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Zheng S, Tsao PS, Pan C. Abdominal aortic aneurysm and cardiometabolic traits share strong genetic susceptibility to lipid metabolism and inflammation. Nat Commun 2024; 15:5652. [PMID: 38969659 DOI: 10.1038/s41467-024-49921-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 06/25/2024] [Indexed: 07/07/2024] Open
Abstract
Abdominal aortic aneurysm has a high heritability and often co-occurs with other cardiometabolic disorders, suggesting shared genetic susceptibility. We investigate this commonality leveraging recent GWAS studies of abdominal aortic aneurysm and 32 cardiometabolic traits. We find significant genetic correlations between abdominal aortic aneurysm and 21 of the cardiometabolic traits investigated, including causal relationships with coronary artery disease, hypertension, lipid traits, and blood pressure. For each trait pair, we identify shared causal variants, genes, and pathways, revealing that cholesterol metabolism and inflammation are shared most prominently. Additionally, we show the tissue and cell type specificity in the shared signals, with strong enrichment across traits in the liver, arteries, adipose tissues, macrophages, adipocytes, and fibroblasts. Finally, we leverage drug-gene databases to identify several lipid-lowering drugs and antioxidants with high potential to treat abdominal aortic aneurysm with comorbidities. Our study provides insight into the shared genetic mechanism between abdominal aortic aneurysm and cardiometabolic traits, and identifies potential targets for pharmacological intervention.
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Affiliation(s)
- Shufen Zheng
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Guangzhou, China
- Center for Evolutionary Biology, Intelligent Medicine Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Philip S Tsao
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA.
- Stanford Cardiovascular Institute, Stanford University, California, USA.
- VA Palo Alto Health Care System, Palo Alto, California, USA.
| | - Cuiping Pan
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Guangzhou, China.
- Center for Evolutionary Biology, Intelligent Medicine Institute, School of Life Sciences, Fudan University, Shanghai, China.
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Chen Y, Liu P, Yi S, Fan C, Zhao W, Liu J. Investigating the shared genetic architecture between attention-deficit/hyperactivity disorder and risk taking behavior: A large-scale genomewide cross-trait analysis. J Affect Disord 2024; 356:22-31. [PMID: 38565336 DOI: 10.1016/j.jad.2024.03.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND This study aims to explore the genetic architecture shared between Attention-Deficit/Hyperactivity Disorder (ADHD) and risk behavior. METHODS Based on the latest large-scale Genome-wide association studies (GWAS), we firstly employed Linkage disequilibrium score regression (LDSC) and Local Analysis of Variant Association (LAVA) to investigate the genetic correlation between risk behavior and ADHD. Then, we conducted cross-trait analysis to identified the Pleiotropic loci. Finally, bidirectional Mendelian randomization analysis (MR) was applied to examine the causal relationship. RESULTS We found a significant positive genetic correlation between ADHD and risk-taking behavior (rg = 0.351, p = 6.50E-37). The cross-trait meta-analysis identified 27 significant SNPs shared between ADHD and risk behavior. The most significant locus, located near the CADM2 gene on chromosome 3, had been identified associated with this two trait (pADHD = 3.07E-05 and prisk-taking behavior = 2.47E-30). The same situation can also be observed near the FOXP2 gene on chromosome 7 (rs8180817, pmeta = 5.72E-21). We found CCDC171 gene and other genes played a significant role in ADHD and risk behavior in mRNA level. Bidirectional MR analysis found a causal relationship between them. LIMITATION The majority of our data sources were of European origin, which may limit the generalizability of our findings to other ethnic populations. CONCLUSION This article reveals in depth the shared genetic structure between ADHD and risk-taking behavior, finding a significant positive genetic correlation between ADHD and risk-taking behavior. Providing insights for the future treatment and management of these two traits.
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Affiliation(s)
- Yanjing Chen
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan Province 410011, People's Republic of China.
| | - Ping Liu
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan Province 410011, People's Republic of China.
| | - Sijie Yi
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan Province 410011, People's Republic of China
| | - Chunhua Fan
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan Province 410011, People's Republic of China
| | - Wei Zhao
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan Province 410011, People's Republic of China; Clinical Research Center for Medical Imaging in Hunan Province, Changsha, Hunan Province 410011, People's Republic of China.
| | - Jun Liu
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, Hunan Province 410011, People's Republic of China; Clinical Research Center for Medical Imaging in Hunan Province, Changsha, Hunan Province 410011, People's Republic of China.
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3
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Wiberg A, Lucey MA, Kleeman S, Kang Y, Ng M, Furniss D. Genetic Correlations between Migraine and Carpal Tunnel Syndrome. Plast Reconstr Surg 2024; 154:126e-134e. [PMID: 37606917 PMCID: PMC11195923 DOI: 10.1097/prs.0000000000010976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 08/02/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Surgical deactivation of extracranial nerve trigger sites is now well established as an effective treatment for migraine headache. Parallels have been drawn to median nerve decompression for carpal tunnel syndrome (CTS), and 2 previous studies have demonstrated an association between migraine and CTS. The authors sought to (1) substantiate these findings in a considerably larger UK cohort, and (2) investigate potential genetic associations between the 2 disorders. METHODS Nested case-control studies were conducted in the UK Biobank cohort of 401,656 individuals. Odds ratios were calculated for the association between migraine and CTS in the overall cohort and sex-stratified subsets. Genetic correlation between migraine and CTS was interrogated by linkage disequilibrium score regression, leveraging data from published genomewide association studies. Regions of genetic overlap were identified by multitrait analysis of genomewide association studies and cross-phenotype association. RESULTS Migraine and CTS show a significant epidemiologic association within UK Biobank (OR, 1.14, 95% CI, 1.04 to 1.25; P = 0.0058), which is specific to women (OR, 1.15; 95% CI, 1.04 to 1.28; P = 0.0057) and not men (OR, 1.07; 95% CI, 0.82 to 1.40; P = 0.61). Genetic analysis demonstrated a significant positive genetic correlation between the 2 disorders ( rg = 0.13; P = 0.0039), and implicated the TRIM32 locus on chromosome 9 as a region of genetic overlap. CONCLUSIONS This study replicates past reports of an epidemiologic association between CTS and migraine, albeit in women only. This association is underpinned by a genetic correlation, with shared genetic susceptibility at the TRIM32 locus. The authors' data add credibility to the notion that an element of entrapment neuropathy underlies migraine pathophysiology. CLINICAL QUESTION/LEVEL OF EVIDENCE Risk, III.
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Affiliation(s)
- Akira Wiberg
- From the Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford
- Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital
| | - Maria A. Lucey
- From the Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford
| | | | - Youngjoo Kang
- From the Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford
| | - Mike Ng
- From the Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford
| | - Dominic Furniss
- From the Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford
- Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital
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Feng X, Zan Y, Li T, Yao Y, Ning Z, Li J, Charati H, Xu W, Wan Q, Zeng D, Zeng Z, Liu Y, Shen X. Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics. Heredity (Edinb) 2024; 133:11-20. [PMID: 38822132 PMCID: PMC11222461 DOI: 10.1038/s41437-024-00688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/07/2024] [Indexed: 06/02/2024] Open
Abstract
Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations. In real data analysis, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary statistics from our GWAS and expression QTL scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis indicates that this locus is co-selected with flowering-time-related genes. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.
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Affiliation(s)
- Xiao Feng
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Guangzhou, China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yanjun Zan
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ting Li
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Guangzhou, China
| | - Yue Yao
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Guangzhou, China
| | - Zheng Ning
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jiabei Li
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Guangzhou, China
| | - Hadi Charati
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Guangzhou, China
| | - Weilin Xu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Qianhui Wan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Mathematics, University of California, Davis, CA, USA
| | - Dongyu Zeng
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Ziyi Zeng
- School of Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China.
| | - Xia Shen
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Guangzhou, China.
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Center for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, UK.
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Wang Q, Wu Y, Wang X, Zhang J, Li L, Wu J, Lu Y, Han L. Genomic correlation, shared loci, and causal relationship between insomnia and psoriasis: a large-scale genome-wide cross-trait analysis. Arch Dermatol Res 2024; 316:425. [PMID: 38904754 DOI: 10.1007/s00403-024-03178-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/08/2024] [Accepted: 06/08/2024] [Indexed: 06/22/2024]
Abstract
Psoriasis and insomnia have co-morbidities, however, their common genetic basis is still unclear. We analyzed psoriasis and insomnia with summary statistics from genome-wide association studies. We first quantified overall genetic correlations, then ascertained multiple effector loci and expression-trait associations, and lastly, we analyzed the causal effects between psoriasis and insomnia. A prevalent genetic link between psoriasis and insomnia was found, four pleiotropic loci affecting psoriasis and insomnia were identified, and 154 genes were shared, indicating a genetic link between psoriasis and insomnia. Yet, there is no causal relationship between psoriasis and insomnia by two-sample Mendelian randomization. We discovered a genetic connection between insomnia and psoriasis driven by biological pleiotropy and unrelated to causation. Cross-trait analysis indicates a common genetic basis for psoriasis and insomnia. The results of this study highlight the importance of sleep management in the pathogenesis of psoriasis.
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Affiliation(s)
- Qing Wang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Research Team of bio-molecular and system biology of Chinese medicine, Guangdong Academy of Traditional Chinese Medicine, Guangzhou, China
| | - Yuan Wu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuehua Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Junhong Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Research Team of bio-molecular and system biology of Chinese medicine, Guangdong Academy of Traditional Chinese Medicine, Guangzhou, China
| | - Li Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Research Team of bio-molecular and system biology of Chinese medicine, Guangdong Academy of Traditional Chinese Medicine, Guangzhou, China
| | - Jingjing Wu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China.
- Research Team of bio-molecular and system biology of Chinese medicine, Guangdong Academy of Traditional Chinese Medicine, Guangzhou, China.
| | - Yue Lu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China.
- Research Team of bio-molecular and system biology of Chinese medicine, Guangdong Academy of Traditional Chinese Medicine, Guangzhou, China.
| | - Ling Han
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China.
- Research Team of bio-molecular and system biology of Chinese medicine, Guangdong Academy of Traditional Chinese Medicine, Guangzhou, China.
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Suzuki Y, Ménager H, Brancotte B, Vernet R, Nerin C, Boetto C, Auvergne A, Linhard C, Torchet R, Lechat P, Troubat L, Cho MH, Bouzigon E, Aschard H, Julienne H. Trait selection strategy in multi-trait GWAS: Boosting SNP discoverability. HGG ADVANCES 2024; 5:100319. [PMID: 38872309 DOI: 10.1016/j.xhgg.2024.100319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
Since the first genome-wide association studies (GWASs), thousands of variant-trait associations have been discovered. However, comprehensively mapping the genetic determinant of complex traits through univariate testing can require prohibitive sample sizes. Multi-trait GWAS can circumvent this issue and improve statistical power by leveraging the joint genetic architecture of human phenotypes. Although many methodological hurdles of multi-trait testing have been solved, the strategy to select traits has been overlooked. In this study, we conducted multi-trait GWAS on approximately 20,000 combinations of 72 traits using an omnibus test as implemented in the Joint Analysis of Summary Statistics. We assessed which genetic features of the sets of traits analyzed were associated with an increased detection of variants compared with univariate screening. Several features of the set of traits, including the heritability, the number of traits, and the genetic correlation, drive the multi-trait test gain. Using these features jointly in predictive models captures a large fraction of the power gain of the multi-trait test (Pearson's r between the observed and predicted gain equals 0.43, p < 1.6 × 10-60). Applying an alternative multi-trait approach (Multi-Trait Analysis of GWAS), we identified similar features of interest, but with an overall 70% lower number of new associations. Finally, selecting sets based on our data-driven models systematically outperformed the common strategy of selecting clinically similar traits. This work provides a unique picture of the determinant of multi-trait GWAS statistical power and outlines practical strategies for multi-trait testing.
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Affiliation(s)
- Yuka Suzuki
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, 75015 Paris, France.
| | - Hervé Ménager
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, 75015 Paris, France
| | - Bryan Brancotte
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, 75015 Paris, France
| | - Raphaël Vernet
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Group of Genomic Epidemiology of Multifactorial Diseases, Paris, France
| | - Cyril Nerin
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, 75015 Paris, France
| | - Christophe Boetto
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, 75015 Paris, France
| | - Antoine Auvergne
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, 75015 Paris, France
| | - Christophe Linhard
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Group of Genomic Epidemiology of Multifactorial Diseases, Paris, France
| | - Rachel Torchet
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, 75015 Paris, France
| | - Pierre Lechat
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, 75015 Paris, France
| | - Lucie Troubat
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, 75015 Paris, France
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emmanuelle Bouzigon
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Group of Genomic Epidemiology of Multifactorial Diseases, Paris, France
| | - Hugues Aschard
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, 75015 Paris, France.
| | - Hanna Julienne
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, 75015 Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, 75015 Paris, France.
