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Moore A, Venkatesh R, Levin MG, Damrauer SM, Reza N, Cappola TP, Ritchie MD. Connecting intermediate phenotypes to disease using multi-omics in heart failure. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.06.24311572. [PMID: 39148828 PMCID: PMC11326335 DOI: 10.1101/2024.08.06.24311572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Heart failure (HF) is one of the most common, complex, heterogeneous diseases in the world, with over 1-3% of the global population living with the condition. Progression of HF can be tracked via MRI measures of structural and functional changes to the heart, namely left ventricle (LV), including ejection fraction, mass, end-diastolic volume, and LV end-systolic volume. Moreover, while genome-wide association studies (GWAS) have been a useful tool to identify candidate variants involved in HF risk, they lack crucial tissue-specific and mechanistic information which can be gained from incorporating additional data modalities. This study addresses this gap by incorporating transcriptome-wide and proteome-wide association studies (TWAS and PWAS) to gain insights into genetically-regulated changes in gene expression and protein abundance in precursors to HF measured using MRI-derived cardiac measures as well as full-stage all-cause HF. We identified several gene and protein overlaps between LV ejection fraction and end-systolic volume measures. Many of the overlaps identified in MRI-derived measurements through TWAS and PWAS appear to be shared with all-cause HF. We implicate many putative pathways relevant in HF associated with these genes and proteins via gene-set enrichment and protein-protein interaction network approaches. The results of this study (1) highlight the benefit of using multi-omics to better understand genetics and (2) provide novel insights as to how changes in heart structure and function may relate to HF.
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Affiliation(s)
- Anni Moore
- Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk Philadelphia, PA, 19104, USA
| | - Rasika Venkatesh
- Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk Philadelphia, PA, 19104, USA
| | - Michael G. Levin
- Division of Cardiovascular Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd Philadelphia, PA, 19104, USA
| | - Scott M. Damrauer
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, 3400 Spruce St Philadelphia, PA 19104
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk Philadelphia, PA, 19104, USA
- Corporal Michael Crescenz VA Medical Center, 3900 Woodland Ave Philadelphia, PA
| | - Nosheen Reza
- Division of Cardiovascular Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd Philadelphia, PA, 19104, USA
| | - Thomas P. Cappola
- Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk Philadelphia, PA, 19104, USA
- Division of Cardiovascular Medicine, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd Philadelphia, PA, 19104, USA
| | - Marylyn D. Ritchie
- Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk Philadelphia, PA, 19104, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, 3700 Hamilton Walk Philadelphia, PA, 19104, USA
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Hybridization chain reaction-mediated Fe2MoO4 bimetallic nanozyme for colorimetric risk prediction of bladder cancer. Biosens Bioelectron 2022; 210:114272. [DOI: 10.1016/j.bios.2022.114272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022]
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Matthews BJ, Melia T, Waxman DJ. Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model. PLoS Genet 2021; 17:e1009588. [PMID: 34752452 PMCID: PMC8664386 DOI: 10.1371/journal.pgen.1009588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/10/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Sex differences in gene expression are widespread in the liver, where many autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57BL/6J and CAST/EiJ, representing two subspecies separated by 0.5-1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24, Tox, and Zfp809, lose their sex-biased expression in CAST/EiJ mouse liver. To elucidate the observed strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of the sex differences in expression between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-dependent gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs apparently lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations.
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Affiliation(s)
- Bryan J. Matthews
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Tisha Melia
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - David J. Waxman
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
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Zou M, Jiang D, Wu T, Zhang X, Zhao Y, Wu D, Sun W, Cui J, Moreland L, Li G. Post-GWAS functional studies reveal an RA-associated CD40-induced NF-kB signal transduction and transcriptional regulation network targeted by class II HDAC inhibitors. Hum Mol Genet 2021; 30:823-835. [PMID: 33517445 PMCID: PMC8161515 DOI: 10.1093/hmg/ddab032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 01/17/2023] Open
Abstract
Currently, it remains difficult to identify which single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are functional and how various functional SNPs (fSNPs) interact and contribute to disease susceptibility. GWAS have identified a CD40 locus that is associated with rheumatoid arthritis (RA). We previously used two techniques developed in our laboratory, single nucleotide polymorphism-next-generation sequencing (SNP-seq) and flanking restriction enhanced DNA pulldown-mass spectrometry (FREP-MS), to determine that the RA risk gene RBPJ regulates CD40 expression via a fSNP at the RA-associated CD40 locus. In the present work, by applying the same approach, we report the identification of six proteins that regulate RBPJ expression via binding to two fSNPs on the RA-associated RBPJ locus. Using these findings, together with the published data, we constructed an RA-associated signal transduction and transcriptional regulation network (STTRN) that functionally connects multiple RA-associated risk genes via transcriptional regulation networks (TRNs) linked by CD40-induced nuclear factor kappa B (NF-kB) signaling. Remarkably, this STTRN provides insight into the potential mechanism of action for the histone deacetylase inhibitor givinostat, an approved therapy for systemic juvenile idiopathic arthritis. Thus, the generation of disease-associated STTRNs based on post-GWAS functional studies is demonstrated as a novel and effective approach to apply GWAS for mechanistic studies and target identification.
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Affiliation(s)
- Meijuan Zou
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Pharmacology, Nanjing Medical University, Nanjing 211166, China
| | - Danli Jiang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Ting Wu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Medicine, Xiangya School of Medicine, Central South University, Changsha 410083, China
| | - Xiaoyu Zhang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Yihan Zhao
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Di Wu
- Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wei Sun
- Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
| | - Jing Cui
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Larry Moreland
- Department of Medicine, Division of Rheumatology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
| | - Gang Li
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
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5
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Yuan Z, Sunduimijid B, Xiang R, Behrendt R, Knight MI, Mason BA, Reich CM, Prowse-Wilkins C, Vander Jagt CJ, Chamberlain AJ, MacLeod IM, Li F, Yue X, Daetwyler HD. Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits. Genet Sel Evol 2021; 53:8. [PMID: 33461502 PMCID: PMC7812657 DOI: 10.1186/s12711-021-00602-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. Conclusions We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.
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Affiliation(s)
- Zehu Yuan
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Institutes of Agricultural Science and Technology Development (Joint International Research Laboratory of Agriculture & Agri-Product Safety), Yangzhou University, Yangzhou, 225000, People's Republic of China
| | - Bolormaa Sunduimijid
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ruidong Xiang
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ralph Behrendt
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Matthew I Knight
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Brett A Mason
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Coralie M Reich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Claire Prowse-Wilkins
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Fadi Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
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6
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Patel RK, West JD, Jiang Y, Fogarty EA, Grimson A. Robust partitioning of microRNA targets from downstream regulatory changes. Nucleic Acids Res 2020; 48:9724-9746. [PMID: 32821933 PMCID: PMC7515711 DOI: 10.1093/nar/gkaa687] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/19/2020] [Accepted: 08/08/2020] [Indexed: 11/14/2022] Open
Abstract
The biological impact of microRNAs (miRNAs) is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high false-positive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present an experimental and computational framework to deconvolute post-transcriptional and transcriptional changes using a combination of RNA-seq and PRO-seq. This novel approach allows us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. Using this approach, we identify miRNA-specific activity of target sites within the open reading frame. Additionally, we show that CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that mediate downstream regulatory changes. Given the robustness of the approach, CARP would be particularly suitable for dissecting miRNA regulatory networks in vivo.
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Affiliation(s)
- Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA
| | - Jessica D West
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ya Jiang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Genetics, Genomics, and Development, Cornell University, Ithaca, New York 14853, USA
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Andrew Grimson
- To whom correspondence should be addressed. Tel: +1 607 254 1307; Fax: +1 607 254 1307;
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7
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Li N, Cui Z, Huang D, Gao M, Li S, Song M, Wang Y, Tong L, Yin Z. Association of LINC00673 rs11655237 polymorphism with cancer susceptibility: A meta-analysis based on 23,478 subjects. Genomics 2020; 112:4148-4154. [PMID: 32650095 DOI: 10.1016/j.ygeno.2020.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 06/05/2020] [Accepted: 07/02/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Some studies on the relationship between LINC00673 polymorphism and cancer susceptibility have been inconsistent. To perform a more comprehensively quantitative assessment of LINC00673 rs11655237 and risk of overall cancer, we operated this meta-analysis for the first time. METHODS A comprehensive search was conducted to obtain relevant literature up to November 20, 2019. Pooled odds ratios and 95% confidence intervals were utilized to assess rs11655237 and cancer susceptibility under five different genetic models. RESULTS Eventually, 11 case-control studies from 9 articles were included. We found that LINC00673 rs11655237 polymorphism increased the susceptibility to overall cancer under all genetic models in the overall population. By dividing ethnicity and cancer type into subgroups, we also obtained similar positive results in subgroups of Chinese population, pancreatic cancer, cervical cancer, neuroblastoma, hepatoblastoma and gastric cancer. CONCLUSION Overall, this meta-analysis has demonstrated for the first time that LINC00673 rs11655237 could increase susceptibility to cancer.
