nature
2023
•2023/9/6
•Vol.621 No.7977 p.7-26
Genome-wide association studiesSARS-CoV-2
10.1038/S41586-023-06355-3
ISSN:0028-0836
GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification
Vasiliki Lagou•Longda Jiang•Anna Ulrich•Liudmila Zudina•Karla Sofia Gutiérrez González等 96 人
Nature Genetics
2023
•2023/9/7
•Vol.55 No.9 p.1448-1461
Conventional measurements of fasting and postprandial blood glucose levels investigated in genome-wide association studies (GWAS) cannot capture the effects of DNA variability on ‘around the clock’ glucoregulatory processes. Here we show that GWAS meta-analysis of glucose measurements under nonstand...
DiseasesGenetics
10.1038/S41588-023-01462-3
ISSN:1061-4036
Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets
Xiaoguang Xu•Chachrit Khunsriraksakul•James M. Eales•Sebastien Rubin•David Scannali等 38 人
Nature Communications
2024
•2024/3/19
•Vol.15 No.1 p.1-29
Genetic mechanisms of blood pressure (BP) regulation remain poorly defined. Using kidney-specific epigenomic annotations and 3D genome information we generated and validated gene expression prediction models for the purpose of transcriptome-wide association studies in 700 human kidneys. We identifie...
Gene expressionGene regulationGenome-wide association studies
10.1038/S41467-024-46132-Y
ISSN:2041-1723
LazySlide: accessible and interoperable whole-slide image analysis
Yimin Zheng•Ernesto Abila•Eva Chrenková•Iva Buljan•Juliane Winkler等 6 人
Nature Methods
2026
•2026/3/20
•Vol.23 No.4 p.728-731
Histopathological data are foundational in both biological research and clinical diagnostics but remain siloed from modern multimodal and single-cell frameworks. Here we introduce LazySlide, an open-source Python package built on the scverse ecosystem for efficient whole-slide image analysis and mul...
Computational platforms and environmentsSoftware
10.1038/S41592-026-03044-7
ISSN:1548-7091
The health impacts and genetic architecture of food liking in cardio-metabolic diseases
Wenbo Jiang•Hang Wang•Yiding Geng•Meijuan Guo•Yingdong Zuo等 16 人
Nature Communications
2025
•2025/5/23
•Vol.16 No.1 p.1-20
We evaluated temporal and genetic relationships between 176 food-liking-traits and cardio-metabolic diseases using data from the UK Biobank (N = 182,087) for observational analyses and summary-level GWAS data from FinnGen and other consortia (N = 406,565–977,323) for genetic analyses. Integrating ob...
CardiologyEndocrine system and metabolic diseasesRisk factors
10.1038/S41467-025-59945-2
ISSN:2041-1723
Cell adhesion molecule KIRREL1 is a feedback regulator of Hippo signaling recruiting SAV1 to cell-cell contact sites
Paul Atanu•Annunziato Stefano•Lu Bo•Sun Tianliang•Evrova Olivera等 20 人
Nature Communications
2022
•2022/2/17
•Vol.13 No.1 p.1-14
The Hippo/YAP pathway controls cell proliferation through sensing physical and spatial organization of cells. How cell-cell contact is sensed by Hippo signaling is poorly understood. Here, we identified the cell adhesion molecule KIRREL1 as an upstream positive regulator of the mammalian Hippo pathw...
CRISPR-Cas9 genome editingCell adhesionCell signallingHIPPO signalling
10.1038/S41467-022-28567-3
ISSN:2041-1723
RIPK1 is a negative mediator in Aquaporin 1-driven triple-negative breast carcinoma progression and metastasis
Zhuming Yin•Wenlin Chen•Jian Yin•Jingyan Sun•Qianrong Xie等 8 人
Npj Breast Cancer
2021
•2021/5/12
•Vol.7 No.1 p.1-11
The triple-negative breast carcinoma (TNBC) is the most aggressive subtype of breast cancer. In TNBC, Aquaporin 1 (AQP1), a water-transporting transmembrane protein, is aberrantly enriched in cytoplasm and causes tumor cell death evasion. However, the carcinogenetic bioactivities of cytoplasmic AQP1...
