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Kleeman SO, Thakir TM, Demestichas B, Mourikis N, Loiero D, Ferrer M, Bankier S, Riazat-Kesh YJ, Lee H, Chantzichristos D, Regan C, Preall J, Sinha S, Rosin N, Yipp B, de Almeida LG, Biernaskie J, Dufour A, Tober-Lau P, Ruusalepp A, Bjorkegren JL, Ralser M, Kurth F, Demichev V, Heywood T, Gao Q, Johannsson G, Koelzer VH, Walker BR, Meyer HV, Janowitz T. Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy. CELL GENOMICS 2023; 3:100347. [PMID: 37601967 PMCID: PMC10435381 DOI: 10.1016/j.xgen.2023.100347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 03/23/2023] [Accepted: 05/30/2023] [Indexed: 08/22/2023]
Abstract
Cystatin C (CyC), a secreted cysteine protease inhibitor, has unclear biological functions. Many patients exhibit elevated plasma CyC levels, particularly during glucocorticoid (GC) treatment. This study links GCs with CyC's systemic regulation by utilizing genome-wide association and structural equation modeling to determine CyC production genetics in the UK Biobank. Both CyC production and a polygenic score (PGS) capturing predisposition to CyC production were associated with increased all-cause and cancer-specific mortality. We found that the GC receptor directly targets CyC, leading to GC-responsive CyC secretion in macrophages and cancer cells. CyC-knockout tumors displayed significantly reduced growth and diminished recruitment of TREM2+ macrophages, which have been connected to cancer immunotherapy failure. Furthermore, the CyC-production PGS predicted checkpoint immunotherapy failure in 685 patients with metastatic cancer from combined clinical trial cohorts. In conclusion, CyC may act as a GC effector pathway via TREM2+ macrophage recruitment and may be a potential target for combination cancer immunotherapy.
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Affiliation(s)
- Sam O. Kleeman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Dominik Loiero
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Miriam Ferrer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Sean Bankier
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | | | - Hassal Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Dimitrios Chantzichristos
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Endocrinology Diabetes and Metabolism, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Claire Regan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Sarthak Sinha
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Nicole Rosin
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Bryan Yipp
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Luiz G.N. de Almeida
- Department of Biochemistry and Molecular Biology and Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Antoine Dufour
- Department of Biochemistry and Molecular Biology and Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | | | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Johan L.M. Bjorkegren
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Florian Kurth
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Todd Heywood
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Qing Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gudmundur Johannsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Endocrinology Diabetes and Metabolism, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Viktor H. Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oncology and Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Brian R. Walker
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Tobias Janowitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cancer Institute, Northwell Health, New Hyde Park, NY, USA
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Luo J, Wu X, Cheng Y, Chen G, Wang J, Song X. Expression quantitative trait locus studies in the era of single-cell omics. Front Genet 2023; 14:1182579. [PMID: 37284065 PMCID: PMC10239882 DOI: 10.3389/fgene.2023.1182579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
Genome-wide association studies have revealed that the regulation of gene expression bridges genetic variants and complex phenotypes. Profiling of the bulk transcriptome coupled with linkage analysis (expression quantitative trait locus (eQTL) mapping) has advanced our understanding of the relationship between genetic variants and gene regulation in the context of complex phenotypes. However, bulk transcriptomics has inherited limitations as the regulation of gene expression tends to be cell-type-specific. The advent of single-cell RNA-seq technology now enables the identification of the cell-type-specific regulation of gene expression through a single-cell eQTL (sc-eQTL). In this review, we first provide an overview of sc-eQTL studies, including data processing and the mapping procedure of the sc-eQTL. We then discuss the benefits and limitations of sc-eQTL analyses. Finally, we present an overview of the current and future applications of sc-eQTL discoveries.
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Affiliation(s)
- Jie Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuan Cheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xijiao Song
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. Brief Bioinform 2021; 22:6330938. [PMID: 34329375 DOI: 10.1093/bib/bbab259] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
Significant innovations in next-generation sequencing techniques and bioinformatics tools have impacted our appreciation and understanding of RNA. Practical RNA sequencing (RNA-Seq) applications have evolved in conjunction with sequence technology and bioinformatic tools advances. In most projects, bulk RNA-Seq data is used to measure gene expression patterns, isoform expression, alternative splicing and single-nucleotide polymorphisms. However, RNA-Seq holds far more hidden biological information including details of copy number alteration, microbial contamination, transposable elements, cell type (deconvolution) and the presence of neoantigens. Recent novel and advanced bioinformatic algorithms developed the capacity to retrieve this information from bulk RNA-Seq data, thus broadening its scope. The focus of this review is to comprehend the emerging bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications. In doing so, we highlight the power of bulk RNA-Seq in providing biological insights.