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Affiliation(s)
- Na Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, PR China.
| | - Zhigang Cui
- School of Nursing, China Medical University, Shenyang 110122, PR China.
| | - Dayang Huang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, 110000, PR China
| | - Min Gao
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, PR China.
| | - Sixuan Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, PR China.
| | - Mingyang Song
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, PR China.
| | - Ying Wang
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, PR China.
| | - Lianwei Tong
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, PR China.
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, PR China.
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8
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Turchin MC, Stephens M. Bayesian multivariate reanalysis of large genetic studies identifies many new associations. PLoS Genet 2019; 15:e1008431. [PMID: 31596850 PMCID: PMC6802844 DOI: 10.1371/journal.pgen.1008431] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/21/2019] [Accepted: 09/17/2019] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have now been conducted for hundreds of phenotypes of relevance to human health. Many such GWAS involve multiple closely-related phenotypes collected on the same samples. However, the vast majority of these GWAS have been analyzed using simple univariate analyses, which consider one phenotype at a time. This is despite the fact that, at least in simulation experiments, multivariate analyses have been shown to be more powerful at detecting associations. Here, we conduct multivariate association analyses on 13 different publicly-available GWAS datasets that involve multiple closely-related phenotypes. These data include large studies of anthropometric traits (GIANT), plasma lipid traits (GlobalLipids), and red blood cell traits (HaemgenRBC). Our analyses identify many new associations (433 in total across the 13 studies), many of which replicate when follow-up samples are available. Overall, our results demonstrate that multivariate analyses can help make more effective use of data from both existing and future GWAS. Genome-wide association studies (GWAS) have become a common and powerful tool for identifying significant correlations between markers of genetic variation and physical traits of interest. Often these studies are conducted by comparing genetic variation against single traits one at a time (‘univariate’); however, it has previously been shown that it is possible to increase your power to detect significant associations by comparing genetic variation against multiple traits simultaneously (‘multivariate’). Despite this apparent increase in power though, researchers still rarely conduct multivariate GWAS, even when studies have multiple traits readily available. Here, we reanalyze 13 previously published GWAS using a multivariate method and find >400 additional associations. Our method makes use of univariate GWAS summary statistics and is available as a software package, thus making it accessible to other researchers interested in conducting the same analyses. We also show, using studies that have multiple releases, that our new associations have high rates of replication. Overall, we argue multivariate approaches in GWAS should no longer be overlooked and how, often, there is low-hanging fruit in the form of new associations by running these methods on data already collected.
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Affiliation(s)
- Michael C. Turchin
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Stephens
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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9
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Zhan M, Wang H, Xu SW, Yang LH, Chen W, Zhao SX, Shen H, Liu Q, Yang RM, Wang J. Variants in oxidative stress-related genes affect the chemosensitivity through Nrf2-mediated signaling pathway in biliary tract cancer. EBioMedicine 2019; 48:143-160. [PMID: 31590928 PMCID: PMC6838379 DOI: 10.1016/j.ebiom.2019.08.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 02/08/2023] Open
Abstract
Background Oxidative stress and their effectors play critical roles in carcinogenesis and chemoresistance. However, the role of oxidative stress-related genes variants in biliary tract cancer (BTC) chemoresistance remains unknown. In this work, we aim to investigate oxidative stress-dependent molecular mechanisms underlying chemoresistance, and find potential biomarkers to predict chemotherapy response for BTC. Methods Sixty-six SNPs in 21 oxidative stress-related genes were genotyped and analyzed in 367 BTC patients. Immunoblot, immunohistochemical, immunofluorescent, quantitative PCR, chromatin immunoprecipitation analysis and study of animal xenograft models were performed to discover oxidative stress-related susceptibility genes underlying chemoresistance mechanism of BTC. Findings We found that 3 functional polymorphisms (CAT_rs769217, GPX4_rs4807542, and GSR_rs3779647), which were shown to affect their respective gene expression levels, modified the effect of chemotherapy on overall survival (OS). We then demonstrated that knockdown of GPX4, CAT, or GSR induced chemoresistance through elevation of ROS level and activation of Nrf2-ABCG2 pathway in BTC cell lines. Moreover, the association between Nrf2 expression and BTC prognosis is only found in patients who received chemotherapy. Knockdown of Nrf2 enhanced chemosensitivity or even eliminated postoperative recurrence in BTC xenograft mouse models. Importantly, upon chemotherapy treatment patients harboring high oxidative stress-related score received higher survival benefit from adjuvant chemotherapy compared with patients with low oxidative stress-related score. Interpretation The result of our study suggests, for the first time, that the oxidative stress-related score calculated by combining variations in CAT, GPX4, and GSR or Nrf2 expression could be used for predicting the chemosensitivity of BTC patients. Fund This work was supported by the National Science Foundation of China, Foundation of Shanghai Shen Kang Hospital Development Center, and Shanghai Outstanding Academic Leaders Plan.
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Affiliation(s)
- Ming Zhan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hui Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Sun-Wang Xu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lin-Hua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuang-Xia Zhao
- The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai 200011, China
| | - Hui Shen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Rui-Meng Yang
- The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai 200011, China.
| | - Jian Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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10
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Taylor DL, Jackson AU, Narisu N, Hemani G, Erdos MR, Chines PS, Swift A, Idol J, Didion JP, Welch RP, Kinnunen L, Saramies J, Lakka TA, Laakso M, Tuomilehto J, Parker SCJ, Koistinen HA, Davey Smith G, Boehnke M, Scott LJ, Birney E, Collins FS. Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle. Proc Natl Acad Sci U S A 2019; 116:10883-10888. [PMID: 31076557 PMCID: PMC6561151 DOI: 10.1073/pnas.1814263116] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We integrate comeasured gene expression and DNA methylation (DNAme) in 265 human skeletal muscle biopsies from the FUSION study with >7 million genetic variants and eight physiological traits: height, waist, weight, waist-hip ratio, body mass index, fasting serum insulin, fasting plasma glucose, and type 2 diabetes. We find hundreds of genes and DNAme sites associated with fasting insulin, waist, and body mass index, as well as thousands of DNAme sites associated with gene expression (eQTM). We find that controlling for heterogeneity in tissue/muscle fiber type reduces the number of physiological trait associations, and that long-range eQTMs (>1 Mb) are reduced when controlling for tissue/muscle fiber type or latent factors. We map genetic regulators (quantitative trait loci; QTLs) of expression (eQTLs) and DNAme (mQTLs). Using Mendelian randomization (MR) and mediation techniques, we leverage these genetic maps to predict 213 causal relationships between expression and DNAme, approximately two-thirds of which predict methylation to causally influence expression. We use MR to integrate FUSION mQTLs, FUSION eQTLs, and GTEx eQTLs for 48 tissues with genetic associations for 534 diseases and quantitative traits. We identify hundreds of genes and thousands of DNAme sites that may drive the reported disease/quantitative trait genetic associations. We identify 300 gene expression MR associations that are present in both FUSION and GTEx skeletal muscle and that show stronger evidence of MR association in skeletal muscle than other tissues, which may partially reflect differences in power across tissues. As one example, we find that increased RXRA muscle expression may decrease lean tissue mass.
