1
|
Tang Y, Zhang J, Li W, Liu X, Chen S, Mi S, Yang J, Teng J, Fang L, Yu Y. Identification and characterization of whole blood gene expression and splicing quantitative trait loci during early to mid-lactation of dairy cattle. BMC Genomics 2024; 25:445. [PMID: 38711039 DOI: 10.1186/s12864-024-10346-7] [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: 09/30/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Characterization of regulatory variants (e.g., gene expression quantitative trait loci, eQTL; gene splicing QTL, sQTL) is crucial for biologically interpreting molecular mechanisms underlying loci associated with complex traits. However, regulatory variants in dairy cattle, particularly in specific biological contexts (e.g., distinct lactation stages), remain largely unknown. In this study, we explored regulatory variants in whole blood samples collected during early to mid-lactation (22-150 days after calving) of 101 Holstein cows and analyzed them to decipher the regulatory mechanisms underlying complex traits in dairy cattle. RESULTS We identified 14,303 genes and 227,705 intron clusters expressed in the white blood cells of 101 cattle. The average heritability of gene expression and intron excision ratio explained by cis-SNPs is 0.28 ± 0.13 and 0.25 ± 0.13, respectively. We identified 23,485 SNP-gene expression pairs and 18,166 SNP-intron cluster pairs in dairy cattle during early to mid-lactation. Compared with the 2,380,457 cis-eQTLs reported to be present in blood in the Cattle Genotype-Tissue Expression atlas (CattleGTEx), only 6,114 cis-eQTLs (P < 0.05) were detected in the present study. By conducting colocalization analysis between cis-e/sQTL and the results of genome-wide association studies (GWAS) from four traits, we identified a cis-e/sQTL (rs109421300) of the DGAT1 gene that might be a key marker in early to mid-lactation for milk yield, fat yield, protein yield, and somatic cell score (PP4 > 0.6). Finally, transcriptome-wide association studies (TWAS) revealed certain genes (e.g., FAM83H and TBC1D17) whose expression in white blood cells was significantly (P < 0.05) associated with complex traits. CONCLUSIONS This study investigated the genetic regulation of gene expression and alternative splicing in dairy cows during early to mid-lactation and provided new insights into the regulatory mechanisms underlying complex traits of economic importance.
Collapse
Affiliation(s)
- Yongjie Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinning Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wenlong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xueqin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Siqian Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Siyuan Mi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinyan Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinyan Teng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
2
|
Fong WJ, Tan HM, Garg R, Teh AL, Pan H, Gupta V, Krishna B, Chen ZH, Purwanto NY, Yap F, Tan KH, Chan KYJ, Chan SY, Goh N, Rane N, Tan ESE, Jiang Y, Han M, Meaney M, Wang D, Keppo J, Tan GCY. Comparing feature selection and machine learning approaches for predicting CYP2D6 methylation from genetic variation. Front Neuroinform 2024; 17:1244336. [PMID: 38449836 PMCID: PMC10915285 DOI: 10.3389/fninf.2023.1244336] [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: 06/22/2023] [Accepted: 10/18/2023] [Indexed: 03/08/2024] Open
Abstract
Introduction Pharmacogenetics currently supports clinical decision-making on the basis of a limited number of variants in a few genes and may benefit paediatric prescribing where there is a need for more precise dosing. Integrating genomic information such as methylation into pharmacogenetic models holds the potential to improve their accuracy and consequently prescribing decisions. Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene conventionally associated with the metabolism of commonly used drugs and endogenous substrates. We thus sought to predict epigenetic loci from single nucleotide polymorphisms (SNPs) related to CYP2D6 in children from the GUSTO cohort. Methods Buffy coat DNA methylation was quantified using the Illumina Infinium Methylation EPIC beadchip. CpG sites associated with CYP2D6 were used as outcome variables in Linear Regression, Elastic Net and XGBoost models. We compared feature selection of SNPs from GWAS mQTLs, GTEx eQTLs and SNPs within 2 MB of the CYP2D6 gene and the impact of adding demographic data. The samples were split into training (75%) sets and test (25%) sets for validation. In Elastic Net model and XGBoost models, optimal hyperparameter search was done using 10-fold cross validation. Root Mean Square Error and R-squared values were obtained to investigate each models' performance. When GWAS was performed to determine SNPs associated with CpG sites, a total of 15 SNPs were identified where several SNPs appeared to influence multiple CpG sites. Results Overall, Elastic Net models of genetic features appeared to perform marginally better than heritability estimates and substantially better than Linear Regression and XGBoost models. The addition of nongenetic features appeared to improve performance for some but not all feature sets and probes. The best feature set and Machine Learning (ML) approach differed substantially between CpG sites and a number of top variables were identified for each model. Discussion The development of SNP-based prediction models for CYP2D6 CpG methylation in Singaporean children of varying ethnicities in this study has clinical application. With further validation, they may add to the set of tools available to improve precision medicine and pharmacogenetics-based dosing.
Collapse
Affiliation(s)
- Wei Jing Fong
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Hong Ming Tan
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Rishabh Garg
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hong Pan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Varsha Gupta
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Bernadus Krishna
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Zou Hui Chen
- Computational Biology, National University of Singapore, Singapore, Singapore
| | | | - Fabian Yap
- KK Women's and Children's Hospital, Singapore, Singapore
| | - Kok Hian Tan
- KK Women's and Children's Hospital, Singapore, Singapore
- Duke NUS Medical School, Singapore, Singapore
| | - Kok Yen Jerry Chan
- KK Women's and Children's Hospital, Singapore, Singapore
- Duke NUS Medical School, Singapore, Singapore
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- National University Hospital, Singapore, Singapore
| | | | - Nikita Rane
- Institute of Mental Health,Singapore, Singapore
| | | | | | - Mei Han
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Michael Meaney
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dennis Wang
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jussi Keppo
- Computational Biology, National University of Singapore, Singapore, Singapore
| | - Geoffrey Chern-Yee Tan
- Computational Biology, National University of Singapore, Singapore, Singapore
- Institute of Mental Health,Singapore, Singapore
| |
Collapse
|
3
|
Antonatos C, Grafanaki K, Georgiou S, Evangelou E, Vasilopoulos Y. Disentangling the complexity of psoriasis in the post-genome-wide association era. Genes Immun 2023; 24:236-247. [PMID: 37717118 DOI: 10.1038/s41435-023-00222-x] [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: 04/23/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
In recent years, genome-wide association studies (GWAS) have been instrumental in unraveling the genetic architecture of complex diseases, including psoriasis. The application of large-scale GWA studies in psoriasis has illustrated several associated loci that participate in the cutaneous inflammation, however explaining a fraction of the disease heritability. With the advent of high-throughput sequencing technologies and functional genomics approaches, the post-GWAS era aims to unravel the functional mechanisms underlying the inter-individual variability in psoriasis patients. In this review, we present the key advances of psoriasis GWAS in under-represented populations, rare, non-coding and structural variants and epistatic phenomena that orchestrate the interplay between different cell types. We further review the gene-gene and gene-environment interactions contributing to the disease predisposition and development of comorbidities through Mendelian randomization studies and pleiotropic effects of psoriasis-associated loci. We finally examine the holistic approaches conducted in psoriasis through system genetics and state-of-the-art transcriptomic analyses, discussing their potential implication in the expanding field of precision medicine and characterization of comorbidities.
Collapse
Affiliation(s)
- Charalabos Antonatos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece
| | - Katerina Grafanaki
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504, Patras, Greece
| | - Sophia Georgiou
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504, Patras, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45110, Ioannina, Greece
- Department of Epidemiology & Biostatistics, MRC Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece.
| |
Collapse
|
4
|
Huggett SB, Ikeda AS, Yuan Q, Benca-Bachman CE, Palmer RHC. Genome- and transcriptome-wide splicing associations with alcohol use disorder. Sci Rep 2023; 13:3950. [PMID: 36894673 PMCID: PMC9998611 DOI: 10.1038/s41598-023-30926-z] [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: 06/15/2022] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Genetic mechanisms of alternative mRNA splicing have been shown in the brain for a variety of neuropsychiatric traits, but not substance use disorders. Our study utilized RNA-sequencing data on alcohol use disorder (AUD) in four brain regions (n = 56; ages 40-73; 100% 'Caucasian'; PFC, NAc, BLA and CEA) and genome-wide association data on AUD (n = 435,563, ages 22-90; 100% European-American). Polygenic scores of AUD were associated with AUD-related alternative mRNA splicing in the brain. We identified 714 differentially spliced genes between AUD vs controls, which included both putative addiction genes and novel gene targets. We found 6463 splicing quantitative trait loci (sQTLs) that linked to the AUD differentially spliced genes. sQTLs were enriched in loose chromatin genomic regions and downstream gene targets. Additionally, the heritability of AUD was enriched for DNA variants in and around differentially spliced genes associated with AUD. Our study also performed splicing transcriptome-wide association studies (TWASs) of AUD and other drug use traits that unveiled specific genes for follow-up and splicing correlations across SUDs. Finally, we showed that differentially spliced genes between AUD vs control were also associated with primate models of chronic alcohol consumption in similar brain regions. Our study found substantial genetic contributions of alternative mRNA splicing in AUD.
Collapse
Affiliation(s)
- Spencer B Huggett
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Ami S Ikeda
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Qingyue Yuan
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Chelsie E Benca-Bachman
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Rohan H C Palmer
- Behavioral Genetics of Addiction Laboratory, Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA.
| |
Collapse
|
5
|
The molecular genetic basis of creativity: a mini review and perspectives. PSYCHOLOGICAL RESEARCH 2023; 87:1-16. [PMID: 35217895 DOI: 10.1007/s00426-022-01649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/16/2022] [Indexed: 01/27/2023]
Abstract
Although creativity is one of the defining features of human species, it is just the beginning of an ambitious attempt for psychologists to understand its genetic basis. With ongoing efforts, great progress has been achieved in molecular genetic studies of creativity. In this mini review, we highlighted recent molecular genetic findings for both domain-general and domain-specific creativity, and provided some perspectives for future studies. It is expected that this work will provide an update on the knowledge regarding the molecular genetic basis of creativity, and contribute to the further development of this field.
Collapse
|
6
|
Fryett JJ, Morris AP, Cordell HJ. Investigating the prediction of CpG methylation levels from SNP genotype data to help elucidate relationships between methylation, gene expression and complex traits. Genet Epidemiol 2022; 46:629-643. [PMID: 35930604 PMCID: PMC9804820 DOI: 10.1002/gepi.22496] [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: 05/16/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023]
Abstract
As popularised by PrediXcan (and related methods), transcriptome-wide association studies (TWAS), in which gene expression is imputed from single-nucleotide polymorphism (SNP) genotypes and tested for association with a phenotype, are a popular approach for investigating the role of gene expression in complex traits. Like gene expression, DNA methylation is an important biological process and, being under genetic regulation, may be imputable from SNP genotypes. Here, we investigate prediction of CpG methylation levels from SNP genotype data to help elucidate relationships between methylation, gene expression and complex traits. We start by examining how well CpG methylation can be predicted from SNP genotypes, comparing three penalised regression approaches and examining whether changing the window size improves prediction accuracy. Although methylation at most CpG sites cannot be accurately predicted from SNP genotypes, for a subset it can be predicted well. We next apply our methylation prediction models (trained using the optimal method and window size) to carry out a methylome-wide association study (MWAS) of primary biliary cholangitis. We intersect the regions identified via MWAS with those identified via TWAS, providing insight into the interplay between CpG methylation, gene expression and disease status. We conclude that MWAS has the potential to improve understanding of biological mechanisms in complex traits.
Collapse
Affiliation(s)
- James J. Fryett
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal ResearchUniversity of ManchesterManchesterUK
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| |
Collapse
|
7
|
Alamin M, Sultana MH, Lou X, Jin W, Xu H. Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS. PLANTS (BASEL, SWITZERLAND) 2022; 11:3277. [PMID: 36501317 PMCID: PMC9739826 DOI: 10.3390/plants11233277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Genome-wide association study (GWAS) is the most popular approach to dissecting complex traits in plants, humans, and animals. Numerous methods and tools have been proposed to discover the causal variants for GWAS data analysis. Among them, linear mixed models (LMMs) are widely used statistical methods for regulating confounding factors, including population structure, resulting in increased computational proficiency and statistical power in GWAS studies. Recently more attention has been paid to pleiotropy, multi-trait, gene-gene interaction, gene-environment interaction, and multi-locus methods with the growing availability of large-scale GWAS data and relevant phenotype samples. In this review, we have demonstrated all possible LMMs-based methods available in the literature for GWAS. We briefly discuss the different LMM methods, software packages, and available open-source applications in GWAS. Then, we include the advantages and weaknesses of the LMMs in GWAS. Finally, we discuss the future perspective and conclusion. The present review paper would be helpful to the researchers for selecting appropriate LMM models and methods quickly for GWAS data analysis and would benefit the scientific society.