Breast cancerOncogenes
10.1038/S41523-021-00261-5
ISSN:2374-4677
The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance
Ferguson Ian D.•Patiño-Escobar Bonell•Tuomivaara Sami T.•Lin Yu-Hsiu T.•Nix Matthew A.等 29 人
Nature Communications
2022
•2022/7/15
•Vol.13 No.1 p.1-17
The myeloma surface proteome (surfaceome) determines tumor interaction with the microenvironment and serves as an emerging arena for therapeutic development. Here, we use glycoprotein capture proteomics to define the myeloma surfaceome at baseline, in drug resistance, and in response to acute drug t...
Mass spectrometryMembrane proteinsMyelomaProteomics
10.1038/S41467-022-31810-6
ISSN:2041-1723
CNK2 promotes cancer cell motility by mediating ARF6 activation downstream of AXL signalling
Guillaume Serwe•David Kachaner•Jessica Gagnon•Cédric Plutoni•Driss Lajoie等 14 人
Nature Communications
2023
•2023/6/15
•Vol.14 No.1 p.1-21
Cell motility is a critical feature of invasive tumour cells that is governed by complex signal transduction events. Particularly, the underlying mechanisms that bridge extracellular stimuli to the molecular machinery driving motility remain partially understood. Here, we show that the scaffold prot...
CancerCell invasionCell signalling
10.1038/S41467-023-39281-Z
ISSN:2041-1723
Targeted activation of ferroptosis in colorectal cancer via LGR4 targeting overcomes acquired drug resistance
Hao Zheng•Jinming Liu•Qi Cheng•Qianping Zhang•Yaoyao Zhang等 22 人
Nature Cancer
2024
•2024/1/30
•00 p.1-18
Acquired drug resistance is a major challenge for cancer therapy and is the leading cause of cancer mortality; however, the mechanisms of drug resistance are diverse and the strategy to specifically target drug-resistant cancer cells remains an unmet clinical issue. Here, we established a colorectal...
CancerGastrointestinal cancer
10.1038/S43018-023-00715-8
ISSN:2662-1347
pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation
Boix Olga•Martinez Marion•Vidal Santiago•Giménez-Alejandre Marta•Palenzuela Lluís等 22 人
Nature Communications
2022
•2022/11/11
•Vol.13 No.1 p.1-22
The human transcriptome contains thousands of small open reading frames (sORFs) that encode microproteins whose functions remain largely unexplored. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary conserved ubiquitin-like protein (UBL) expressed in many epithelia and upregulated upon...
CancerMechanisms of disease
10.1038/S41467-022-34529-6
ISSN:2041-1723
Genome-wide analysis highlights contribution of immune system pathways to the genetic architecture of asthma
Yi Han•Qiong Jia•Pedram Shafiei Jahani•Benjamin P. Hurrell•Calvin Pan等 13 人
Nature Communications
2020
•2020/4/15
•Vol.11 No.1 p.1-13
Asthma is a chronic and genetically complex respiratory disease that affects over 300 million people worldwide. Here, we report a genome-wide analysis for asthma using data from the UK Biobank and the Trans-National Asthma Genetic Consortium. We identify 66 previously unknown asthma loci and demonst...
AsthmaGenome-wide association studiesImmunogenetics
10.1038/S41467-020-15649-3
ISSN:2041-1723
Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations
David S. M. Lee•Louis R. Ghanem•Yoseph Barash
Nature Communications
2020
•2020/1/27
•Vol.11 No.1 p.1-12
G-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5’ and 3’ UTRs are selectively ...
Genetic association studyGenetic variationRNARNA folding
10.1038/S41467-020-14404-Y
ISSN:2041-1723
Targeted inhibition of the methyltransferase SETD8 synergizes with the Wee1 inhibitor adavosertib in restraining glioblastoma growth
Rosa Della Monica•Michela Buonaiuto•Mariella Cuomo•Cristina Pagano•Federica Trio等 23 人
Cell Death & Disease
2023
•2023/9/27
•Vol.14 No.9 p.1-13
Despite intense research efforts, glioblastoma remains an incurable brain tumor with a dismal median survival time of 15 months. Thus, identifying new therapeutic targets is an urgent need. Here, we show that the lysine methyltransferase SETD8 is overexpressed in 50% of high-grade gliomas. The small...