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Affiliation(s)
- D Leland Taylor
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
- European Molecular Biology Laboratory, European Bioinformatics Institute, CB10 1SD Hinxton, United Kingdom
| | - Anne U Jackson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Narisu Narisu
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN Bristol, United Kingdom
| | - Michael R Erdos
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Peter S Chines
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Amy Swift
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jackie Idol
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - John P Didion
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ryan P Welch
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Leena Kinnunen
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
| | - Jouko Saramies
- Rehabilitation Center, South Karelia Social and Health Care District EKSOTE, Fl-53130 Lappeenranta, Finland
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Fl-70211 Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Fl-70211 Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Fl-70100 Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, FI-70210 Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, FI-70210 Kuopio, Finland
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- Department of Public Health, University of Helsinki, Fl-00014 Helsinki, Finland
- Saudi Diabetes Research Group, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Stephen C J Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Heikki A Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, FI-00029 Helsinki, Finland
- Minerva Foundation Institute for Medical Research, FI-00290 Helsinki, Finland
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, BS8 2BN Bristol, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Laura J Scott
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109;
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, CB10 1SD Hinxton, United Kingdom;
| | - Francis S Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892;
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11
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Yi X, Xu E, Xiao Y, Cai X. Evaluation of the Relationship Between Common Variants in the TLR-9 Gene and Hip Osteoarthritis Susceptibility. Genet Test Mol Biomarkers 2019; 23:373-379. [PMID: 31066581 DOI: 10.1089/gtmb.2019.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Objective: Hip osteoarthritis (HOA) is one of the most common types of osteoarthritis and affects nearly 10% of men and 18% of women who are >60 years of age worldwide. It has been demonstrated to be a genetic disease with a 50% heritability risk. Recently, the TLR-9 gene has been associated with knee OA in both Turkish and Chinese populations, but the relationship between the TLR-9 gene and HOA has not been evaluated. In this study, we aimed to evaluate the relationship between the common genetic variants in the TLR-9 gene and the predisposition of Han Chinese individuals to HOA. Methods: A total of 730 HOA patients and 1220 healthy controls were recruited in a hospital-based case-control study. Six common single nucleotide polymorphisms (SNPs) of the TLR-9 gene were selected for genotyping, and genetic association analyses were performed using both single-marker and haplotype-based methods. Results: The SNP rs187084 was found to be significantly associated with the risk of HOA after a Bonferroni correction (adjusted allelic p-values with age, gender, and body mass index [BMI] = 0.0008). The results indicated that the A allele of rs187084 is a risk allele for HOA and is likely to be a predisposing factor leading to an increased risk of HOA (adjusted odds ratio with age, gender, and BMI = 1.26, 95% confidence interval = 1.10-1.43). The results of the haplotype analyses confirmed a similar pattern to the SNP analyses. Conclusions: Our study provides strong evidence that variations in the TLR-9 gene are closely linked with genetic susceptibility to HOA in the Han Chinese population. This finding furthers the role of TLR-9 in the development and occurrence of OA in general.
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Affiliation(s)
- Xiaoqing Yi
- 1 Department of Pediatrics, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Erdi Xu
- 1 Department of Pediatrics, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yanfeng Xiao
- 1 Department of Pediatrics, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xuan Cai
- 2 Department of Orthopaedic Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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12
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Angelin-Bonnet O, Biggs PJ, Vignes M. Gene Regulatory Networks: A Primer in Biological Processes and Statistical Modelling. Methods Mol Biol 2019; 1883:347-383. [PMID: 30547408 DOI: 10.1007/978-1-4939-8882-2_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Modelling gene regulatory networks requires not only a thorough understanding of the biological system depicted, but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to familiarize the reader with the biological processes and molecular factors at play in the process of gene expression regulation. We first describe the different interactions controlling each step of the expression process, from transcription to mRNA and protein decay. In the second section, we provide statistical tools to accurately represent this biological complexity in the form of mathematical models. Among other considerations, we discuss the topological properties of biological networks, the application of deterministic and stochastic frameworks, and the quantitative modelling of regulation. We particularly focus on the use of such models for the simulation of expression data that can serve as a benchmark for the testing of network inference algorithms.
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Affiliation(s)
- Olivia Angelin-Bonnet
- Institute of Fundamental Sciences, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- Institute of Fundamental Sciences, Palmerston North, New Zealand
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Matthieu Vignes
- Institute of Fundamental Sciences, Palmerston North, New Zealand.
- School of Veterinary Science, Massey University, Palmerston North, New Zealand.
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13
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5-bp insertion/deletion polymorphism in the promoter region of LncRNA GAS5 and cancer risk: A meta-analysis of 7005 cases and 8576 controls. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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14
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Tagging SNPs in the HOTAIR gene are associated with bladder cancer risk in a Chinese population. Gene 2018; 664:22-26. [DOI: 10.1016/j.gene.2018.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 12/21/2022]
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15
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Chu H, Chen Y, Yuan Q, Hua Q, Zhang X, Wang M, Tong N, Zhang W, Chen J, Zhang Z. The HOTAIR, PRNCR1 and POLR2E polymorphisms are associated with cancer risk: a meta-analysis. Oncotarget 2018; 8:43271-43283. [PMID: 28159929 PMCID: PMC5522144 DOI: 10.18632/oncotarget.14920] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (LncRNAs) have been widely studied and aberrant expression of lncRNAs are involved in diverse cancers. Genetic variation in lncRNAs can influence the lncRNAs expression and function. At present, there are many studies to investigate the association between lncRNAs polymorphisms and cancer susceptibility. However, it has no systematic study to evaluate the association. We performed a meta-analysis to summarize the results of common lncRNAs (HOTAIR, PRNCR1, POLR2E and H19) polymorphisms on cancer risk, by using the random-effect model to obtain the odds ratio (ORs) and 95% confidence interval (95%CI). We also applied the meta-regression and publication bias analysis to seek the source of heterogeneity and evaluate the stability of results, respectively. The summary results indicated that HOTAIR rs920778 increased the cancer risk in recessive model (OR = 1.61, 95% CI = 1.08-2.41, Pheterogeneity<0.001). For PRNCR1 (rs1016343, rs16901946) and POLR2E (rs3787016), we also found the significant association with incresed risk of cancer (all P<0.05). However, we did not observe any significant association between H19 rs2107425 and cancer risk. Our meta-analysis results revealed that these four lncRNAs polymorphisms (HOTAIR rs920778, PRNCR1 rs1016343 and rs16901946, POLR2E rs3787016) can contribute to cancer risk. Further studies should confirm these findings.
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Affiliation(s)
- Haiyan Chu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yaoyao Chen
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qinbo Yuan
- Department of Urology, Huaiyin Hospital of Huai'an City, Huai'an, China.,Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiuhan Hua
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xu Zhang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Na Tong
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinfei Chen
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
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16
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Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution. Nat Commun 2017; 8:1092. [PMID: 29061983 PMCID: PMC5653656 DOI: 10.1038/s41467-017-01037-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/09/2017] [Indexed: 12/23/2022] Open
Abstract
Noncoding regulatory variants play a central role in the genetics of human diseases and in evolution. Here we measure allele-specific transcription factor binding occupancy of three liver-specific transcription factors between crosses of two inbred mouse strains to elucidate the regulatory mechanisms underlying transcription factor binding variations in mammals. Our results highlight the pre-eminence of cis-acting variants on transcription factor occupancy divergence. Transcription factor binding differences linked to cis-acting variants generally exhibit additive inheritance, while those linked to trans-acting variants are most often dominantly inherited. Cis-acting variants lead to local coordination of transcription factor occupancies that decay with distance; distal coordination is also observed and may be modulated by long-range chromatin contacts. Our results reveal the regulatory mechanisms that interplay to drive transcription factor occupancy, chromatin state, and gene expression in complex mammalian cell states.
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Affiliation(s)
- Emily S Wong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Bianca M Schmitt
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | | | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Aisling Redmond
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Frances Connor
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Tim F Rayner
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Christine Feig
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | | | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK-Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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17
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Association between TLR-9 gene rs187084 polymorphism and knee osteoarthritis in a Chinese population. Biosci Rep 2017; 37:BSR20170844. [PMID: 28916728 PMCID: PMC5643737 DOI: 10.1042/bsr20170844] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/02/2017] [Accepted: 09/13/2017] [Indexed: 12/02/2022] Open
Abstract
Osteoarthritis (OA) is a complex disease that is induced by many genetic risk variants and other factors. To examine the role of toll-like receptor 9 (TLR-9) in OA patients, we conducted a case–control study involving 215 knee OA (KOA) patients and 215 controls in a Chinese population. Genotyping with a custom-by-design 48-Plex single nucleotide polymorphism Scan™ Kit showed the TLR-9 gene rs187084 polymorphism was associated with an increased risk of KOA. Stratification analyses further validated this finding among old people (age ≥ 55 years). In conclusion, TLR-9 gene rs187084 polymorphism is positively correlated with susceptibility to KOA, especially among old people. Nevertheless, this finding should be confirmed by larger size studies with more ethnic populations.