Collapse
Affiliation(s)
- Md. Alamin
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | | | - Xiangyang Lou
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
8
|
Castaldi PJ, Abood A, Farber CR, Sheynkman GM. Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. Hum Mol Genet 2022; 31:R123-R136. [PMID: 35960994 PMCID: PMC9585682 DOI: 10.1093/hmg/ddac196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023] Open
Abstract
Aberrant splicing underlies many human diseases, including cancer, cardiovascular diseases and neurological disorders. Genome-wide mapping of splicing quantitative trait loci (sQTLs) has shown that genetic regulation of alternative splicing is widespread. However, identification of the corresponding isoform or protein products associated with disease-associated sQTLs is challenging with short-read RNA-seq, which cannot precisely characterize full-length transcript isoforms. Furthermore, contemporary sQTL interpretation often relies on reference transcript annotations, which are incomplete. Solutions to these issues may be found through integration of newly emerging long-read sequencing technologies. Long-read sequencing offers the capability to sequence full-length mRNA transcripts and, in some cases, to link sQTLs to transcript isoforms containing disease-relevant protein alterations. Here, we provide an overview of sQTL mapping approaches, the use of long-read sequencing to characterize sQTL effects on isoforms, the linkage of RNA isoforms to protein-level functions and comment on future directions in the field. Based on recent progress, long-read RNA sequencing promises to be part of the human disease genetics toolkit to discover and treat protein isoforms causing rare and complex diseases.
Collapse
Affiliation(s)
- Peter J Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of General Medicine and Primary Care, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Abdullah Abood
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Charles R Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gloria M Sheynkman
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
| |
Collapse
|
9
|
Pattee J, Vanderlinden LA, Mahaffey S, Hoffman P, Tabakoff B, Saba LM. Evaluation and characterization of expression quantitative trait analysis methods in the Hybrid Rat Diversity Panel. Front Genet 2022; 13:947423. [PMID: 36186443 PMCID: PMC9515987 DOI: 10.3389/fgene.2022.947423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/26/2022] [Indexed: 01/07/2023] Open
Abstract
The Hybrid Rat Diversity Panel (HRDP) is a stable and well-characterized set of more than 90 inbred rat strains that can be leveraged for systems genetics approaches to understanding the genetic and genomic variation associated with complex disease. The HRDP exhibits substantial between-strain diversity while retaining substantial within-strain isogenicity, allowing for the precise mapping of genetic variation associated with complex phenotypes and providing statistical power to identify associated variants. In order to robustly identify associated genetic variants, it is important to account for the population structure induced by inbreeding. To this end, we investigate the performance of four plausible approaches towards modeling quantitative traits in the HRDP and quantify their operating characteristics. In particular, we investigate three approaches based on genome-wide mixed model analysis, and one approach based on ordinary least squares linear regression. Towards facilitating study planning and design, we conduct extensive simulations to investigate the power of genetic association analyses in the HRDP, and characterize the impressive attained power. In simulation of eQTL data in the HRDP, we find that a mixed model approach that leverages leave-one-chromosome-out kinship estimation attains the highest power while controlling type I error.
Collapse
Affiliation(s)
- Jack Pattee
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lauren A. Vanderlinden
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Paula Hoffman
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,*Correspondence: Laura M. Saba,
| |
Collapse
|
10
|
Wang X, Gharahkhani P, Levine DM, Fitzgerald RC, Gockel I, Corley DA, Risch HA, Bernstein L, Chow WH, Onstad L, Shaheen NJ, Lagergren J, Hardie LJ, Wu AH, Pharoah PDP, Liu G, Anderson LA, Iyer PG, Gammon MD, Caldas C, Ye W, Barr H, Moayyedi P, Harrison R, Watson RGP, Attwood S, Chegwidden L, Love SB, MacDonald D, deCaestecker J, Prenen H, Ott K, Moebus S, Venerito M, Lang H, Mayershofer R, Knapp M, Veits L, Gerges C, Weismüller J, Reeh M, Nöthen MM, Izbicki JR, Manner H, Neuhaus H, Rösch T, Böhmer AC, Hölscher AH, Anders M, Pech O, Schumacher B, Schmidt C, Schmidt T, Noder T, Lorenz D, Vieth M, May A, Hess T, Kreuser N, Becker J, Ell C, Tomlinson I, Palles C, Jankowski JA, Whiteman DC, MacGregor S, Schumacher J, Vaughan TL, Buas MF, Dai JY. eQTL Set-Based Association Analysis Identifies Novel Susceptibility Loci for Barrett Esophagus and Esophageal Adenocarcinoma. Cancer Epidemiol Biomarkers Prev 2022; 31:1735-1745. [PMID: 35709760 PMCID: PMC9444939 DOI: 10.1158/1055-9965.epi-22-0096] [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: 01/28/2022] [Revised: 04/13/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Over 20 susceptibility single-nucleotide polymorphisms (SNP) have been identified for esophageal adenocarcinoma (EAC) and its precursor, Barrett esophagus (BE), explaining a small portion of heritability. METHODS Using genetic data from 4,323 BE and 4,116 EAC patients aggregated by international consortia including the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON), we conducted a comprehensive transcriptome-wide association study (TWAS) for BE/EAC, leveraging Genotype Tissue Expression (GTEx) gene-expression data from six tissue types of plausible relevance to EAC etiology: mucosa and muscularis from the esophagus, gastroesophageal (GE) junction, stomach, whole blood, and visceral adipose. Two analytical approaches were taken: standard TWAS using the predicted gene expression from local expression quantitative trait loci (eQTL), and set-based SKAT association using selected eQTLs that predict the gene expression. RESULTS Although the standard approach did not identify significant signals, the eQTL set-based approach identified eight novel associations, three of which were validated in independent external data (eQTL SNP sets for EXOC3, ZNF641, and HSP90AA1). CONCLUSIONS This study identified novel genetic susceptibility loci for EAC and BE using an eQTL set-based genetic association approach. IMPACT This study expanded the pool of genetic susceptibility loci for EAC and BE, suggesting the potential of the eQTL set-based genetic association approach as an alternative method for TWAS analysis.
Collapse
Affiliation(s)
- Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David M. Levine
- Department of Biostatistics, University of Washington, School of Public Health, Seattle, Washington, USA
| | - Rebecca C. Fitzgerald
- Medical Research Council (MRC) Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Douglas A. Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
- San Francisco Medical Center, Kaiser Permanente Northern California, San Francisco, California, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, California, USA
| | - Wong-Ho Chow
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Lynn Onstad
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicholas J. Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jesper Lagergren
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- School of Cancer and Pharmaceutical Sciences, King’s College London
| | | | - Anna H. Wu
- Department of Population and Public Health Sciences, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Paul D. P. Pharoah
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Geoffrey Liu
- Pharmacogenomic Epidemiology, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Lesley A. Anderson
- Department of Epidemiology and Public Health, Queen's University of Belfast, Royal Group of Hospitals, Northern Ireland
| | - Prasad G. Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Marilie D. Gammon
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Weimin Ye
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Hugh Barr
- Department of Upper GI Surgery, Gloucestershire Royal Hospital, Gloucester, UK
| | - Paul Moayyedi
- Farncombe Family Digestive Health Research Institute, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Rebecca Harrison
- Department of Pathology, Leicester Royal Infirmary, Leicester, UK
| | - RG Peter Watson
- Department of Medicine, Institute of Clinical Science, Royal Victoria Hospital, Belfast, UK
| | - Stephen Attwood
- Department of General Surgery, North Tyneside General Hospital, North Shields, UK
| | - Laura Chegwidden
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - Sharon B. Love
- Centre for Statistics in Medicine and Oxford Clinical Trials Research Unit, Oxford, UK
| | - David MacDonald
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - John deCaestecker
- Digestive Diseases Centre, University Hospitals of Leicester, Leicester, UK
| | - Hans Prenen
- Oncology Department, University Hospital Antwerp, Edegem, Belgium
| | - Katja Ott
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- Department of General, Visceral and Thorax Surgery, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Susanne Moebus
- Institute for Urban Public Health, University Hospitals, University of Duisburg-Essen, Essen, Germany
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | | | - Michael Knapp
- Institute for Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Lothar Veits
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Christian Gerges
- Department of Internal Medicine, Evangelisches Krankenhaus, Düsseldorf, Germany
| | | | - Matthias Reeh
- Department of General, Visceral and Thoracic Surgery, Asklepios Harzklinik Goslar, Goslar, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jakob R. Izbicki
- General, Visceral and Thoracic Surgery Department and Clinic. University Medical Center Hamburg-Eppendorf. Hamburg. Germany
| | - Hendrik Manner
- Department of Internal Medicine II, Frankfurt Hoechst Hospital, Frankfurt, Germany
| | - Horst Neuhaus
- Department of Internal Medicine, Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Thomas Rösch
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Anne C. Böhmer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Arnulf H. Hölscher
- Clinic for General, Visceral and Trauma Surgery, Contilia Center for Esophageal Diseases. Elisabeth Hospital Essen, Germany
| | - Mario Anders
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Department of Gastroenterology and Interdisciplinary Endoscopy, Vivantes Wenckebach-Klinikum, Berlin, Germany
| | - Oliver Pech
- Department of Gastroenterology and Interventional Endoscopy, St. John of God Hospital, Regensburg, Germany
| | - Brigitte Schumacher
- Department of Internal Medicine, Evangelisches Krankenhaus, Düsseldorf, Germany
- Department of Internal Medicine and Gastroenterology, Elisabeth Hospital, Essen, Germany
| | - Claudia Schmidt
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Thomas Schmidt
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Tania Noder
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Dietmar Lorenz
- Department of General and Visceral Surgery, Sana Klinikum, Offenbach, Germany
| | - Michael Vieth
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Andrea May
- Department of Gastroenterology, Oncology and Pneumology, Asklepios Paulinen Klinik, Wiesbaden, Germany
| | - Timo Hess
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Nicole Kreuser
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Jessica Becker
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Christian Ell
- Department of Medicine II, Sana Klinikum, Offenbach, Germany
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - David C. Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Thomas L. Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, Washington, USA
| | - Matthew F. Buas
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263 USA
| | - James Y. Dai
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington, School of Public Health, Seattle, Washington, USA
| |
Collapse
|
11
|
Genetic variant rs9848497 up-regulates MST1R expression, thereby influencing leadership phenotypes. Proc Natl Acad Sci U S A 2022; 119:e2207847119. [PMID: 35787185 PMCID: PMC9303931 DOI: 10.1073/pnas.2207847119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
12
|
Olayinka OA, O’Neill NK, Farrer LA, Wang G, Zhang X. Molecular Quantitative Trait Locus Mapping in Human Complex Diseases. Curr Protoc 2022; 2:e426. [PMID: 35587224 PMCID: PMC9186089 DOI: 10.1002/cpz1.426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mapping quantitative trait loci (QTLs) for molecular traits from chromatin to metabolites (i.e., xQTLs) provides insight into the locations and effect modes of genetic variants that influence these molecular phenotypes and the propagation of functional consequences of each variant. xQTL studies indirectly interrogate the functional landscape of the molecular basis of complex diseases, including the impact of non-coding regulatory variants, the tissue specificity of regulatory elements, and their contribution to disease by integrating with genome-wide association studies (GWAS). We summarize a variety of molecular xQTL studies in human tissues and cells. In addition, using the Alzheimer's Disease Sequencing Project (ADSP) as an example, we describe the ADSP xQTL project, a collaborative effort across the ADSP Functional Genomics Consortium (ADSP-FGC). The project's ultimate goal is a reference map of Alzheimer's-related QTLs using existing datasets from multiple omics layers to help us study the consequences of genetic variants identified in the ADSP. xQTL studies enable the identification of the causal genes and pathways in GWAS loci, which will likely aid in the discovery of novel biomarkers and therapeutic targets for complex diseases. © 2022 Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Oluwatosin A. Olayinka
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Nicholas K. O’Neill
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A. Farrer
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA,Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA,Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Gao Wang
- Department of Neurology, Columbia University, New York, NY, USA,Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Xiaoling Zhang
- Bioinformatics Program, Boston University, Boston, MA, USA,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA,Correspondence: Xiaoling Zhang, M.D., Ph.D., , Boston University School of Medicine, 72 East Concord Street, E223, Boston, MA 02118
| |
Collapse
|
13
|
Tian J, Chen C, Rao M, Zhang M, Lu Z, Cai Y, Ying P, Li B, Wang H, Wang L, Li Y, Huang J, Fan L, Cai X, Ning C, Li Y, Zhang F, Wang W, Jiang Y, Liu Y, Wang M, Li H, Huang C, Yang Z, Chang J, Zhu Y, Yang X, Miao X. Aberrant RNA splicing is a primary link between genetic variation and pancreatic cancer risk. Cancer Res 2022; 82:2084-2096. [PMID: 35363263 DOI: 10.1158/0008-5472.can-21-4367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022]
Abstract
Understanding the genetic variation underlying transcript splicing is essential for fully dissecting the molecular mechanisms of common diseases. The available evidence from splicing quantitative trait locus (sQTL) studies using pancreatic ductal adenocarcinoma (PDAC) tissues have been limited to small sample sizes. Here we present a genome-wide sQTL analysis to identify single nucleotide polymorphisms (SNPs) that control mRNA splicing in 176 PDAC samples from TCGA. From this analysis, 16,175 sQTLs were found to be significantly enriched in RNA binding protein (RBP) binding sites and chromatin regulatory elements and overlapped with known loci from PDAC genome-wide association studies (GWAS). sQTLs and expression QTLs (eQTL) showed mostly non-overlapping patterns, suggesting sQTLs provide additional insights into the etiology of disease. Target genes affected by sQTLs were closely related to cancer signaling pathways, high mutational burden, immune infiltration, and pharmaceutical targets, which will be helpful for clinical applications. Integration of a large-scale population consisting of 2,782 PDAC patients and 7,983 healthy controls identified an sQTL variant rs1785932-T allele that promotes alternative splicing of ELP2 exon 6 and leads to a lower level of the ELP2 full-length isoform (ELP2_V1) and a higher level of a truncated ELP2 isoform (ELP2_V2), resulting in decreased risk of PDAC (OR=0.83, 95%CI=0.77-0.89, P=1.16×10-6). The ELP2_V2 isoform functioned as a potential tumor suppressor gene, inhibiting PDAC cell proliferation by exhibiting stronger binding affinity to JAK1/STAT3 than ELP2_V1 and subsequently blocking the pathological activation of the p-STAT3 pathway. Collectively, these findings provide an informative sQTL resource and insights into the regulatory mechanisms linking splicing variants to PDAC risk.