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Affiliation(s)
- Amarinder Singh Thind
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Isha Monga
- Columbia University, New York City, NY, USA
| | | | - Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | | | - Marie Ranson
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Bruce Ashford
- University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
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Crawford AA, Bankier S, Altmaier E, Barnes CLK, Clark DW, Ermel R, Friedrich N, van der Harst P, Joshi PK, Karhunen V, Lahti J, Mahajan A, Mangino M, Nethander M, Neumann A, Pietzner M, Sukhavasi K, Wang CA, Bakker SJL, Bjorkegren JLM, Campbell H, Eriksson J, Gieger C, Hayward C, Jarvelin MR, McLachlan S, Morris AP, Ohlsson C, Pennell CE, Price J, Rudan I, Ruusalepp A, Spector T, Tiemeier H, Völzke H, Wilson JF, Michoel T, Timpson NJ, Smith GD, Walker BR. Variation in the SERPINA6/SERPINA1 locus alters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expression in peripheral tissues, and risk of cardiovascular disease. J Hum Genet 2021; 66:625-636. [PMID: 33469137 PMCID: PMC8144017 DOI: 10.1038/s10038-020-00895-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023]
Abstract
The stress hormone cortisol modulates fuel metabolism, cardiovascular homoeostasis, mood, inflammation and cognition. The CORtisol NETwork (CORNET) consortium previously identified a single locus associated with morning plasma cortisol. Identifying additional genetic variants that explain more of the variance in cortisol could provide new insights into cortisol biology and provide statistical power to test the causative role of cortisol in common diseases. The CORNET consortium extended its genome-wide association meta-analysis for morning plasma cortisol from 12,597 to 25,314 subjects and from ~2.2 M to ~7 M SNPs, in 17 population-based cohorts of European ancestries. We confirmed the genetic association with SERPINA6/SERPINA1. This locus contains genes encoding corticosteroid binding globulin (CBG) and α1-antitrypsin. Expression quantitative trait loci (eQTL) analyses undertaken in the STARNET cohort of 600 individuals showed that specific genetic variants within the SERPINA6/SERPINA1 locus influence expression of SERPINA6 rather than SERPINA1 in the liver. Moreover, trans-eQTL analysis demonstrated effects on adipose tissue gene expression, suggesting that variations in CBG levels have an effect on delivery of cortisol to peripheral tissues. Two-sample Mendelian randomisation analyses provided evidence that each genetically-determined standard deviation (SD) increase in morning plasma cortisol was associated with increased odds of chronic ischaemic heart disease (0.32, 95% CI 0.06-0.59) and myocardial infarction (0.21, 95% CI 0.00-0.43) in UK Biobank and similarly in CARDIoGRAMplusC4D. These findings reveal a causative pathway for CBG in determining cortisol action in peripheral tissues and thereby contributing to the aetiology of cardiovascular disease.
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Affiliation(s)
- Andrew A Crawford
- BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sean Bankier
- BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Catriona L K Barnes
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - David W Clark
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Raili Ermel
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
- German Center for Cardiovascular Disease (DZHK e.V.), partner site Greifswald, 17475, Greifswald, Germany
| | - Pim van der Harst
- Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, PO box 30.001, 9700 RB, The Netherlands
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England Centre for Environment and Health, Imperial College London, London, UK
- Centre for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
- Turku Institute of Advanced Studies, University of Turku, Turku, Finland
| | - Anubha Mahajan
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College, Lambeth Palace Road, London, SE1 7EH, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Maria Nethander
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Maik Pietzner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
- German Center for Cardiovascular Disease (DZHK e.V.), partner site Greifswald, 17475, Greifswald, Germany
| | | | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Newcastle, NSW, 2308, Australia
| | - Stephan J L Bakker
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Johan L M Bjorkegren
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
- Department of Genetics & Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Clinical Gene Networks AB, Stockholm, Sweden
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Johan Eriksson
- Folkhälsan Research Center, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Helsinki, Singapore
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England Centre for Environment and Health, Imperial College London, London, UK
- Centre for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Stela McLachlan
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Andrew P Morris
- Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Centre for Human genetics, University of Oxford, Oxford, UK
| | - Claes Ohlsson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, University of Newcastle, Newcastle, NSW, 2308, Australia
| | - Jackie Price
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
- Clinical Gene Networks AB, Stockholm, Sweden
| | - Tim Spector
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Social and Behavioural Science, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Walther-Rathenau-Str. 48, 17489, Greifswald, Germany
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Tom Michoel
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Computational Biology Unit, Department of Informatics, University of Bergen, PO Box 7803, 5020, Bergen, Norway
| | - Nicolas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Brian R Walker
- BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Clinical and Translational Research Institute, Newcastle University, Newcastle upon Tyne, UK.