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Zhou P, Li L, Lin Z, Ming X, Feng Y, Hu Y, Chen X. Exploring the Shared Genetic Architecture Between Obstructive Sleep Apnea and Body Mass Index. Nat Sci Sleep 2024; 16:711-723. [PMID: 38863482 PMCID: PMC11166156 DOI: 10.2147/nss.s459136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024] Open
Abstract
Purpose The reciprocal comorbidity of obstructive sleep apnea (OSA) and body mass index (BMI) has been observed, yet the shared genetic architecture between them remains unclear. This study aimed to explore the genetic overlaps between them. Methods Summary statistics were acquired from the genome-wide association studies (GWASs) on OSA (Ncase = 41,704; Ncontrol = 335,573) and BMI (Noverall = 461,460). A comprehensive genome-wide cross-trait analysis was performed to quantify global and local genetic correlation, infer the bidirectional causal relationships, detect independent pleiotropic loci, and investigate potential comorbid genes. Results A positive significant global genetic correlation between OSA and BMI was observed (r g = 0.52, P = 2.85e-122), which was supported by three local signal. The Mendelian randomization analysis confirmed bidirectional causal associations. In the meta-analysis of cross-traits GWAS, a total of 151 single-nucleotide polymorphisms were found to be pleiotropic between OSA and BMI. Additionally, we discovered that the genetic association between OSA and BMI is concentrated in 12 brain regions. Finally, a total 134 expression-tissue pairs were observed to have a significant impact on both OSA and BMI within the specified brain regions. Conclusion Our comprehensive genome-wide cross-trait analysis indicates a shared genetic architecture between OSA and BMI, offering new perspectives on the possible mechanisms involved.
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Affiliation(s)
- Peng Zhou
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Ling Li
- Department of Nuclear Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Zehua Lin
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Xiaoping Ming
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Yiwei Feng
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Yifan Hu
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Xiong Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
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Chen Z, Gao N, Wang X, Chen X, Zeng Y, Li C, Yang X, Cai Q, Wang X. Shared genetic aetiology of respiratory diseases: a genome-wide multitraits association analysis. BMJ Open Respir Res 2024; 11:e002148. [PMID: 38834332 PMCID: PMC11163672 DOI: 10.1136/bmjresp-2023-002148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 05/10/2024] [Indexed: 06/06/2024] Open
Abstract
OBJECTIVE This study aims to explore the common genetic basis between respiratory diseases and to identify shared molecular and biological mechanisms. METHODS This genome-wide pleiotropic association study uses multiple statistical methods to systematically analyse the shared genetic basis between five respiratory diseases (asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, lung cancer and snoring) using the largest publicly available genome wide association studies summary statistics. The missions of this study are to evaluate global and local genetic correlations, to identify pleiotropic loci, to elucidate biological pathways at the multiomics level and to explore causal relationships between respiratory diseases. Data were collected from 27 November 2022 to 30 March 2023 and analysed from 14 April 2023 to 13 July 2023. MAIN OUTCOMES AND MEASURES The primary outcomes are shared genetic loci, pleiotropic genes, biological pathways and estimates of genetic correlations and causal effects. RESULTS Significant genetic correlations were found for 10 paired traits in 5 respiratory diseases. Cross-Phenotype Association identified 12 400 significant potential pleiotropic single-nucleotide polymorphism at 156 independent pleiotropic loci. In addition, multitrait colocalisation analysis identified 15 colocalised loci and a subset of colocalised traits. Gene-based analyses identified 432 potential pleiotropic genes and were further validated at the transcriptome and protein levels. Both pathway enrichment and single-cell enrichment analyses supported the role of the immune system in respiratory diseases. Additionally, five pairs of respiratory diseases have a causal relationship. CONCLUSIONS AND RELEVANCE This study reveals the common genetic basis and pleiotropic genes among respiratory diseases. It provides strong evidence for further therapeutic strategies and risk prediction for the phenomenon of respiratory disease comorbidity.
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Affiliation(s)
- Zhe Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University Department of Thoracic Surgery, Changsha, Hunan, China
| | - Ning Gao
- Department of Cardiovascular Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xuanye Wang
- Department of Oncology, Xi'an Jiaotong University Second Affiliated Hospital Department of Oncology, Xi'an, Shaanxi, China
| | - Xiangming Chen
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - YaQi Zeng
- Department of Psychiatry, Brain Hospital of Hunan Province, Changsha, Hunan, China
| | - Cong Li
- Department of Radiology, The Second Xiangya Hospital of Central South University Department of Radiology, Changsha, Hunan, China
| | - Xiahong Yang
- Department of Anesthesiology, The Second Xiangya Hospital of Central South University Department of Anesthesiology, Changsha, Hunan, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University Department of Thoracic Surgery, Changsha, Hunan, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University Department of Thoracic Surgery, Changsha, Hunan, China
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Deng Q, Song C, Lin S. An adaptive and robust method for multi-trait analysis of genome-wide association studies using summary statistics. Eur J Hum Genet 2024; 32:681-690. [PMID: 37237036 PMCID: PMC11153499 DOI: 10.1038/s41431-023-01389-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human traits or diseases in the past decade. Nevertheless, much of the heritability of many traits is still unaccounted for. Commonly used single-trait analysis methods are conservative, while multi-trait methods improve statistical power by integrating association evidence across multiple traits. In contrast to individual-level data, GWAS summary statistics are usually publicly available, and thus methods using only summary statistics have greater usage. Although many methods have been developed for joint analysis of multiple traits using summary statistics, there are many issues, including inconsistent performance, computational inefficiency, and numerical problems when considering lots of traits. To address these challenges, we propose a multi-trait adaptive Fisher method for summary statistics (MTAFS), a computationally efficient method with robust power performance. We applied MTAFS to two sets of brain imaging derived phenotypes (IDPs) from the UK Biobank, including a set of 58 Volumetric IDPs and a set of 212 Area IDPs. Through annotation analysis, the underlying genes of the SNPs identified by MTAFS were found to exhibit higher expression and are significantly enriched in brain-related tissues. Together with results from a simulation study, MTAFS shows its advantage over existing multi-trait methods, with robust performance across a range of underlying settings. It controls type 1 error well and can efficiently handle a large number of traits.
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Affiliation(s)
- Qiaolan Deng
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
- Department of Statistics, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Shili Lin
- Department of Statistics, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA.
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10
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Chen J, Hui Q, Titanji BK, So-Armah K, Freiberg M, Justice AC, Xu K, Zhu X, Gwinn M, Marconi VC, Sun YV. A multi-trait epigenome-wide association study identified DNA methylation signature of inflammation among people with HIV. RESEARCH SQUARE 2024:rs.3.rs-4419840. [PMID: 38854093 PMCID: PMC11160930 DOI: 10.21203/rs.3.rs-4419840/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inflammation underlies many conditions causing excess morbidity and mortality among people with HIV (PWH). A handful of single-trait epigenome-wide association studies (EWAS) have suggested that inflammation is associated with DNA methylation (DNAm) among PWH. Multi-trait EWAS may further improve statistical power and reveal pathways in common between different inflammatory markers. We conducted single-trait EWAS of three inflammatory markers (soluble CD14, D-dimers, and interleukin 6) in the Veteran Aging Cohort Study (n = 920). The study population was all male PWH with an average age of 51 years, and 82.3% self-reported as Black. We then applied two multi-trait EWAS methods-CPASSOC and OmniTest-to combine single-trait EWAS results. CPASSOC and OmniTest identified 189 and 157 inflammation-associated DNAm sites respectively, of which 112 overlapped. Among the identified sites, 56% were not significant in any single-trait EWAS. Top sites were mapped to inflammation-related genes including IFITM1, PARP9 and STAT1. These genes were significantly enriched in pathways such as "type I interferon signaling" and "immune response to virus". We demonstrate that multi-trait EWAS can improve the discovery of inflammation-associated DNAm sites, genes, and pathways. These DNAm sites suggest molecular mechanisms in response to inflammation associated with HIV and might hold the key to addressing persistent inflammation in PWH.
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Affiliation(s)
| | | | | | - Kaku So-Armah
- Boston University Chobanian and Avedisian School of Medicine
| | - Matthew Freiberg
- Vanderbilt University School of Medicine and Tennessee Valley Healthcare System
| | | | - Ke Xu
- Connecticut Veteran Health System
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11
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Guo Y, Liu Q, Zheng Z, Qing M, Yao T, Wang B, Zhou M, Wang D, Ke Q, Ma J, Shan Z, Chen W. Genetic association of inflammatory marker GlycA with lung function and respiratory diseases. Nat Commun 2024; 15:3751. [PMID: 38704398 PMCID: PMC11069551 DOI: 10.1038/s41467-024-47845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
Association of circulating glycoprotein acetyls (GlycA), a systemic inflammation biomarker, with lung function and respiratory diseases remain to be investigated. We examined the genetic correlation, shared genetics, and potential causality of GlycA (N = 115,078) with lung function and respiratory diseases (N = 497,000). GlycA showed significant genetic correlation with FEV1 (rg = -0.14), FVC (rg = -0.18), asthma (rg = 0.21) and COPD (rg = 0.31). We consistently identified ten shared loci (including chr3p21.31 and chr8p23.1) at both SNP and gene level revealing potential shared biological mechanisms involving ubiquitination, immune response, Wnt/β-catenin signaling, cell growth and differentiation in tissues or cells including blood, epithelium, fibroblast, fetal thymus, and fetal intestine. Genetically elevated GlycA was significantly correlated with lung function and asthma susceptibility (354.13 ml decrement of FEV1, 442.28 ml decrement of FVC, and 144% increased risk of asthma per SD increment of GlycA) from MR analyses. Our findings provide insights into biological mechanisms of GlycA in relating to lung function, asthma, and COPD.
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Affiliation(s)
- Yanjun Guo
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
- Department of Epidemiology, Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
| | - Quanhong Liu
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Zhilin Zheng
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Mengxia Qing
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Tianci Yao
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Wang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Min Zhou
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Dongming Wang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Qinmei Ke
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jixuan Ma
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Zhilei Shan
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weihong Chen
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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12
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Kerns S, Owen KA, Schwalbe D, Grammer AC, Lipsky PE. Examination of the shared genetic architecture between multiple sclerosis and systemic lupus erythematosus facilitates discovery of novel lupus risk loci. Hum Genet 2024; 143:703-719. [PMID: 38609570 DOI: 10.1007/s00439-024-02672-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease with heterogeneous manifestations, including neurological and psychiatric symptoms. Genetic association studies in SLE have been hampered by insufficient sample size and limited power compared to many other diseases. Multiple Sclerosis (MS) is a chronic relapsing autoimmune disease of the central nervous system (CNS) that also manifests neurological and immunological features. Here, we identify a method of leveraging large-scale genome wide association studies (GWAS) in MS to identify novel genetic risk loci in SLE. Statistical genetic comparison methods including linkage disequilibrium score regression (LDSC) and cross-phenotype association analysis (CPASSOC) to identify genetic overlap in disease pathophysiology, traditional 2-sample and novel PPI-based mendelian randomization to identify causal associations and Bayesian colocalization were applied to association studies conducted in MS to facilitate discovery in the smaller, more limited datasets available for SLE. Pathway analysis using SNP-to-gene mapping identified biological networks composed of molecular pathways with causal implications for CNS disease in SLE specifically, as well as pathways likely causal of both pathologies, providing key insights for therapeutic selection.
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Affiliation(s)
- Sophia Kerns
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA.
- The RILITE Research Institute, Charlottesville, VA, 22902, USA.
| | - Katherine A Owen
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Dana Schwalbe
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Amrie C Grammer
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
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13
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Wu X, Yang C, Zou Y, Jones SE, Zhao X, Zhang L, Han Z, Hao Y, Xiao J, Xiao C, Zhang W, Yan P, Cui H, Tang M, Wang Y, Chen L, Zhang L, Yao Y, Liu Z, Li J, Jiang X, Zhang B. Using human genetics to understand the phenotypic association between chronotype and breast cancer. J Sleep Res 2024; 33:e13973. [PMID: 37380357 DOI: 10.1111/jsr.13973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/23/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023]
Abstract
Little is known regarding the shared genetic influences underlying the observed phenotypic association between chronotype and breast cancer in women. Leveraging summary statistics from the hitherto largest genome-wide association study conducted in each trait, we investigated the genetic correlation, pleiotropic loci, and causal relationship of chronotype with overall breast cancer, and with its subtypes defined by the status of oestrogen receptor. We identified a negative genomic correlation between chronotype and overall breast cancer (r g = -0.06, p = 3.00 × 10-4), consistent across oestrogen receptor-positive (r g = -0.05, p = 3.30 × 10-3) and oestrogen receptor-negative subtypes (r g = -0.05, p = 1.11 × 10-2). Five specific genomic regions were further identified as contributing a significant local genetic correlation. Cross-trait meta-analysis identified 78 loci shared between chronotype and breast cancer, of which 23 were novel. Transcriptome-wide association study revealed 13 shared genes, targeting tissues of the nervous, cardiovascular, digestive, and exocrine/endocrine systems. Mendelian randomisation demonstrated a significantly reduced risk of overall breast cancer (odds ratio 0.89, 95% confidence interval 0.83-0.94; p = 1.30 × 10-4) for genetically predicted morning chronotype. No reverse causality was found. Our work demonstrates an intrinsic link underlying chronotype and breast cancer, which may provide clues to inform management of sleep habits to improve female health.