Collapse
Affiliation(s)
| | | | | | - Ming Zhang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zequn Lu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yimin Cai
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pingting Ying
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Li
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoxue Wang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lu Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
| | - Yao Li
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, China
| | - Jinyu Huang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Linyun Fan
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaomin Cai
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Caibo Ning
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yanmin Li
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fuwei Zhang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenzhuo Wang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | | | | | - Min Wang
- Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Heng Li
- Tongji Hospital, Wuhan, Hubei, China
| | | | | | - Jiang Chang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, China
| | | | | | | |
Collapse
|
14
|
Liu A, Liu Y, Su KJ, Greenbaum J, Bai Y, Tian Q, Zhao LJ, Deng HW, Shen H. A transcriptome-wide association study to detect novel genes for volumetric bone mineral density. Bone 2021; 153:116106. [PMID: 34252604 PMCID: PMC8478845 DOI: 10.1016/j.bone.2021.116106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 01/02/2023]
Abstract
Transcriptome-wide association studies (TWAS) systematically investigate the association of genetically predicted gene expression with disease risk, providing an effective approach to identify novel susceptibility genes. Osteoporosis is the most common metabolic bone disease, associated with reduced bone mineral density (BMD) and increased risk of osteoporotic fractures, whereas genetic factors explain approximately 70% of the variance in phenotypes associated with bone. BMD is commonly assessed using dual-energy X-ray absorptiometry (DXA) to obtain measurements (g/cm2) of areal BMD. However, quantitative computed tomography (QCT) measured 3D volumetric BMD (vBMD) (g/cm3) has important advantages compared with DXA since it can evaluate cortical and trabecular microstructural features of bone quality, which can be used to directly predict fracture risk. Here, we performed the first TWAS for volumetric BMD (vBMD) by integrating genome-wide association studies (GWAS) data from two independent cohorts, namely the Framingham Heart Study (FHS, n = 3298) and the Osteoporotic Fractures in Men (MrOS, n = 4641), with tissue-specific gene expression data from the Genotype-Tissue Expression (GTEx) project. We first used stratified linkage disequilibrium (LD) score regression approach to identify 12 vBMD-relevant tissues, for which vBMD heritability is enriched in tissue-specific genes of the given tissue. Focusing on these tissues, we subsequently leveraged GTEx expression reference panels to predict tissue-specific gene expression levels based on the genotype data from FHS and MrOS. The associations between predicted gene expression levels and vBMD variation were then tested by MultiXcan, an innovative TWAS method that integrates information available across multiple tissues. We identified 70 significant genes associated with vBMD, including some previously identified osteoporosis-related genes such as LYRM2 and NME8, as well as some novel loci such as DNAAF2 and SPAG16. Our findings provide novel insights into the pathophysiological mechanisms of osteoporosis and highlight several novel vBMD-associated genes that warrant further investigation.
Collapse
Affiliation(s)
- Anqi Liu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Yong Liu
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Yuelu, Changsha, Hunan Province, PR China
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Jonathan Greenbaum
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Yuntong Bai
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA; Department of Biomedical Engineering, Tulane University, New Orleans, LA, USA
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Lan-Juan Zhao
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA; Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Yuelu, Changsha, Hunan Province, PR China
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA.
| |
Collapse
|
15
|
Zhu M, Yin P, Hu F, Jiang J, Yin L, Li Y, Wang S. Integrating genome-wide association and transcriptome prediction model identifies novel target genes for osteoporosis. Osteoporos Int 2021; 32:2493-2503. [PMID: 34142171 PMCID: PMC8608767 DOI: 10.1007/s00198-021-06024-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
UNLABELLED In this study, we integrated large-scale GWAS summary data and used the predicted transcriptome-wide association study method to discover novel genes associated with osteoporosis. We identified 204 candidate genes, which provide novel clues for understanding the genetic mechanism of osteoporosis and indicate potential therapeutic targets. INTRODUCTION Osteoporosis is a highly polygenetic disease characterized by low bone mass and deterioration of the bone microarchitecture. Our objective was to discover novel candidate genes associated with osteoporosis. METHODS To identify potential causal genes of the associated loci, we investigated trait-gene expression associations using the transcriptome-wide association study (TWAS) method. This method directly imputes gene expression effects from genome-wide association study (GWAS) data using a statistical prediction model trained on GTEx reference transcriptome data. We then performed a colocalization analysis to evaluate the posterior probability of biological patterns: associations characterized by a single causal variant or multiple distinct causal variants. Finally, a functional enrichment analysis of gene sets was performed using the VarElect and CluePedia tools, which assess the causal relationships between genes and a disease and search for potential gene's functional pathways. The osteoporosis-associated genes were further confirmed based on the differentially expressed genes profiled from mRNA expression data of bone tissue. RESULTS Our analysis identified 204 candidate genes, including 154 genes that have been previously associated with osteoporosis, 50 genes that have not been previously discovered. A biological function analysis found that 20 of the candidate genes were directly associated with osteoporosis. Further analysis of multiple gene expression profiles showed that 15 genes were differentially expressed in patients with osteoporosis. Among these, SLC11A2, MAP2K5, NFATC4, and HSP90B1 were enriched in four pathways, namely, mineral absorption pathway, MAPK signaling pathway, Wnt signaling pathway, and PI3K-Akt signaling pathway, which indicates a causal relationship with the occurrence of osteoporosis. CONCLUSIONS We demonstrated that transcriptome fine-mapping identifies more osteoporosis-related genes and provides key insight into the development of novel targeted therapeutics for the treatment of osteoporosis.
Collapse
Affiliation(s)
- M Zhu
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - P Yin
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - F Hu
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - J Jiang
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - L Yin
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Y Li
- AnLan AI, Shenzhen, China
| | - S Wang
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| |
Collapse
|
16
|
Ma M, Li P, Liu L, Cheng S, Cheng B, Liang CJ, Tan S, Li W, Wen Y, Guo X, Wu C. Integrating Transcriptome-Wide Association Study and mRNA Expression Profiling Identifies Novel Genes Associated With Osteonecrosis of the Femoral Head. Front Genet 2021; 12:663080. [PMID: 34163523 PMCID: PMC8215574 DOI: 10.3389/fgene.2021.663080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/29/2021] [Indexed: 12/04/2022] Open
Abstract
Objective This study aims to identify novel candidate genes associated with osteonecrosis of the femoral head (ONFH). Methods A transcriptome-wide association study (TWAS) was performed by integrating the genome-wide association study dataset of osteonecrosis (ON) in the UK Biobank with pre-computed mRNA expression reference weights of muscle skeleton (MS) and blood. The ON-associated genes identified by TWAS were further subjected to gene ontology (GO) analysis by the DAVID tool. Finally, a trans-omics comparative analysis of TWAS and genome-wide mRNA expression profiling was conducted to identify the common genes and the GO terms shared by both DNA-level TWAS and mRNA-level expression profile for ONFH. Results TWAS totally identified 564 genes that were with PTWAS value <0.05 for MS and blood, such as CBX1 (PTWAS = 0.0001 for MS), SRPK2 (PTWAS = 0.0002 for blood), and MYO5A (PTWAS = 0.0005 for blood). After comparing the genes detected by TWAS with the differentially expressed genes identified by mRNA expression profiling, we detected 59 overlapped genes, such as STEAP4 [PTWAS = 0.0270, FC (fold change)mRNA = 7.03], RABEP1 (PTWAS = 0.010, FCmRNA = 2.22), and MORC3 (PTWAS = 0.0053, FCmRNA = 2.92). The GO analysis of TWAS-identified genes discovered 53 GO terms for ON. Further comparing the GO results of TWAS and mRNA expression profiling identified four overlapped GO terms, including cysteine-type endopeptidase activity (PTWAS = 0.0006, PmRNA = 0.0227), extracellular space (PTWAS = 0.0342, PmRNA = 0.0012), protein binding (PTWAS = 0.0112, PmRNA = 0.0106), and ATP binding (PTWAS = 0.0464, PmRNA = 0.0033). Conclusion Several ONFH-associated genes and GO terms were identified by integrating TWAS and mRNA expression profiling. It provides novel clues to reveal the pathogenesis of ONFH.
Collapse
Affiliation(s)
- Mei Ma
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Peilin Li
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chu Jun Liang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Sijia Tan
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Wenyu Li
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiong Guo
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Cuiyan Wu
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
17
|
Eales JM, Jiang X, Xu X, Saluja S, Akbarov A, Cano-Gamez E, McNulty MT, Finan C, Guo H, Wystrychowski W, Szulinska M, Thomas HB, Pramanik S, Chopade S, Prestes PR, Wise I, Evangelou E, Salehi M, Shakanti Y, Ekholm M, Denniff M, Nazgiewicz A, Eichinger F, Godfrey B, Antczak A, Glyda M, Król R, Eyre S, Brown J, Berzuini C, Bowes J, Caulfield M, Zukowska-Szczechowska E, Zywiec J, Bogdanski P, Kretzler M, Woolf AS, Talavera D, Keavney B, Maffia P, Guzik TJ, O'Keefe RT, Trynka G, Samani NJ, Hingorani A, Sampson MG, Morris AP, Charchar FJ, Tomaszewski M. Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney. Nat Genet 2021; 53:630-637. [PMID: 33958779 DOI: 10.1038/s41588-021-00835-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/04/2021] [Indexed: 02/02/2023]
Abstract
The kidney is an organ of key relevance to blood pressure (BP) regulation, hypertension and antihypertensive treatment. However, genetically mediated renal mechanisms underlying susceptibility to hypertension remain poorly understood. We integrated genotype, gene expression, alternative splicing and DNA methylation profiles of up to 430 human kidneys to characterize the effects of BP index variants from genome-wide association studies (GWASs) on renal transcriptome and epigenome. We uncovered kidney targets for 479 (58.3%) BP-GWAS variants and paired 49 BP-GWAS kidney genes with 210 licensed drugs. Our colocalization and Mendelian randomization analyses identified 179 unique kidney genes with evidence of putatively causal effects on BP. Through Mendelian randomization, we also uncovered effects of BP on renal outcomes commonly affecting patients with hypertension. Collectively, our studies identified genetic variants, kidney genes, molecular mechanisms and biological pathways of key relevance to the genetic regulation of BP and inherited susceptibility to hypertension.