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SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data. BMC Bioinformatics 2020; 21:184. [PMID: 32393315 PMCID: PMC7216638 DOI: 10.1186/s12859-020-3534-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/05/2020] [Indexed: 11/16/2022] Open
Abstract
Background With the rapid development of single-cell genomics, technologies for parallel sequencing of the transcriptome and genome in each single cell is being explored in several labs and is becoming available. This brings us the opportunity to uncover association between genotypes and gene expression phenotypes at single-cell level by eQTL analysis on single-cell data. New method is needed for such tasks due to special characteristics of single-cell sequencing data. Results We developed an R package SCeQTL that uses zero-inflated negative binomial regression to do eQTL analysis on single-cell data. It can distinguish two type of gene-expression differences among different genotype groups. It can also be used for finding gene expression variations associated with other grouping factors like cell lineages or cell types. Conclusions The SCeQTL method is capable for eQTL analysis on single-cell data as well as detecting associations of gene expression with other grouping factors. The R package of the method is available at https://github.com/XuegongLab/SCeQTL/.
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Wang L, Audenaert P, Michoel T. High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering. Front Genet 2019; 10:1196. [PMID: 31921278 PMCID: PMC6933017 DOI: 10.3389/fgene.2019.01196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/29/2019] [Indexed: 11/23/2022] Open
Abstract
Studying the impact of genetic variation on gene regulatory networks is essential to understand the biological mechanisms by which genetic variation causes variation in phenotypes. Bayesian networks provide an elegant statistical approach for multi-trait genetic mapping and modelling causal trait relationships. However, inferring Bayesian gene networks from high-dimensional genetics and genomics data is challenging, because the number of possible networks scales super-exponentially with the number of nodes, and the computational cost of conventional Bayesian network inference methods quickly becomes prohibitive. We propose an alternative method to infer high-quality Bayesian gene networks that easily scales to thousands of genes. Our method first reconstructs a node ordering by conducting pairwise causal inference tests between genes, which then allows to infer a Bayesian network via a series of independent variable selection problems, one for each gene. We demonstrate using simulated and real systems genetics data that this results in a Bayesian network with equal, and sometimes better, likelihood than the conventional methods, while having a significantly higher overlap with groundtruth networks and being orders of magnitude faster. Moreover our method allows for a unified false discovery rate control across genes and individual edges, and thus a rigorous and easily interpretable way for tuning the sparsity level of the inferred network. Bayesian network inference using pairwise node ordering is a highly efficient approach for reconstructing gene regulatory networks when prior information for the inclusion of edges exists or can be inferred from the available data.
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Affiliation(s)
- Lingfei Wang
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Pieter Audenaert
- IDLab, Ghent University—imec, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Tom Michoel
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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Drag MH, Kogelman LJA, Maribo H, Meinert L, Thomsen PD, Kadarmideen HN. Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis. Physiol Genomics 2019; 51:488-499. [PMID: 31373884 DOI: 10.1152/physiolgenomics.00125.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Characterization of genetic variants affecting genome-wide gene expression levels (expression quantitative trait loci or eQTLs) in pig testes may improve our understanding of genetic architecture of boar taint (an animal welfare trait) and helps in genome-assisted or genomic selection programs. The aims of this study were to identify eQTLs associated with androstenone, to find candidate eQTLs for low androstenone, and to validate the top eQTL by reverse transcriptase quantitative PCR (RT-qPCR). Gene expression profiles were obtained by RNA sequencing in testis from Danish cross-bred pigs and genotype data by 80K single nucleotide polymorphism panel. A total of 262 eQTLs [false discovery rate (FDR) < 0.05] were identified by using two software packages: Matrix eQTL and Krux eQTL. Of these, 149 cis-acting eQTLs were significantly associated with androstenone concentrations and gene expression (FDR < 0.05). The eQTLs were associated with several genes of boar taint relevance including CYP1A2, CYB5D1, and SPHK2. One eQTL gene, AMPH, was differentially expressed (FDR < 0.05) and affected by chicory. Five candidate eQTLs associated with low androstenone concentrations were discovered, including the top eQTL associated with CYP1A2. RT-qPCR confirmed target gene expression to be significantly (P < 0.05) different based on eQTL genotypes. Furthermore, eQTLs were enriched as QTLs for 15 boar taint related traits from the PigQTLdb. This is the first study to report eQTLs in testes of commercial crossbred pigs used in pork production and to reveal genetic architecture of boar taint. Potential applications include development of a DNA test and in advanced genomic selection models for boar taint.