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18
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Su Y, Yang C, Zhang Z. The Association Between XPG Gene Polymorphism and Gastric Cancer Risk. Genet Test Mol Biomarkers 2017; 21:619-624. [PMID: 28832189 DOI: 10.1089/gtmb.2017.0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
PURPOSE Studies exploring the association between the Xeroderma pigmentosum group G (XPG) gene polymorphisms and gastric cancer (GC) risk provide conflicting findings. Thus, this meta-analysis was performed. MATERIALS AND METHODS The PubMed and EMBASE databases were comprehensively searched to identify studies for the inclusion in the meta-analysis. The strength of the association was evaluated by calculating pooled odds ratios and 95% confidence intervals. RESULTS Nine case-control studies involving 3540 cases and 3953 controls were included in the meta-analysis, which revealed that the XPG rs751402 polymorphism is positively associated with GC risk and could be viewed as a risk factor of GC in three genetic models. CONCLUSION The XPG gene rs751402 polymorphism is associated with an increased risk of GC in Chinese Han populations. This finding should be verified by larger studies that include additional ethnic groups.
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Affiliation(s)
- Yanyan Su
- Department of General Surgery, Hangzhou Red Cross Hospital/Zhe Jiang Chinese Medicine and Western Medicine Integrated Hospital , Hangzhou, China
| | - Chong Yang
- Department of General Surgery, Hangzhou Red Cross Hospital/Zhe Jiang Chinese Medicine and Western Medicine Integrated Hospital , Hangzhou, China
| | - Zongxiang Zhang
- Department of General Surgery, Hangzhou Red Cross Hospital/Zhe Jiang Chinese Medicine and Western Medicine Integrated Hospital , Hangzhou, China
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19
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Fan Y, Zhang S, Liang F, Zhou Y. Association of insulin-like growth factor I gene polymorphisms with the risk of osteoporosis in a Chinese population. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:8443-8451. [PMID: 31966696 PMCID: PMC6965436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/13/2017] [Indexed: 06/10/2023]
Abstract
Osteoporosis is a systemic metabolic and serious skeletal disease commonly observed among the elderly. Insulin-like growth factors (IGFs) are critical regulators for bone cell function. We estimated the role of IGF-I rs35767, rs2288377 and rs5742612 polymorphisms in the susceptibility to osteoporosis in a population of China, and assessed gene-environment interactions. A total of 346 patients with osteoporosis and 346 controls were enrolled. Genotyping of IGF-I rs35767, rs2288377 and rs5742612 was amplified and performed with the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The TA and AA genotypes displayed elevated risk of developing osteoporosis (TA vs TT: OR=1.54, 95% CI=1.11-2.15; AA vs TT: OR=3.65, 95% CI=2.09-6.37). Compared with TT individuals, individuals with the TA+AA genotype had a substantial increased susceptibility to osteoporosis (OR=1.80, 95% CI=1.31-2.46). In recessive model, the AA genotype of rs2288377 displayed 2.89 folds risk of osteoporosis (adjusted OR=2.89, 95% CI=1.70-4.89). A significant negative interaction was found between IGF-I rs2288377 and BMD levels for femoral neck (r=-0.14, P<0.001), total hip (r=-0.09, P<0.001) and trochanter (r=-0.13, P<0.001). In conclusion, we suggest that IGF-I rs2288377 polymorphism had a strong influence on osteoporosis susceptibility in this Chinese population.
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Affiliation(s)
- Yakun Fan
- Department of Geriatrics, The First Hospital of Shijiazhuang Shijiazhuang 050000, Hebei, China
| | - Shiyang Zhang
- Department of Geriatrics, The First Hospital of Shijiazhuang Shijiazhuang 050000, Hebei, China
| | - Fang Liang
- Department of Geriatrics, The First Hospital of Shijiazhuang Shijiazhuang 050000, Hebei, China
| | - Yanyan Zhou
- Department of Geriatrics, The First Hospital of Shijiazhuang Shijiazhuang 050000, Hebei, China
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20
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Time-dependent genetic effects on gene expression implicate aging processes. Genome Res 2017; 27:545-552. [PMID: 28302734 PMCID: PMC5378173 DOI: 10.1101/gr.207688.116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/23/2017] [Indexed: 01/04/2023]
Abstract
Gene expression is dependent on genetic and environmental factors. In the last decade, a large body of research has significantly improved our understanding of the genetic architecture of gene expression. However, it remains unclear whether genetic effects on gene expression remain stable over time. Here, we show, using longitudinal whole-blood gene expression data from a twin cohort, that the genetic architecture of a subset of genes is unstable over time. In addition, we identified 2213 genes differentially expressed across time points that we linked with aging within and across studies. Interestingly, we discovered that most differentially expressed genes were affected by a subset of 77 putative causal genes. Finally, we observed that putative causal genes and down-regulated genes were affected by a loss of genetic control between time points. Taken together, our data suggest that instability in the genetic architecture of a subset of genes could lead to widespread effects on the transcriptome with an aging signature.
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21
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The Genetic Architecture of Gene Expression in Peripheral Blood. Am J Hum Genet 2017; 100:228-237. [PMID: 28065468 DOI: 10.1016/j.ajhg.2016.12.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/14/2016] [Indexed: 01/28/2023] Open
Abstract
We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits. Of the set of expressed probes (15,966), 10,580 (66%) had an estimated narrow-sense heritability (h2) greater than zero with a mean (median) value of 0.192 (0.142). Across these probes, on average the proportion of genetic variance explained by all eQTL (hCOJO2) was 31% (0.060/0.192), meaning that 69% is missing, with the sentinel SNP of the largest eQTL explaining 87% (0.052/0.060) of the variance attributed to all identified cis- and trans-eQTL. For the same set of probes, the genetic variance attributed to genome-wide common (MAF > 0.01) HapMap 3 SNPs (hg2) accounted for on average 48% (0.093/0.192) of h2. Taken together, the evidence suggests that approximately half the genetic variance for gene expression is not tagged by common SNPs, and of the variance that is tagged by common SNPs, a large proportion can be attributed to identifiable eQTL of large effect, typically in cis. Finally, we present evidence that, compared with a meta-analysis, using individual-level data results in an increase of approximately 50% in power to detect eQTL.
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22
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Ji SG, Juran BD, Mucha S, Folseraas T, Jostins L, Melum E, Kumasaka N, Atkinson EJ, Schlicht EM, Liu JZ, Shah T, Gutierrez-Achury J, Boberg KM, Bergquist A, Vermeire S, Eksteen B, Durie PR, Farkkila M, Müller T, Schramm C, Sterneck M, Weismüller TJ, Gotthardt DN, Ellinghaus D, Braun F, Teufel A, Laudes M, Lieb W, Jacobs G, Beuers U, Weersma RK, Wijmenga C, Marschall HU, Milkiewicz P, Pares A, Kontula K, Chazouillères O, Invernizzi P, Goode E, Spiess K, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J, Floreani A, Gulamhusein AF, Eaton JE, Schreiber S, Coltescu C, Bowlus CL, Luketic VA, Odin JA, Chopra KB, Kowdley KV, Chalasani N, Manns MP, Srivastava B, Mells G, Sandford RN, Alexander G, Gaffney DJ, Chapman RW, Hirschfield GM, de Andrade M, Rushbrook SM, Franke A, Karlsen TH, Lazaridis KN, Anderson CA. Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease. Nat Genet 2017; 49:269-273. [PMID: 27992413 PMCID: PMC5540332 DOI: 10.1038/ng.3745] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 11/18/2016] [Indexed: 02/07/2023]
Abstract
Primary sclerosing cholangitis (PSC) is a rare progressive disorder leading to bile duct destruction; ∼75% of patients have comorbid inflammatory bowel disease (IBD). We undertook the largest genome-wide association study of PSC (4,796 cases and 19,955 population controls) and identified four new genome-wide significant loci. The most associated SNP at one locus affects splicing and expression of UBASH3A, with the protective allele (C) predicted to cause nonstop-mediated mRNA decay and lower expression of UBASH3A. Further analyses based on common variants suggested that the genome-wide genetic correlation (rG) between PSC and ulcerative colitis (UC) (rG = 0.29) was significantly greater than that between PSC and Crohn's disease (CD) (rG = 0.04) (P = 2.55 × 10-15). UC and CD were genetically more similar to each other (rG = 0.56) than either was to PSC (P < 1.0 × 10-15). Our study represents a substantial advance in understanding of the genetics of PSC.