CheckpointsTargeted therapies
10.1038/S41419-023-06167-3
ISSN:2041-4889
Brain tissue- and cell type-specific eQTL Mendelian randomization reveals efficacy of FADS1 and FADS2 on cognitive function
Xueyan Wu•Lei Jiang•Hongyan Qi•Chunyan Hu•Xiaojing Jia等 19 人
Translational Psychiatry
2024
•2024/2/5
•Vol.14 No.1 p.1-9
Epidemiological studies suggested an association between omega-3 fatty acids and cognitive function. However, the causal role of the fatty acid desaturase (FADS) gene, which play a key role in regulating omega-3 fatty acids biosynthesis, on cognitive function is unclear. Hence, we used two-sample Me...
Drug discoveryMedical genetics
10.1038/S41398-024-02784-4
ISSN:2158-3188
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis
Dan Zhou•Yi Jiang•Xue Zhong•Nancy J. Cox•Chunyu Liu等 6 人
Nature Genetics
2020
•2020/10/5
•Vol.52 No.11 p.1239-1246
Here, we present a joint-tissue imputation (JTI) approach and a Mendelian randomization framework for causal inference, MR-JTI. JTI borrows information across transcriptomes of different tissues, leveraging shared genetic regulation, to improve prediction performance in a tissue-dependent manner. No...
Computational biology and bioinformaticsDiseasesGenetics
10.1038/S41588-020-0706-2
ISSN:1061-4036
A visual–omics foundation model to bridge histopathology with spatial transcriptomics
Weiqing Chen•Pengzhi Zhang•Tu N Tran•Yiwei Xiao•Shengyu Li等 20 人
Nature Methods
2025
•2025/5/29
•00 p.1-15
Artificial intelligence has revolutionized computational biology. Recent developments in omics technologies, including single-cell RNA sequencing and spatial transcriptomics, provide detailed genomic data alongside tissue histology. However, current computational models focus on either omics or imag...
Computational modelsComputational platforms and environmentsMachine learningSoftware
10.1038/S41592-025-02707-1
ISSN:1548-7091
Reference SVA insertion polymorphisms are associated with Parkinson’s Disease progression and differential gene expression
Abigail L. Pfaff•Vivien J. Bubb•John P. Quinn•Sulev Koks
Npj Parkinson's Disease
2021
•2021/5/25
•Vol.7 No.1 p.1-9
The development of Parkinson’s disease (PD) involves a complex interaction of genetic and environmental factors. Genome-wide association studies using extensive single nucleotide polymorphism datasets have identified many loci involved in disease. However much of the heritability of Parkinson’s dise...
GenomicsParkinson's disease
10.1038/S41531-021-00189-4
ISSN:2373-8057
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
Self-assembly of hybrid 3D cultures by integrating living and synthetic cells
Nils Piernitzki•Ning Gao•Gilles Gasparoni•Louisa M. Krauß•Julia Schulze-Hentrich等 10 人
Nature Communications
2025
•2025/12/10
•Vol.16 No.1 p.110730
Self-assembly is a fundamental property of living matter that drives the three-dimensional organization of cell collectives such as tissues and organs. Here, the co-assembly of synthetic and natural cells is leveraged to create hybrid living 3D cancer cultures. We screen a range of synthetic cell mo...
Bioinspired materialsCancer models
10.1038/S41467-025-66789-3
ISSN:2041-1723
Therapeutic target prediction for orphan diseases integrating genome-wide and transcriptome-wide association studies
Satoko Namba•Michio Iwata•Shin-Ichi Nureki•Noriko Yuyama Otani•Yoshihiro Yamanishi
Nature Communications
2025
•2025/4/18
•Vol.16 No.1 p.1-15
Therapeutic target identification is challenging in drug discovery, particularly for rare and orphan diseases. Here, we propose a disease signature, TRESOR, which characterizes the functional mechanisms of each disease through genome-wide association study (GWAS) and transcriptome-wide association s...