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Affiliation(s)
- Markus H Drag
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lisette J A Kogelman
- Department of Neurology, Danish Headache Center, Rigshospitalet Glostrup, Faculty of Health and Medical Sciences, University of Copenhagen, Glostrup, Denmark
| | - Hanne Maribo
- SEGES, Danish Pig Research Center, Copenhagen, Denmark
| | - Lene Meinert
- Danish Meat Research Institute (DMRI), Danish Technological Institute, Taastrup, Denmark
| | - Preben D Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Haja N Kadarmideen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
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Lu YH, Wang BH, Jiang F, Mo XB, Wu LF, He P, Lu X, Deng FY, Lei SF. Multi-omics integrative analysis identified SNP-methylation-mRNA: Interaction in peripheral blood mononuclear cells. J Cell Mol Med 2019; 23:4601-4610. [PMID: 31106970 PMCID: PMC6584519 DOI: 10.1111/jcmm.14315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/18/2019] [Accepted: 03/14/2019] [Indexed: 11/29/2022] Open
Abstract
Genetic variants have potential influence on DNA methylation and thereby regulate mRNA expression. This study aimed to comprehensively reveal the relationships among SNP, methylation and mRNA, and identify methylation-mediated regulation patterns in human peripheral blood mononuclear cells (PBMCs). Based on in-house multi-omics datasets from 43 Chinese Han female subjects, genome-wide association trios were constructed by simultaneously testing the following three association pairs: SNP-methylation, methylation-mRNA and SNP-mRNA. Causal inference test (CIT) was used to identify methylation-mediated genetic effects on mRNA. A total of 64,184 significant cis-methylation quantitative trait loci (meQTLs) were identified (FDR < 0.05). Among the 745 constructed trios, 464 trios formed SNP-methylation-mRNA regulation chains (CIT). Network analysis (Cytoscape 3.3.0) constructed multiple complex regulation networks among SNP, methylation and mRNA (eg a total of 43 SNPs simultaneously connected to cg22517527 and further to PRMT2, DIP2A and YBEY). The regulation chains were supported by the evidence from 4DGenome database, relevant to immune or inflammatory related diseases/traits, and overlapped with previous eQTLs from dbGaP and GTEx. The results provide new insights into the regulation patterns among SNP, DNA methylation and mRNA expression, especially for the methylation-mediated effects, and also increase our understanding of functional mechanisms underlying the established associations.
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Affiliation(s)
- Yi-Hua Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Department of Epidemiology and Health Statistics, School of Public Health, Nantong University, Nantong, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Bing-Hua Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Fei Jiang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Xing-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Long-Fei Wu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
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9
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Microbial community and ovine host response varies with early and late stages of Haemonchus contortus infection. Vet Res Commun 2017; 41:263-277. [PMID: 29098532 DOI: 10.1007/s11259-017-9698-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/17/2017] [Indexed: 01/07/2023]
Abstract
The interactions between gastric microbiota, ovine host, and Haemonchus contortus portray the ovine gastric environment as a complex ecosystem, where all factors play a pertinent role in fine-tuning each other and in haemeostasis. We delineated the impact of early and late Haemonchus infection on abomasal and ruminal microbial community, as well as the ovine host. Twelve, parasite-naive lambs were divided into four groups, 7 days post-infection (dpi) and time-matched uninfected-control groups; 50 dpi and time-matched uninfected control groups were used for the experiment. Six sheep were inoculated with 5000 H. contortus infective larvae and followed for 7 or 50 days with their corresponding uninfected-control ones. Ovine abomasal tissues were collected for histological analysis and gastric fluids were collected for PH value measurements, microbial community isolation and Illumina MiSeq platform and bioinformatic analysis. Our results showed that Haemonchus infection increased the abomasal gastric pH (P = 0.05) and resulted in necrotizing and inflammatory changes that were more severe during acute infection. Furthermore, infection increased the abomasal bacterial load and decreased the ruminal microbiome. A 7-day infection of sheep with H. contortus significantly altered approximately 98% and 94% of genera in the abomasal and ruminal bacterial profile, respectively (P = 0.04-0.05). However, the approximate altered genera 50 days after infection in the ovine abomasal and ruminal microbiome were about 62% and 69%, correspondingly (P = 0.04-0.05) with increase in some bacteria and decrease in others. Overall, these results indicate that Haemonchus infection plays a crucial role in shaping stomach microbial community composition, and diversity.