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Affiliation(s)
- Sun-Gou Ji
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Brian D Juran
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom,Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, United Kingdom
| | - Espen Melum
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Natsuhiko Kumasaka
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Erik M Schlicht
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Jimmy Z Liu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tejas Shah
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Javier Gutierrez-Achury
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kirsten M Boberg
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Annika Bergquist
- Department of Gastroenterology and Hepatology, Karolinska University Hospital Huddinge, Karolinska Instituet, Stockholm, Sweden
| | - Severine Vermeire
- Department of Clinical and Experimental Medicine, Katholieke Universiteit Leuven, Lueven, Belgium,Department of Gastroenterology, University Hospital Lueven, Lueven, Belgium
| | - Bertus Eksteen
- Snyder Institute for Chronic Diseases, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Peter R Durie
- Physiology and Experimental Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Martti Farkkila
- Helsinki University and Helsinki University Hospital, Clinic of Gastroenterology, Helsinki, Finland
| | - Tobias Müller
- Department of Internal Medicine, Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martina Sterneck
- Department of Hepatobiliary Surgery and Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias J Weismüller
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany,Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany,Department of Internal Medicine 1, University Hospital of Bonn, Bonn, Germany
| | - Daniel N Gotthardt
- Department of Medicine, University Hospital of Heidelberg, Heidelberg, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Felix Braun
- Department of General, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andreas Teufel
- Department of Medicine I, University Medical Center, Regensburg, Germany
| | - Mattias Laudes
- Clinic of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gunnar Jacobs
- Institute of Epidemiology and Biobank PopGen, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ulrich Beuers
- Department of Gastroenterology and Hepatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Piotr Milkiewicz
- Liver and Internal Medicine Unit, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Albert Pares
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Kimmo Kontula
- Helsinki University, Department of Medicine, University of Helsinki, Helsinki, Finland
| | - Olivier Chazouillères
- AP-HP Hôpital Saint Antoine, Department of Hepatology, UPMC University Paris 06, Paris, France
| | - Pietro Invernizzi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Milano, Italy
| | - Elizabeth Goode
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Kelly Spiess
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Carmel Moore
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom
| | - Jennifer Sambrook
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,Department of Hematology, University of Cambridge, Long Road, Cambridge CB2 0PT, United Kingdom
| | - Willem H Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,Department of Hematology, University of Cambridge, Long Road, Cambridge CB2 0PT, United Kingdom,NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, United Kingdom
| | - David J Roberts
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,NHS Blood and Transplant - Oxford Centre, Level 2, John Radcliffe Hospital, Headley Way, Oxford OX3 9BQ, United Kingdom,Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, United Kingdom
| | - John Danesh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom
| | - Annarosa Floreani
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, Italy
| | - Aliya F Gulamhusein
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - John E Eaton
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany,Department for General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel 24105, Germany
| | | | - Christopher L Bowlus
- Division of Gastroenterology and Hepatology, University of California, Davis, California, United States of America
| | - Velimir A Luketic
- Gastroenterology and Hepatology Section, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Joseph A Odin
- Department of Medicine, The Mount Sinai School of Medicine, New York, New York, United States of America
| | - Kapil B Chopra
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kris V Kowdley
- Liver Care Network and Organ Care Research, Swedish Medical Center, Seattle, Washington, United States of America
| | - Naga Chalasani
- Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Michael P Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany,Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany
| | - Brijesh Srivastava
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - George Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom,Division of Gastroenterology and Hepatology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Graeme Alexander
- Department of Medicine, Division of Hepatology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel J Gaffney
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Roger W Chapman
- Department of Translational Gastroenterology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Gideon M Hirschfield
- Centre for Liver Research, NIHR Biomedical Research Unit, University of Birmingham, Birmingham, United Kingdom,University of Toronto and Liver Center, Toronto Western Hospital, Toronto, ON, Canada
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | | | | | | | - Simon M Rushbrook
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom H Karlsen
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Konstantinos N Lazaridis
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America,Corresponding authors: Correspondence should be addressed to C.A.A. () or K.N.L. () or
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom,Corresponding authors: Correspondence should be addressed to C.A.A. () or K.N.L. () or
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23
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Chen J, Xie J, Chen B, Quan M, Li Y, Li B, Zhang D. Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus. THE NEW PHYTOLOGIST 2016; 212:150-60. [PMID: 27265357 DOI: 10.1111/nph.14040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/28/2016] [Indexed: 05/22/2023]
Abstract
Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus. We used RNA-seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA-target pairs showed significant co-expression. Gene ontology (GO) term analysis showed that most of the genes in the co-regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single-SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA-target pairs associated with the same traits. Multi-SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co-expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis.
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Affiliation(s)
- Jinhui Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Beibei Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Ying Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
| | - Bailian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Department of Forestry, North Carolina State University, Raleigh, NC, 27695-8203, USA
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China
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24
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Jacobson E, Perry JK, Long DS, Vickers MH, O'Sullivan JM. A potential role for genome structure in the translation of mechanical force during immune cell development. Nucleus 2016; 7:462-475. [PMID: 27673560 PMCID: PMC5120600 DOI: 10.1080/19491034.2016.1238998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/11/2016] [Accepted: 09/13/2016] [Indexed: 12/29/2022] Open
Abstract
Immune cells react to a wide range of environments, both chemical and physical. While the former has been extensively studied, there is growing evidence that physical and in particular mechanical forces also affect immune cell behavior and development. In order to elicit a response that affects immune cell behavior or development, environmental signals must often reach the nucleus. Chemical and mechanical signals can initiate signal transduction pathways, but mechanical forces may also have a more direct route to the nucleus, altering nuclear shape via mechanotransduction. The three-dimensional organization of DNA allows for the possibility that altering nuclear shape directly remodels chromatin, redistributing critical regulatory elements and proteins, and resulting in wide-scale gene expression changes. As such, integrating mechanotransduction and genome architecture into the immunology toolkit will improve our understanding of immune development and disease.
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Affiliation(s)
- Elsie Jacobson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Jo K. Perry
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - David S. Long
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Mark H. Vickers
- Liggins Institute, University of Auckland, Auckland, New Zealand
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25
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Transethnic Genetic-Correlation Estimates from Summary Statistics. Am J Hum Genet 2016; 99:76-88. [PMID: 27321947 DOI: 10.1016/j.ajhg.2016.05.001] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 05/03/2016] [Indexed: 11/22/2022] Open
Abstract
The increasing number of genetic association studies conducted in multiple populations provides an unprecedented opportunity to study how the genetic architecture of complex phenotypes varies between populations, a problem important for both medical and population genetics. Here, we have developed a method for estimating the transethnic genetic correlation: the correlation of causal-variant effect sizes at SNPs common in populations. This methods takes advantage of the entire spectrum of SNP associations and uses only summary-level data from genome-wide association studies. This avoids the computational costs and privacy concerns associated with genotype-level information while remaining scalable to hundreds of thousands of individuals and millions of SNPs. We applied our method to data on gene expression, rheumatoid arthritis, and type 2 diabetes and overwhelmingly found that the genetic correlation was significantly less than 1. Our method is implemented in a Python package called Popcorn.
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26
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Kamkina P, Snoek LB, Grossmann J, Volkers RJM, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE. Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans. Mol Cell Proteomics 2016; 15:1670-80. [PMID: 26944343 DOI: 10.1074/mcp.m115.052548] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Indexed: 11/06/2022] Open
Abstract
Natural genetic variation is the raw material of evolution and influences disease development and progression. An important question is how this genetic variation translates into variation in protein abundance. To analyze the effects of the genetic background on gene and protein expression in the nematode Caenorhabditis elegans, we quantitatively compared the two genetically highly divergent wild-type strains N2 and CB4856. Gene expression was analyzed by microarray assays, and proteins were quantified using stable isotope labeling by amino acids in cell culture. Among all transcribed genes, we found 1,532 genes to be differentially transcribed between the two wild types. Of the total 3,238 quantified proteins, 129 proteins were significantly differentially expressed between N2 and CB4856. The differentially expressed proteins were enriched for genes that function in insulin-signaling and stress-response pathways, underlining strong divergence of these pathways in nematodes. The protein abundance of the two wild-type strains correlates more strongly than protein abundance versus transcript abundance within each wild type. Our findings indicate that in C. elegans only a fraction of the changes in protein abundance can be explained by the changes in mRNA abundance. These findings corroborate with the observations made across species.