Collapse
Affiliation(s)
- James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Eddie Cano-Gamez
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Michelle T McNulty
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Christopher Finan
- Institute of Cardiovascular Science, University College London, London, UK
| | - Hui Guo
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Wojciech Wystrychowski
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Monika Szulinska
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Huw B Thomas
- Division of Evolution and Genomic Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Sanjeev Pramanik
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,East Lancashire Hospitals NHS Trust, Blackburn, UK
| | - Sandesh Chopade
- Institute of Cardiovascular Science, University College London, London, UK
| | - Priscilla R Prestes
- Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | - Ingrid Wise
- Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, Queensland, Australia
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.,Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Mahan Salehi
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Yusif Shakanti
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Mikael Ekholm
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Alicja Nazgiewicz
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Felix Eichinger
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Bradley Godfrey
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Maciej Glyda
- Department of Transplantology and General Surgery Poznan, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Robert Król
- Department of General, Vascular and Transplant Surgery, Medical University of Silesia, Katowice, Poland
| | - Stephen Eyre
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Jason Brown
- Division of Research and Innovation, Manchester University NHS Foundation Trust, Manchester, UK
| | - Carlo Berzuini
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - John Bowes
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Mark Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,National Institute for Health Research, Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | | | - Joanna Zywiec
- Department of Internal Medicine, Diabetology and Nephrology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Bogdanski
- Department of Obesity, Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | | | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Royal Manchester Children's Hospital and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Division of Cardiology and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Pasquale Maffia
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tomasz J Guzik
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Department of Internal and Agricultural Medicine, Jagiellonian University College of Medicine, Kraków, Poland
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Gosia Trynka
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK.,Open Targets, Wellcome Genome Campus, Cambridge, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,National Institute for Health Research, Leicester Biomedical Research Centre, Leicester, UK
| | - Aroon Hingorani
- Institute of Cardiovascular Science, University College London, London, UK
| | - Matthew G Sampson
- Division of Nephrology, Boston Children's Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Andrew P Morris
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.,Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Fadi J Charchar
- Health Innovation and Transformation Centre, School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,Department of Physiology, University of Melbourne, Parkville, Victoria, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK. .,Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.
| |
Collapse
|
18
|
Patel D, Zhang X, Farrell JJ, Chung J, Stein TD, Lunetta KL, Farrer LA. Cell-type-specific expression quantitative trait loci associated with Alzheimer disease in blood and brain tissue. Transl Psychiatry 2021; 11:250. [PMID: 33907181 PMCID: PMC8079392 DOI: 10.1038/s41398-021-01373-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/24/2021] [Accepted: 04/08/2021] [Indexed: 02/02/2023] Open
Abstract
Because regulation of gene expression is heritable and context-dependent, we investigated AD-related gene expression patterns in cell types in blood and brain. Cis-expression quantitative trait locus (eQTL) mapping was performed genome-wide in blood from 5257 Framingham Heart Study (FHS) participants and in brain donated by 475 Religious Orders Study/Memory & Aging Project (ROSMAP) participants. The association of gene expression with genotypes for all cis SNPs within 1 Mb of genes was evaluated using linear regression models for unrelated subjects and linear-mixed models for related subjects. Cell-type-specific eQTL (ct-eQTL) models included an interaction term for the expression of "proxy" genes that discriminate particular cell type. Ct-eQTL analysis identified 11,649 and 2533 additional significant gene-SNP eQTL pairs in brain and blood, respectively, that were not detected in generic eQTL analysis. Of note, 386 unique target eGenes of significant eQTLs shared between blood and brain were enriched in apoptosis and Wnt signaling pathways. Five of these shared genes are established AD loci. The potential importance and relevance to AD of significant results in myeloid cell types is supported by the observation that a large portion of GWS ct-eQTLs map within 1 Mb of established AD loci and 58% (23/40) of the most significant eGenes in these eQTLs have previously been implicated in AD. This study identified cell-type-specific expression patterns for established and potentially novel AD genes, found additional evidence for the role of myeloid cells in AD risk, and discovered potential novel blood and brain AD biomarkers that highlight the importance of cell-type-specific analysis.
Collapse
Affiliation(s)
- Devanshi Patel
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Department of Veterans Affairs Medical Center, Bedford, MA, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Lindsay A Farrer
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
| |
Collapse
|
19
|
Díez-Obrero V, Dampier CH, Moratalla-Navarro F, Devall M, Plummer SJ, Díez-Villanueva A, Peters U, Bien S, Huyghe JR, Kundaje A, Ibáñez-Sanz G, Guinó E, Obón-Santacana M, Carreras-Torres R, Casey G, Moreno V. Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci. Cell Mol Gastroenterol Hepatol 2021; 12:181-197. [PMID: 33601062 PMCID: PMC8102177 DOI: 10.1016/j.jcmgh.2021.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS The association of genetic variation with tissue-specific gene expression and alternative splicing guides functional characterization of complex trait-associated loci and may suggest novel genes implicated in disease. Here, our aims were as follows: (1) to generate reference profiles of colon mucosa gene expression and alternative splicing and compare them across colon subsites (ascending, transverse, and descending), (2) to identify expression and splicing quantitative trait loci (QTLs), (3) to find traits for which identified QTLs contribute to single-nucleotide polymorphism (SNP)-based heritability, (4) to propose candidate effector genes, and (5) to provide a web-based visualization resource. METHODS We collected colonic mucosal biopsy specimens from 485 healthy adults and performed bulk RNA sequencing. We performed genome-wide SNP genotyping from blood leukocytes. Statistical approaches and bioinformatics software were used for QTL identification and downstream analyses. RESULTS We provided a complete quantification of gene expression and alternative splicing across colon subsites and described their differences. We identified thousands of expression and splicing QTLs and defined their enrichment at genome-wide regulatory regions. We found that part of the SNP-based heritability of diseases affecting colon tissue, such as colorectal cancer and inflammatory bowel disease, but also of diseases affecting other tissues, such as psychiatric conditions, can be explained by the identified QTLs. We provided candidate effector genes for multiple phenotypes. Finally, we provided the Colon Transcriptome Explorer web application. CONCLUSIONS We provide a large characterization of gene expression and splicing across colon subsites. Our findings provide greater etiologic insight into complex traits and diseases influenced by transcriptomic changes in colon tissue.
Collapse
Affiliation(s)
- Virginia Díez-Obrero
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Colorectal Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL) Program, Bellvitge Biomedical Research Institute, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Christopher H Dampier
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia; Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia; Department of Surgery, University of Virginia, Charlottesville, Virginia
| | - Ferran Moratalla-Navarro
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Matthew Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia; Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Sarah J Plummer
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia; Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Anna Díez-Villanueva
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Colorectal Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL) Program, Bellvitge Biomedical Research Institute, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
| | - Ulrike Peters
- Epidemiology Department, University of Washington, Seattle, Washington; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephanie Bien
- Epidemiology Department, University of Washington, Seattle, Washington; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jeroen R Huyghe
- Epidemiology Department, University of Washington, Seattle, Washington; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California
| | - Gemma Ibáñez-Sanz
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Colorectal Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL) Program, Bellvitge Biomedical Research Institute, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain; Gastroenterology Department, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Elisabeth Guinó
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Colorectal Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL) Program, Bellvitge Biomedical Research Institute, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
| | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Colorectal Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL) Program, Bellvitge Biomedical Research Institute, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
| | - Robert Carreras-Torres
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Colorectal Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL) Program, Bellvitge Biomedical Research Institute, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia; Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia.
| | - Víctor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain; Colorectal Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL) Program, Bellvitge Biomedical Research Institute, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Madrid, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
| |
Collapse
|
20
|
Xiang R, MacLeod IM, Daetwyler HD, de Jong G, O’Connor E, Schrooten C, Chamberlain AJ, Goddard ME. Genome-wide fine-mapping identifies pleiotropic and functional variants that predict many traits across global cattle populations. Nat Commun 2021; 12:860. [PMID: 33558518 PMCID: PMC7870883 DOI: 10.1038/s41467-021-21001-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 11/23/2020] [Indexed: 02/08/2023] Open
Abstract
The difficulty in finding causative mutations has hampered their use in genomic prediction. Here, we present a methodology to fine-map potentially causal variants genome-wide by integrating the functional, evolutionary and pleiotropic information of variants using GWAS, variant clustering and Bayesian mixture models. Our analysis of 17 million sequence variants in 44,000+ Australian dairy cattle for 34 traits suggests, on average, one pleiotropic QTL existing in each 50 kb chromosome-segment. We selected a set of 80k variants representing potentially causal variants within each chromosome segment to develop a bovine XT-50K genotyping array. The custom array contains many pleiotropic variants with biological functions, including splicing QTLs and variants at conserved sites across 100 vertebrate species. This biology-informed custom array outperformed the standard array in predicting genetic value of multiple traits across populations in independent datasets of 90,000+ dairy cattle from the USA, Australia and New Zealand.
Collapse
Affiliation(s)
- Ruidong Xiang
- grid.1008.90000 0001 2179 088XFaculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC Australia
| | - Iona M. MacLeod
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC Australia
| | - Hans D. Daetwyler
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC Australia ,grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC Australia
| | | | | | | | - Amanda J. Chamberlain
- grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC Australia
| | - Michael E. Goddard
- grid.1008.90000 0001 2179 088XFaculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC Australia
| |
Collapse
|
21
|
Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874
expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
|
22
|
Novel directions in data pre-processing and genome-wide association study (GWAS) methodologies to overcome ongoing challenges. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
23
|
Chen G, Tang C, Qi J, Wang Y, Shi X. A fusion method based on alignment software with SNP and Indel detection methods. Comb Chem High Throughput Screen 2020; 25:519-527. [PMID: 33308124 DOI: 10.2174/1386207323666201211095018] [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: 07/18/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND With the advent of the second generation sequencing technology, the discovery of sequence alignment and sequence variation is a long-standing challenge. RESULTS A method based on general alignment software, SNP and Indel software tools was proposed in this paper. By comparing the advantages of traditional alignment software, we can produce the best alignment. SNP and Indel detection tools fusion research found that different depth of sequencing effect is different. When the sequence depth reaches a certain value, select one of the software for testing. CONCLUSIONS Finally, the experimental verification shows that SNP and Indel have certain advantages in the comparison of the effects of the fusion method.
Collapse
Affiliation(s)
- Guobing Chen
- Chongqing Key Laboratory of Spatial Data Mining and Big Data Integration for Ecology and Environment, Rongzhi College of Chongqing Technology and Business University , Chongqing 401320. China
| | - Chao Tang
- Radiation & Cancer Biology Laboratory, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing 400030. China
| | - Jun Qi
- Radiation & Cancer Biology Laboratory, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing 400030. China
| | - Ying Wang
- Radiation & Cancer Biology Laboratory, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing 400030. China
| | - Xiaolong Shi
- Radiation & Cancer Biology Laboratory, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing 400030. China
| |
Collapse
|
24
|
Liu Y, Shen H, Greenbaum J, Liu A, Su KJ, Zhang LS, Zhang L, Tian Q, Hu HG, He JS, Deng HW. Gene Expression and RNA Splicing Imputation Identifies Novel Candidate Genes Associated with Osteoporosis. J Clin Endocrinol Metab 2020; 105:5895512. [PMID: 32827035 PMCID: PMC7736639 DOI: 10.1210/clinem/dgaa572] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
CONTEXT Though genome-wide association studies (GWASs) have identified hundreds of genetic variants associated with osteoporosis related traits, such as bone mineral density (BMD) and fracture, it remains a challenge to interpret their biological functions and underlying biological mechanisms. OBJECTIVE Integrate diverse expression quantitative trait loci and splicing quantitative trait loci data with several powerful GWAS datasets to identify novel candidate genes associated with osteoporosis. DESIGN, SETTING, AND PARTICIPANTS Here, we conducted a transcriptome-wide association study (TWAS) for total body BMD (TB-BMD) (n = 66 628 for discovery and 7697 for validation) and fracture (53 184 fracture cases and 373 611 controls for discovery and 37 857 cases and 227 116 controls for validation), respectively. We also conducted multi-SNP-based summarized mendelian randomization analysis to further validate our findings. RESULTS In total, we detected 88 genes significantly associated with TB-BMD or fracture through expression or ribonucleic acid splicing. Summarized mendelian randomization analysis revealed that 78 of the significant genes may have potential causal effects on TB-BMD or fracture in at least 1 specific tissue. Among them, 64 genes have been reported in previous GWASs or TWASs for osteoporosis, such as ING3, CPED1, and WNT16, as well as 14 novel genes, such as DBF4B, GRN, TMUB2, and UNC93B1. CONCLUSIONS Overall, our findings provide novel insights into the pathogenesis mechanisms of osteoporosis and highlight the power of a TWAS to identify and prioritize potential causal genes.