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10
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Wang L, Michoel T. Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data. PLoS Comput Biol 2017; 13:e1005703. [PMID: 28821014 PMCID: PMC5576763 DOI: 10.1371/journal.pcbi.1005703] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 08/30/2017] [Accepted: 07/26/2017] [Indexed: 02/07/2023] Open
Abstract
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster. Findr is publicly available at https://github.com/lingfeiwang/findr. Understanding how genetic variation between individuals determines variation in observable traits or disease risk is one of the core aims of genetics. It is known that genetic variation often affects gene regulatory DNA elements and directly causes variation in expression of nearby genes. This effect in turn cascades down to other genes via the complex pathways and gene interaction networks that ultimately govern how cells operate in an ever changing environment. In theory, when genetic variation and gene expression levels are measured simultaneously in a large number of individuals, the causal effects of genes on each other can be inferred using statistical models similar to those used in randomized controlled trials. We developed a novel method and ultra-fast software Findr which, unlike existing methods, takes into account the complex but unknown network context when predicting causality between specific gene pairs. Findr’s predictions have a significantly higher overlap with known gene networks compared to existing methods, using both simulated and real data. Findr is also nearly a million times faster, and hence the only software in its class that can handle modern datasets where the expression levels of ten-thousands of genes are simultaneously measured in hundreds to thousands of individuals.
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Affiliation(s)
- Lingfei Wang
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Tom Michoel
- Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- * E-mail:
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11
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Haitjema S, Meddens CA, van der Laan SW, Kofink D, Harakalova M, Tragante V, Foroughi Asl H, van Setten J, Brandt MM, Bis JC, O’Donnell C, Cheng C, Hoefer IE, Waltenberger J, Biessen E, Jukema JW, Doevendans PA, Nieuwenhuis EE, Erdmann J, Björkegren JL, Pasterkamp G, Asselbergs FW, den Ruijter HM, Mokry M. Additional Candidate Genes for Human Atherosclerotic Disease Identified Through Annotation Based on Chromatin Organization. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.116.001664. [DOI: 10.1161/circgenetics.116.001664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 12/12/2016] [Indexed: 11/16/2022]
Abstract
Background—
As genome-wide association efforts, such as CARDIoGRAM and METASTROKE, are ongoing to reveal susceptibility loci for their underlying disease—atherosclerotic disease—identification of candidate genes explaining the associations of these loci has proven the main challenge. Many disease susceptibility loci colocalize with DNA regulatory elements, which influence gene expression through chromatin interactions. Therefore, the target genes of these regulatory elements can be considered candidate genes. Applying these biological principles, we used an alternative approach to annotate susceptibility loci and identify candidate genes for human atherosclerotic disease based on circular chromosome conformation capture followed by sequencing.
Methods and Results—
In human monocytes and coronary endothelial cells, we generated 63 chromatin interaction data sets for 37 active DNA regulatory elements that colocalize with known susceptibility loci for coronary artery disease (CARDIoGRAMplusC4D) and large artery stroke (METASTROKE). By circular chromosome conformation capture followed by sequencing, we identified a physical 3-dimensional interaction with 326 candidate genes expressed in at least 1 of these cell types, of which 294 have not been reported before. We highlight 16 genes based on expression quantitative trait loci.
Conclusions—
Our findings provide additional candidate-gene annotation for 37 disease susceptibility loci for human atherosclerotic disease that are of potential interest to better understand the complex pathophysiology of cardiovascular diseases.
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12
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El-Ashram S, Suo X. Exploring the microbial community (microflora) associated with ovine Haemonchus contortus (macroflora) field strains. Sci Rep 2017; 7:70. [PMID: 28250429 PMCID: PMC5427911 DOI: 10.1038/s41598-017-00171-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/13/2017] [Indexed: 01/02/2023] Open
Abstract
High-throughput sequencing technology has shown tremendous promise for microbial community composition and diversity. Illumina MiSeq platform was exploited to study the microbial community associated with the different stages of the life-cycle of ovine Haemonchus contortus field strains using two distinct amplification primer sets (targeting V3–V4, and V5–V7). Scanning electron microscope and polymerase chain reaction coupled with Illumina MiSeq platform were employed to confirm the absence of any parasite surface contamination by intact bacteria or their DNA products. Results showed 48 (V3–V4 tags) and 28 (V5–V7 tags) bacterial genera comprised the microbial flora of H. contortus microbiome. The dominant bacterial genera belonged to Escherichia-Shigella, Pseudomonas and Ochrobactrum, which were shared in all the stages of the parasite life-cycle using V3–V4 and V5–V7 amplicons. Moreover, the parasite microbiome could reflect the external micro-organisms (i.e. micro- and macro-habitats). There is abundant room for further progress in comparing microbiome of different helminths, which has, and will continue to offer considerable potential for better understanding a wide-variety of devastating animal and human diseases.