BioinformaticsDrug developmentGenome-wide analysis of gene expressionMachine learningTarget identification
10.1038/S41467-025-58464-4
ISSN:2041-1723
Large-scale integration of the plasma proteome with genetics and disease
Ferkingstad Egil•Sulem Patrick•Atlason Bjarni A.•Sveinbjornsson Gardar•Magnusson Magnus I.等 40 人
Nature Genetics
2021
•2021/12/2
•00 p.1-10
The plasma proteome can help bridge the gap between the genome and diseases. Here we describe genome-wide association studies (GWASs) of plasma protein levels measured with 4,907 aptamers in 35,559 Icelanders. We found 18,084 associations between sequence variants and levels of proteins in plasma (p...
Genetics researchGenome-wide association studiesProteome informatics
10.1038/S41588-021-00978-W
ISSN:1061-4036
A sequence of SVA retrotransposon insertions in ASIP shaped human pigmentation
Nolan Kamitaki•Margaux L. A. Hujoel•Ronen E. Mukamel•Edward Gebara•Steven A. McCarroll等 6 人
Nature Genetics
2024
•2024/7/24
•Vol.56 No.8 p.1583-1591
Retrotransposons comprise about 45% of the human genome1, but their contributions to human trait variation and evolution are only beginning to be explored2,3. Here, we find that a sequence of SVA retrotransposon insertions in an early intron of the ASIP (agouti signaling protein) gene has probably s...
Gene expressionGenetic association studyPopulation geneticsSkin cancer
10.1038/S41588-024-01841-4
ISSN:1061-4036
GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements
Dixon Peter H.•Levine Adam P.•Cebola Inês•Chan Melanie M. Y.•Amin Aliya S.等 22 人
Nature Communications
2022
•2022/8/17
•Vol.13 No.1 p.1-18
Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse o...
Gene expression profilingGenome-wide association studiesLiver diseases
10.1038/S41467-022-29931-Z
ISSN:2041-1723
Genetic risk factors for COVID-19 and influenza are largely distinct
Jack A. Kosmicki•Anthony Marcketta•Deepika Sharma•Silvio Alessandro Di Gioia•Samantha Batista等 55 人
Nature Genetics
2024
•2024/8/5
•Vol.56 No.8 p.1592-1596
Coronavirus disease 2019 (COVID-19) and influenza are respiratory illnesses caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses, respectively. Both diseases share symptoms and clinical risk factors1, but the extent to which these conditions have a common ...
DNA sequencingGenome-wide association studies
10.1038/S41588-024-01844-1
ISSN:1061-4036
Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers
Rebecca J. Deyell•Yaoqing Shen•Emma Titmuss•Katherine Dixon•Laura M. Williamson等 31 人
Nature Communications
2024
•2024/5/16
•Vol.15 No.1 p.1-15
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in chi...
Cancer geneticsCancer genomicsGene expressionPaediatric cancer
10.1038/S41467-024-48363-5
ISSN:2041-1723
Adolescent multi-omics and Mendelian randomization reveal transdiagnostic molecular mechanisms in psychiatric disorders
Luheng Qian•Runye Shi•Xinyang Yu•Di Chen•Tobias Banaschewski等 26 人
Nature Mental Health
2026
•2026/6/5
•00 p.1-14
The biological mechanisms underlying major neuropsychiatric disorders remain largely elusive. Given the frequent association of immune dysregulation with these conditions, we used blood-derived multi-omics data from 1,274 healthy adolescents in the IMAGEN cohort to identify transdiagnostic biomarker...
DNA methylationGene expressionPsychiatric disorders
10.1038/S44220-026-00660-2
ISSN:2731-6076
Risk factors associated with age at onset of Parkinson’s disease in the UK Biobank
Yuanfeng Huang•Qian Chen•Zheng Wang•Yijing Wang•Aojie Lian等 11 人
Npj Parkinson's Disease
2024
•2024/1/2
•Vol.10 No.1 p.1-8
Substantial evidence shown that the age at onset (AAO) of Parkinson’s disease (PD) is a major determinant of clinical heterogeneity. However, the mechanisms underlying heterogeneity in the AAO remain unclear. To investigate the risk factors with the AAO of PD, a total of 3156 patients with PD from t...
