1
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Koch RL, Stanton JB, McClatchy S, Churchill GA, Craig SW, Williams DN, Johns ME, Chase KR, Thiesfeldt DL, Flynt JC, Pazdro R. Discovery of genomic loci for liver health and steatosis reveals overlap with glutathione redox genetics. Redox Biol 2024; 75:103248. [PMID: 38917671 PMCID: PMC11254179 DOI: 10.1016/j.redox.2024.103248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/27/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver condition in the United States, encompassing a wide spectrum of liver pathologies including steatosis, steatohepatitis, fibrosis, and cirrhosis. Despite its high prevalence, there are no medications currently approved by the Food and Drug Administration for the treatment of NAFLD. Recent work has suggested that NAFLD has a strong genetic component and identifying causative genes will improve our understanding of the molecular mechanisms contributing to NAFLD and yield targets for future therapeutic investigations. Oxidative stress is known to play an important role in NAFLD pathogenesis, yet the underlying mechanisms accounting for disturbances in redox status are not entirely understood. To better understand the relationship between the glutathione redox system and signs of NAFLD in a genetically-diverse population, we measured liver weight, serum biomarkers aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and graded liver pathology in a large cohort of Diversity Outbred mice. We compared hepatic endpoints to those of the glutathione redox system previously measured in the livers and kidneys of the same mice, and we screened for statistical and genetic associations using the R/qtl2 software. We discovered several novel genetic loci associated with markers of liver health, including loci that were associated with both liver steatosis and glutathione redox status. Candidate genes within each locus point to possible new mechanisms underlying the complex relationship between NAFLD and the glutathione redox system, which could have translational implications for future studies targeting NAFLD pathology.
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Affiliation(s)
- Rebecca L Koch
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - James B Stanton
- Department of Pathology, University of Georgia, Athens, GA, USA, 30602
| | | | | | - Steven W Craig
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Darian N Williams
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Mallory E Johns
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Kylah R Chase
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Dana L Thiesfeldt
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Jessica C Flynt
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, Athens, GA, USA, 30602.
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2
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Philip VM, He H, Saul MC, Dickson PE, Bubier JA, Chesler EJ. Gene expression genetics of the striatum of Diversity Outbred mice. Sci Data 2023; 10:522. [PMID: 37543624 PMCID: PMC10404230 DOI: 10.1038/s41597-023-02426-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/28/2023] [Indexed: 08/07/2023] Open
Abstract
Brain transcriptional variation is a heritable trait that mediates complex behaviors, including addiction. Expression quantitative trait locus (eQTL) mapping reveals genomic regions harboring genetic variants that influence transcript abundance. In this study, we profiled transcript abundance in the striatum of 386 Diversity Outbred (J:DO) mice of both sexes using RNA-Seq. All mice were characterized using a behavioral battery of widely-used exploratory and risk-taking assays prior to transcriptional profiling. We performed eQTL mapping, incorporated the results into a browser-based eQTL viewer, and deposited co-expression network members in GeneWeaver. The eQTL viewer allows researchers to query specific genes to obtain allelic effect plots, analyze SNP associations, assess gene expression correlations, and apply mediation analysis to evaluate whether the regulatory variant is acting through the expression of another gene. GeneWeaver allows multi-species comparison of gene sets using statistical and combinatorial tools. This data resource allows users to find genetic variants that regulate differentially expressed transcripts and place them in the context of other studies of striatal gene expression and function in addiction-related behavior.
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Affiliation(s)
- Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04605, USA
| | - Hao He
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Michael C Saul
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04605, USA
| | - Price E Dickson
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine Marshall University, Huntington, WV, 25703, USA
| | - Jason A Bubier
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04605, USA
| | - Elissa J Chesler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04605, USA.