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Affiliation(s)
- Saeed El-Ashram
- State Key Laboratory for Agrobiotechnology & College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China. .,National Animal Protozoa Laboratory & College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China. .,Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, Beijing, 100193, China. .,Faculty of Science, Kafr El-Sheikh University, Kafr El-Sheikh, Egypt.
| | - Xun Suo
- State Key Laboratory for Agrobiotechnology & College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.,National Animal Protozoa Laboratory & College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.,Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, Beijing, 100193, China
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13
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Xia W, Zhu XW, Mo XB, Wu LF, Wu J, Guo YF, Zeng KQ, Wang MJ, Lin X, Qiu YH, Wang L, He P, Xie FF, Bing PF, Lu X, Liu YZ, Yi NJ, Deng FY, Lei SF. Integrative multi-omics analysis revealed SNP-lncRNA-mRNA (SLM) networks in human peripheral blood mononuclear cells. Hum Genet 2017; 136:451-462. [PMID: 28243742 DOI: 10.1007/s00439-017-1771-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/20/2017] [Indexed: 12/11/2022]
Abstract
Long non-coding RNAs (lncRNAs) serve as important controller of cellular functions via regulating RNA transcription, degradation and translation. However, what are the regulation patterns of lncRNAs on downstream mRNA and how the upstream genetic variants regulate lncRNAs are largely unknown. We first performed a comprehensive expression quantitative trait locus (eQTL) analysis (MatrixeQTL package, R) using genome-wide lncRNA expression and SNP genotype data from human peripheral blood mononuclear cells (PBMCs) of 43 unrelated individuals. Subsequently, multi-omics integrative network analysis was applied to construct SNP-lncRNA-mRNA (SLM) interaction networks. The causal inference test (CIT) was used to identify lncRNA-mediated (epi-) genetic regulation on mRNA expressions. Our eQTL analysis detected 707 pairs of cis-effect associations (p < 5.64E-06) and 6657 trans-effect associations (p < 3.51E-08), respectively. We also found that top significant cis-eSNPs were enriched around the lncRNA transcription start site regions, and that enrichment patterns of cis-eSNPs differs among different lncRNA sizes (small, medium and large).The constructed SLM interaction networks (1 primary networks and four small separate networks) showed various complex interaction patterns. Especially, the in-depth CIT detected 50 significant lncRNA-mediated SLM trios, and some hotspots (e.g., SNPs: rs926370, rs7716167 and rs16880521; lncRNAs: HIT000061975 and ENST00000579057.1). This study represents the first effort of dissecting the SLM interaction patterns in PBMCs by multi-omics integrative network analysis and causal inference test for clearing the regulation chain. The results provide novel insights into the regulation patterns of lncRNA, and may facilitate investigations of PBMC-related immune physiological process and immunological diseases in the future.
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Affiliation(s)
- Wei Xia
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Department of Statistical, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Xiao-Wei Zhu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xin-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Long-Fei Wu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Jian Wu
- Department of Rheumatology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Yu-Fan Guo
- Department of Rheumatology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Ke-Qin Zeng
- Department of Rheumatology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Ming-Jun Wang
- Department of Rheumatology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
| | - Xiang Lin
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Ying-Hua Qiu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Lan Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Fang-Fei Xie
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Peng-Fei Bing
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Yao-Zhong Liu
- Department of Biostatistics and Bioinformatics, Center of Genomics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Neng-Jun Yi
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China. .,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
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14
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Abstract
The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i.e., testing for association of all transcript-marker pairs. However these "one at-a-time" strategies are (1) unable to control the number of false-positives when an intricate Linkage Disequilibrium structure is present and (2) are often underpowered to detect the full spectrum of trans-acting regulatory effects. Here we present our viewpoint on the most recent advances on eQTL mapping approaches, with a focus on Bayesian methodology. We review the advantages of the Bayesian approach over frequentist methods and provide an empirical example of polygenic eQTL mapping to illustrate the different properties of frequentist and Bayesian methods. Finally, we discuss how multivariate eQTL mapping approaches have distinctive features with respect to detection of polygenic effects, accuracy, and interpretability of the results.