Parkinson's diseaseRisk factors
10.1038/S41531-023-00623-9
ISSN:2373-8057
Mapping rare protein-coding variants on multi-organ imaging traits
Yijun Fan•Jie Chen•Zirui Fan•Julio Chirinos•Jason L. Stein等 23 人
Nature Communications
2025
•2025/12/23
0Human organ structure and function are important endophenotypes for clinical outcomes. Genome-wide association studies (GWAS) have identified numerous common variants associated with phenotypes derived from magnetic resonance imaging (MRI) of the brain and body. However, the role of rare protein-cod...
Genetic association studyGenomics
10.1038/S41467-025-67431-Y
ISSN:2041-1723
An integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease
Ariella T. Cohain•William T. Barrington•Daniel M. Jordan•Noam D. Beckmann•Carmen A. Argmann等 26 人
Nature Communications
2021
•2021/1/22
•Vol.12 No.1 p.1-13
Elevated plasma cholesterol and type 2 diabetes (T2D) are associated with coronary artery disease (CAD). Individuals treated with cholesterol-lowering statins have increased T2D risk, while individuals with hypercholesterolemia have reduced T2D risk. We explore the relationship between lipid and glu...
Cardiovascular diseasesComputational biology and bioinformaticsMetabolic disordersRegulatory networks
10.1038/S41467-020-20750-8
ISSN:2041-1723
Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy
Krzysztof Kiryluk•Elena Sanchez-Rodriguez•Xu-Jie Zhou•Francesca Zanoni•Lili Liu等 188 人
Nature Genetics
2023
•2023/6/19
•00 p.1-15
IgA nephropathy (IgAN) is a progressive form of kidney disease defined by glomerular deposition of IgA. Here we performed a genome-wide association study of 10,146 kidney-biopsy-diagnosed IgAN cases and 28,751 controls across 17 international cohorts. We defined 30 genome-wide significant risk loci ...
Genome-wide association studiesIgA nephropathy
10.1038/S41588-023-01422-X
ISSN:1061-4036
RSPO3 is important for trabecular bone and fracture risk in mice and humans
Nilsson Karin H.•Henning Petra•Shahawy Maha El•Nethander Maria•Andersen Thomas Levin等 21 人
Nature Communications
2021
•2021/8/13
•Vol.12 No.1 p.1-18
With increasing age of the population, countries across the globe are facing a substantial increase in osteoporotic fractures. Genetic association signals for fractures have been reported at the RSPO3 locus, but the causal gene and the underlying mechanism are unknown. Here we show that the fracture...
BoneOsteoblasts
10.1038/S41467-021-25124-2
ISSN:2041-1723
PFKM governs metabolic shifts throughout skeletal muscle differentiation
Melissa Campos•Steven T. Nguyen•Xiangduo Kong•Ying Yang•Richard L. Watson等 23 人
Nature Metabolism
2026
•2026/2/24
•Vol.8 No.2 p.489-505
Metabolism is known to influence cell identity, but the underlying mechanisms remain unclear. Here we reveal spatiotemporal dynamics of phosphofructokinase 1 (PFK1), a key glycolytic enzyme, within the skeletal muscle lineage. The expression of PFKM (the muscle isoform of PFK1) is low in muscle stem...
AutophagyDifferentiationLysosomesMetabolismMuscle stem cells
10.1038/S42255-026-01457-4
ISSN:2522-5812
Genome-wide association study meta-analysis provides insights into the etiology of heart failure and its subtypes
Albert Henry•Xiaodong Mo•Chris Finan•Mark D. Chaffin•Doug Speed等 181 人
Nature Genetics
2025
•2025/3/4
•00 p.1-14
Heart failure (HF) is a major contributor to global morbidity and mortality. While distinct clinical subtypes, defined by etiology and left ventricular ejection fraction, are well recognized, their genetic determinants remain inadequately understood. In this study, we report a genome-wide associatio...