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Affiliation(s)
- Polina Kamkina
- From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; §Ph.D. Program in Molecular Life Sciences Zurich, 8057 Zurich, Switzerland
| | - L Basten Snoek
- ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Jonas Grossmann
- **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland
| | - Rita J M Volkers
- ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Mark G Sterken
- ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Michael Daube
- From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Bernd Roschitzki
- **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland
| | - Claudia Fortes
- **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland
| | - Ralph Schlapbach
- **Functional Genomics Center Zurich, University of Zurich and Swiss Federal Institute of Technology Zurich, 8057 Zurich, Switzerland
| | - Alexander Roth
- From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Christian von Mering
- From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Michael O Hengartner
- From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Sabine P Schrimpf
- From the ‡Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
| | - Jan E Kammenga
- ‖Laboratory of Nematology, Wageningen University, Wageningen 6708 PB, The Netherlands;
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27
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Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. A survey of best practices for RNA-seq data analysis. Genome Biol 2016; 17:13. [PMID: 26813401 PMCID: PMC4728800 DOI: 10.1186/s13059-016-0881-8] [Citation(s) in RCA: 1384] [Impact Index Per Article: 173.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
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Affiliation(s)
- Ana Conesa
- Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA. .,Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012, Valencia, Spain.
| | - Pedro Madrigal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery, University of Cambridge, Cambridge, CB2 0SZ, UK.
| | - Sonia Tarazona
- Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012, Valencia, Spain.,Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, 46020, Valencia, Spain
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 171 77, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 17177, Stockholm, Sweden.,Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176, Stockholm, Sweden.,Science for Life Laboratory, 17121, Solna, Sweden
| | - Alejandra Cervera
- Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, 00014, Helsinki, Finland
| | - Andrew McPherson
- School of Computing Science, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada
| | - Michał Wojciech Szcześniak
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Daniel J Gaffney
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Laura L Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Xuegong Zhang
- Key Lab of Bioinformatics/Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA. .,Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA.
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28
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Sveen A, Kilpinen S, Ruusulehto A, Lothe RA, Skotheim RI. Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. Oncogene 2015; 35:2413-27. [PMID: 26300000 DOI: 10.1038/onc.2015.318] [Citation(s) in RCA: 333] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023]
Abstract
Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations.
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Affiliation(s)
- A Sveen
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - R A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - R I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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29
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Feuerborn A, Cook PR. Why the activity of a gene depends on its neighbors. Trends Genet 2015; 31:483-90. [PMID: 26259670 DOI: 10.1016/j.tig.2015.07.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/25/2015] [Accepted: 07/15/2015] [Indexed: 11/15/2022]
Abstract
Sixty years ago, the position of a gene on a chromosome was seen to be a major determinant of gene activity; however, position effects are rarely central to current discussions of gene expression. We describe a comprehensive and simplifying view of how position in 1D sequence and 3D nuclear space underlies expression. We suggest that apparently-different regulatory motifs including enhancers, silencers, insulators, barriers, and boundaries act similarly - they are active promoters that tether target genes close to, or distant from, appropriate transcription sites or 'factories'. We also suggest that any active transcription unit regulates the firing of its neighbors - and thus can be categorized as one or other type of motif; this is consistent with expression quantitative trait loci (eQTLs) being widely dispersed.
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Affiliation(s)
- Alexander Feuerborn
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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30
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Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015; 16:197-212. [DOI: 10.1038/nrg3891] [Citation(s) in RCA: 684] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Evolutionary genetic bases of longevity and senescence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 847:1-44. [PMID: 25916584 DOI: 10.1007/978-1-4939-2404-2_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Senescence, as a time-dependent developmental process, affects all organisms at every stage in their development and growth. During this process, genetic, epigenetic and environmental factors are known to introduce a wide range of variation for longevity among individuals. As an important life-history trait, longevity shows ontogenetic relationships with other complex traits, and hence may be viewed as a composite trait. Factors that influence the origin and maintenance of diversity of life are ultimately governed by Darwinian processes. Here we review evolutionary genetic mechanisms underlying longevity and senescence in humans from a life-history and genotype-epigenetic-phenotype (G-E-P) map prospective. We suggest that synergistic and cascading effects of cis-ruptive mechanisms in the genome, and epigenetic disruptive processes in relation to environmental factors may lead to sequential slippage in the G-E-P space. These mechanisms accompany age, stage and individual specific senescent processes, influenced by positive pleiotropy of certain genes, superior genome integrity, negative-frequency dependent selection and other factors that universally regulate rarity in nature. Finally we interpret life span as an inherent property of self-organizing systems that, accordingly, maintain species-specific limits for the entire complex of fitness traits. We conclude that Darwinian approaches provide unique opportunities to discover the biological bases of longevity as well as devise individual specific medical or other interventions toward improving health span.
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Xue Y, Gu D, Ma G, Zhu L, Hua Q, Chu H, Tong N, Chen J, Zhang Z, Wang M. Genetic variants in lncRNA HOTAIR are associated with risk of colorectal cancer. Mutagenesis 2014; 30:303-10. [PMID: 25432874 DOI: 10.1093/mutage/geu076] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA HOX transcript antisenseRNA (HOTAIR) has been widely identified to participate in tumour pathogenesis, acting as a promoter in colorectal cancer carcinogenesis. However, the association between genetic variants in HOTAIR and cancer risk has not yet been reported. In the present study, we performed a two-stage case-control study to investigate the association between HOTAIR tagSNPs and the risk of colorectal cancer. We found that individuals with rs7958904 CC genotype had a significantly decreased risk of colorectal cancer in both Stage 1 and 2, compared with those carrying GG genotype [odds ratio (OR) = 0.70, 95% confidence interval (CI) = 0.51-0.97 in Stage 1; OR = 0.58, 95% CI = 0.37-0.91 in Stage 2; OR = 0.67, 95% CI = 0.51-0.87 in combined stage]. The subsequently stratified analyses showed that the protective effect of rs7958904 was more pronounced in several subgroups. In summary, our study showed that genetic variants in HOTAIR were associated with risk of colorectal cancer and rs7958904 may act as a potential biomarker for predicting the risk of colorectal cancer.
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Affiliation(s)
- Yao Xue
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University
| | - Gaoxiang Ma
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health
| | - Lingjun Zhu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiuhan Hua
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center
| | - Na Tong
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health,
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health,
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Abstract
Large-scale genome-wide association studies (GWAS) have identified 46 loci that are associated with coronary heart disease (CHD). Additionally, 104 independent candidate variants (false discovery rate of 5 %) have been identified (Schunkert H, Konig IR, Kathiresan S, Reilly MP, Assimes TL, Holm H et al. Nat Genet 43:333-8, 2011; Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR et al. Nat Genet 45:25-33, 2012; C4D Genetics Consortium. Nat Genet 43:339-44, 2011). The majority of the causal genes in these loci function independently of conventional risk factors. It is postulated that a number of the CHD-associated genes regulate basic processes in the vascular cells involved in atherosclerosis, and that study of the signaling pathways that are modulated in this cell type by causal regulatory variation will provide critical new insights for targeting the initiation and progression of disease. In this review, we will discuss the types of experimental approaches and data that are critical to understanding the molecular processes that underlie the disease risk at 9p21.3, TCF21, SORT1, and other CHD-associated loci.
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Shen SQ, Turro E, Corbo JC. Hybrid mice reveal parent-of-origin and Cis- and trans-regulatory effects in the retina. PLoS One 2014; 9:e109382. [PMID: 25340786 PMCID: PMC4207689 DOI: 10.1371/journal.pone.0109382] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022] Open
Abstract
A fundamental challenge in genomics is to map DNA sequence variants onto changes in gene expression. Gene expression is regulated by cis-regulatory elements (CREs, i.e., enhancers, promoters, and silencers) and the trans factors (e.g., transcription factors) that act upon them. A powerful approach to dissecting cis and trans effects is to compare F1 hybrids with F0 homozygotes. Using this approach and taking advantage of the high frequency of polymorphisms in wild-derived inbred Cast/EiJ mice relative to the reference strain C57BL/6J, we conducted allele-specific mRNA-seq analysis in the adult mouse retina, a disease-relevant neural tissue. We found that cis effects account for the bulk of gene regulatory divergence in the retina. Many CREs contained functional (i.e., activating or silencing) cis-regulatory variants mapping onto altered expression of genes, including genes associated with retinal disease. By comparing our retinal data with previously published liver data, we found that most of the cis effects identified were tissue-specific. Lastly, by comparing reciprocal F1 hybrids, we identified evidence of imprinting in the retina for the first time. Our study provides a framework and resource for mapping cis-regulatory variants onto changes in gene expression, and underscores the importance of studying cis-regulatory variants in the context of retinal disease.