Collapse
Affiliation(s)
- Yong Liu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Jonathan Greenbaum
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Anqi Liu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Li-Shu Zhang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, China
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Hong-Gang Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Hong-Wen Deng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
- Correspondence and Reprint Requests: Hong-Wen Deng, PhD, Professor, Director, Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, 1440 Canal St., Suite 2001, New Orleans, LA 70112.
| |
Collapse
|
25
|
Kim-Hellmuth S, Aguet F, Oliva M, Muñoz-Aguirre M, Kasela S, Wucher V, Castel SE, Hamel AR, Viñuela A, Roberts AL, Mangul S, Wen X, Wang G, Barbeira AN, Garrido-Martín D, Nadel BB, Zou Y, Bonazzola R, Quan J, Brown A, Martinez-Perez A, Soria JM, Getz G, Dermitzakis ET, Small KS, Stephens M, Xi HS, Im HK, Guigó R, Segrè AV, Stranger BE, Ardlie KG, Lappalainen T. Cell type-specific genetic regulation of gene expression across human tissues. Science 2020; 369:eaaz8528. [PMID: 32913075 PMCID: PMC8051643 DOI: 10.1126/science.aaz8528] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
The Genotype-Tissue Expression (GTEx) project has identified expression and splicing quantitative trait loci in cis (QTLs) for the majority of genes across a wide range of human tissues. However, the functional characterization of these QTLs has been limited by the heterogeneous cellular composition of GTEx tissue samples. We mapped interactions between computational estimates of cell type abundance and genotype to identify cell type-interaction QTLs for seven cell types and show that cell type-interaction expression QTLs (eQTLs) provide finer resolution to tissue specificity than bulk tissue cis-eQTLs. Analyses of genetic associations with 87 complex traits show a contribution from cell type-interaction QTLs and enables the discovery of hundreds of previously unidentified colocalized loci that are masked in bulk tissue.
Collapse
Affiliation(s)
- Sarah Kim-Hellmuth
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany.
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Meritxell Oliva
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya (UPC), Barcelona, Catalonia, Spain
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Valentin Wucher
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Stephane E Castel
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrew R Hamel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Amy L Roberts
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Serghei Mangul
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Gao Wang
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Diego Garrido-Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Brian B Nadel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuxin Zou
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Rodrigo Bonazzola
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jie Quan
- Inflammation & Immunology, Pfizer, Cambridge, MA, USA
| | - Andrew Brown
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Population Health and Genomics, University of Dundee, Dundee, Scotland, UK
| | - Angel Martinez-Perez
- Unit of Genomic of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - José Manuel Soria
- Unit of Genomic of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Hualin S Xi
- Foundational Neuroscience Center, AbbVie, Cambridge, MA, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Ayellet V Segrè
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Center for Genetic Medicine, Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA
| |
Collapse
|
26
|
Kahraman A, Karakulak T, Szklarczyk D, von Mering C. Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. Sci Rep 2020; 10:14453. [PMID: 32879328 PMCID: PMC7468103 DOI: 10.1038/s41598-020-71221-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/17/2020] [Indexed: 01/01/2023] Open
Abstract
Under normal conditions, cells of almost all tissue types express the same predominant canonical transcript isoform at each gene locus. In cancer, however, splicing regulation is often disturbed, leading to cancer-specific switches in the most dominant transcripts (MDT). To address the pathogenic impact of these switches, we have analyzed isoform-specific protein-protein interaction disruptions in 1,209 cancer samples covering 27 different cancer types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the International Cancer Genomics Consortium (ICGC). Our study revealed large variations in the number of cancer-specific MDT (cMDT) with the highest frequency in cancers of female reproductive organs. Interestingly, in contrast to the mutational load, cancers arising from the same primary tissue had a similar number of cMDT. Some cMDT were found in 100% of all samples in a cancer type, making them candidates for diagnostic biomarkers. cMDT tend to be located at densely populated network regions where they disrupted protein interactions in the proximity of pathogenic cancer genes. A gene ontology enrichment analysis showed that these disruptions occurred mostly in protein translation and RNA splicing pathways. Interestingly, samples with mutations in the spliceosomal complex tend to have higher number of cMDT, while other transcript expressions correlated with mutations in non-coding splice-site and promoter regions of their genes. This work demonstrates for the first time the large extent of cancer-specific alterations in alternative splicing for 27 different cancer types. It highlights distinct and common patterns of cMDT and suggests novel pathogenic transcripts and markers that induce large network disruptions in cancers.
Collapse
Affiliation(s)
- Abdullah Kahraman
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tülay Karakulak
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| |
Collapse
|
27
|
The Role of Noncoding Variants in Heritable Disease. Trends Genet 2020; 36:880-891. [PMID: 32741549 DOI: 10.1016/j.tig.2020.07.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022]
Abstract
The genetic basis of disease has largely focused on coding regions. However, it has become clear that a large proportion of the noncoding genome is functional and harbors genetic variants that contribute to disease etiology. Here, we review recent examples of inherited noncoding alterations that are responsible for Mendelian disorders or act to influence complex traits. We explore both rare and common genetic variants and discuss the wide range of mechanisms by which they affect gene regulation to promote disease. We also debate the challenges and progress associated with identifying and interpreting the functional and clinical significance of genetic variation in the context of the noncoding regulatory landscape.
Collapse
|
28
|
Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2020; 80:100874. [PMID: 32553897 DOI: 10.1016/j.preteyeres.2020.100874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
Abstract
Mutations which induce aberrant transcript splicing represent a distinct class of disease-causing genetic variants in retinal disease genes. Such mutations may either weaken or erase regular splice sites or create novel splice sites which alter exon recognition. While mutations affecting the canonical GU-AG dinucleotides at the splice donor and splice acceptor site are highly predictive to cause a splicing defect, other variants in the vicinity of the canonical splice sites or those affecting additional cis-acting regulatory sequences within exons or introns are much more difficult to assess or even to recognize and require additional experimental validation. Splicing mutations are unique in that the actual outcome for the transcript (e.g. exon skipping, pseudoexon inclusion, intron retention) and the encoded protein can be quite different depending on the individual mutation. In this article, we present an overview on the current knowledge about and impact of splicing mutations in inherited retinal diseases. We introduce the most common sub-classes of splicing mutations including examples from our own work and others and discuss current strategies for the identification and validation of splicing mutations, as well as therapeutic approaches, open questions, and future perspectives in this field of research.
Collapse
|
29
|
Tian J, Wang Z, Mei S, Yang N, Yang Y, Ke J, Zhu Y, Gong Y, Zou D, Peng X, Wang X, Wan H, Zhong R, Chang J, Gong J, Han L, Miao X. CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. Nucleic Acids Res 2020; 47:D909-D916. [PMID: 30329095 PMCID: PMC6324030 DOI: 10.1093/nar/gky954] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing (AS) is a widespread process that increases structural transcript variation and proteome diversity. Aberrant splicing patterns are frequently observed in cancer initiation, progress, prognosis and therapy. Increasing evidence has demonstrated that AS events could undergo modulation by genetic variants. The identification of splicing quantitative trait loci (sQTLs), genetic variants that affect AS events, might represent an important step toward fully understanding the contribution of genetic variants in disease development. However, no database has yet been developed to systematically analyze sQTLs across multiple cancer types. Using genotype data from The Cancer Genome Atlas and corresponding AS values calculated by TCGASpliceSeq, we developed a computational pipeline to identify sQTLs from 9 026 tumor samples in 33 cancer types. We totally identified 4 599 598 sQTLs across all cancer types. We further performed survival analyses and identified 17 072 sQTLs associated with patient overall survival times. Furthermore, using genome-wide association study (GWAS) catalog data, we identified 1 180 132 sQTLs overlapping with known GWAS linkage disequilibrium regions. Finally, we constructed a user-friendly database, CancerSplicingQTL (http://www.cancersplicingqtl-hust.com/) for users to conveniently browse, search and download data of interest. This database provides an informative sQTL resource for further characterizing the potential functional roles of SNPs that control transcript isoforms in human cancer.
Collapse
Affiliation(s)
- Jianbo Tian
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Zhihua Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Shufang Mei
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Nan Yang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Yang Yang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Juntao Ke
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Ying Zhu
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Yajie Gong
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Danyi Zou
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Xiating Peng
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Xiaoyang Wang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Hao Wan
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Rong Zhong
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Jiang Chang
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Jing Gong
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.,HubeiKey Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Xiaoping Miao
- Key Laboratory of Environmental Health of Ministry of Education, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| |
Collapse
|
30
|
Yang C, Wan X, Lin X, Chen M, Zhou X, Liu J. CoMM: a collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information. Bioinformatics 2020; 35:1644-1652. [PMID: 30295737 DOI: 10.1093/bioinformatics/bty865] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/15/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Genome-wide association studies (GWASs) have been successful in identifying many genetic variants associated with complex traits. However, the mechanistic links between these variants and complex traits remain elusive. A scientific hypothesis is that genetic variants influence complex traits at the organismal level via affecting cellular traits, such as regulating gene expression and altering protein abundance. Although earlier works have already presented some scientific insights about this hypothesis and their findings are very promising, statistical methods that effectively harness multilayered data (e.g. genetic variants, cellular traits and organismal traits) on a large scale for functional and mechanistic exploration are highly demanding. RESULTS In this study, we propose a collaborative mixed model (CoMM) to investigate the mechanistic role of associated variants in complex traits. The key idea is built upon the emerging scientific evidence that genetic effects at the cellular level are much stronger than those at the organismal level. Briefly, CoMM combines two models: the first model relating gene expression with genotype and the second model relating phenotype with predicted gene expression using the first model. The two models are fitted jointly in CoMM, such that the uncertainty in predicting gene expression has been fully accounted. To demonstrate the advantages of CoMM over existing methods, we conducted extensive simulation studies, and also applied CoMM to analyze 25 traits in NFBC1966 and Genetic Epidemiology Research on Aging (GERA) studies by integrating transcriptome information from the Genetic European in Health and Disease (GEUVADIS) Project. The results indicate that by leveraging regulatory information, CoMM can effectively improve the power of prioritizing risk variants. Regarding the computational efficiency, CoMM can complete the analysis of NFBC1966 dataset and GERA datasets in 2 and 18 min, respectively. AVAILABILITY AND IMPLEMENTATION The developed R package is available at https://github.com/gordonliu810822/CoMM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Can Yang
- Department of Mathematics, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiang Wan
- Shenzhen Research Institute of Big Data, Shenzhen, China
| | - Xinyi Lin
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore
| | - Mengjie Chen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Jin Liu
- Centre for Quantitative Medicine, Program in Health Services and Systems Research, Duke-NUS Medical School, Singapore
| |
Collapse
|
31
|
Gauthier L, Stynen B, Serohijos AWR, Michnick SW. Genetics' Piece of the PI: Inferring the Origin of Complex Traits and Diseases from Proteome-Wide Protein-Protein Interaction Dynamics. Bioessays 2019; 42:e1900169. [PMID: 31854021 DOI: 10.1002/bies.201900169] [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: 09/16/2019] [Revised: 11/15/2019] [Indexed: 11/07/2022]
Abstract
How do common and rare genetic polymorphisms contribute to quantitative traits or disease risk and progression? Multiple human traits have been extensively characterized at the genomic level, revealing their complex genetic architecture. However, it is difficult to resolve the mechanisms by which specific variants contribute to a phenotype. Recently, analyses of variant effects on molecular traits have uncovered intermediate mechanisms that link sequence variation to phenotypic changes. Yet, these methods only capture a fraction of genetic contributions to phenotype. Here, in reviewing the field, it is proposed that complex traits can be understood by characterizing the dynamics of biochemical networks within living cells, and that the effects of genetic variation can be captured on these networks by using protein-protein interaction (PPI) methodologies. This synergy between PPI methodologies and the genetics of complex traits opens new avenues to investigate the molecular etiology of human diseases and to facilitate their prevention or treatment.