Genome-wide association studiesHeart failure
10.1038/S41588-024-02064-3
ISSN:1061-4036
Genetic suppression features ABHD18 as a Barth syndrome therapeutic target
Sanna N. Masud•Anchal Srivastava•Patricia Mero•Victoria Saba Echezarreta•Eve Anderson等 49 人
Nature
2025
•2025/9/3
•00 p.1-10
Cardiolipin (CL) is the signature phospholipid of the inner mitochondrial membrane, where it stabilizes electron transport chain protein complexes1. The final step in CL biosynthesis relates to its remodelling: the exchange of nascent acyl chains with longer, unsaturated chains1. However, the enzyme...
Genetic interactionHydrolasesMetabolic disorders
10.1038/S41586-025-09373-5
ISSN:0028-0836
Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility
Wen Wanqing•Chen Zhishan•Bao Jiandong•Long Quan•Shu Xiao-ou等 7 人
Nature Communications
2021
•2021/9/13
•Vol.12 No.1 p.1-12
Identifying transcription factors (TFs) whose DNA bindings are altered by genetic variants that regulate susceptibility genes is imperative to understand transcriptional dysregulation in disease etiology. Here, we develop a statistical framework to analyze extensive ChIP-seq and GWAS data and identi...
Breast cancerCancer epigenetics
10.1038/S41467-021-25670-9
ISSN:2041-1723
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data
Greta Pintacuda•Frederik H. Lassen•Yu-Han H. Hsu•April Kim•Jacqueline M. Martín等 10 人
Nature Communications
2021
•2021/5/10
•Vol.12 No.1 p.1-10
Combining genetic and cell-type-specific proteomic datasets can generate biological insights and therapeutic hypotheses, but a technical and statistical framework for such analyses is lacking. Here, we present an open-source computational tool called Genoppi (lagelab.org/genoppi) that enables robust...
Amyotrophic lateral sclerosisProtein–protein interaction networksProteome informatics
10.1038/S41467-021-22648-5
ISSN:2041-1723
Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention
Wang Zhe•Emmerich Andrew•Pillon Nicolas J.•Moore Tim•Hemerich Daiane等 218 人
Nature Genetics
2022
•2022/9/7
•Vol.54 No.9 p.1332-1344
Although physical activity and sedentary behavior are moderately heritable, little is known about the mechanisms that influence these traits. Combining data for up to 703,901 individuals from 51 studies in a multi-ancestry meta-analysis of genome-wide association studies yields 99 loci that associat...
Genetics researchGenome-wide association studiesTranslational research
10.1038/S41588-022-01165-1
ISSN:1061-4036
Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries
Puya Gharahkhani•Eric Jorgenson•Pirro Hysi•Anthony P. Khawaja•Sarah Pendergrass等 79 人
Nature Communications
2021
•2021/2/24
•Vol.12 No.1 p.1-16
Primary open-angle glaucoma (POAG), is a heritable common cause of blindness world-wide. To identify risk loci, we conduct a large multi-ethnic meta-analysis of genome-wide association studies on a total of 34,179 cases and 349,321 controls, identifying 44 previously unreported risk loci and confirm...
Genome-wide association studiesOptic nerve diseases
10.1038/S41467-020-20851-4
ISSN:2041-1723
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus
Downes Damien J.•Cross Amy R.•Hua Peng•Roberts Nigel•Schwessinger Ron等 19 人
Nature Genetics
2021
•2021/11/4
•Vol.53 No.11 p.1606-1615
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19) pandemic has caused millions of deaths worldwide. Genome-wide association studies identified the 3p21.31 region as conferring a twofold increased risk of respiratory failure. Here, using a combined multiomics and mac...
Gene regulationGenome-wide association studiesGenomicsRespiratory tract diseasesSARS-CoV-2
10.1038/S41588-021-00955-3
ISSN:1061-4036
Shared genetic pathways contribute to risk of hypertrophic and dilated cardiomyopathies with opposite directions of effect
Rafik Tadros•Catherine Francis•Xiao Xu•Alexa M. C. Vermeer•Andrew R. Harper等 70 人
Nature Genetics
2021
•2021/1/25
•Vol.53 No.2 p.128-134
The heart muscle diseases hypertrophic (HCM) and dilated (DCM) cardiomyopathies are leading causes of sudden death and heart failure in young, otherwise healthy, individuals. We conducted genome-wide association studies and multi-trait analyses in HCM (1,733 cases), DCM (5,521 cases) and nine left v...