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Affiliation(s)
- Martha Imprialou
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Box 238, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Department of Mathematics, Imperial College London, 180 Queen's Gate, London, SW7 2AZ, UK.
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15
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Abstract
MicroRNAs (miRNAs) are small RNA molecules that play key regulatory roles in general biological processes and disease pathogenesis. These small RNA molecules interact with their target mRNAs to induce mRNA degradation and/or inhibit the translation of mRNAs into proteins. Therefore, identifying miRNA targets is an essential step to fully understand the regulatory effects of miRNAs. Here, we describe a regularized regression approach that integrates the sequence information with the miRNA and mRNA expression profiles for detecting miRNA targets. This method takes into account the full spectrum of gene sequence features of miRNA targets, including the thermodynamic stability, the accessibility energy, and the context features of the target sites,. Given these sequence features for each putative miRNA-mRNA interaction and their expression values, this model is able to quantify the down-regulation effect of each miRNA on its targets while simultaneously estimating the contribution of each sequence feature for predicting functional miRNA-mRNA interactions.
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16
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Fine-mapping analysis revealed complex pleiotropic effect and tissue-specific regulatory mechanism of TNFSF15 in primary biliary cholangitis, Crohn's disease and leprosy. Sci Rep 2016; 6:31429. [PMID: 27507062 PMCID: PMC4979016 DOI: 10.1038/srep31429] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/18/2016] [Indexed: 12/17/2022] Open
Abstract
Genetic polymorphism within the 9q32 locus is linked with increased risk of several diseases, including Crohn’s disease (CD), primary biliary cholangitis (PBC) and leprosy. The most likely disease-causing gene within 9q32 is TNFSF15, which encodes the pro-inflammatory cytokine TNF super-family member 15, but it was unknown whether these disparate diseases were associated with the same genetic variance in 9q32, and how variance within this locus might contribute to pathology. Using genetic data from published studies on CD, PBC and leprosy we revealed that bearing a T allele at rs6478108/rs6478109 (r2 = 1) or rs4979462 was significantly associated with increased risk of CD and decreased risk of leprosy, while the T allele at rs4979462 was associated with significantly increased risk of PBC. In vitro analyses showed that the rs6478109 genotype significantly affected TNFSF15 expression in cells from whole blood of controls, while functional annotation using publicly-available data revealed the broad cell type/tissue-specific regulatory potential of variance at rs6478109 or rs4979462. In summary, we provide evidence that variance within TNFSF15 has the potential to affect cytokine expression across a range of tissues and thereby contribute to protection from infectious diseases such as leprosy, while increasing the risk of immune-mediated diseases including CD and PBC.
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17
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Skjærven L, Jariwala S, Yao XQ, Grant BJ. Online interactive analysis of protein structure ensembles with Bio3D-web. Bioinformatics 2016; 32:3510-3512. [PMID: 27423893 PMCID: PMC5181562 DOI: 10.1093/bioinformatics/btw482] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/17/2016] [Accepted: 07/10/2016] [Indexed: 01/30/2023] Open
Abstract
Summary: Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics. Availability: Bio3D-web is based on the Bio3D and Shiny R packages. All major browsers are supported and full source code is available under a GPL2 license from http://thegrantlab.org/bio3d-web. Contact:bjgrant@umich.edu or lars.skjarven@uib.no
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Affiliation(s)
- Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Xin-Qiu Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Barry J Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
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18
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Tempelman RJ. Statistical and Computational Challenges in Whole Genome Prediction and Genome-Wide Association Analyses for Plant and Animal Breeding. JOURNAL OF AGRICULTURAL, BIOLOGICAL, AND ENVIRONMENTAL STATISTICS 2015. [DOI: 10.1007/s13253-015-0225-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Wang Z, Xu W, Liu Y. Integrating full spectrum of sequence features into predicting functional microRNA-mRNA interactions. Bioinformatics 2015; 31:3529-36. [PMID: 26130578 DOI: 10.1093/bioinformatics/btv392] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 06/23/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION MicroRNAs (miRNAs) play important roles in general biological processes and diseases pathogenesis. Identifying miRNA target genes is an essential step to fully understand the regulatory effects of miRNAs. Many computational methods based on the sequence complementary rules and the miRNA and mRNA expression profiles have been developed for this purpose. It is noted that there have been many sequence features of miRNA targets available, including the context features of the target sites, the thermodynamic stability and the accessibility energy for miRNA-mRNA interaction. However, most of current computational methods that combine sequence and expression information do not effectively integrate full spectrum of these features; instead, they perceive putative miRNA-mRNA interactions from sequence-based prediction as equally meaningful. Therefore, these sequence features have not been fully utilized for improving miRNA target prediction. RESULTS We propose a novel regularized regression approach that is based on the adaptive Lasso procedure for detecting functional miRNA-mRNA interactions. Our method fully takes into account the gene sequence features and the miRNA and mRNA expression profiles. Given a set of sequence features for each putative miRNA-mRNA interaction and their expression values, our model quantifies the down-regulation effect of each miRNA on its targets while simultaneously estimating the contribution of each sequence feature to predicting functional miRNA-mRNA interactions. By applying our model to the expression datasets from two cancer studies, we have demonstrated our prediction results have achieved better sensitivity and specificity and are more biologically meaningful compared with those based on other methods. AVAILABILITY AND IMPLEMENTATION The source code is available at: http://nba.uth.tmc.edu/homepage/liu/miRNALasso. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT Yin.Liu@uth.tmc.edu.