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Affiliation(s)
- Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southwest Medical University, Luzhou, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Samuel E Jones
- Institute for Molecular Medicine, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Xunying Zhao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhitong Han
- School of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Hao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jinyu Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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14
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Wu X, Xiao C, Rasooly D, Zhao X, Morton CC, Jiang X, Gallagher CS. A comprehensive genome-wide cross-trait analysis of sexual factors and uterine leiomyoma. PLoS Genet 2024; 20:e1011268. [PMID: 38701081 PMCID: PMC11095738 DOI: 10.1371/journal.pgen.1011268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/15/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Age at first sexual intercourse (AFS) and lifetime number of sexual partners (NSP) may influence the pathogenesis of uterine leiomyoma (UL) through their associations with hormonal concentrations and uterine infections. Leveraging summary statistics from large-scale genome-wide association studies conducted in European ancestry for each trait (NAFS = 214,547; NNSP = 370,711; NUL = 302,979), we observed a significant negative genomic correlation for UL with AFS (rg = -0.11, P = 7.83×10-4), but not with NSP (rg = 0.01, P = 0.62). Four specific genomic regions were identified as contributing significant local genetic correlations to AFS and UL, including one genomic region further identified for NSP and UL. Partitioning SNP-heritability with cell-type-specific annotations, a close clustering of UL with both AFS and NSP was identified in immune and blood-related components. Cross-trait meta-analysis revealed 15 loci shared between AFS/NSP and UL, including 7 novel SNPs. Univariable two-sample Mendelian randomization (MR) analysis suggested no evidence for a causal association between genetically predicted AFS/NSP and risk of UL, nor vice versa. Multivariable MR adjusting for age at menarche or/and age at natural menopause revealed a significant causal effect of genetically predicted higher AFS on a lower risk of UL. Such effect attenuated to null when age at first birth was further included. Utilizing participant-level data from the UK Biobank, one-sample MR based on genetic risk scores yielded consistent null findings among both pre-menopausal and post-menopausal females. From a genetic perspective, our study demonstrates an intrinsic link underlying sexual factors (AFS and NSP) and UL, highlighting shared biological mechanisms rather than direct causal effects. Future studies are needed to elucidate the specific mechanisms involved in the shared genetic influences and their potential impact on UL development.
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Affiliation(s)
- Xueyao Wu
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- National Cancer Institute, Rockville, Maryland, United States of America
| | - Changfeng Xiao
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Danielle Rasooly
- Division of Aging, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xunying Zhao
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cynthia Casson Morton
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Manchester Centre for Audiology and Deafness, Manchester Academic Health Science Center, University of Manchester, Manchester, United Kingdom
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - C. Scott Gallagher
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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15
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Xu Z, Wei P. A novel statistical framework for meta-analysis of total mediation effect with high-dimensional omics mediators in large-scale genomic consortia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591700. [PMID: 38746374 PMCID: PMC11092451 DOI: 10.1101/2024.04.29.591700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Meta-analysis is used to aggregate the effects of interest across multiple studies, while its methodology is largely underexplored in mediation analysis, particularly in estimating the total mediation effect of high-dimensional omics mediators. Large-scale genomic consortia, such as the Trans-Omics for Precision Medicine (TOPMed) program, comprise multiple cohorts with diverse technologies to elucidate the genetic architecture and biological mechanisms underlying complex human traits and diseases. Leveraging the recent established asymptotic standard error of the R-squared R 2 -based mediation effect estimation for high-dimensional omics mediators, we have developed a novel meta-analysis framework requiring only summary statistics and allowing inter-study heterogeneity. Whereas the proposed meta-analysis can uniquely evaluate and account for potential effect heterogeneity across studies due to, for example, varying genomic profiling platforms, our extensive simulations showed that the developed method was more computationally efficient and yielded satisfactory operating characteristics comparable to analysis of the pooled individual-level data when there was no inter-study heterogeneity. We applied the developed method to 8 TOPMed studies with over 5800 participants to estimate the mediation effects of gene expression on age-related variation in systolic blood pressure and sex-related variation in high-density lipoprotein (HDL) cholesterol. The proposed method is available in R package MetaR2M on GitHub.
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Affiliation(s)
- Zhichao Xu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center
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16
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Ma J, Liu D, Zhao J, Fang X, Bu D. Unraveling the immunogenetic landscape of autism spectrum disorder: a comprehensive bioinformatics approach. Front Immunol 2024; 15:1347139. [PMID: 38726016 PMCID: PMC11080648 DOI: 10.3389/fimmu.2024.1347139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/05/2024] [Indexed: 05/12/2024] Open
Abstract
Background Autism spectrum disorder (ASD) is a disease characterized by social disorder. Recently, the population affected by ASD has gradually increased around the world. There are great difficulties in diagnosis and treatment at present. Methods The ASD datasets were obtained from the Gene Expression Omnibus database and the immune-relevant genes were downloaded from a previously published compilation. Subsequently, we used WGCNA to screen the modules related to the ASD and immune. We also choose the best combination and screen out the core genes from Consensus Machine Learning Driven Signatures (CMLS). Subsequently, we evaluated the genetic correlation between immune cells and ASD used GNOVA. And pleiotropic regions identified by PLACO and CPASSOC between ASD and immune cells. FUMA was used to identify pleiotropic regions, and expression trait loci (EQTL) analysis was used to determine their expression in different tissues and cells. Finally, we use qPCR to detect the gene expression level of the core gene. Results We found a close relationship between neutrophils and ASD, and subsequently, CMLS identified a total of 47 potential candidate genes. Secondly, GNOVA showed a significant genetic correlation between neutrophils and ASD, and PLACO and CPASSOC identified a total of 14 pleiotropic regions. We annotated the 14 regions mentioned above and identified a total of 6 potential candidate genes. Through EQTL, we found that the CFLAR gene has a specific expression pattern in neutrophils, suggesting that it may serve as a potential biomarker for ASD and is closely related to its pathogenesis. Conclusions In conclusion, our study yields unprecedented insights into the molecular and genetic heterogeneity of ASD through a comprehensive bioinformatics analysis. These valuable findings hold significant implications for tailoring personalized ASD therapies.
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Affiliation(s)
- Jieying Ma
- Department of Psychiatric Medicine, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, China
| | - Deyang Liu
- Department of Rehabilitation Medicine, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Jianzhong Zhao
- Department of Clinical Laboratory, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Xiaolu Fang
- Department of Clinical Laboratory, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Dengyin Bu
- Department of Psychiatric Medicine, Xiangyang Central Hospital, Hubei University of Arts and Science, Xiangyang, China
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17
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Lorincz-Comi N, Yang Y, Li G, Zhu X. MRBEE: A bias-corrected multivariable Mendelian randomization method. HGG ADVANCES 2024; 5:100290. [PMID: 38582968 PMCID: PMC11053334 DOI: 10.1016/j.xhgg.2024.100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024] Open
Abstract
Mendelian randomization (MR) is an instrumental variable approach used to infer causal relationships between exposures and outcomes, which is becoming increasingly popular because of its ability to handle summary statistics from genome-wide association studies. However, existing MR approaches often suffer the bias from weak instrumental variables, horizontal pleiotropy and sample overlap. We introduce MRBEE (MR using bias-corrected estimating equation), a multivariable MR method capable of simultaneously removing weak instrument and sample overlap bias and identifying horizontal pleiotropy. Our extensive simulations and real data analyses reveal that MRBEE provides nearly unbiased estimates of causal effects, well-controlled type I error rates and higher power than comparably robust methods and is computationally efficient. Our real data analyses result in consistent causal effect estimates and offer valuable guidance for conducting multivariable MR studies, elucidating the roles of pleiotropy, and identifying total 42 horizontal pleiotropic loci missed previously that are associated with myopia, schizophrenia, and coronary artery disease.
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Affiliation(s)
- Noah Lorincz-Comi
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yihe Yang
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Gen Li
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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18
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Zhang W, Zhu J, Wu X, Feng T, Liao W, Li X, Chen J, Zhang L, Xiao C, Cui H, Yang C, Yan P, Wang Y, Tang M, Chen L, Liu Y, Zou Y, Wu X, Zhang L, Yang C, Yao Y, Li J, Liu Z, Jiang X, Zhang B. Phenotypic and genetic effect of carotid intima-media thickness on the risk of stroke. Hum Genet 2024:10.1007/s00439-024-02666-1. [PMID: 38578439 DOI: 10.1007/s00439-024-02666-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
While carotid intima-media thickness (cIMT) as a noninvasive surrogate measure of atherosclerosis is widely considered a risk factor for stroke, the intrinsic link underlying cIMT and stroke has not been fully understood. We aimed to evaluate the clinical value of cIMT in stroke through the investigation of phenotypic and genetic relationships between cIMT and stroke. We evaluated phenotypic associations using observational data from UK Biobank (N = 21,526). We then investigated genetic relationships leveraging genomic data conducted in predominantly European ancestry for cIMT (N = 45,185) and any stroke (AS, Ncase/Ncontrol=40,585/406,111). Observational analyses suggested an increased hazard of stroke per one standard deviation increase in cIMT (cIMTmax-AS: hazard ratio (HR) = 1.39, 95%CI = 1.09-1.79; cIMTmean-AS: HR = 1.39, 95%CI = 1.09-1.78; cIMTmin-AS: HR = 1.32, 95%CI = 1.04-1.68). A positive global genetic correlation was observed (cIMTmax-AS: [Formula: see text]=0.23, P=9.44 × 10-5; cIMTmean-AS: [Formula: see text]=0.21, P=3.00 × 10-4; cIMTmin-AS: [Formula: see text]=0.16, P=6.30 × 10-3). This was further substantiated by five shared independent loci and 15 shared expression-trait associations. Mendelian randomization analyses suggested no causal effect of cIMT on stroke (cIMTmax-AS: odds ratio (OR)=1.12, 95%CI=0.97-1.28; cIMTmean-AS: OR=1.09, 95%CI=0.93-1.26; cIMTmin-AS: OR=1.03, 95%CI = 0.90-1.17). A putative association was observed for genetically predicted stroke on cIMT (AS-cIMTmax: beta=0.07, 95%CI = 0.01-0.13; AS-cIMTmean: beta=0.08, 95%CI = 0.01-0.15; AS-cIMTmin: beta = 0.08, 95%CI = 0.01-0.16) in the reverse direction MR, which attenuated to non-significant in sensitivity analysis. Our work does not find evidence supporting causal associations between cIMT and stroke. The pronounced cIMT-stroke association is intrinsic, and mostly attributed to shared genetic components. The clinical value of cIMT as a surrogate marker for stroke risk in the general population is likely limited.
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Affiliation(s)
- Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Jingwei Zhu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Xuan Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Tianle Feng
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Wei Liao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Xuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Jianci Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Chenghan Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Ling Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yuqin Yao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Zhenmi Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China.
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
- Department of Clinical Neuroscience, Karolinskaa Institutet, Stockholm, Sweden.
| | - Ben Zhang
- Hainan General Hospital and Hainan Affiliated Hospital, Hainan Medical University, Haikou, China; West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
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Xiao C, Wu X, Gallagher CS, Rasooly D, Jiang X, Morton CC. Genetic contribution of reproductive traits to risk of uterine leiomyomata: a large-scale, genome-wide, cross-trait analysis. Am J Obstet Gynecol 2024; 230:438.e1-438.e15. [PMID: 38191017 DOI: 10.1016/j.ajog.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/03/2023] [Accepted: 12/26/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Although phenotypic associations between female reproductive characteristics and uterine leiomyomata have long been observed in epidemiologic investigations, the shared genetic architecture underlying these complex phenotypes remains unclear. OBJECTIVE We aimed to investigate the shared genetic basis, pleiotropic effects, and potential causal relationships underlying reproductive traits (age at menarche, age at natural menopause, and age at first birth) and uterine leiomyomata. STUDY DESIGN With the use of large-scale, genome-wide association studies conducted among women of European ancestry for age at menarche (n=329,345), age at natural menopause (n=201,323), age at first birth (n=418,758), and uterine leiomyomata (ncases/ncontrols=35,474/267,505), we performed a comprehensive, genome-wide, cross-trait analysis to examine systematically the common genetic influences between reproductive traits and uterine leiomyomata. RESULTS Significant global genetic correlations were identified between uterine leiomyomata and age at menarche (rg, -0.17; P=3.65×10-10), age at natural menopause (rg, 0.23; P=3.26×10-07), and age at first birth (rg, -0.16; P=1.96×10-06). Thirteen genomic regions were further revealed as contributing significant local correlations (P<.05/2353) to age at natural menopause and uterine leiomyomata. A cross-trait meta-analysis identified 23 shared loci, 3 of which were novel. A transcriptome-wide association study found 15 shared genes that target tissues of the digestive, exo- or endocrine, nervous, and cardiovascular systems. Mendelian randomization suggested causal relationships between a genetically predicted older age at menarche (odds ratio, 0.88; 95% confidence interval, 0.85-0.92; P=1.50×10-10) or older age at first birth (odds ratio, 0.95; 95% confidence interval, 0.90-0.99; P=.02) and a reduced risk for uterine leiomyomata and between a genetically predicted older age at natural menopause and an increased risk for uterine leiomyomata (odds ratio, 1.08; 95% confidence interval, 1.06-1.09; P=2.30×10-27). No causal association in the reverse direction was found. CONCLUSION Our work highlights that there are substantial shared genetic influences and putative causal links that underlie reproductive traits and uterine leiomyomata. The findings suggest that early identification of female reproductive risk factors may facilitate the initiation of strategies to modify potential uterine leiomyomata risk.
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Affiliation(s)
- Changfeng Xiao
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Danielle Rasooly
- Division of Aging, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China; Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Stockholm, Sweden.
| | - Cynthia Casson Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Manchester Centre for Audiology and Deafness, Manchester Academic Health Science Center, University of Manchester, Manchester, United Kingdom.