CardiomyopathiesGenetic testingGenetics researchGenome-wide association studiesPopulation genetics
10.1038/S41588-020-00762-2
ISSN:1061-4036
Functional synapses between neurons and small cell lung cancer
Vignesh Sakthivelu•Anna Schmitt•Franka Odenthal•Kristiano Ndoci•Marian Touet等 75 人
Nature
2025
•2025/9/10
•00 p.1-11
Small cell lung cancer (SCLC) is a highly aggressive type of lung cancer, characterized by rapid proliferation, early metastatic spread, frequent early relapse and a high mortality rate1–3. Recent evidence has suggested that innervation has an important role in the development and progression o...
Cancer genomicsCancer microenvironmentNeuroscienceSmall-cell lung cancerTargeted therapies
10.1038/S41586-025-09434-9
ISSN:0028-0836
A comprehensive SARS-CoV-2–human protein–protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets
Zhou Yadi•Liu Yuan•Gupta Shagun•Paramo Mauricio I.•Hou Yuan等 23 人
Nature Biotechnology
2022
•2022/10/10
•Vol.41 No.1 p.128-139
Studying viral–host protein–protein interactions can facilitate the discovery of therapies for viral infection. We use high-throughput yeast two-hybrid experiments and mass spectrometry to generate a comprehensive SARS-CoV-2–human protein–protein interactome network consisting of 739 high-confidence...
Biochemical networksNetwork topology
10.1038/S41587-022-01474-0
ISSN:1087-0156
Uncovering structural themes across cilia microtubule inner proteins with implications for human cilia function
Jens S. Andersen•Aaran Vijayakumaran•Christopher Godbehere•Esben Lorentzen•Vito Mennella等 6 人
Nature Communications
2024
•2024/3/27
•Vol.15 No.1 p.1-17
Centrosomes and cilia are microtubule-based superstructures vital for cell division, signaling, and motility. The once thought hollow lumen of their microtubule core structures was recently found to hold a rich meshwork of microtubule inner proteins (MIPs). To address the outstanding question of how...
CiliaComputational biology and bioinformaticsMicrotubulesProtein structure predictions
10.1038/S41467-024-46737-3
ISSN:2041-1723
Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery
Zhou Tian•Zhu Xinyi•Ye Zhizhong•Wang Yong-Fei•Yao Chao等 25 人
Nature Communications
2022
•2022/4/6
•Vol.13 No.1 p.1-16
Despite strong evidence that human genetic variants affect the expression of many key transcription factors involved in autoimmune diseases, establishing biological links between non-coding risk variants and the gene targets they regulate remains a considerable challenge. Here, we combine genetic, e...
CRISPR-Cas9 genome editingDNA methylationEpigenomicsGene regulationSystemic lupus erythematosus
10.1038/S41467-022-29514-Y
ISSN:2041-1723
Elevated NEGR1 in brain induces anxiety or depression-like phenotypes and synaptic dysfunction
Ya-Qi Zhang•Qing Zhang•Yi Yang•Li-Li Yu•Ning-Lin Fan等 14 人
Molecular Psychiatry
2025
•2025/5/17
•00 p.1-14
Single nucleotide polymorphisms (SNPs) within 1p31.1 region have shown significant associations with depression, and our prior functional genomics pinpointed a regulatory variant rs3101339 among them. However, its precise role in depression pathogenesis remains elusive. In this study, we employed a ...
DepressionGeneticsMolecular biologyNeuroscience
10.1038/S41380-025-03052-7
ISSN:1359-4184
ZNF410 represses fetal globin by singular control of CHD4
Divya S. Vinjamur•Qiuming Yao•Mitchel A. Cole•Connor McGuckin•Chunyan Ren等 11 人
Nature Genetics
2021
•2021/4/15
•Vol.53 No.5 p.719-728
Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes enco...