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Affiliation(s)
- Susan Q. Shen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ernest Turro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Abstract
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosome profiling to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes. Allele specific measurements in the diploid hybrid between the two strains revealed roughly half as many cis-acting effects on translation as were observed for mRNA levels. In both the parents and the hybrid, most effects on translation were of small magnitude, such that the direction of an mRNA difference was typically reflected in a concordant footprint difference. The relative importance of cis and trans acting variation on footprint levels was similar to that for mRNA levels. There was a tendency for translation to cause larger footprint differences than expected given the respective mRNA differences. This is in contrast to translational differences between yeast species that have been reported to more often oppose than reinforce mRNA differences. Finally, we catalogued instances of premature translation termination in the two yeast strains and also found several instances where erroneous reference gene annotations lead to apparent nonsense mutations that in fact reside outside of the translated gene body. Overall, genetic influences on translation subtly modulate gene expression differences, and translation does not create strong discrepancies between genetic influences on mRNA and protein levels. Individuals in a species differ from each other in many ways. For many traits, a fraction of this variation is genetic—it is caused by DNA sequence variants in the genome of each individual. Some of these variants influence traits by altering how much certain genes are expressed, i.e. how many mRNA and protein molecules are made in different individuals. Surprisingly, earlier work has found that the effects of genetic variants on mRNA and protein levels for the same genes appear to be very different. Many variants appeared to influence only mRNA (but not protein) levels, and vice versa. In this paper, we studied this question by using a technique called “ribosome profiling” to measure translation (the cellular process of reading mRNA molecules and synthesizing protein molecules) in two yeast strains. We found that the genetic differences between these two strains influence translation for hundreds of genes. Because most of these effects were small in magnitude, they explain at most a small fraction of the discrepancies between the effects of genetic variants on mRNA and protein levels.
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Castillo J, Amaral A, Azpiazu R, Vavouri T, Estanyol JM, Ballesca JL, Oliva R. Genomic and proteomic dissection and characterization of the human sperm chromatin. Mol Hum Reprod 2014; 20:1041-53. [DOI: 10.1093/molehr/gau079] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Mäkinen VP, Civelek M, Meng Q, Zhang B, Zhu J, Levian C, Huan T, Segrè AV, Ghosh S, Vivar J, Nikpay M, Stewart AFR, Nelson CP, Willenborg C, Erdmann J, Blakenberg S, O'Donnell CJ, März W, Laaksonen R, Epstein SE, Kathiresan S, Shah SH, Hazen SL, Reilly MP, Lusis AJ, Samani NJ, Schunkert H, Quertermous T, McPherson R, Yang X, Assimes TL. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS Genet 2014; 10:e1004502. [PMID: 25033284 PMCID: PMC4102418 DOI: 10.1371/journal.pgen.1004502] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/27/2014] [Indexed: 12/13/2022] Open
Abstract
The majority of the heritability of coronary artery disease (CAD) remains unexplained, despite recent successes of genome-wide association studies (GWAS) in identifying novel susceptibility loci. Integrating functional genomic data from a variety of sources with a large-scale meta-analysis of CAD GWAS may facilitate the identification of novel biological processes and genes involved in CAD, as well as clarify the causal relationships of established processes. Towards this end, we integrated 14 GWAS from the CARDIoGRAM Consortium and two additional GWAS from the Ottawa Heart Institute (25,491 cases and 66,819 controls) with 1) genetics of gene expression studies of CAD-relevant tissues in humans, 2) metabolic and signaling pathways from public databases, and 3) data-driven, tissue-specific gene networks from a multitude of human and mouse experiments. We not only detected CAD-associated gene networks of lipid metabolism, coagulation, immunity, and additional networks with no clear functional annotation, but also revealed key driver genes for each CAD network based on the topology of the gene regulatory networks. In particular, we found a gene network involved in antigen processing to be strongly associated with CAD. The key driver genes of this network included glyoxalase I (GLO1) and peptidylprolyl isomerase I (PPIL1), which we verified as regulatory by siRNA experiments in human aortic endothelial cells. Our results suggest genetic influences on a diverse set of both known and novel biological processes that contribute to CAD risk. The key driver genes for these networks highlight potential novel targets for further mechanistic studies and therapeutic interventions. Sudden death due to heart attack ranks among the top causes of death in the world, and family studies have shown that genetics has a substantial effect on heart disease risk. Recent studies suggest that multiple genetic factors each with modest effects are necessary for the development of CAD, but the genes and molecular processes involved remain poorly understood. We conducted an integrative genomics study where we used the information of gene-gene interactions to capture groups of genes that are most likely to increase heart disease risk. We not only confirmed the importance of several known CAD risk processes such as the metabolism and transport of cholesterol, immune response, and blood coagulation, but also revealed many novel processes such as neuroprotection, cell cycle, and proteolysis that were not previously implicated in CAD. In particular, we highlight several genes such as GLO1 with key regulatory roles within these processes not detected by the first wave of genetic analyses. These results highlight the value of integrating population genetic data with diverse resources that functionally annotate the human genome. Such integration facilitates the identification of novel molecular processes involved in the pathogenesis of CAD as well as potential novel targets for the development of efficacious therapeutic interventions.
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Affiliation(s)
- Ville-Petteri Mäkinen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Mete Civelek
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Candace Levian
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Tianxiao Huan
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Ayellet V. Segrè
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Sujoy Ghosh
- Department of Cardiovascular and Metabolic Research, Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, North Carolina, United States of America
- Program in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore
| | - Juan Vivar
- Department of Cardiovascular and Metabolic Research, Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, North Carolina, United States of America
| | - Majid Nikpay
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Alexandre F. R. Stewart
- John and Jennifer Ruddy Canadian Cardiovascular Research Center, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Christopher P. Nelson
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Christina Willenborg
- Institut für Integrative und Experimentelle Genomik, University of Lübeck, Lübeck, Germany
| | - Jeanette Erdmann
- Institut für Integrative und Experimentelle Genomik, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg, Kiel, Lübeck, Germany
| | - Stefan Blakenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Christopher J. O'Donnell
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Cardiology Division, Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Winfried März
- Mannheim Institute of Public Health, Social and Preventive Medicine, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
- Synlab Academy, Mannheim, Germany
| | - Reijo Laaksonen
- Science Center, Tampere University Hospital, Tampere, Finland
| | - Stephen E. Epstein
- Cardiovascular Research Institute, Washington Hospital Center, Washington, D.C., United States of America
| | - Sekar Kathiresan
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Cardiology Division, Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Svati H. Shah
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Muredach P. Reilly
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Aldons J. Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Heribert Schunkert
- DZHK (German Research Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ruth McPherson
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail: (XY); (TLA)
| | - Themistocles L. Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (XY); (TLA)
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Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G, Dermitzakis ET. Cis and trans effects of human genomic variants on gene expression. PLoS Genet 2014; 10:e1004461. [PMID: 25010687 PMCID: PMC4091791 DOI: 10.1371/journal.pgen.1004461] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.
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Affiliation(s)
- Julien Bryois
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - David M. Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - John P. Kemp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Department of Pathology and Genetics, Stanford University, Stanford, California, United States of America
| | | | - Karen M. Ho
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kindom
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
- Center of Excellence for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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Zhang X, Gierman HJ, Levy D, Plump A, Dobrin R, Goring HHH, Curran JE, Johnson MP, Blangero J, Kim SK, O’Donnell CJ, Emilsson V, Johnson AD. Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics 2014; 15:532. [PMID: 24973796 PMCID: PMC4102726 DOI: 10.1186/1471-2164-15-532] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 06/18/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Gene expression genetic studies in human tissues and cells identify cis- and trans-acting expression quantitative trait loci (eQTLs). These eQTLs provide insights into regulatory mechanisms underlying disease risk. However, few studies systematically characterized eQTL results across cell and tissues types. We synthesized eQTL results from >50 datasets, including new primary data from human brain, peripheral plaque and kidney samples, in order to discover features of human eQTLs. RESULTS We find a substantial number of robust cis-eQTLs and far fewer trans-eQTLs consistent across tissues. Analysis of 45 full human GWAS scans indicates eQTLs are enriched overall, and above nSNPs, among positive statistical signals in genetic mapping studies, and account for a significant fraction of the strongest human trait effects. Expression QTLs are enriched for gene centricity, higher population allele frequencies, in housekeeping genes, and for coincidence with regulatory features, though there is little evidence of 5' or 3' positional bias. Several regulatory categories are not enriched including microRNAs and their predicted binding sites and long, intergenic non-coding RNAs. Among the most tissue-ubiquitous cis-eQTLs, there is enrichment for genes involved in xenobiotic metabolism and mitochondrial function, suggesting these eQTLs may have adaptive origins. Several strong eQTLs (CDK5RAP2, NBPFs) coincide with regions of reported human lineage selection. The intersection of new kidney and plaque eQTLs with related GWAS suggest possible gene prioritization. For example, butyrophilins are now linked to arterial pathogenesis via multiple genetic and expression studies. Expression QTL and GWAS results are made available as a community resource through the NHLBI GRASP database [http://apps.nhlbi.nih.gov/grasp/]. CONCLUSIONS Expression QTLs inform the interpretation of human trait variability, and may account for a greater fraction of phenotypic variability than protein-coding variants. The synthesis of available tissue eQTL data highlights many strong cis-eQTLs that may have important biologic roles and could serve as positive controls in future studies. Our results indicate some strong tissue-ubiquitous eQTLs may have adaptive origins in humans. Efforts to expand the genetic, splicing and tissue coverage of known eQTLs will provide further insights into human gene regulation.