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Chen Y, Liu P, Zhang Z, Ye Y, Yi S, Fan C, Zhao W, Liu J. Genetic overlap and causality between COVID-19 and multi-site chronic pain: the importance of immunity. Front Immunol 2024; 15:1277720. [PMID: 38633255 PMCID: PMC11022998 DOI: 10.3389/fimmu.2024.1277720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/13/2024] [Indexed: 04/19/2024] Open
Abstract
Background The existence of chronic pain increases susceptibility to virus and is now widely acknowledged as a prominent feature recognized as a major manifestation of long-term coronavirus disease 2019 (COVID-19) infection. Given the ongoing COVID-19 pandemic, it is imperative to explore the genetic associations between chronic pain and predisposition to COVID-19. Methods We conducted genetic analysis at the single nucleotide polymorphism (SNP), gene, and molecular levels using summary statistics of genome-wide association study (GWAS) and analyzed the drug targets by summary data-based Mendelian randomization analysis (SMR) to alleviate the multi-site chronic pain in COVID-19. Additionally, we performed a latent causal variable (LCV) method to investigate the causal relationship between chronic pain and susceptibility to COVID-19. Results The cross-trait meta-analysis identified 19 significant SNPs shared between COVID-19 and chronic pain. Coloc analysis indicated that the posterior probability of association (PPH4) for three loci was above 70% in both critical COVID-19 and COVID-19, with the corresponding top three SNPs being rs13135092, rs7588831, and rs13135092. A total of 482 significant overlapped genes were detected from MAGMA and CPASSOC results. Additionally, the gene ANAPC4 was identified as a potential drug target for treating chronic pain (P=7.66E-05) in COVID-19 (P=8.23E-03). Tissue enrichment analysis highlighted that the amygdala (P=7.81E-04) and prefrontal cortex (P=8.19E-05) as pivotal in regulating chronic pain of critical COVID-19. KEGG pathway enrichment further revealed the enrichment of pleiotropic genes in both COVID-19 (P=3.20E-03,Padjust=4.77E-02,hsa05171) and neurotrophic pathways (P=9.03E-04,Padjust =2.55E-02,hsa04621). Finally, the latent causal variable (LCV) model was applied to find the genetic component of critical COVID-19 was causal for multi-site chronic pain (P=0.015), with a genetic causality proportion (GCP) of was 0.60. Conclusions In this study, we identified several functional genes and underscored the pivotal role of the inflammatory system in the correlation between the paired traits. Notably, heat shock proteins emerged as potential objective biomarkers for chronic pain symptoms in individuals with COVID-19. Additionally, the ubiquitin system might play a role in mediating the impact of COVID-19 on chronic pain. These findings contribute to a more comprehensive understanding of the pleiotropy between COVID-19 and chronic pain, offering insights for therapeutic trials.
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Affiliation(s)
- Yanjing Chen
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Ping Liu
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhiyi Zhang
- Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yingling Ye
- Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Sijie Yi
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Chunhua Fan
- Department of Radiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhao
- Clinical Research Center for Medical Imaging in Hunan Province, Changsha, Hunan, China
| | - Jun Liu
- Clinical Research Center for Medical Imaging in Hunan Province, Changsha, Hunan, China
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Wu Y, Huang M, Chen X, Wu J, Li L, Wei J, Lu C, Han L, Lu Y. A genome-wide cross-trait analysis identifies shared loci and causal relationships of obesity and lipidemic traits with psoriasis. Front Immunol 2024; 15:1328297. [PMID: 38550599 PMCID: PMC10972863 DOI: 10.3389/fimmu.2024.1328297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 04/02/2024] Open
Abstract
Background Obesity and dyslipidemia, major global health concerns, have been linked to psoriasis, but previous studies faced methodological limitations and their shared genetic basis remains unclear. This study examines various obesity-related and lipidemic traits as potential contributors to psoriasis development, aiming to clarify their genetic associations and potential causal links. Methods Summary statistics from genome-wide association studies (GWAS) conducted for obesity-related traits (body mass index (BMI), waist-to-hip ratio (WHR), and waist-to-hip ratio adjusted for the body mass index (WHRadjBMI)) and lipidemic traits (high-density lipoprotein (HDL), LDL, triglyceride (TG), total Cholesterol (TC), apolipoprotein A1 (apoA1), apolipoprotein B (apoB), and apolipoprotein E (apoE)) and psoriasis, all in populations of European ancestry, were used. We quantified genetic correlations, identified shared loci and explored causal relationship across traits. Results We found positive genetic correlation between BMI and psoriasis (rg=0.22, p=2.44×10-18), and between WHR and psoriasis (rg=0.19, p=1.41×10-12). We further found the positive genetic correlation between psoriasis and WHRadjBMI(rg=0.07, p=1.81×10-2) the genetic correlation, in while the effect of BMI was controlled for. We identified 14 shared loci underlying psoriasis and obesity-related traits and 43 shared loci between psoriasis and lipidemic traits via cross-trait meta-analysis. Mendelian randomization (MR) supported the causal roles of BMI (IVW OR=1.483, 95%CI=1.333-1.649), WHR (IVW OR=1.393, 95%CI=1.207-1.608) and WHRadjBMI (IVW OR=1.18, 95%CI=1.047-1.329) in psoriasis, but not observe any significant association between lipidemic traits and the risk of psoriasis. Genetic predisposition to psoriasis did not appear to affect the risk of obesity and lipidemic traits. Conclusions An intrinsic link between obesity-related traits and psoriasis has been demonstrated. The genetic correlation and causal role of obesity-related traits in psoriasis highlight the significance of weight management in both the prevention and treatment of this condition.
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Affiliation(s)
- Yuan Wu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mengfen Huang
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xueru Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jingjing Wu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianan Wei
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chuanjian Lu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ling Han
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yue Lu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Zhang M, Bai Y, Wang Y, Cui H, Zhang W, Zhang L, Yan P, Tang M, Liu Y, Jiang X, Zhang B. Independent association of general and central adiposity with risk of gallstone disease: observational and genetic analyses. Front Endocrinol (Lausanne) 2024; 15:1367229. [PMID: 38529389 PMCID: PMC10961427 DOI: 10.3389/fendo.2024.1367229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Background General obesity is a well-established risk factor for gallstone disease (GSD), but whether central obesity contributes additional independent risk remains controversial. We aimed to comprehensively clarify the effect of body fat distribution on GSD. Methods We first investigated the observational association of central adiposity, characterized by waist-to-hip ratio (WHR), with GSD risk using data from UK Biobank (N=472,050). We then explored the genetic relationship using summary statistics from the largest genome-wide association study of GSD (ncase=43,639, ncontrol=506,798) as well as WHR, with and without adjusting for body mass index (BMI) (WHR: n=697,734; WHRadjBMI: n=694,649). Results Observational analysis demonstrated an increased risk of GSD with one unit increase in WHR (HR=1.18, 95%CI=1.14-1.21). A positive WHR-GSD genetic correlation (r g =0.41, P=1.42×10-52) was observed, driven by yet independent of BMI (WHRadjBMI: r g =0.19, P=6.89×10-16). Cross-trait meta-analysis identified four novel pleiotropic loci underlying WHR and GSD with biological mechanisms outside of BMI. Mendelian randomization confirmed a robust WHR-GSD causal relationship (OR=1.50, 95%CI=1.35-1.65) which attenuated yet remained significant after adjusting for BMI (OR=1.17, 95%CI=1.09-1.26). Furthermore, observational analysis confirmed a positive association between general obesity and GSD, corroborated by a shared genetic basis (r g =0.40, P=2.16×10-43), multiple novel pleiotropic loci (N=11) and a causal relationship (OR=1.67, 95%CI=1.56-1.78). Conclusion Both observational and genetic analyses consistently provide evidence on an association of central obesity with an increased risk of GSD, independent of general obesity. Our work highlights the need of considering both general and central obesity in the clinical management of GSD.
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Affiliation(s)
- Min Zhang
- Clinical and Public Health Research Center, Chongqing Research Center for Prevention & Control of Maternal and Child Diseases and Public Health, Chongqing Health Center for Women and Children, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Ye Bai
- Gene Diagnosis Center, the First Affiliated Hospital of Jilin University, Jilin, China
| | - Yutong Wang
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huijie Cui
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenqiang Zhang
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Zhang
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peijing Yan
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingshuang Tang
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunjie Liu
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xia Jiang
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ben Zhang
- Department of Epidemiology and Health Statistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
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Wu KCH, Liu L, Xu A, Chan YH, Cheung BMY. Shared genetic architecture between periodontal disease and type 2 diabetes: a large scale genome-wide cross-trait analysis. Endocrine 2024:10.1007/s12020-024-03766-8. [PMID: 38460073 DOI: 10.1007/s12020-024-03766-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
PURPOSE To investigate the relationship between abnormal glucose metabolism, type 2 diabetes (T2D), and periodontal disease (PER) independent of Body Mass Index (BMI), we employed a genome-wide cross-trait approach to clarify the association. METHODS Our study utilized the most extensive genome-wide association studies conducted for populations of European ancestry, including PER, T2D, fasting glucose, fasting insulin, 2-hour glucose after an oral glucose challenge, HOMA-β, HOMA-IR (unadjusted or adjusted for BMI) and HbA1c. RESULTS With this approach, we were able to identify pleiotropic loci, establish expression-trait associations, and quantify global and local genetic correlations. There was a significant positive global genetic correlation between T2D (rg = 0.261, p = 2.65 × 10-13), HbA1c (rg = 0.182, p = 4.14 × 10-6) and PER, as well as for T2D independent of BMI (rg = 0.158, p = 2.34 × 10-6). A significant local genetic correlation was also observed between PER and glycemic traits or T2D. We also identified 62 independent pleiotropic loci that impact both PER and glycemic traits, including T2D. Nine significant pathways were identified between the shared genes between T2D, glycemic traits and PER. Genetically liability of HOMA-βadjBMI was causally associated with the risk of PER. CONCLUSION Our research has revealed a genetic link between T2D, glycemic traits, and PER that is influenced by biological pleiotropy. Notably, some of these links are not related to BMI. Our research highlights an underlying link between patients with T2D and PER, regardless of their BMI.
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Affiliation(s)
- Kevin Chun Hei Wu
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Lin Liu
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Aimin Xu
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yap Hang Chan
- Division of Cardiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Bernard Man Yung Cheung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Institute of Cardiovascular Science and Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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Tang M, Wu X, Zhang W, Cui H, Zhang L, Yan P, Yang C, Wang Y, Chen L, Xiao C, Liu Y, Zou Y, Yang C, Zhang L, Yao Y, Liu Z, Li J, Jiang X, Zhang B. Epidemiological and Genetic Analyses of Schizophrenia and Breast Cancer. Schizophr Bull 2024; 50:317-326. [PMID: 37467357 PMCID: PMC10919785 DOI: 10.1093/schbul/sbad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
BACKGROUND AND HYPOTHESIS While the phenotypic association between schizophrenia and breast cancer has been observed, the underlying intrinsic link is not adequately understood. We aim to conduct a comprehensive interrogation on both phenotypic and genetic relationships between schizophrenia and breast cancer. STUDY DESIGN We first used data from UK Biobank to evaluate a phenotypic association and performed an updated meta-analysis incorporating existing cohort studies. We then leveraged genomic data to explore the shared genetic architecture through a genome-wide cross-trait design. STUDY RESULTS Incorporating results of our observational analysis, meta-analysis of cohort studies suggested a significantly increased incidence of breast cancer among women with schizophrenia (RR = 1.30, 95% CIs = 1.14-1.48). A positive genomic correlation between schizophrenia and overall breast cancer was observed (rg = 0.12, P = 1.80 × 10-10), consistent across ER+ (rg = 0.10, P = 5.74 × 10-7) and ER- subtypes (rg = 0.09, P = .003). This was further corroborated by four local signals. Cross-trait meta-analysis identified 23 pleiotropic loci between schizophrenia and breast cancer, including five novel loci. Gene-based analysis revealed 27 shared genes. Mendelian randomization demonstrated a significantly increased risk of overall breast cancer (OR = 1.07, P = 4.81 × 10-10) for genetically predisposed schizophrenia, which remained robust in subgroup analysis (ER+: OR = 1.10, P = 7.26 × 10-12; ER-: OR = 1.08, P = 3.50 × 10-6). No mediation effect and reverse causality was found. CONCLUSIONS Our study demonstrates an intrinsic link underlying schizophrenia and breast cancer, which may inform tailored screening and management of breast cancer in schizophrenia.
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Affiliation(s)
- Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, College of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Liu L, Yan R, Guo P, Ji J, Gong W, Xue F, Yuan Z, Zhou X. Conditional transcriptome-wide association study for fine-mapping candidate causal genes. Nat Genet 2024; 56:348-356. [PMID: 38279040 DOI: 10.1038/s41588-023-01645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 12/08/2023] [Indexed: 01/28/2024]
Abstract
Transcriptome-wide association studies (TWASs) aim to integrate genome-wide association studies with expression-mapping studies to identify genes with genetically predicted expression (GReX) associated with a complex trait. In the present report, we develop a method, GIFT (gene-based integrative fine-mapping through conditional TWAS), that performs conditional TWAS analysis by explicitly controlling for GReX of all other genes residing in a local region to fine-map putatively causal genes. GIFT is frequentist in nature, explicitly models both expression correlation and cis-single nucleotide polymorphism linkage disequilibrium across multiple genes and uses a likelihood framework to account for expression prediction uncertainty. As a result, GIFT produces calibrated P values and is effective for fine-mapping. We apply GIFT to analyze six traits in the UK Biobank, where GIFT narrows down the set size of putatively causal genes by 32.16-91.32% compared with existing TWAS fine-mapping approaches. The genes identified by GIFT highlight the importance of vessel regulation in determining blood pressures and lipid metabolism for regulating lipid levels.
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Affiliation(s)
- Lu Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ran Yan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ping Guo
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiadong Ji
- Institute for Financial Studies, Shandong University, Jinan, China
| | - Weiming Gong
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.