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Affiliation(s)
- Zixing Wang
- Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston and
| | - Wenlong Xu
- Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston and
| | - Yin Liu
- Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston and University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
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20
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Björkegren JLM, Kovacic JC, Dudley JT, Schadt EE. Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders. J Am Coll Cardiol 2015; 65:830-845. [PMID: 25720628 DOI: 10.1016/j.jacc.2014.12.033] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 12/19/2014] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies (GWAS) have been extensively used to study common complex diseases such as coronary artery disease (CAD), revealing 153 suggestive CAD loci, of which at least 46 have been validated as having genome-wide significance. However, these loci collectively explain <10% of the genetic variance in CAD. Thus, we must address the key question of what factors constitute the remaining 90% of CAD heritability. We review possible limitations of GWAS, and contextually consider some candidate CAD loci identified by this method. Looking ahead, we propose systems genetics as a complementary approach to unlocking the CAD heritability and etiology. Systems genetics builds network models of relevant molecular processes by combining genetic and genomic datasets to ultimately identify key "drivers" of disease. By leveraging systems-based genetic approaches, we can help reveal the full genetic basis of common complex disorders, enabling novel diagnostic and therapeutic opportunities.
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Affiliation(s)
- Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Department of Pathological Anatomy and Forensic Medicine, University of Tartu, Tartu, Estonia.
| | - Jason C Kovacic
- Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
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Variants in ALOX5, ALOX5AP and LTA4H are not associated with atherosclerotic plaque phenotypes: the Athero-Express Genomics Study. Atherosclerosis 2015; 239:528-38. [PMID: 25721704 DOI: 10.1016/j.atherosclerosis.2015.01.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/07/2015] [Accepted: 01/13/2015] [Indexed: 11/22/2022]
Abstract
BACKGROUND The eicosanoid genes ALOX5, ALOX5AP and LTA4H have been implicated in atherosclerosis. We assessed the impact of common variants in these genes on gene expression, circulating protein levels, and atherosclerotic plaque phenotypes. METHODS We included patients from the Stockholm Atherosclerosis Gene Expression study (STAGE, N = 109), and the Athero-Express Biobank Study (AE, N = 1443). We tested 1453 single-nucleotide variants (SNVs) in ALOX5, ALOX5AP and LTA4H for association with gene expression in STAGE. We also tested these SNVs for association with seven histologically defined plaque phenotypes in the AE (which included calcification, collagen, cellular content, atheroma size, and intraplaque vessel density and hemorrhage). RESULTS We replicate a known cis-eQTL (rs6538697, p = 1.96 × 10(-6)) for LTA4H expression in whole blood of patients from STAGE. We found no significant association for any of the SNVs tested with serum levels of ALOX5 or ALOX5AP (p > 5.79 × 10(-4)). For atherosclerotic plaque phenotypes the strongest associations were found for intraplaque vessel density and smooth muscle cells in the ALOX5AP locus (p > 1.67 × 10(-4)). CONCLUSIONS We replicate a known eQTL for LTA4H expression in whole blood using STAGE data. We found no associations of variants in and around ALOX5, ALOX5AP and LTA4H with serum ALOX5 or ALOX5AP levels, or plaque phenotypes. On the supposition that these genes play a causal role in atherosclerosis, these results suggest that common variants in these loci play a limited role (if any) in influencing advanced atherosclerotic plaque morphology to the extent that it impacts atherosclerotic disease.
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