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3
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Philip VM, He H, Saul MC, Dickson PE, Bubier JA, Chesler EJ. Gene expression genetics of the striatum of Diversity Outbred mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540390. [PMID: 37214980 PMCID: PMC10197688 DOI: 10.1101/2023.05.11.540390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Brain transcriptional variation is a heritable trait that mediates complex behaviors, including addiction. Expression quantitative trait locus (eQTL) mapping reveals genomic regions harboring genetic variants that influence transcript abundance. In this study, we profiled transcript abundance in the striatum of 386 Diversity Outbred (J:DO) mice of both sexes using RNA-Seq. All mice were characterized using a behavioral battery of widely-used exploratory and risk-taking assays prior to transcriptional profiling. We performed eQTL mapping, incorporated the results into a browser-based eQTL viewer, and deposited co-expression network members in GeneWeaver. The eQTL viewer allows researchers to query specific genes to obtain allelic effect plots, analyze SNP associations, assess gene expression correlations, and apply mediation analysis to evaluate whether the regulatory variant is acting through the expression of another gene. GeneWeaver allows multi-species comparison of gene sets using statistical and combinatorial tools. This data resource allows users to find genetic variants that regulate differentially expressed transcripts and place them in the context of other studies of striatal gene expression and function in addiction-related behavior.
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Affiliation(s)
- Vivek M. Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME 04605
| | - Hao He
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032
| | - Michael C. Saul
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME 04605
| | - Price E. Dickson
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine Marshall University, 1700 3rd Ave. Huntington, WV 25703
| | - Jason A. Bubier
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME 04605
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4
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Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VM, Chen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, Vitas LP, Laznik-Bogoslavski D, Ordonez M, Liu X, Chen X, Wang Y, Liu W, Tran N, Liu Y, Zhang Y, Cypess AM, White AP, He Y, Deng R, Schöder H, Paulo JA, Jedrychowski MP, Banks AS, Tseng YH, Cohen P, Tsai LT, Rosen ED, Klein S, Chondronikola M, McAllister FE, Van Bruggen N, Huttlin EL, Spiegelman BM, Churchill GA, Gygi SP, Chouchani ET. Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. Cell 2022; 185:4654-4673.e28. [PMID: 36334589 PMCID: PMC10040263 DOI: 10.1016/j.cell.2022.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/18/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Brown adipose tissue (BAT) regulates metabolic physiology. However, nearly all mechanistic studies of BAT protein function occur in a single inbred mouse strain, which has limited the understanding of generalizable mechanisms of BAT regulation over physiology. Here, we perform deep quantitative proteomics of BAT across a cohort of 163 genetically defined diversity outbred mice, a model that parallels the genetic and phenotypic variation found in humans. We leverage this diversity to define the functional architecture of the outbred BAT proteome, comprising 10,479 proteins. We assign co-operative functions to 2,578 proteins, enabling systematic discovery of regulators of BAT. We also identify 638 proteins that correlate with protection from, or sensitivity to, at least one parameter of metabolic disease. We use these findings to uncover SFXN5, LETMD1, and ATP1A2 as modulators of BAT thermogenesis or adiposity, and provide OPABAT as a resource for understanding the conserved mechanisms of BAT regulation over metabolic physiology.
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Affiliation(s)
- Haopeng Xiao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Luiz H M Bozi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yizhi Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher L Riley
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mandy Chen
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Evanna L Mills
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Margo P Emont
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Wenfei Sun
- Department of Bioengineering, Stanford University, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, CA 94305, USA
| | - Anita Reddy
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan Garrity
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jiani Long
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tobias Becher
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Laura Potano Vitas
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Martha Ordonez
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiong Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yun Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Weihai Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nhien Tran
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yitong Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yang Zhang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Aaron M Cypess
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew P White
- Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yuchen He
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Rebecca Deng
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Heiko Schöder
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark P Jedrychowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander S Banks
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Linus T Tsai
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Evan D Rosen
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | | | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce M Spiegelman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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5
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Ouellette AR, Hadad N, Deighan A, Robinson L, O'Connell K, Freund A, Churchill GA, Kaczorowski CC. Life-long dietary restrictions have negligible or damaging effects on late-life cognitive performance: A key role for genetics in outcomes. Neurobiol Aging 2022; 118:108-116. [PMID: 35914473 PMCID: PMC9583241 DOI: 10.1016/j.neurobiolaging.2022.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/22/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022]
Abstract
Several studies report that caloric restriction (CR) or intermittent fasting (IF) can improve cognition, while others report limited or no cognitive benefits. Here, we compare the effects of 20% CR, 40% CR, 1-day IF, and 2-day IF feeding paradigms to ad libitum controls on Y-maze working memory (WM) and contextual fear memory (CFM) in a large population of Diversity Outbred mice that model the genetic diversity of humans. While CR and IF interventions improve lifespan, we observed no enhancement of working memory or CFM in mice on these feeding paradigms, and report 40% CR to be damaging to recall of CFM. Using Quantitative Trait Loci mapping, we identified the gene Slc16a7 to be associated with CFM outcomes in aged mice on lifespan promoting feeding paradigms. Limited utility of dieting and fasting on memory in mice that recapitulate genetic diversity in the human population highlights the need for anti-aging therapeutics that promote cognitive function, with the neuronal monocarboxylate transporter MCT2 encoded by Slc16a7 highlighted as novel target.