Collapse
Affiliation(s)
- Louis Gauthier
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Bram Stynen
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Adrian W R Serohijos
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| | - Stephen W Michnick
- Departement de Biochimie, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada.,Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, 2900 Édouard-Montpetit, Montréal, Quebec, H3T 1J4, Canada
| |
Collapse
|
32
|
Chong WC, Cain JE. Lessons learned from the developmental origins of childhood renal cancer. Anat Rec (Hoboken) 2019; 303:2561-2577. [DOI: 10.1002/ar.24315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 08/14/2019] [Accepted: 10/05/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Wai Chin Chong
- Centre for Cancer ResearchHudson Institute of Medical Research Clayton Victoria Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health SciencesMonash University Clayton Victoria Australia
| | - Jason E. Cain
- Centre for Cancer ResearchHudson Institute of Medical Research Clayton Victoria Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health SciencesMonash University Clayton Victoria Australia
| |
Collapse
|
33
|
Malhotra R, Mauer AC, Lino Cardenas CL, Guo X, Yao J, Zhang X, Wunderer F, Smith AV, Wong Q, Pechlivanis S, Hwang SJ, Wang J, Lu L, Nicholson CJ, Shelton G, Buswell MD, Barnes HJ, Sigurslid HH, Slocum C, Rourke CO, Rhee DK, Bagchi A, Nigwekar SU, Buys ES, Campbell CY, Harris T, Budoff M, Criqui MH, Rotter JI, Johnson AD, Song C, Franceschini N, Debette S, Hoffmann U, Kälsch H, Nöthen MM, Sigurdsson S, Freedman BI, Bowden DW, Jöckel KH, Moebus S, Erbel R, Feitosa MF, Gudnason V, Thanassoulis G, Zapol WM, Lindsay ME, Bloch DB, Post WS, O'Donnell CJ. HDAC9 is implicated in atherosclerotic aortic calcification and affects vascular smooth muscle cell phenotype. Nat Genet 2019; 51:1580-1587. [PMID: 31659325 PMCID: PMC6858575 DOI: 10.1038/s41588-019-0514-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/16/2019] [Indexed: 01/16/2023]
Abstract
Aortic calcification is an important independent predictor of future cardiovascular events. We performed a genome-wide association meta-analysis to determine single nucleotide polymorphisms (SNPs) associated with the extent of abdominal (AAC, n = 9,417) or descending thoracic (TAC, n = 8,422) aortic calcification. Two genetic loci, HDAC9 and RAP1GAP, were associated with AAC at a genome-wide level (P < 5.0 × 10−8). No SNPs were associated with TAC at the genome-wide threshold. Increased expression of HDAC9 in human aortic smooth muscle cells (HASMCs) promoted calcification and reduced contractility, while inhibition of HDAC9 in HASMCs inhibited calcification and enhanced cell contractility. In matrix Gla protein (MGP)-deficient mice, a model of human vascular calcification, mice lacking HDAC9 had a 40% reduction in aortic calcification and improved survival. This translational genomic study identifies the first genetic risk locus associated with calcification of the abdominal aorta and describes a novel role for HDAC9 in the development of vascular calcification. Genome-wide analyses identify variants near HDAC9 associated with abdominal aortic calcification and other cardiovascular phenotypes. Functional work shows that HDAC9 promotes an osteogenic vascular smooth muscle cell phenotype, enhancing calcification and reducing contractility.
Collapse
Affiliation(s)
- Rajeev Malhotra
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Andreas C Mauer
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christian L Lino Cardenas
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiaoling Zhang
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA.,Department of Medicine (Biomedical Genetics Section), Boston University School of Medicine, Boston, MA, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Florian Wunderer
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Albert V Smith
- Icelandic Heart Association, Kópavogur, Iceland.,Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Shih-Jen Hwang
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA.,National Heart, Lung and Blood Institute, Population Sciences Branch, Division of Intramural Research, Bethesda, MD, USA
| | - Judy Wang
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Lingyi Lu
- Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Christopher J Nicholson
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Georgia Shelton
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mary D Buswell
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hanna J Barnes
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Haakon H Sigurslid
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Charles Slocum
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caitlin O' Rourke
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David K Rhee
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Aranya Bagchi
- Harvard Medical School, Boston, MA, USA.,Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sagar U Nigwekar
- Harvard Medical School, Boston, MA, USA.,Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emmanuel S Buys
- Harvard Medical School, Boston, MA, USA.,Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Matthew Budoff
- Division of Cardiology, Department of Medicine and Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael H Criqui
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA.,National Heart, Lung and Blood Institute, Population Sciences Branch, Division of Intramural Research, Bethesda, MD, USA
| | - Ci Song
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA.,National Heart, Lung and Blood Institute, Population Sciences Branch, Division of Intramural Research, Bethesda, MD, USA.,Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Stephanie Debette
- Inserm U1219, University of Bordeaux, Bordeaux, France.,Department of Neurology, University Hospital of Bordeaux, Bordeaux, France
| | - Udo Hoffmann
- Harvard Medical School, Boston, MA, USA.,Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Hagen Kälsch
- Department of Cardiology, Alfried Krupp Hospital, Essen, Germany.,Witten/Herdecke University, Witten, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain GmbH, University of Bonn, Bonn, Germany
| | | | | | | | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany.,Centre for Urban Epidemiology, University Hospital Essen, Essen, Germany
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Mary F Feitosa
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kópavogur, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - George Thanassoulis
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA.,Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Warren M Zapol
- Harvard Medical School, Boston, MA, USA.,Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mark E Lindsay
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Donald B Bloch
- Harvard Medical School, Boston, MA, USA.,Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.,Division of Rheumatology, Allergy, and Immunology; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher J O'Donnell
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA. .,U.S. Department of Veterans Affairs, Boston, MA, USA.
| |
Collapse
|
34
|
Dorris ER, Linehan E, Trenkmann M, Veale DJ, Fearon U, Wilson AG. Association of the Rheumatoid Arthritis Severity Variant rs26232 with the Invasive Activity of Synovial Fibroblasts. Cells 2019; 8:cells8101300. [PMID: 31652652 PMCID: PMC6829881 DOI: 10.3390/cells8101300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/19/2022] Open
Abstract
rs26232, located in intron one of C5orf30, is associated with the susceptibility to and severity of rheumatoid arthritis (RA). Here, we investigate the relationship between this variant and the biological activities of rheumatoid arthritis synovial fibroblasts (RASFs). RASFs were isolated from the knee joints of 33 RA patients. The rs26232 genotype was determined and cellular migration, invasion, and apoptosis were compared using in vitro techniques. The production of adhesion molecules, chemokines, and proteases was measured by ELISA or flow cytometry. Cohort genotypes were CC n = 16; CT n = 14; TT n = 3. In comparison with the RASFs of the CT genotype, the CC genotype showed a 1.48-fold greater invasiveness in vitro (p = 0.02), 1.6-fold higher expression intracellular adhesion molecule (ICAM)-1 (p = 0.001), and 5-fold IFN-γ inducible protein-10 (IP-10) (p = 0.01). There was no association of the rs26232 genotype with the expression levels of either total C5orf30 mRNA or any of the three transcript variants. The rs26232 C allele, which has previously been associated with both the risk and severity of RA, is associated with greater invasive activity of RASFs in vitro, and with higher expression of ICAM-1 and IP-10. In resting RASFs, rs26232 is not a quantitative trait locus for C5orf30 mRNA, indicating a more complex mechanism underlying the genotype‒phenotype relationship.
Collapse
Affiliation(s)
- Emma R Dorris
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland.
| | - Eimear Linehan
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland.
| | - Michelle Trenkmann
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland.
| | - Douglas J Veale
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland.
| | - Ursula Fearon
- Molecular Rheumatology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin D06 R590, Ireland.
| | - Anthony G Wilson
- University College Dublin Centre for Arthritis Research, Conway Institute, University College Dublin, Dublin D04 W6F6, Ireland.
| |
Collapse
|
35
|
Vandiedonck C. Genetic association of molecular traits: A help to identify causative variants in complex diseases. Clin Genet 2019; 93:520-532. [PMID: 29194587 DOI: 10.1111/cge.13187] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022]
Abstract
In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies. The genetic variants that modulate them are called expression quantitative trait loci. Their study has been extended to other molecular quantitative trait loci (molQTLs) that regulate gene expression at the various levels, from chromatin state to cellular responses. Altogether, these studies have generated a wealth of basic information on the genome-wide patterns of gene expression and their inter-individual variation. Most importantly, molQTLs have become an invaluable asset in the genetic study of complex diseases. Although the identification of the disease-causing variants on the basis of their overlap with molQTLs requires caution, molQTLs can help to prioritize the relevant candidate gene(s) in the disease-associated regions and bring a functional interpretation of the associated variants, therefore, bridging the gap between genotypes and clinical phenotypes.
Collapse
Affiliation(s)
- C Vandiedonck
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
36
|
Wheeler HE, Ploch S, Barbeira AN, Bonazzola R, Andaleon A, Fotuhi Siahpirani A, Saha A, Battle A, Roy S, Im HK. Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits. Genet Epidemiol 2019; 43:596-608. [PMID: 30950127 PMCID: PMC6687523 DOI: 10.1002/gepi.22205] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/15/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022]
Abstract
Regulation of gene expression is an important mechanism through which genetic variation can affect complex traits. A substantial portion of gene expression variation can be explained by both local (cis) and distal (trans) genetic variation. Much progress has been made in uncovering cis-acting expression quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate. Here we take advantage of our ability to predict the cis component of gene expression coupled with gene mapping methods such as PrediXcan to identify high confidence candidate trans-acting genes and their targets. That is, we correlate the cis component of gene expression with observed expression of genes in different chromosomes. Leveraging the shared cis-acting regulation across tissues, we combine the evidence of association across all available Genotype-Tissue Expression Project tissues and find 2,356 trans-acting/target gene pairs with high mappability scores. Reassuringly, trans-acting genes are enriched in transcription and nucleic acid binding pathways and target genes are enriched in known transcription factor binding sites. Interestingly, trans-acting genes are more significantly associated with selected complex traits and diseases than target or background genes, consistent with percolating trans effects. Our scripts and summary statistics are publicly available for future studies of trans-acting gene regulation.
Collapse
Affiliation(s)
- Heather E. Wheeler
- Department of BiologyLoyola University ChicagoChicagoIllinois
- Department of Computer ScienceLoyola University ChicagoChicagoIllinois
- Department of Public Health SciencesStritch School of Medicine, Loyola University ChicagoMaywoodIllinois
| | - Sally Ploch
- Department of BiologyLoyola University ChicagoChicagoIllinois
| | - Alvaro N. Barbeira
- Section of Genetic Medicine, Department of MedicineUniversity of ChicagoChicagoIllinois
| | - Rodrigo Bonazzola
- Section of Genetic Medicine, Department of MedicineUniversity of ChicagoChicagoIllinois
| | - Angela Andaleon
- Department of BiologyLoyola University ChicagoChicagoIllinois
| | | | - Ashis Saha
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMaryland
| | - Alexis Battle
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMaryland
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMaryland
| | - Sushmita Roy
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin‐MadisonMadisonWisconsin
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of MedicineUniversity of ChicagoChicagoIllinois
| |
Collapse
|
37
|
Zhu M, Xu K, Chen Y, Gu Y, Zhang M, Luo F, Liu Y, Gu W, Hu J, Xu H, Xie Z, Sun C, Li Y, Sun M, Xu X, Hsu HT, Chen H, Fu Q, Shi Y, Xu J, Ji L, Liu J, Bian L, Zhu J, Chen S, Xiao L, Li X, Jiang H, Shen M, Huang Q, Fang C, Li X, Huang G, Fan J, Jiang Z, Jiang Y, Dai J, Ma H, Zheng S, Cai Y, Dai H, Zheng X, Zhou H, Ni S, Jin G, She JX, Yu L, Polychronakos C, Hu Z, Zhou Z, Weng J, Shen H, Yang T. Identification of Novel T1D Risk Loci and Their Association With Age and Islet Function at Diagnosis in Autoantibody-Positive T1D Individuals: Based on a Two-Stage Genome-Wide Association Study. Diabetes Care 2019; 42:1414-1421. [PMID: 31152121 DOI: 10.2337/dc18-2023] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/03/2019] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Type 1 diabetes (T1D) is a highly heritable disease with much lower incidence but more adult-onset cases in the Chinese population. Although genome-wide association studies (GWAS) have identified >60 T1D loci in Caucasians, less is known in Asians. RESEARCH DESIGN AND METHODS We performed the first two-stage GWAS of T1D using 2,596 autoantibody-positive T1D case subjects and 5,082 control subjects in a Chinese Han population and evaluated the associations between the identified T1D risk loci and age and fasting C-peptide levels at T1D diagnosis. RESULTS We observed a high genetic correlation between children/adolescents and adult T1D case subjects (r g = 0.87), as well as subgroups of autoantibody status (r g ≥ 0.90). We identified four T1D risk loci reaching genome-wide significance in the Chinese Han population, including two novel loci, rs4320356 near BTN3A1 (odds ratio [OR] 1.26, P = 2.70 × 10-8) and rs3802604 in GATA3 (OR 1.24, P = 2.06 × 10-8), and two previously reported loci, rs1770 in MHC (OR 4.28, P = 2.25 × 10-232) and rs705699 in SUOX (OR 1.46, P = 7.48 × 10-20). Further fine mapping in the MHC region revealed five independent variants, including another novel locus, HLA-C position 275 (omnibus P = 9.78 × 10-12), specific to the Chinese population. Based on the identified eight variants, we achieved an area under the curve value of 0.86 (95% CI 0.85-0.88). By building a genetic risk score (GRS) with these variants, we observed that the higher GRS were associated with an earlier age of T1D diagnosis (P = 9.08 × 10-11) and lower fasting C-peptide levels (P = 7.19 × 10-3) in individuals newly diagnosed with T1D. CONCLUSIONS Our results extend current knowledge on genetic contributions to T1D risk. Further investigations in different populations are needed for genetic heterogeneity and subsequent precision medicine.