AnaemiaGene regulationHigh-throughput screening
10.1038/S41588-021-00843-W
ISSN:1061-4036
Genomics of perivascular space burden unravels early mechanisms of cerebral small vessel disease
Duperron Marie-Gabrielle•Knol Maria J.•Le Grand Quentin•Evans Tavia E.•Mishra Aniket等 88 人
Nature Medicine
2023
•2023/4/17
•00 p.1-13
Perivascular space (PVS) burden is an emerging, poorly understood, magnetic resonance imaging marker of cerebral small vessel disease, a leading cause of stroke and dementia. Genome-wide association studies in up to 40,095 participants (18 population-based cohorts, 66.3 ± 8.6 yr, 96.9% European ance...
Genome-wide association studiesNeurologyStroke
10.1038/S41591-023-02268-W
ISSN:1078-8956
Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson’s disease
Ganqiang Liu•Jiajie Peng•Zhixiang Liao•Joseph J. Locascio•Jean-Christophe Corvol等 39 人
Nature Genetics
2021
•2021/5/6
•Vol.53 No.6 p.787-793
A key driver of patients’ well-being and clinical trials for Parkinson’s disease (PD) is the course that the disease takes over time (progression and prognosis). To assess how genetic variation influences the progression of PD over time to dementia, a major determinant for quality of life, we perfor...
Genome-wide association studiesParkinson's disease
10.1038/S41588-021-00847-6
ISSN:1061-4036
Integrative analysis of risk factors for immune-related adverse events of checkpoint blockade therapy in cancer
Changhwan Sung•Jinhyeon An•Soohyeon Lee•Jaesoon Park•Kang Seon Lee等 25 人
Nature Cancer
2023
•2023/6/12
•Vol.4 No.6 p.844-859
Immune-related adverse events (irAEs) induced by checkpoint inhibitors involve a multitude of different risk factors. Here, to interrogate the multifaceted underlying mechanisms, we compiled germline exomes and blood transcriptomes with clinical data, before and after checkpoint inhibitor treatment,...
CancerCancer geneticsCancer immunotherapyPredictive medicineTumour biomarkers
10.1038/S43018-023-00572-5
ISSN:2662-1347
Hypergraph factorization for multi-tissue gene expression imputation
Ramon Viñas•Chaitanya K. Joshi•Dobrik Georgiev•Phillip Lin•Bianca Dumitrascu等 7 人
Nature Machine Intelligence
2023
•2023/7/17
•Vol.5 No.7 p.739-753
Integrating gene expression across tissues and cell types is crucial for understanding the coordinated biological mechanisms that drive disease and characterize homoeostasis. However, traditional multi-tissue integration methods either cannot handle uncollected tissues or rely on genotype informatio...
Machine learningTranscriptomics
10.1038/S42256-023-00684-8
ISSN:2522-5839
SUMMIT: An integrative approach for better transcriptomic data imputation improves causal gene identification
Zhang Zichen•Bae Ye Eun•Bradley Jonathan R.•Wu Lang•Wu Chong
Nature Communications
2022
•2022/10/25
•Vol.13 No.1 p.1-12
Genes with moderate to low expression heritability may explain a large proportion of complex trait etiology, but such genes cannot be sufficiently captured in conventional transcriptome-wide association studies (TWASs), partly due to the relatively small available reference datasets for developing e...
Gene expressionPopulation geneticsQuantitative trait lociTranscriptomics
10.1038/S41467-022-34016-Y
ISSN:2041-1723
The genetic architecture of biological age in nine human organ systems
Junhao Wen•Ye Ella Tian•Ioanna Skampardoni•Zhijian Yang•Yuhan Cui等 11 人
Nature Aging
2024
•2024/6/28
•00 p.1-18
Investigating the genetic underpinnings of human aging is essential for unraveling the etiology of and developing actionable therapies for chronic diseases. Here, we characterize the genetic architecture of the biological age gap (BAG; the difference between machine learning-predicted age and chrono...
AgeingData miningGenome-wide association studies
10.1038/S43587-024-00662-8
ISSN:2662-8465