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26
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Yan P, Zhang L, Yang C, Zhang W, Wang Y, Zhang M, Cui H, Tang M, Chen L, Wu X, Zhao X, Zou Y, Xiao J, Liu Y, Xiao C, Yang Y, Zhang L, Yao Y, Li J, Liu Z, Yang C, Jiang X, Zhang B. Observational and genetic analyses clarify the relationship between type 2 diabetes mellitus and gallstone disease. Front Endocrinol (Lausanne) 2024; 14:1337071. [PMID: 38356679 PMCID: PMC10864641 DOI: 10.3389/fendo.2023.1337071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024] Open
Abstract
Background The relationship between type 2 diabetes mellitus (T2DM) and gallstone disease (GSD) have been incompletely understood. We aimed to investigate their phenotypic and genetic associations and evaluate the biological mechanisms underlying these associations. Methods We first evaluated the phenotypic association between T2DM and GSD using data from the UK Biobank (n>450,000) using a prospective observational design. We then conducted genetic analyses using summary statistics from a meta-analysis of genome-wide association studies of T2DM, with and without adjusting for body mass index (BMI) (Ncase=74,124, Ncontrol=824,006; T2DMadjBMI: Ncase=50,409, Ncontrol=523,897) and GSD (Ncase=43,639, Ncontrol=506,798). Results A unidirectional phenotypic association was observed, where individuals with T2DM exhibited a higher GSD risk (hazard ratio (HR)=1.39, P<0.001), but not in the reverse direction (GSD→T2DM: HR=1.00, P=0.912). The positive T2DM-GSD genetic correlation (rg=0.35, P=7.71×10-23) remained even after adjusting for BMI (T2DMadjBMI: rg=0.22, P=4.48×10-10). Mendelian randomization analyses provided evidence of a unidirectional causal relationship (T2DM→GSD: odds ratio (OR)=1.08, P=4.6×10-8; GSD→T2DM: OR=1.02, P=0.48), even after adjusting for important metabolic confounders (OR=1.02, P=0.02). This association was further corroborated through a comprehensive functional analysis reflected by 23 pleiotropic single nucleotide polymorphisms, as well as multiple neural and motor-enriched tissues. Conclusion Through comprehensive observational and genetic analyses, our study clarified the causal relationship between T2DM and GSD, but not in the reverse direction. These findings might provide new insights into prevention and treatment strategies for T2DM and GSD.
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Affiliation(s)
- Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- School of Public Health, Southwest Medical University, Luzhou, Sichuan, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Min Zhang
- Clinical Research Center, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xunying Zhao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinyu Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yanfang Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Chen D, Zhou Y, Zhang Y, Zeng H, Wu L, Liu Y. Unraveling shared susceptibility loci and Mendelian genetic associations linking educational attainment with multiple neuropsychiatric disorders. Front Psychiatry 2024; 14:1303430. [PMID: 38250258 PMCID: PMC10797721 DOI: 10.3389/fpsyt.2023.1303430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Background Empirical studies have demonstrated that educational attainment (EA) is associated with neuropsychiatric disorders (NPDs), suggesting a shared etiological basis between them. However, little is known about the shared genetic mechanisms and causality behind such associations. Methods This study explored the shared genetic basis and causal relationships between EA and NPDs using the high-definition likelihood (HDL) method, cross phenotype association study (CPASSOC), transcriptome-wide association study (TWAS), and bidirectional Mendelian randomization (MR) with summary-level data for EA (N = 293,723) and NPDs (N range = 9,725 to 455,258). Results Significant genetic correlations between EA and 12 NPDs (rg range - 0.49 to 0.35; all p < 3.85 × 10-3) were observed. CPASSOC identified 37 independent loci shared between EA and NPDs, one of which was novel (rs71351952, mapped gene: ARFGEF2). Functional analyses and TWAS found shared genes were enriched in brain tissue, especially in the cerebellum and highlighted the regulatory role of neuronal signaling, purine nucleotide metabolic process, and cAMP-mediated signaling pathways. CPASSOC and TWAS supported the role of three regions of 6q16.1, 3p21.31, and 17q21.31 might account for the shared causes between EA and NPDs. MR confirmed higher genetically predicted EA lower the risk of ADHD (ORIVW: 0.50; 95% CI: 0.39 to 0.63) and genetically predicted ADHD decreased the risk of EA (Causal effect: -2.8 months; 95% CI: -3.9 to -1.8). Conclusion These findings provided evidence of shared genetics and causation between EA and NPDs, advanced our understanding of EA, and implicated potential biological pathways that might underlie both EA and NPDs.
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Affiliation(s)
- Dongze Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yi Zhou
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Yali Zhang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Huatang Zeng
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Liqun Wu
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Yuyang Liu
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
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28
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Buchardt AS, Zhou X, Ekstrøm CT. Joint regression analysis of multiple traits based on genetic relationships. BIOINFORMATICS ADVANCES 2024; 4:vbad192. [PMID: 38264461 PMCID: PMC10805347 DOI: 10.1093/bioadv/vbad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 12/11/2023] [Accepted: 12/31/2023] [Indexed: 01/25/2024]
Abstract
Motivation Polygenic scores (PGSs) are widely available and employed in genomic data analyses for predicting and understanding genetic architectures. Existing approaches either require information on SNP level, do not infer clusters of traits sharing genetic characteristic, or do not have any immediate predictive properties. Results Here, we present geneJAM, which is a novel clustering and estimation method using PGSs for inferring a genetic relationship among multiple, simultaneously measured and potentially correlated traits in a multivariate GWAS.Using graphical lasso, we estimate a sparse covariance matrix of the PGSs and obtain clusters of traits sharing genetic characteristics. We use the clusters to specify the structure of the error covariance matrix of a generalized least squares (GLS) model and use the feasible GLS estimator for estimating a linear regression model with a certain unknown degree of correlation between the residuals.The method suits many biology studies well with traits embedded in some genetic functioning groups and facilitates development of the PGS research. We compare the method with fully parametric techniques on simulated data and illustrate the utility of the methods by examining a heterogeneous stock mouse data set from the Wellcome Trust Centre for Human Genetics. We demonstrate that the method successfully identifies clusters of traits and increases precision, power, and computational efficiency. Availability and implementation GeneJAM is implemented in R and available at: https://github.com/abuchardt/geneJAM.
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Affiliation(s)
- Ann-Sophie Buchardt
- Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Claus Thorn Ekstrøm
- Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
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29
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Cao R, Olawsky E, McFowland E, Marcotte E, Spector L, Yang T. Subset scanning for multi-trait analysis using GWAS summary statistics. Bioinformatics 2024; 40:btad777. [PMID: 38191683 PMCID: PMC11087659 DOI: 10.1093/bioinformatics/btad777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/23/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
MOTIVATION Multi-trait analysis has been shown to have greater statistical power than single-trait analysis. Most of the existing multi-trait analysis methods only work with a limited number of traits and usually prioritize high statistical power over identifying relevant traits, which heavily rely on domain knowledge. RESULTS To handle diseases and traits with obscure etiology, we developed TraitScan, a powerful and fast algorithm that identifies potential pleiotropic traits from a moderate or large number of traits (e.g. dozens to thousands) and tests the association between one genetic variant and the selected traits. TraitScan can handle either individual-level or summary-level GWAS data. We evaluated TraitScan using extensive simulations and found that it outperformed existing methods in terms of both testing power and trait selection when sparsity was low or modest. We then applied it to search for traits associated with Ewing Sarcoma, a rare bone tumor with peak onset in adolescence, among 754 traits in UK Biobank. Our analysis revealed a few promising traits worthy of further investigation, highlighting the use of TraitScan for more effective multi-trait analysis as biobanks emerge. We also extended TraitScan to search and test association with a polygenic risk score and genetically imputed gene expression. AVAILABILITY AND IMPLEMENTATION Our algorithm is implemented in an R package "TraitScan" available at https://github.com/RuiCao34/TraitScan.
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Affiliation(s)
- Rui Cao
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN 55414, United States
| | - Evan Olawsky
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN 55414, United States
| | - Edward McFowland
- Technology and Operations Management, Harvard Business School, Harvard University, Boston, MA 02163, United States
| | - Erin Marcotte
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, United States
| | - Logan Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, United States
| | - Tianzhong Yang
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN 55414, United States
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, United States
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Singh S, Choudhury A, Hazelhurst S, Crowther NJ, Boua PR, Sorgho H, Agongo G, Nonterah EA, Micklesfield LK, Norris SA, Kisiangani I, Mohamed S, Gómez-Olivé FX, Tollman SM, Choma S, Brandenburg JT, Ramsay M. Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study. Nat Commun 2023; 14:8376. [PMID: 38104120 PMCID: PMC10725455 DOI: 10.1038/s41467-023-44079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Most hypertension-related genome-wide association studies (GWASs) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure (BP)-related traits (systolic and diastolic BP, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N = 10,775), identifies two novel genome-wide significant signals (p < 5E-08): systolic BP near P2RY1 (rs77846204; intergenic variant, p = 4.95E-08) and pulse pressure near LINC01256 (rs80141533; intergenic variant, p = 1.76E-08). No genome-wide signals are detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p < 5E-06) are observed for all traits, with 29 SNPs associating with more than one trait and several replicating known associations. Polygenic risk scores (PRSs) developed from studies on different ancestries have limited transferability, with multi-ancestry PRS providing better prediction. This study provides insights into the genetics of BP variation in African populations.
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Affiliation(s)
- Surina Singh
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Lisa K Micklesfield
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Health and Human Development, University of Southampton, Southampton, UK
| | | | - Shukri Mohamed
- African Population and Health Research Center, Nairobi, Kenya
| | - Francesc X Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen M Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Solomon Choma
- Department of Medical Science, Public Health and Health Promotion, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - J-T Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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31
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Guo Y, Chung W, Shan Z, Zhu Z, Costenbader KH, Liang L. Genome-Wide Assessment of Shared Genetic Architecture Between Rheumatoid Arthritis and Cardiovascular Diseases. J Am Heart Assoc 2023; 12:e030211. [PMID: 37947095 PMCID: PMC10727280 DOI: 10.1161/jaha.123.030211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Background Patients with rheumatoid arthritis (RA) have a 2- to 10-fold increased risk of cardiovascular disease (CVD), but the biological mechanisms and existence of causality underlying such associations remain to be investigated. We aimed to investigate the genetic associations and underlying mechanisms between RA and CVD by leveraging large-scale genomic data and genetic cross-trait analytic approaches. Methods and Results Within UK Biobank data, we examined the genetic correlation, shared genetics, and potential causality between RA (Ncases=6754, Ncontrols=452 384) and cardiovascular diseases (CVD, Ncases=44 238, Ncontrols=414 900) using linkage disequilibrium score regression, cross-trait meta-analysis, and Mendelian randomization. We observed significant genetic correlations of RA with myocardial infarction (rg:0.40 [95% CI, 0.24-0.56), angina (rg:0.42 [95% CI, 0.28-0.56]), coronary heart diseases (rg:0.41 [95% CI, 0.27-0.55]), and CVD (rg:0.43 [95% CI, 0.29-0.57]) after correcting for multiple testing (P<0.05/5). When stratified by frequent use of analgesics, we found increased genetic correlation between RA and CVD among participants without aspirin usage (rg:0.54 [95% CI, 0.30-0.78] for angina; Pvalue=6.69×10-6) and among participants with paracetamol usage (rg:0.75 [95% CI, 0.20-1.29] for myocardial infarction; Pvalue=8.90×10-3), whereas others remained similar. Cross-trait meta-analysis identified 9 independent shared loci between RA and CVD, including PTPN22 at chr1p13.2, BCL2L11 at chr2q13, and CCR3 at chr3p21.31 (Psingle trait<1×10-3 and Pmeta<5×10-8), highlighting potential shared pathogenesis including accelerating atherosclerosis, upregulating oxidative stress, and vascular permeability. Finally, Mendelian randomization estimates showed limited evidence of causality between RA and CVD. Conclusions Our results supported shared genetic pathogenesis rather than causality in explaining the observed association between RA and CVD. The identified shared genetic factors provided insights into potential novel therapeutic target for RA-CVD comorbidities.