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Affiliation(s)
- Xiaoling Zhang
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
| | - Hinco J Gierman
- />Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Daniel Levy
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
| | - Andrew Plump
- />Sanofi Aventis Pharmaceuticals, Bridgewater, NJ 08807 USA
| | - Radu Dobrin
- />Johnson & Johnson Pharmaceutical Research and Development, Radnor, PA 19477 USA
| | - Harald HH Goring
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Joanne E Curran
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Matthew P Johnson
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - John Blangero
- />Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Stuart K Kim
- />Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Christopher J O’Donnell
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
- />Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Andrew D Johnson
- />Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA USA
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Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L, Gaffney D. Genetic background drives transcriptional variation in human induced pluripotent stem cells. PLoS Genet 2014; 10:e1004432. [PMID: 24901476 PMCID: PMC4046971 DOI: 10.1371/journal.pgen.1004432] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/25/2014] [Indexed: 12/18/2022] Open
Abstract
Human iPS cells have been generated using a diverse range of tissues from a variety of donors using different reprogramming vectors. However, these cell lines are heterogeneous, which presents a limitation for their use in disease modeling and personalized medicine. To explore the basis of this heterogeneity we generated 25 iPS cell lines under normalised conditions from the same set of somatic tissues across a number of donors. RNA-seq data sets from each cell line were compared to identify the majority contributors to transcriptional heterogeneity. We found that genetic differences between individual donors were the major cause of transcriptional variation between lines. In contrast, residual signatures from the somatic cell of origin, so called epigenetic memory, contributed relatively little to transcriptional variation. Thus, underlying genetic background variation is responsible for most heterogeneity between human iPS cell lines. We conclude that epigenetic effects in hIPSCs are minimal, and that hIPSCs are a stable, robust and powerful platform for large-scale studies of the function of genetic differences between individuals. Our data also suggest that future studies using hIPSCs as a model system should focus most effort on collection of large numbers of donors, rather than generating large numbers of lines from the same donor. Human induced pluripotent stem (hiPS) cells are a potentially powerful model system for studying human disease and development, and a resource for personalized medicine. However, it has been reported that hiPS cells exhibit substantial heterogeneity which could limit their use as model systems. Clearly, knowledge of the source of heterogeneity is key for deeper understanding of the use of human iPS cells for basic and therapeutic applications. One source of this heterogeneity has been presumed to be “memory” of the adult somatic cell from which the hIPS cells were derived, but the evidence to support this view is scant. We have generated a set of human iPS cells from a set of somatic cell types from different donors. Our study shows that cell lines from different somatic sources but from the same donor (i.e. with the same genome) are more similar than cell lines isolated from the same tissue type but from different donors. Once genetic changes are accounted for, all aspects of gene expression, including mRNA levels, splicing and imprinting are highly similar between iPS cells derived from different human tissues. Thus, most of the previously described transcriptional variation between cell lines is likely to be genetic in origin.
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Affiliation(s)
- Foad Rouhani
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | | | - Allan Bradley
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- University of Cambridge, Cambridge, Cambridge, United Kingdom
| | - Daniel Gaffney
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- * E-mail:
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Abstract
Transcription factor binding sites (TFBSs) on the DNA are generally accepted as the key nodes of gene control. However, the multitudes of TFBSs identified in genome-wide studies, some of them seemingly unconstrained in evolution, have prompted the view that in many cases TF binding may serve no biological function. Yet, insights from transcriptional biochemistry, population genetics and functional genomics suggest that rather than segregating into 'functional' or 'non-functional', TFBS inputs to their target genes may be generally cumulative, with varying degrees of potency and redundancy. As TFBS redundancy can be diminished by mutations and environmental stress, some of the apparently 'spurious' sites may turn out to be important for maintaining adequate transcriptional regulation under these conditions. This has significant implications for interpreting the phenotypic effects of TFBS mutations, particularly in the context of genome-wide association studies for complex traits.
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42
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Parts L, Liu YC, Tekkedil MM, Steinmetz LM, Caudy AA, Fraser AG, Boone C, Andrews BJ, Rosebrock AP. Heritability and genetic basis of protein level variation in an outbred population. Genome Res 2014; 24:1363-70. [PMID: 24823668 PMCID: PMC4120089 DOI: 10.1101/gr.170506.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The genetic basis of heritable traits has been studied for decades. Although recent mapping efforts have elucidated genetic determinants of transcript levels, mapping of protein abundance has lagged. Here, we analyze levels of 4084 GFP-tagged yeast proteins in the progeny of a cross between a laboratory and a wild strain using flow cytometry and high-content microscopy. The genotype of trans variants contributed little to protein level variation between individual cells but explained >50% of the variance in the population’s average protein abundance for half of the GFP fusions tested. To map trans-acting factors responsible, we performed flow sorting and bulk segregant analysis of 25 proteins, finding a median of five protein quantitative trait loci (pQTLs) per GFP fusion. Further, we find that cis-acting variants predominate; the genotype of a gene and its surrounding region had a large effect on protein level six times more frequently than the rest of the genome combined. We present evidence for both shared and independent genetic control of transcript and protein abundance: More than half of the expression QTLs (eQTLs) contribute to changes in protein levels of regulated genes, but several pQTLs do not affect their cognate transcript levels. Allele replacements of genes known to underlie trans eQTL hotspots confirmed the correlation of effects on mRNA and protein levels. This study represents the first genome-scale measurement of genetic contribution to protein levels in single cells and populations, identifies more than a hundred trans pQTLs, and validates the propagation of effects associated with transcript variation to protein abundance.
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Affiliation(s)
- Leopold Parts
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S3E1, Canada
| | - Yi-Chun Liu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada
| | - Manu M Tekkedil
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Amy A Caudy
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S3E1, Canada
| | - Andrew G Fraser
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S3E1, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S3E1, Canada
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, M5S3E1, Canada
| | - Adam P Rosebrock
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada;
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43
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Bolouri H. Modeling genomic regulatory networks with big data. Trends Genet 2014; 30:182-91. [PMID: 24630831 DOI: 10.1016/j.tig.2014.02.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 02/06/2023]
Abstract
High-throughput sequencing, large-scale data generation projects, and web-based cloud computing are changing how computational biology is performed, who performs it, and what biological insights it can deliver. I review here the latest developments in available data, methods, and software, focusing on the modeling and analysis of the gene regulatory interactions in cells. Three key findings are: (i) although sophisticated computational resources are increasingly available to bench biologists, tailored ongoing education is necessary to avoid the erroneous use of these resources. (ii) Current models of the regulation of gene expression are far too simplistic and need updating. (iii) Integrative computational analysis of large-scale datasets is becoming a fundamental component of molecular biology. I discuss current and near-term opportunities and challenges related to these three points.
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Affiliation(s)
- Hamid Bolouri
- Division of Human Biology, Fred Hutchinson Cancer Research Center (FHCRC), 1100 Fairview Avenue North, PO Box 19024, Seattle, WA 98109, USA.
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44
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Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, Jostins L, Plant K, Andrews R, McGee C, Knight JC. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 2014; 343:1246949. [PMID: 24604202 PMCID: PMC4064786 DOI: 10.1126/science.1246949] [Citation(s) in RCA: 541] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-γ (IFN-γ) or differing durations of lipopolysaccharide and mapped expression quantitative trait loci (eQTLs). More than half of cis-eQTLs identified, involving hundreds of genes and associated pathways, are detected specifically in stimulated monocytes. Induced innate immune activity reveals multiple master regulatory trans-eQTLs including the major histocompatibility complex (MHC), coding variants altering enzyme and receptor function, an IFN-β cytokine network showing temporal specificity, and an interferon regulatory factor 2 (IRF2) transcription factor-modulated network. Induced eQTL are significantly enriched for genome-wide association study loci, identifying context-specific associations to putative causal genes including CARD9, ATM, and IRF8. Thus, applying pathophysiologically relevant immune stimuli assists resolution of functional genetic variants.
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Affiliation(s)
- Benjamin P. Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Seiko Makino
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel Wong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Evelyn Lau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Katharine Plant
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Robert Andrews
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton CB10 1SA, UK
| | - Chris McGee
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton CB10 1SA, UK
| | - Julian C. Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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