Collapse
Affiliation(s)
- Meng Zhu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Kuanfeng Xu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Chen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Gu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mei Zhang
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feihong Luo
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yu Liu
- Department of Endocrinology and Metabolism, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Wei Gu
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ji Hu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Haixia Xu
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiguo Xie
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Chengjun Sun
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yuxiu Li
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Min Sun
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xinyu Xu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hsiang-Ting Hsu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Chen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Fu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Shi
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jingjing Xu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Ji
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jin Liu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lingling Bian
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Zhu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuang Chen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Xiao
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Li
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hemin Jiang
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Shen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qianwen Huang
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chen Fang
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xia Li
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Gan Huang
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Jingyi Fan
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Zhu Jiang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Shuai Zheng
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Cai
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Dai
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xuqin Zheng
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongwen Zhou
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shining Ni
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA
| | - Liping Yu
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
| | - Constantin Polychronakos
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Canada
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China .,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiguang Zhou
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China .,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Jianping Weng
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China .,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tao Yang
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China .,Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, China
| |
Collapse
|
38
|
Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene. PLoS Genet 2019; 15:e1008229. [PMID: 31269066 PMCID: PMC6634423 DOI: 10.1371/journal.pgen.1008229] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 07/16/2019] [Accepted: 06/04/2019] [Indexed: 11/19/2022] Open
Abstract
While many disease-associated single nucleotide polymorphisms (SNPs) are associated with gene expression (expression quantitative trait loci, eQTLs), a large proportion of complex disease genome-wide association study (GWAS) variants are of unknown function. Some of these SNPs may contribute to disease by regulating gene splicing. Here, we investigate whether SNPs that are associated with alternative splicing (splice QTL or sQTL) can identify novel functions for existing GWAS variants or suggest new associated variants in chronic obstructive pulmonary disease (COPD). RNA sequencing was performed on whole blood from 376 subjects from the COPDGene Study. Using linear models, we identified 561,060 unique sQTL SNPs associated with 30,333 splice sites corresponding to 6,419 unique genes. Similarly, 708,928 unique eQTL SNPs involving 15,913 genes were detected at 10% FDR. While there is overlap between sQTLs and eQTLs, 55.3% of sQTLs are not eQTLs. Co-localization analysis revealed that 7 out of 21 loci associated with COPD (p<1x10-6) in a published GWAS have at least one shared causal variant between the GWAS and sQTL studies. Among the genes identified to have splice sites associated with top GWAS SNPs was FBXO38, in which a novel exon was discovered to be protective against COPD. Importantly, the sQTL in this locus was validated by qPCR in both blood and lung tissue, demonstrating that splice variants relevant to lung tissue can be identified in blood. Other identified genes included CDK11A and SULT1A2. Overall, these data indicate that analysis of alternative splicing can provide novel insights into disease mechanisms. In particular, we demonstrated that SNPs in a known COPD GWAS locus on chromosome 5q32 influence alternative splicing in the gene FBXO38.
Collapse
|
39
|
Integrative analysis of transcriptome-wide association study data and mRNA expression profiles identified candidate genes and pathways associated with atrial fibrillation. Heart Vessels 2019; 34:1882-1888. [PMID: 31065785 DOI: 10.1007/s00380-019-01418-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/19/2019] [Indexed: 01/18/2023]
Abstract
Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia characterized by extensive structural, contractile and electrophysiological remodeling. The genetic basis of AF remained elusive until now. Transcriptome-wide association study (TWAS) was conducted by FUSION tool using gene expression weights of 7 tissues combined with a large-scale genome-wide association study (GWAS) dataset of AF, totally involving 8180 AF cases and 28,612 controls. Significant genes identified by TWAS were then subjected to gene ontology (GO) and pathway enrichment analysis. The genome-wide mRNA gene expression profiling of AF was compared with the results of TWAS to detect common genes shared by TWAS and mRNA expression profiling of AF. TWAS detected a group of candidate genes with PTWAS values < 0.05 across the seven tissues for AF, such as CMAH (PTWAS = 3.15 × 10-25 for whole blood), INCENP (PTWAS = 1.77 × 10-22 for artery aorta), CMAHP (PTWAS = 4.57 × 10-20 for artery aorta). Pathway enrichment analysis identified multiple candidate pathways, such as protein K48-linked ubiquitination (P value = 0.0124), positive regulation of leukocyte chemotaxis (P value = 0.0046) and fatty acid degradation (P value = 0.0295). Further comparing the GO results of TWAS and mRNA expression profiling, 2 common GO terms were identified, including actin binding (PTWAS = 0.0446, PmRNA = 7.00 × 10-4) and extracellular matrix (PTWAS = 0.0037, PmRNA = 3.00 × 10-6). We detected multiple novel candidate genes, GO terms and pathways for AF, providing novel clues for understanding the genetic mechanism of AF.
Collapse
|
40
|
Hecker M, Rüge A, Putscher E, Boxberger N, Rommer PS, Fitzner B, Zettl UK. Aberrant expression of alternative splicing variants in multiple sclerosis - A systematic review. Autoimmun Rev 2019; 18:721-732. [PMID: 31059848 DOI: 10.1016/j.autrev.2019.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Alternative splicing is an important form of RNA processing that affects nearly all human genes. The differential expression of specific transcript and protein isoforms holds the potential of novel biomarkers for complex diseases. In this systematic review, we compiled the existing literature on aberrant alternative splicing events in multiple sclerosis (MS). METHODS A systematic literature search in the PubMed database was carried out and supplemented by screening the reference lists of the identified articles. We selected only MS-related original research studies which compared the levels of different isoforms of human protein-coding genes. A narrative synthesis of the research findings was conducted. Additionally, we performed a case-control analysis using high-density transcriptome microarray data to reevaluate the genes that were examined in the reviewed studies. RESULTS A total of 160 records were screened. Of those, 36 studies from the last two decades were included. Most commonly, peripheral blood samples were analyzed (32 studies), and PCR-based techniques were usually employed (27 studies) for measuring the expression of selected genes. Two studies used an exploratory genome-wide approach. Overall, 27 alternatively spliced genes were investigated. Nine of these genes appeared in at least two studies (CD40, CFLAR, FOXP3, IFNAR2, IL7R, MOG, PTPRC, SP140 and TNFRSF1A). The microarray data analysis confirmed differential alternative pre-mRNA splicing for 19 genes. CONCLUSIONS An altered RNA processing of genes mediating immune signaling pathways has been repeatedly implicated in MS. The analysis of individual exon-level expression patterns is stimulated by the advancement of transcriptome profiling technologies. In particular, the examination of genes encoded in MS-associated genetic regions may provide important insights into the pathogenesis of the disease and help to identify new biomarkers.
Collapse
Affiliation(s)
- Michael Hecker
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany.
| | - Annelen Rüge
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Elena Putscher
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Nina Boxberger
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Paulus Stefan Rommer
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany; Medical University of Vienna, Department of Neurology, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Brit Fitzner
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Uwe Klaus Zettl
- University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| |
Collapse
|
41
|
Pérez-Núñez I, Karaky M, Fedetz M, Barrionuevo C, Izquierdo G, Matesanz F, Alcina A. Splice-site variant in ACSL5: a marker promoting opposing effect on cell viability and protein expression. Eur J Hum Genet 2019; 27:1836-1844. [PMID: 31053784 PMCID: PMC6871522 DOI: 10.1038/s41431-019-0414-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 02/21/2019] [Accepted: 04/06/2019] [Indexed: 01/15/2023] Open
Abstract
Long-chain Acyl-CoA synthetases (ACSLs) activate fatty acids (FAs) by thioesterification with Coenzyme A (CoA), generating FA-CoAs. These products are essential for lipid metabolism and carcinogenesis. In previous study, we identified an intronic variant rs2256368:A>G, whose G allele promotes exon 20 skipping in up to 43% of ACSL5 transcripts but its functional relevance is unclear. Here, we compared the expression of splice (Spl) and nonsplice (NSpl) ACSL5 variants and the effect on cell viability under culture conditions that force cells to metabolize fatty acids. We found that lymphoblastoid cell lines from 1000 Genomes Project, bearing Spl genotypes, showed a reduced expression of total ACSL5 protein due to an inefficient translation of the Spl RNA. These cells impaired growth in cultures with phorbol myristate acetate-ionomycin (PMA-Io) or medium deprived of glucose, while production of reactive oxygen species increased in PMA-Io. Specific ACSL5-isoform transfection in HEK239T (kidney), U87 (astroglioma), and HOG (oligodendrocyte) cells showed the Spl protein to be the causal factor of cell-growth inhibition, despite its reduced protein expression. Our findings indicate that the variant rs2256368:A>G can predict a growth inhibitory activity, caused by the Spl isoform of ACSL5 protein, opposed to the activity of the NSpl. Deep understanding of its functioning might have application in metabolic diseases and cancer.
Collapse
Affiliation(s)
- Iván Pérez-Núñez
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Mohamad Karaky
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - María Fedetz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Cristina Barrionuevo
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Guillermo Izquierdo
- Unidad de Esclerosis Múltiple, Hospital Universitario Virgen Macarena, 41009, Sevilla, Spain
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain.
| | - Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain.
| |
Collapse
|
42
|
S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing. Nat Genet 2019; 51:755-763. [PMID: 30804562 DOI: 10.1038/s41588-019-0348-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 01/10/2019] [Indexed: 01/01/2023]
Abstract
Exome analysis of patients with a likely monogenic disease does not identify a causal variant in over half of cases. Splice-disrupting mutations make up the second largest class of known disease-causing mutations. Each individual (singleton) exome harbors over 500 rare variants of unknown significance (VUS) in the splicing region. The existing relevant pathogenicity prediction tools tackle all non-coding variants as one amorphic class and/or are not calibrated for the high sensitivity required for clinical use. Here we calibrate seven such tools and devise a novel tool called Splicing Clinically Applicable Pathogenicity prediction (S-CAP) that is over twice as powerful as all previous tools, removing 41% of patient VUS at 95% sensitivity. We show that S-CAP does this by using its own features and not via meta-prediction over previous tools, and that splicing pathogenicity prediction is distinct from predicting molecular splicing changes. S-CAP is an important step on the path to deriving non-coding causal diagnoses.
Collapse
|
43
|
Wang X, Yang M, Ren D, Terzaghi W, Deng XW, He G. Cis-regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:555-570. [PMID: 30375060 DOI: 10.1111/tpj.14142] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/19/2018] [Accepted: 10/23/2018] [Indexed: 05/14/2023]
Abstract
Alternative splicing (AS) plays key roles in plant development and the responses of plants to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from AS) in plant accessions and its contribution to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0 and Ler-1, as well as their F1 hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing. We found that most of the divergent AS events in Arabidopsis accessions were cis-regulated by sequence variation, including those in core splice site and splicing motifs. Many genes that differed in AS between Col-0 and Bur-0 were involved in stimulus responses. Further genome-wide association analyses of 22 environmental variables showed that single nucleotide polymorphisms influencing known splice site strength were also associated with environmental stress responses. These results demonstrate that cis-variation in genomic sequences among Arabidopsis accessions was the dominant contributor to AS divergence, and it may contribute to differences in environmental responses among Arabidopsis accessions.