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Affiliation(s)
- Yanjun Guo
- Department of Occupational and Environmental Health, School of Public HealthTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
- Division of Preventive MedicineBrigham and Women’s HospitalBostonMA
- Harvard Medical SchoolBostonMA
| | - Wonil Chung
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
- Department of Statistics and Actuarial ScienceSoongsil UniversitySeoulKorea
| | - Zhilei Shan
- Department of NutritionHarvard T.H. Chan School of Public HealthBostonMA
| | - Zhaozhong Zhu
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Karen H. Costenbader
- Division of Preventive MedicineBrigham and Women’s HospitalBostonMA
- Division of Rheumatology, Inflammation and Immunity, Department of MedicineBrigham and Women’s HospitalBostonMA
| | - Liming Liang
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMAUSA
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMA
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32
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Zhang W, Zhang L, Zhu J, Xiao C, Cui H, Yang C, Yan P, Tang M, Wang Y, Chen L, Liu Y, Zou Y, Wu X, Zhang L, Yang C, Yao Y, Li J, Liu Z, Jiang X, Zhang B. Additional Evidence for the Relationship Between Type 2 Diabetes and Stroke Through Observational and Genetic Analyses. Diabetes 2023; 72:1671-1681. [PMID: 37552871 DOI: 10.2337/db22-0954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
While type 2 diabetes mellitus (T2DM) is commonly considered a putative causal risk factor for stroke, the effect of stroke on T2DM remains unclear. The intrinsic link underlying T2DM and stroke has not been thoroughly examined. We aimed to evaluate the phenotypic and genetic relationships underlying T2DM and stroke. We evaluated phenotypic associations using data from the UK Biobank (N = 472,050). We then investigated genetic relationships by leveraging genomic data in European ancestry for T2DM, with and without adjusting (adj) for BMI (T2DM: n = 74,124 case subjects/824,006 control subjects; T2DMadjBMI: n = 50,409 case subjects/523,897 control subjects), and for stroke (n = 73,652 case subjects/1,234,808 control subjects). We performed additional analyses using genomic data in East Asian ancestry for T2DM (n = 77,418 case subjects/356,122 control subjects) and for stroke (n = 27,413 case subjects/237,242 control subjects). Observational analyses suggested a significantly increased hazard of stroke among individuals with T2DM (hazard ratio 2.28 [95% CI 1.97-2.64]), but a slightly increased hazard of T2DM among individuals with stroke (1.22 [1.03-1.45]) which attenuated to 1.14 (0.96-1.36) in sensitivity analysis. A positive global T2DM-stroke genetic correlation was observed (rg = 0.35; P = 1.46 × 10-27), largely independent of BMI (T2DMadjBMI-stroke: rg = 0.27; P = 3.59 × 10-13). This was further corroborated by 38 shared independent loci and 161 shared expression-trait associations. Mendelian randomization analyses suggested a putative causal effect of T2DM on stroke in Europeans (odds ratio 1.07 [95% CI 1.06-1.09]), which remained significant in East Asians (1.03 [1.01-1.06]). Conversely, despite a putative causal effect of stroke on T2DM also observed in Europeans (1.21 [1.07-1.37]), it attenuated to 1.04 (0.91-1.19) in East Asians. Our study provides additional evidence to underscore the significant relationship between T2DM and stroke. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Jingwei Zhu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Chenghan Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Ling Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Yuqin Yao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
| | - Zhenmi Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C.C. Chen Institute of Health, West China School of Public Health, and West China Fourth Hospital, Sichuan University, Chengdu
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Qu Y, Xiao C, Wu X, Zhu J, Qin C, He L, Cui H, Zhang L, Zhang W, Yang C, Yao Y, Li J, Liu Z, Zhang B, Wang W, Jiang X. Genetic Correlation, Shared Loci, and Causal Association Between Sex Hormone-Binding Globulin and Bone Mineral Density: Insights From a Large-Scale Genomewide Cross-Trait Analysis. J Bone Miner Res 2023; 38:1635-1644. [PMID: 37615194 DOI: 10.1002/jbmr.4904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/20/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Although the impact of sex hormones on bone metabolism is well-documented, effect of their primary modulator, sex hormone-binding globulin (SHBG), remains inconclusive. This study aims to elucidate the genetic overlap between SHBG and heel estimated bone mineral density (eBMD), a widely-accepted tool for osteoporosis management and fracture risk assessment. Using summary statistics from large-scale genomewide association studies conducted for SHBG (N = 370,125), SHBG adjusted for body mass index (SHBGa, N = 368,929), and eBMD (N = 426,824), a comprehensive genomewide cross-trait approach was performed to quantify global and local genetic correlations, identify pleiotropic loci, and infer causal associations. A significant overall inverse genetic correlation was found for SHBG and eBMD (rg = -0.11, p = 3.34 × 10-10 ), which was further supported by the significant local genetic correlations observed in 11 genomic regions. Cross-trait meta-analysis revealed 219 shared loci, of which seven were novel. Notably, four novel loci (rs6542680, rs8178616, rs147110934, and rs815625) were further demonstrated to colocalize. Mendelian randomization identified a robust causal effect of SHBG on eBMD (beta = -0.22, p = 3.04 × 10-13 ), with comparable effect sizes observed in both men (beta = -0.16, p = 1.99 × 10-6 ) and women (beta = -0.19, p = 2.73 × 10-9 ). Replacing SHBG with SHBGa, the observed genetic correlations, pleiotropic loci and causal associations did not change substantially. Our work reveals a shared genetic basis between SHBG and eBMD, substantiated by multiple pleiotropic loci and a robust causal relationship. Although SHBG has been implicated in preventing and screening aging-related diseases, our findings support its etiological role in osteoporosis. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Yang Qu
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Changfeng Xiao
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jingwei Zhu
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chenjiarui Qin
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lin He
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Wenzhi Wang
- Department of Osteoporosis/Rheumatology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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34
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Suzuki Y, Ménager H, Brancotte B, Vernet R, Nerin C, Boetto C, Auvergne A, Linhard C, Torchet R, Lechat P, Troubat L, Cho MH, Bouzigon E, Aschard H, Julienne H. Trait selection strategy in multi-trait GWAS: Boosting SNPs discoverability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564319. [PMID: 37961722 PMCID: PMC10634875 DOI: 10.1101/2023.10.27.564319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Since the first Genome-Wide Association Studies (GWAS), thousands of variant-trait associations have been discovered. However, the sample size required to detect additional variants using standard univariate association screening is increasingly prohibitive. Multi-trait GWAS offers a relevant alternative: it can improve statistical power and lead to new insights about gene function and the joint genetic architecture of human phenotypes. Although many methodological hurdles of multi-trait testing have been discussed, the strategy to select trait, among overwhelming possibilities, has been overlooked. In this study, we conducted extensive multi-trait tests using JASS (Joint Analysis of Summary Statistics) and assessed which genetic features of the analysed sets were associated with an increased detection of variants as compared to univariate screening. Our analyses identified multiple factors associated with the gain in the association detection in multi-trait tests. Together, these factors of the analysed sets are predictive of the gain of the multi-trait test (Pearson's ρ equal to 0.43 between the observed and predicted gain, P < 1.6 × 10-60). Applying an alternative multi-trait approach (MTAG, multi-trait analysis of GWAS), we found that in most scenarios but particularly those with larger numbers of traits, JASS outperformed MTAG. Finally, we benchmark several strategies to select set of traits including the prevalent strategy of selecting clinically similar traits, which systematically underperformed selecting clinically heterogenous traits or selecting sets that issued from our data-driven models. This work provides a unique picture of the determinant of multi-trait GWAS statistical power and outline practical strategies for multi-trait testing.
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Affiliation(s)
- Yuka Suzuki
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, Paris, 75015 France
| | - Hervé Ménager
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, F-75015 Paris, France
| | - Bryan Brancotte
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, F-75015 Paris, France
| | - Raphaël Vernet
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Group of Genomic Epidemiology of Multifactorial Diseases, Paris, France
| | - Cyril Nerin
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, Paris, 75015 France
| | - Christophe Boetto
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, Paris, 75015 France
| | - Antoine Auvergne
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, Paris, 75015 France
| | - Christophe Linhard
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Group of Genomic Epidemiology of Multifactorial Diseases, Paris, France
| | - Rachel Torchet
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, F-75015 Paris, France
| | - Pierre Lechat
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, F-75015 Paris, France
| | - Lucie Troubat
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, Paris, 75015 France
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Ave, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Emmanuelle Bouzigon
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Group of Genomic Epidemiology of Multifactorial Diseases, Paris, France
| | - Hugues Aschard
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, Paris, 75015 France
| | - Hanna Julienne
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, Paris, 75015 France
- Institut Pasteur, Université Paris Cité, Bioinformatics of Biostatistics Hub, F-75015 Paris, France
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35
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Zhu X, Yang Y, Lorincz-Comi N, Li G, Bentley A, de Vries PS, Brown M, Morrison AC, Rotimi C, James Gauderman W, Rao DC, Aschard H. A new Approach to Identify Gene-Environment Interactions and Reveal New Biological Insight in Complex traits. RESEARCH SQUARE 2023:rs.3.rs-3338723. [PMID: 37886448 PMCID: PMC10602131 DOI: 10.21203/rs.3.rs-3338723/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
There is a long-standing debate about the magnitude of the contribution of gene-environment interactions to phenotypic variations of complex traits owing to the low statistical power and few reported interactions to date. To address this issue, the CHARGE Gene-Lifestyle Interactions Working Group has been spearheading efforts to investigate G × E in large and diverse samples through meta-analysis. Here, we present a powerful new approach to screen for interactions across the genome, an approach that shares substantial similarity to the Mendelian randomization framework. We identified and confirmed 5 loci (6 independent signals) interacting with either cigarette smoking or alcohol consumption for serum lipids, and empirically demonstrated that interaction and mediation are the major contributors to genetic effect size heterogeneity across populations. The estimated lower bound of the interaction and environmentally mediated contribution ranges from 1.76% to 14.05% of SNP heritability of serum lipids in Cross-Population data. Our study improves the understanding of the genetic architecture and environmental contributions to complex traits.
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Affiliation(s)
- Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yihe Yang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Noah Lorincz-Comi
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Gen Li
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Amy Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Michael Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - W. James Gauderman
- Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - DC Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hugues Aschard
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
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Tian Y, Ma G, Li H, Zeng Y, Zhou S, Wang X, Shan S, Xu Y, Xiong J, Cheng G. Shared Genetics and Comorbid Genes of Amyotrophic Lateral Sclerosis and Parkinson's Disease. Mov Disord 2023; 38:1813-1821. [PMID: 37534731 DOI: 10.1002/mds.29572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/15/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Comorbidity exists between amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD), but the role of genetic factors is unclear. OBJECTIVE We aim to investigate genetic correlation, causal relationship, and comorbid genes between ALS and PD. METHODS Leveraging the largest genome-wide association study data (ALS: 27,205 cases, 110,881 controls; PDG: 33,674 cases, 449,056 controls), we used linkage disequilibrium score regression and Mendelian randomization analysis for genetic correlation and causal inference. We performed genome-wide cross-trait analysis via Multi-Trait Analysis of Genome-Wide Association Studies and Cross-Phenotype Association to identify specific single-nucleotide polymorphisms, followed by functional mapping and annotation. Integrating expression quantitative trait loci data from 13 brain regions, we conducted a transcriptome-wide association study via functional summary-based imputation and joint-tissue imputation to explore comorbid genes, followed by pathway enrichment analysis. RESULTS We found that PD positively correlates with ALS (rg = 0.144, P = 0.026) and confers a causal effect (odds ratio = 1.09, 95% confidence interval: 1.03-1.15, P = 3.00 × 10-3 ). We identified nine single-nucleotide polymorphisms (eight new), associating with three risk loci (chromosomes 4, 10, and 17) and seven genes (TMEM175, MAPT, NSF, LRRC37A2, ARHGAP27, GAK, and FGFRL1). In transcriptome-wide association study analysis, we showed six previously unreported pleiotropic genes (KANSL1, ARL17B, EFNA1, WNT3, ERCC8, and ADAM15), and we found these candidate genes are mainly enriched in negative regulation of neuron projection development (GO:0010977). CONCLUSIONS Our work demonstrates shared genetic architecture between ALS and PD, reports new pleiotropic genes, and sheds light on the comorbid mechanism. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Ye Tian
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Guochen Ma
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Haoqi Li
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yaxian Zeng
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Siquan Zhou
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xiaoyu Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Shufang Shan
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yujie Xu
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jingyuan Xiong
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Guo Cheng
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
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Wang Y, Zhang L, Zhang W, Tang M, Cui H, Wu X, Zhao X, Chen L, Yan P, Yang C, Xiao C, Zou Y, Liu Y, Zhang L, Yang C, Yao Y, Li J, Liu Z, Jiang X, Zhang B. Understanding the relationship between circulating lipids and risk of chronic kidney disease: a prospective cohort study and large-scale genetic analyses. J Transl Med 2023; 21:671. [PMID: 37759214 PMCID: PMC10537816 DOI: 10.1186/s12967-023-04509-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND This study aims to comprehensively investigate the phenotypic and genetic relationships between four common lipids (high-density lipoprotein cholesterol, HDL-C; low-density lipoprotein cholesterol, LDL-C; total cholesterol, TC; and triglycerides, TG), chronic kidney disease (CKD), and estimated glomerular filtration rate (eGFR). METHODS We first investigated the observational association of lipids (exposures) with CKD (primary outcome) and eGFR (secondary outcome) using data from UK Biobank. We then explored the genetic relationship using summary statistics from the largest genome-wide association study of four lipids (N = 1,320,016), CKD (Ncase = 41,395, Ncontrol = 439,303), and eGFR(N = 567,460). RESULTS There were significant phenotypic associations (HDL-C: hazard ratio (HR) = 0.76, 95%CI = 0.60-0.95; TG: HR = 1.08, 95%CI = 1.02-1.13) and global genetic correlations (HDL-C: [Formula: see text] = - 0.132, P = 1.00 × 10-4; TG: [Formula: see text] = 0.176; P = 2.66 × 10-5) between HDL-C, TG, and CKD risk. Partitioning the whole genome into 2353 LD-independent regions, twelve significant regions were observed for four lipids and CKD. The shared genetic basis was largely explained by 29 pleiotropic loci and 36 shared gene-tissue pairs. Mendelian randomization revealed an independent causal relationship of genetically predicted HDL-C (odds ratio = 0.91, 95%CI = 0.85-0.98), but not for LDL-C, TC, or TG, with the risk of CKD. Regarding eGFR, a similar pattern of correlation and pleiotropy was observed. CONCLUSIONS Our work demonstrates a putative causal role of HDL-C in CKD and a significant biological pleiotropy underlying lipids and CKD in populations of European ancestry. Management of low HDL-C levels could potentially benefit in reducing the long-term risk of CKD.
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Affiliation(s)
- Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Xunying Zhao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China.
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, Sichuan, China.