Collapse
Affiliation(s)
- Xuncheng Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Mei Yang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Diqiu Ren
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, PA, 18766, USA
| | - Xing-Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Guangming He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
44
|
Chong R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YHE, Jones EM, Goodman DB, Xiao X, Kosuri S. A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions. Mol Cell 2019; 73:183-194.e8. [PMID: 30503770 PMCID: PMC6599603 DOI: 10.1016/j.molcel.2018.10.037] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/19/2018] [Accepted: 10/23/2018] [Indexed: 11/23/2022]
Abstract
Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter and found that 3.8% (1,050) of variants, most of which are extremely rare, led to large-effect splice-disrupting variants (SDVs). Importantly, we find that 83% of SDVs are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predict a priori. Our results indicate extant, rare genetic variants can have large functional effects on splicing at appreciable rates, even outside the context of disease, and MFASS enables their empirical assessment at scale.
Collapse
Affiliation(s)
- Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kimberly D Insigne
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David Yao
- Department of Genetics, Stanford University, Stanford, CA 94035, USA
| | - Christina P Burghard
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jeffrey Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yun-Hua E Hsiao
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric M Jones
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel B Goodman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
45
|
Park JH, Woo YM, Youm EM, Hamad N, Won HH, Naka K, Park EJ, Park JH, Kim HJ, Kim SH, Kim HJ, Ahn JS, Sohn SK, Moon JH, Jung CW, Park S, Lipton JH, Kimura S, Kim JW, Kim DDH. HMGCLL1 is a predictive biomarker for deep molecular response to imatinib therapy in chronic myeloid leukemia. Leukemia 2018; 33:1439-1450. [PMID: 30555164 PMCID: PMC6756062 DOI: 10.1038/s41375-018-0321-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/27/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
Achieving a deep molecular response (DMR) to tyrosine kinase inhibitor (TKI) therapy for chronic myeloid leukemia (CML) remains challenging and at present, there is no biomarker to predict DMR in this setting. Herein, we report that an HMGCLL1 genetic variant located in 6p12.1 can be used as a predictive genetic biomarker for intrinsic sensitivity to imatinib (IM) therapy. We measured DMR rate according to HMGCLL1 variant in a discovery set of CML patients (n = 201) and successfully replicated it in a validation set (n = 270). We also investigated the functional relevance of HMGCLL1 blockade with respect to response to TKI therapy and showed that small interfering RNA mediated blockade of HMGCLL1 isoform 3 results in significant decrease in viability of BCR-ABL1-positive cells including K562, CML-T1 or BaF3 cell lines with or without ABL1 kinase domain mutations such as T315I mutation. Decreased cell viability was also demonstrated in murine CML stem cells and human hematopoietic progenitor cells. RNA sequencing showed that blockade of HMGCLL1 was associated with G0/G1 arrest and the cell cycle. In summary, the HMGCLL1 gene polymorphism is a novel genetic biomarker for intrinsic sensitivity to IM therapy in CML patients that predicts DMR in this setting.
Collapse
Affiliation(s)
- Jong-Ho Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Young Min Woo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Emilia Moonkyung Youm
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Nada Hamad
- Department of Haematology, St Vincent's Hospital, University of New South Wales, Sydney, Australia
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Samsung Medical Center, Seoul, Korea
| | - Kazuhito Naka
- Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Eun-Ju Park
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - June-Hee Park
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Hee-Jin Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun-Hee Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyeoung-Joon Kim
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Jae Sook Ahn
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Sang Kyun Sohn
- Department of Hematology/Oncology, Kyungpook National University Hospital, Daegu, Korea
| | - Joon Ho Moon
- Department of Hematology/Oncology, Kyungpook National University Hospital, Daegu, Korea
| | - Chul Won Jung
- Department of Hematology/Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Silvia Park
- Department of Hematology/Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeffrey H Lipton
- Department of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Shinya Kimura
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga, 849-8501, Japan
| | - Jong-Won Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea. .,Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Samsung Medical Center, Seoul, Korea. .,Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| |
Collapse
|
46
|
Lagou V, Garcia-Perez JE, Smets I, Van Horebeek L, Vandebergh M, Chen L, Mallants K, Prezzemolo T, Hilven K, Humblet-Baron S, Moisse M, Van Damme P, Boeckxstaens G, Bowness P, Dubois B, Dooley J, Liston A, Goris A. Genetic Architecture of Adaptive Immune System Identifies Key Immune Regulators. Cell Rep 2018; 25:798-810.e6. [PMID: 30332657 PMCID: PMC6205839 DOI: 10.1016/j.celrep.2018.09.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
The immune system is highly diverse, but characterization of its genetic architecture has lagged behind the vast progress made by genome-wide association studies (GWASs) of emergent diseases. Our GWAS for 54 functionally relevant phenotypes of the adaptive immune system in 489 healthy individuals identifies eight genome-wide significant associations explaining 6%-20% of variance. Coding and splicing variants in PTPRC and COMMD10 are involved in memory T cell differentiation. Genetic variation controlling disease-relevant T helper cell subsets includes RICTOR and STON2 associated with Th2 and Th17, respectively, and the interferon-lambda locus controlling regulatory T cell proliferation. Early and memory B cell differentiation stages are associated with variation in LARP1B and SP4. Finally, the latrophilin family member ADGRL2 correlates with baseline pro-inflammatory interleukin-6 levels. Suggestive associations reveal mechanisms of autoimmune disease associations, in particular related to pro-inflammatory cytokine production. Pinpointing these key human immune regulators offers attractive therapeutic perspectives.
Collapse
Affiliation(s)
- Vasiliki Lagou
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Josselyn E Garcia-Perez
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Ide Smets
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Lies Van Horebeek
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Marijne Vandebergh
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Liye Chen
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Klara Mallants
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Teresa Prezzemolo
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Kelly Hilven
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Stephanie Humblet-Baron
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Matthieu Moisse
- Leuven Brain Institute (LBI), Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium; KU Leuven Department of Neurosciences, Experimental Neurology, 3000 Leuven, Belgium
| | - Philip Van Damme
- Leuven Brain Institute (LBI), Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium; KU Leuven Department of Neurosciences, Experimental Neurology, 3000 Leuven, Belgium
| | - Guy Boeckxstaens
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for GI Disorders (TARGID), 3000 Leuven, Belgium; Department of Gastroenterology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Paul Bowness
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Bénédicte Dubois
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium; Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - James Dooley
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium
| | - Adrian Liston
- VIB Center for Brain & Disease Research, Laboratory for Translational Immunology, 3000 Leuven, Belgium; KU Leuven Department of Immunology and Microbiology, Laboratory for Translational Immunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium.
| | - An Goris
- KU Leuven Department of Neurosciences, Laboratory for Neuroimmunology, 3000 Leuven, Belgium; Leuven Brain Institute (LBI), Leuven, Belgium.
| |
Collapse
|
47
|
Wang L, Perez J, Heard-Costa N, Chu AY, Joehanes R, Munson PJ, Levy D, Fox CS, Cupples LA, Liu CT. Integrating genetic, transcriptional, and biological information provides insights into obesity. Int J Obes (Lond) 2018; 43:457-467. [PMID: 30232418 PMCID: PMC6405310 DOI: 10.1038/s41366-018-0190-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/18/2018] [Accepted: 07/22/2018] [Indexed: 02/07/2023]
Abstract
Objective: Indices of body fat distribution are heritable, but few genetic signals have been reported from genome-wide association studies (GWAS) of computed tomography (CT) imaging measurements of body fat distribution. We aimed to identify genes associated with adiposity traits and the key drivers that are central to adipose regulatory networks. Subjects: We analyzed gene transcript expression data in blood from participants in the Framingham Heart Study, a large community-based cohort (n up to 4,303), as well as implemented an integrative analysis of these data and existing biological information. Results: Our association analyses identified unique and common gene expression signatures across several adiposity traits, including body mass index, waist-hip ratio, waist circumference, and CT-measured indices, including volume and quality of visceral and subcutaneous adipose tissues. We identified six enriched KEGG pathways and two co-expression modules for further exploration of adipose regulatory networks. The integrative analysis revealed four gene sets (Apoptosis, p53 signaling pathway, Proteasome, Ubiquitin mediated proteolysis) and two co-expression modules with significant genetic variants and 94 key drivers/genes whose local networks were enriched with adiposity-associated genes, suggesting that these enriched pathways or modules have genetic effects on adiposity. Most identified key driver genes are involved in essential biological processes such as controlling cell cycle, DNA repair and degradation of regulatory proteins and are cancer related. Conclusion: Our integrative analysis of genetic, transcriptional and biological information provides a list of compelling candidates for further follow-up functional studies to uncover the biological mechanisms underlying obesity. These candidates highlight the value of examining CT-derived and central adiposity traits.
Collapse
Affiliation(s)
- Lan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Jeremiah Perez
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | | | - Audrey Y Chu
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - Roby Joehanes
- Hebrew SeniorLife, Harvard Medical School, Boston, MA, 02131, USA
| | - Peter J Munson
- Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - Caroline S Fox
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.,The Framingham Heart Study, Framingham, MA, 01702, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA.
| |
Collapse
|
48
|
Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 2018; 34:211-224.e6. [PMID: 30078747 PMCID: PMC9844097 DOI: 10.1016/j.ccell.2018.07.001] [Citation(s) in RCA: 483] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/30/2018] [Accepted: 07/02/2018] [Indexed: 01/19/2023]
Abstract
Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alternative splicing events than normal samples. Association analysis of somatic variants with alternative splicing events confirmed known trans associations with variants in SF3B1 and U2AF1 and identified additional trans-acting variants (e.g., TADA1, PPP2R1A). Many tumors have thousands of alternative splicing events not detectable in normal samples; on average, we identified ≈930 exon-exon junctions ("neojunctions") in tumors not typically found in GTEx normals. From Clinical Proteomic Tumor Analysis Consortium data available for breast and ovarian tumor samples, we confirmed ≈1.7 neojunction- and ≈0.6 single nucleotide variant-derived peptides per tumor sample that are also predicted major histocompatibility complex-I binders ("putative neoantigens").
Collapse
Affiliation(s)
- André Kahles
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Kjong-Van Lehmann
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Nora C Toussaint
- ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Matthias Hüser
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Stefan G Stark
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Timo Sachsenberg
- University of Tübingen, Department of Computer Science, Tübingen, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Oliver Kohlbacher
- University of Tübingen, Department of Computer Science, Tübingen, Germany; Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Quantitative Biology Center, University of Tübingen, Tübingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Institute for Translational Bioinformatics, University Medical Center, Tübingen, Germany
| | - Chris Sander
- Dana-Farber Cancer Institute, cBio Center, Department of Biostatistics and Computational Biology, Boston, MA, USA; Harvard Medical School, CompBio Collaboratory, Department of Cell Biology, Boston, USA
| | | | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; ETH Zurich, Department of Biology, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
| |
Collapse
|
49
|
Abstract
In this issue of Cancer Cell, Kahles et al. perform a comprehensive analysis of RNA splicing across cancer types and identify novel correlations between genetic alterations and splicing in cancer. In addition, they identify that tumor-specific splicing has the potential to generate a large new class of tumor-specific neoantigens.
Collapse
Affiliation(s)
- Luisa Escobar Hoyos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, 408 E. 69th Street, New York, NY 10065, USA; David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Stony Brook University, New York, NY 10065, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, 408 E. 69th Street, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
50
|
Mogil LS, Andaleon A, Badalamenti A, Dickinson SP, Guo X, Rotter JI, Johnson WC, Im HK, Liu Y, Wheeler HE. Genetic architecture of gene expression traits across diverse populations. PLoS Genet 2018; 14:e1007586. [PMID: 30096133 PMCID: PMC6105030 DOI: 10.1371/journal.pgen.1007586] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 08/22/2018] [Accepted: 07/24/2018] [Indexed: 01/14/2023] Open
Abstract
For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression quantitative trait loci (eQTL) mapping in each population and show genetic correlation of gene expression depends on shared ancestry proportions. Using elastic net modeling with cross validation to optimize genotypic predictors of gene expression in each population, we show the genetic architecture of gene expression for most predictable genes is sparse. We found the best predicted gene in each population, TACSTD2 in AFA and CHURC1 in CAU and HIS, had similar prediction performance across populations with R2 > 0.8 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at https://github.com/WheelerLab/DivPop.
Collapse
Affiliation(s)
- Lauren S. Mogil
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Angela Andaleon
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Alexa Badalamenti
- Program in Bioinformatics, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Scott P. Dickinson
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Heather E. Wheeler
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Computer Science, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| |
Collapse
|