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Zhao X, Wu X, Xiao J, Zhang L, Hao Y, Xiao C, Zhang B, Li J, Jiang X. A large-scale genome-wide cross-trait analysis for the effect of COVID-19 on female-specific cancers. iScience 2023; 26:107497. [PMID: 37636041 PMCID: PMC10450412 DOI: 10.1016/j.isci.2023.107497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/24/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Little is known regarding the long-term adverse effects of COVID-19 on female-specific cancers, nor the shared genetic influences underlying these conditions. We performed a comprehensive genome-wide cross-trait analysis to investigate the shared genetic architecture between COVID-19 (infection, hospitalization, and critical illness) with three female-specific cancers (breast cancer (BC), epithelial ovarian cancer (EOC), and endometrial cancer (EC)). We identified significant genome-wide genetic correlations with EC for both hospitalization (r g = 0.19, p = 0.01) and critical illness (r g = 0.29, p = 3.00 × 10-4). Mendelian randomization demonstrated no valid association of COVID-19 with any cancer of interest, except for suggestive associations of genetically predicted hospitalization (ORIVW = 1.09, p = 0.04) and critical illness (ORIVW = 1.06, p = 0.04) with EC risk, none withstanding multiple correction. Cross-trait meta-analysis identified 20 SNPs shared between COVID-19 with BC, 15 with EOC, and 5 with EC; and transcriptome-wide association studies revealed multiple shared genes. Findings support intrinsic links underlying these complex traits, highlighting shared mechanisms rather than causal associations.
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Affiliation(s)
- Xunying Zhao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jinyu Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yu Hao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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Jiang Y, Liu Q, Alfredsson L, Klareskog L, Kockum I, Jiang X. A genome-wide cross-trait analysis identifies genomic correlation, pleiotropic loci, and causal relationship between sex hormone-binding globulin and rheumatoid arthritis. Hum Genomics 2023; 17:81. [PMID: 37644603 PMCID: PMC10466838 DOI: 10.1186/s40246-023-00528-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Our study aims to investigate an intrinsic link underlying sex hormone-binding globulin (SHBG) and rheumatoid arthritis (RA), which remains inconclusive in observational settings. METHODS Summary statistics were collected from the largest GWAS(s) on SHBG adjusted for BMI (SHBGadjBMI; Noverall = 368,929; Nmen = 180,094; Nwomen = 188,908), crude SHBG (Noverall = 370,125; Nmen = 180,726; Nwomen = 189,473), and RA (Ncase = 22,350; Ncontrol = 74,823). A genome-wide cross-trait design was performed to quantify global and local genetic correlation, identify pleiotropic loci, and infer a causal relationship. RESULTS Among the overall population, a significant global genetic correlation was observed for SHBGadjBMI and RA ([Formula: see text] = 0.11, P = 1.0 × 10-4) which was further supported by local signal (1q25.2). A total of 18 independent pleiotropic SNPs were identified, of which three were highly likely causal variants and four were found to have effects on both traits through gene expression mediation. A putative causal association of SHBGadjBMI on RA was demonstrated (OR = 1.20, 95% CI = 1.01-1.43) without evidence of reverse causality (OR = 0.999, 95% CI = 0.997-1.000). Sex-specific analyses revealed distinct shared genetic regions (men: 1q32.1-q32.2 and 5p13.1; women: 1q25.2 and 22q11.21-q11.22) and diverse pleiotropic SNPs (16 in men and 18 in women, nearly half were sex-specific) underlying SHBGadjBMI and RA, demonstrating biological disparities between sexes. Replacing SHBGadjBMI with crude SHBG, a largely similar yet less significant pattern of results was observed. CONCLUSION Our cross-trait analysis suggests an intrinsic, as well as a sex-specific, link underlying SHBG and RA, providing novel insights into disease etiology.
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Affiliation(s)
- Yuan Jiang
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
| | - Qianwen Liu
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
| | - Lars Alfredsson
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden
| | - Xia Jiang
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Visionsgatan 18, 171 77, Solna, Stockholm, Sweden.
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China.
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Zheng C, Liu H, Zhao P, Lu W, Song S, He T, Fan J, Wang D, Yang P, Jie Q, Zheng HF, Luo Z, Yang L. Targeting sulfation-dependent mechanoreciprocity between matrix and osteoblasts to mitigate bone loss. Sci Transl Med 2023; 15:eadg3983. [PMID: 37611084 DOI: 10.1126/scitranslmed.adg3983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 08/04/2023] [Indexed: 08/25/2023]
Abstract
Sulfation is a widespread modification of biomolecules that has been incompletely explored to date. Through cross-phenotype meta-analysis of bone mineral density in up to 426,824 genotyped human participants along with phenotypic characterization of multiple mutant mouse lines, we identified a causative role for sulfate transporter solute carrier family 26 member A2 (SLC26A2) deficiency in osteoporosis. Ablation of SLC26A2 in osteoblasts caused severe bone loss and accumulation of immature bone cells and elicited peculiar pericellular matrix (PCM) production characterized by undersulfation coupled with decreased stiffness. These altered chemophysical properties of the PCM disrupted the formation of focal adhesions in osteoblasts. Bulk RNA sequencing and functional assays revealed that the mechanoreciprocal inhibition of focal adhesion kinase (FAK) and Yes1-associated transcriptional regulator (YAP)/WW domain containing transcription regulator 1 (TAZ) signaling impinged osteoblast maturation upon SLC26A2 deficiency. Moreover, pharmacological abrogation of the Hippo kinases and forced wheel-running ameliorated SLC26A2-deficient osteoporosis by promoting YAP/TAZ activity. Analysis of mouse single-cell RNA sequencing data suggested coordination among sulfate metabolism, focal adhesion, and YAP/TAZ activity during osteoblast-to-osteocyte transition. In addition to the SLC26A2-deficient setting, altered FAK and YAP/TAZ signaling was also observed in bone cells of ovariectomized mice and patients with osteoporosis, and pharmacological enforcing of YAP/TAZ activity ameliorated bone loss in ovariectomized mice. Collectively, these data unveil a role for sulfation in the developmental mechanoreciprocity between matrix and osteoblasts, which could be leveraged to prevent bone loss.
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Affiliation(s)
- Chao Zheng
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - He Liu
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Pianpian Zhao
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
| | - Weiguang Lu
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Shiju Song
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Ting He
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Jing Fan
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Di Wang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Pengfei Yang
- Key Laboratory for Space Bioscience and Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Qiang Jie
- Department of Orthopedic Surgery, Hong Hui Hospital, Xi'an Jiaotong University, College of Medicine, Xi'an 710049, China
- Research Center for Skeletal Developmental Deformity and Injury repair, College of Life Science and Medicine, Northwest University, Xi'an 710069, China
| | - Hou-Feng Zheng
- Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
| | - Zhuojing Luo
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
- Medical Research Institute, Northwestern Polytechnical University, Xi'an 710072, China
| | - Liu Yang
- Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
- Medical Research Institute, Northwestern Polytechnical University, Xi'an 710072, China
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Zhang Y, Jiang X, Mentzer AJ, McVean G, Lunter G. Topic modeling identifies novel genetic loci associated with multimorbidities in UK Biobank. CELL GENOMICS 2023; 3:100371. [PMID: 37601973 PMCID: PMC10435382 DOI: 10.1016/j.xgen.2023.100371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 05/04/2023] [Accepted: 07/07/2023] [Indexed: 08/22/2023]
Abstract
Many diseases show patterns of co-occurrence, possibly driven by systemic dysregulation of underlying processes affecting multiple traits. We have developed a method (treeLFA) for identifying such multimorbidities from routine health-care data, which combines topic modeling with an informative prior derived from medical ontology. We apply treeLFA to UK Biobank data and identify a variety of topics representing multimorbidity clusters, including a healthy topic. We find that loci identified using topic weights as traits in a genome-wide association study (GWAS) analysis, which we validated with a range of approaches, only partially overlap with loci from GWASs on constituent single diseases. We also show that treeLFA improves upon existing methods like latent Dirichlet allocation in various ways. Overall, our findings indicate that topic models can characterize multimorbidity patterns and that genetic analysis of these patterns can provide insight into the etiology of complex traits that cannot be determined from the analysis of constituent traits alone.
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Affiliation(s)
- Yidong Zhang
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Department of Radiation Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Xilin Jiang
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge CB2 0SR, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge CB2 0BB, UK
| | - Alexander J. Mentzer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, the Netherlands
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Zhang W, Zhang L, Yang L, Xiao C, Wu X, Yan P, Cui H, Yang C, Zhu J, Wu X, Tang M, Wang Y, Chen L, Liu Y, Zou Y, Zhang L, Yang C, Yao Y, Li J, Liu Z, Zhang B, Jiang X. Migraine, chronic kidney disease and kidney function: observational and genetic analyses. Hum Genet 2023; 142:1185-1200. [PMID: 37306871 PMCID: PMC10449948 DOI: 10.1007/s00439-023-02575-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023]
Abstract
Epidemiological studies demonstrate an association between migraine and chronic kidney disease (CKD), while the genetic basis underlying the phenotypic association has not been investigated. We aimed to help avoid unnecessary interventions in individuals with migraine through the investigation of phenotypic and genetic relationships underlying migraine, CKD, and kidney function. We first evaluated phenotypic associations using observational data from UK Biobank (N = 255,896). We then investigated genetic relationships leveraging genomic data in European ancestry for migraine (Ncase/Ncontrol = 48,975/540,381), CKD (Ncase/Ncontrol = 41,395/439,303), and two traits of kidney function (estimated glomerular filtration rate [eGFR, N = 567,460] and urinary albumin-to-creatinine ratio [UACR, N = 547,361]). Observational analyses suggested no significant association of migraine with the risk of CKD (HR = 1.13, 95% CI = 0.85-1.50). While we did not find any global genetic correlation in general, we identified four specific genomic regions showing significant for migraine with eGFR. Cross-trait meta-analysis identified one candidate causal variant (rs1047891) underlying migraine, CKD, and kidney function. Transcriptome-wide association study detected 28 shared expression-trait associations between migraine and kidney function. Mendelian randomization analysis suggested no causal effect of migraine on CKD (OR = 1.03, 95% CI = 0.98-1.09; P = 0.28). Despite a putative causal effect of migraine on an increased level of UACR (log-scale-beta = 0.02, 95% CI = 0.01-0.04; P = 1.92 × 10-3), it attenuated to null when accounting for both correlated and uncorrelated pleiotropy. Our work does not find evidence supporting a causal association between migraine and CKD. However, our study highlights significant biological pleiotropy between migraine and kidney function. The value of a migraine prophylactic treatment for reducing future CKD in people with migraine is likely limited.
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Affiliation(s)
- Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Luo Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
- Department of Urology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chenghan Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Jingwei Zhu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Xuan Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Ling Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Yuqin Yao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
| | - Zhenmi Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041 China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Lorincz-Comi N, Yang Y, Li G, Zhu X. MRBEE: A novel bias-corrected multivariable Mendelian Randomization method. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523480. [PMID: 37066391 PMCID: PMC10103949 DOI: 10.1101/2023.01.10.523480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mendelian randomization (MR) is an instrumental variable approach used to infer causal relationships between exposures and outcomes and can apply to summary data from genome-wide association studies (GWAS). Since GWAS summary statistics are subject to estimation errors, most existing MR approaches suffer from measurement error bias, whose scale and direction are influenced by weak instrumental variables and GWAS sample overlap, respectively. We introduce MRBEE (MR using Bias-corrected Estimating Equation), a novel multivariable MR method capable of simultaneously removing measurement error bias and identifying horizontal pleiotropy. In simulations, we showed that MRBEE is capable of effectively removing measurement error bias in the presence of weak instrumental variables and sample overlap. In two independent real data analyses, we discovered that the causal effect of BMI on coronary artery disease risk is entirely mediated by blood pressure, and that existing MR methods may underestimate the causal effect of cannabis use disorder on schizophrenia risk compared to MRBEE. MRBEE possesses significant potential for advancing genetic research by providing a valuable tool to study causality between multiple risk factors and disease outcomes, particularly as a large number of GWAS summary statistics become publicly available.
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Affiliation(s)
- Noah Lorincz-Comi
- Department of Population and Quantitative Health Sciences, School of Medicine
- Case Western Reserve University, Cleveland, OH 44106, USA June 12, 2023
| | - Yihe Yang
- Department of Population and Quantitative Health Sciences, School of Medicine
- Case Western Reserve University, Cleveland, OH 44106, USA June 12, 2023
| | - Gen Li
- Department of Population and Quantitative Health Sciences, School of Medicine
- Case Western Reserve University, Cleveland, OH 44106, USA June 12, 2023
| | - Xiaofeng Zhu
- This work was supported by grant HG011052 (to X.Z.) from the National Human Genome Research Institute (NHGRI), USA.
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Wen YP, Yu ZG. Identifying shared genetic loci and common risk genes of rheumatoid arthritis associated with three autoimmune diseases based on large-scale cross-trait genome-wide association studies. Front Immunol 2023; 14:1160397. [PMID: 37377963 PMCID: PMC10291128 DOI: 10.3389/fimmu.2023.1160397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction Substantial links between autoimmune diseases have been shown by an increasing number of studies, and one hypothesis for this comorbidity is that there is a common genetic cause. Methods In this paper, a large-scale cross-trait Genome-wide Association Studies (GWAS) was conducted to investigate the genetic overlap among rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease and type 1 diabetes. Results and discussion Through the local genetic correlation analysis, 2 regions with locally significant genetic associations between rheumatoid arthritis and multiple sclerosis, and 4 regions with locally significant genetic associations between rheumatoid arthritis and type 1 diabetes were discovered. By cross-trait meta-analysis, 58 independent loci associated with rheumatoid arthritis and multiple sclerosis, 86 independent loci associated with rheumatoid arthritis and inflammatory bowel disease, and 107 independent loci associated with rheumatoid arthritis and type 1 diabetes were identified with genome-wide significance. In addition, 82 common risk genes were found through genetic identification. Based on gene set enrichment analysis, it was found that shared genes are enriched in exposed dermal system, calf, musculoskeletal, subcutaneous fat, thyroid and other tissues, and are also significantly enriched in 35 biological pathways. To verify the association between diseases, Mendelian randomized analysis was performed, which shows possible causal associations between rheumatoid arthritis and multiple sclerosis, and between rheumatoid arthritis and type 1 diabetes. The common genetic structure of rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease and type 1 diabetes was explored by these studies, and it is believed that this important discovery will lead to new ideas for clinical treatment.
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Affiliation(s)
- Ya-Ping Wen
- National Center for Applied Mathematics in Hunan, Xiangtan University, Hunan, China
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan, China
| | - Zu-Guo Yu
- National Center for Applied Mathematics in Hunan, Xiangtan University, Hunan, China
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Hunan, China
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Zeng R, Jiang R, Huang W, Wang J, Zhang L, Ma Y, Wu Y, Meng M, Lan H, Lian Q, Leung FW, Sha W, Chen H. Dissecting shared genetic architecture between obesity and multiple sclerosis. EBioMedicine 2023; 93:104647. [PMID: 37300932 PMCID: PMC10363440 DOI: 10.1016/j.ebiom.2023.104647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Observational studies have associated obesity with an increased risk of multiple sclerosis (MS). However, the role of genetic factors in their comorbidity remains largely unknown. Our study aimed to investigate the shared genetic architecture underlying obesity and MS. METHODS By leveraging data from genome-wide association studies, we investigated the genetic correlation of body mass index (BMI) and MS by linkage disequilibrium score regression and genetic covariance analyser. The casualty was identified by bidirectional Mendelian randomisation. Linkage disequilibrium score regression in specifically expressed genes and multimarker analysis of GenoMic annotation was utilised to explore single-nucleotide polymorphism (SNP) enrichment at the tissue and cell-type levels. Shared risk SNPs were derived using cross-trait meta-analyses and Heritability Estimation from Summary Statistics. We explored the potential functional genes using summary-data-based Mendelian randomization (SMR). The expression profiles of the risk gene in tissues were further examined. FINDINGS We found a significantly positive genetic correlation between BMI and MS, and the causal association of BMI with MS was supported (β = 0.22, P = 8.03E-05). Cross-trait analysis yielded 39 shared risk SNPs, and the risk gene GGNBP2 was consistently identified in SMR. We observed tissue-specific level SNP heritability enrichment for BMI mainly in brain tissues for MS in immune-related tissues, and cell-type-specific level SNP heritability enrichment in 12 different immune cell types in brain, spleen, lung, and whole blood. The expressions of GGNBP2 were significantly altered in the tissues of patients with obesity or MS compared to those of control subjects. INTERPRETATION Our study indicates the genetic correlation and shared risk genes between obesity and MS. These findings provide insights into the potential mechanisms behind their comorbidity and the future development of therapeutics. FUNDING This work was funded by the National Natural Science Foundation of China (82171698, 82170561, 81300279, and 81741067), the Program for High-level Foreign Expert Introduction of China (G2022030047L), the Natural Science Foundation for Distinguished Young Scholars of Guangdong Province (2021B1515020003), Natural Science Foundation of Guangdong Province (2022A1515012081), the Foreign Distinguished Teacher Program of Guangdong Science and Technology Department (KD0120220129), the Climbing Programme of Introduced Talents and High-level Hospital Construction Project of Guangdong Provincial People's Hospital (DFJH201803, KJ012019099, KJ012021143, and KY012021183), and in part by VA Clinical Merit and ASGE clinical research funds (FWL).
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Affiliation(s)
- Ruijie Zeng
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Rui Jiang
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Wentao Huang
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiaxuan Wang
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Lijun Zhang
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Yuying Ma
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yanjun Wu
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Meijun Meng
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Hekui Lan
- Department of Paediatrics, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Qizhou Lian
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China; Cord Blood Bank, Guangzhou Institute of Eugenics and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR, China
| | - Felix W Leung
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Sepulveda Ambulatory Care Center, Veterans Affairs Greater Los Angeles Healthcare System, North Hills, CA, USA.
| | - Weihong Sha
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; School of Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China.
| | - Hao Chen
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; School of Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China.
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Wu X, Zhang W, Zhao X, Zhang L, Xu M, Hao Y, Xiao J, Zhang B, Li J, Kraft P, Smoller JW, Jiang X. Investigating the relationship between depression and breast cancer: observational and genetic analyses. BMC Med 2023; 21:170. [PMID: 37143087 PMCID: PMC10161423 DOI: 10.1186/s12916-023-02876-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Both depression and breast cancer (BC) contribute to a substantial global burden of morbidity and mortality among women, and previous studies have observed a potential depression-BC link. We aimed to comprehensively characterize the phenotypic and genetic relationships between depression and BC. METHODS We first evaluated phenotypic association using longitudinal follow-up data from the UK Biobank (N = 250,294). We then investigated genetic relationships leveraging summary statistics from the hitherto largest genome-wide association study of European individuals conducted for depression (N = 500,199), BC (N = 247,173), and its subtypes based on the status of estrogen receptor (ER + : N = 175,475; ER - : N = 127,442). RESULTS Observational analysis suggested an increased hazard of BC in depression patients (HR = 1.10, 95%CIs = 0.95-1.26). A positive genetic correlation between depression and overall BC was observed ([Formula: see text] = 0.08, P = 3.00 × 10-4), consistent across ER + ([Formula: see text] = 0.06, P = 6.30 × 10-3) and ER - subtypes ([Formula: see text] = 0.08, P = 7.20 × 10-3). Several specific genomic regions showed evidence of local genetic correlation, including one locus at 9q31.2, and four loci at, or close, to 6p22.1. Cross-trait meta-analysis identified 17 pleiotropic loci shared between depression and BC. TWAS analysis revealed five shared genes. Bi-directional Mendelian randomization suggested risk of depression was causally associated with risk of overall BC (OR = 1.12, 95%Cis = 1.04-1.19), but risk of BC was not causally associated with risk of depression. CONCLUSIONS Our work demonstrates a shared genetic basis, pleiotropic loci, and a putative causal relationship between depression and BC, highlighting a biological link underlying the observed phenotypic relationship; these findings may provide important implications for future studies aimed reducing BC risk.
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Affiliation(s)
- Xueyao Wu
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Wenqiang Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xunying Zhao
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Li Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Minghan Xu
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yu Hao
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jinyu Xiao
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Ben Zhang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiayuan Li
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Psychiatry, Massachusetts General Hospital, MA, Boston, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, MA, Cambridge, USA
| | - Xia Jiang
- Department of Epidemiology and Health Statistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, No. 16 Ren Min Nan Lu, Chengdu, Sichuan, 610041, People's Republic of China.
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Solna, Sweden.
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
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Qiu S, Zheng K, Hu Y, Liu G. Genetic correlation, causal relationship, and shared loci between vitamin D and COVID-19: A genome-wide cross-trait analysis. J Med Virol 2023; 95:e28780. [PMID: 37212302 DOI: 10.1002/jmv.28780] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/25/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023]
Abstract
Observational studies have shown that vitamin D supplementation reduces the risk of COVID-19 infection, yet little is known about the shared genomic architectures between them. Leveraging large-scale genome-wide association study (GWAS) summary statistics, we investigated the genetic correlation and causal relationship between genetically determined vitamin D and COVID-19 using linkage disequilibrium score regression and Mendelian randomization (MR) analyses, and conducted a cross-trait GWAS meta-analysis to identify the overlapping susceptibility loci of them. We observed a significant genetic correlation between genetically predicted vitamin D and COVID-19 (rg = -0.143, p = 0.011), and the risk of COVID-19 infection would decrease by 6% for every 0.76 nmol L-1 increase of serum 25 hydroxyvitamin D (25OHD) concentrations in generalized MR (OR = 0.94, 95% CI: 0.89-0.99, p = 0.019). We identified rs4971066 (EFNA1) as a risk locus for the joint phenotype of vitamin D and COVID-19. In conclusion, genetically determined vitamin D is associated with COVID-19. Increased levels of serum 25OHD concentration may benefit the prevention and treatment of COVID-19.
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Affiliation(s)
- Shizheng Qiu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Keyang Zheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yang Hu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Guiyou Liu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Key Laboratory of Cerebral Microcirculation in Universities of Shandong, Department of Neurology, Second Affiliated Hospital, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong, China
- Beijing Key Laboratory of Hypoxia Translational Medicine, National Engineering Laboratory of Internet Medical Diagnosis and Treatment Technology, Xuanwu Hospital, Capital Medical University, Beijing, China
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Nosková A, Mehrotra A, Kadri NK, Lloret-Villas A, Neuenschwander S, Hofer A, Pausch H. Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs. BMC Genomics 2023; 24:192. [PMID: 37038103 PMCID: PMC10084639 DOI: 10.1186/s12864-023-09295-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/04/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Genetic correlations between complex traits suggest that pleiotropic variants contribute to trait variation. Genome-wide association studies (GWAS) aim to uncover the genetic underpinnings of traits. Multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS enable detecting variants associated with multiple phenotypes. In this study, we used array-derived genotypes and phenotypes for 24 reproduction, production, and conformation traits to explore differences between the two methods and used imputed sequence variant genotypes to fine-map six quantitative trait loci (QTL). RESULTS We considered genotypes at 44,733 SNPs for 5,753 pigs from the Swiss Large White breed that had deregressed breeding values for 24 traits. Single-trait association analyses revealed eleven QTL that affected 15 traits. Multi-trait association testing and the meta-analysis of the single-trait GWAS revealed between 3 and 6 QTL, respectively, in three groups of traits. The multi-trait methods revealed three loci that were not detected in the single-trait GWAS. Four QTL that were identified in the single-trait GWAS, remained undetected in the multi-trait analyses. To pinpoint candidate causal variants for the QTL, we imputed the array-derived genotypes to the sequence level using a sequenced reference panel consisting of 421 pigs. This approach provided genotypes at 16 million imputed sequence variants with a mean accuracy of imputation of 0.94. The fine-mapping of six QTL with imputed sequence variant genotypes revealed four previously proposed causal mutations among the top variants. CONCLUSIONS Our findings in a medium-size cohort of pigs suggest that multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS provide very similar results. Although multi-trait association methods provide a useful overview of pleiotropic loci segregating in mapping populations, the investigation of single-trait association studies is still advised, as multi-trait methods may miss QTL that are uncovered in single-trait GWAS.
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Affiliation(s)
- A Nosková
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland.
| | - A Mehrotra
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | - N K Kadri
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | | | | | - A Hofer
- SUISAG, Allmend 10, 6204, Sempach, Switzerland
| | - H Pausch
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
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Wang N, Yu B, Jun G, Qi Q, Durazo-Arvizu RA, Lindstrom S, Morrison AC, Kaplan RC, Boerwinkle E, Chen H. StocSum: stochastic summary statistics for whole genome sequencing studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535886. [PMID: 37066281 PMCID: PMC10104122 DOI: 10.1101/2023.04.06.535886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Genomic summary statistics, usually defined as single-variant test results from genome-wide association studies, have been widely used to advance the genetics field in a wide range of applications. Applications that involve multiple genetic variants also require their correlations or linkage disequilibrium (LD) information, often obtained from an external reference panel. In practice, it is usually difficult to find suitable external reference panels that represent the LD structure for underrepresented and admixed populations, or rare genetic variants from whole genome sequencing (WGS) studies, limiting the scope of applications for genomic summary statistics. Here we introduce StocSum, a novel reference-panel-free statistical framework for generating, managing, and analyzing stochastic summary statistics using random vectors. We develop various downstream applications using StocSum including single-variant tests, conditional association tests, gene-environment interaction tests, variant set tests, as well as meta-analysis and LD score regression tools. We demonstrate the accuracy and computational efficiency of StocSum using two cohorts from the Trans-Omics for Precision Medicine Program. StocSum will facilitate sharing and utilization of genomic summary statistics from WGS studies, especially for underrepresented and admixed populations.
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Affiliation(s)
- Nannan Wang
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Goo Jun
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ramon A. Durazo-Arvizu
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, California
- Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sara Lindstrom
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, School of Public Health, University of Washington, 3980 15th Ave NE, Seattle, WA, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Robert C. Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
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50
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Wei Q, Chen L, Zhou Y, Wang H. An adaptive test based on principal components for detecting multiple phenotype associations using GWAS summary data. Genetica 2023; 151:97-104. [PMID: 36656460 DOI: 10.1007/s10709-023-00179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023]
Abstract
Extensive evidence from genome-wide association studies (GWAS) has shown that jointly analyzing multiple phenotypes can improve the power of the association test compared to the traditional single variant versus single trait approach. Here we propose an adaptive test based on principal components (ATPC) that is powerful and efficient for discovering the association between a single variant and multiple traits. Our method only needs GWAS summary statistics that are often available. We first estimate the trait correlation matrix by LD score regression. Then, based on the correlation matrix, we construct a series of test statistics that contain different numbers of principal components. The ultimate test statistic combines the P values of these principal component-based statistics by using the aggregated Cauchy association test. The analytical P-value of the test statistic can be computed quickly without the permutation process, which is the notable feature of our proposed method. The extensive simulation studies demonstrate that ATPC can control the type I error rates and have powerful and robust performance compared to several existing tests in a wide range of simulation settings. The analysis of the lipids GWAS summary data from the Global Lipids Genetics Consortium shows that ATPC identifies 230 new SNPs that are missed by the original single trait association analysis. By searching the GWAS Catalog, some SNPs and mapped genes identified by ATPC are reported to be associated with lipid traits. Through further analysis for GWAS results, we also find some Gene Ontology terms and biological pathways related to lipids.
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Affiliation(s)
- Qianran Wei
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University, Harbin, 150080, China
| | - Lili Chen
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University, Harbin, 150080, China.
| | - Yajing Zhou
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University, Harbin, 150080, China
| | - Huiyi Wang
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University, Harbin, 150080, China
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