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Affiliation(s)
- Andrew R Ouellette
- The University of Maine, Graduate School of Biomedical Science and Engineering, Orono ME, USA; The Jackson Laboratory, Bar Harbor ME, USA
| | | | | | | | | | - Adam Freund
- Calico Life Sciences LLC, San Francisco CA, USA
| | | | - Catherine C Kaczorowski
- The University of Maine, Graduate School of Biomedical Science and Engineering, Orono ME, USA; The Jackson Laboratory, Bar Harbor ME, USA.
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6
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Orschell CM, Wu T, Patterson AM. Impact of Age, Sex, and Genetic Diversity in Murine Models of the Hematopoietic Acute Radiation Syndrome (H-ARS) and the Delayed Effects of Acute Radiation Exposure (DEARE). CURRENT STEM CELL REPORTS 2022; 8:139-149. [PMID: 36798890 PMCID: PMC9928166 DOI: 10.1007/s40778-022-00214-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2022] [Indexed: 10/17/2022]
Abstract
Purpose of review Malicious or accidental radiation exposure increases risk for the hematopoietic acute radiation syndrome (H-ARS) and the delayed effects of acute radiation exposure (DEARE). Radiation medical countermeasure (MCM) development relies on robust animal models reflective of all age groups and both sexes. This review details critical considerations in murine H-ARS and DEARE model development including divergent radiation responses dependent on age, sex, and genetic diversity. Recent findings Radioresistance increases with murine age from pediatrics through geriatrics. Between sexes, radioresistance is higher in male weanlings, pubescent females, and aged males, corresponding with accelerated myelopoiesis. Jackson diversity outbred (JDO) mice resemble non-human primates in radiation response for modeling human diversity. Weanlings and JDO models exhibit less DEARE than other models. Summary Highly characterized age-, sex- and diversity-conscious murine models of H-ARS and DEARE provide powerful and essential tools in MCM development for all radiation victims.
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Affiliation(s)
| | - Tong Wu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Andrea M. Patterson
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
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7
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Lin CX, Li HD, Deng C, Liu W, Erhardt S, Wu FX, Zhao XM, Guan Y, Wang J, Wang D, Hu B, Wang J. An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease. Brief Bioinform 2022; 23:bbab522. [PMID: 34953465 PMCID: PMC8769916 DOI: 10.1093/bib/bbab522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/26/2021] [Accepted: 11/13/2021] [Indexed: 09/24/2024] Open
Abstract
Alzheimer's disease (AD) has a strong genetic predisposition. However, its risk genes remain incompletely identified. We developed an Alzheimer's brain gene network-based approach to predict AD-associated genes by leveraging the functional pattern of known AD-associated genes. Our constructed network outperformed existing networks in predicting AD genes. We then systematically validated the predictions using independent genetic, transcriptomic, proteomic data, neuropathological and clinical data. First, top-ranked genes were enriched in AD-associated pathways. Second, using external gene expression data from the Mount Sinai Brain Bank study, we found that the top-ranked genes were significantly associated with neuropathological and clinical traits, including the Consortium to Establish a Registry for Alzheimer's Disease score, Braak stage score and clinical dementia rating. The analysis of Alzheimer's brain single-cell RNA-seq data revealed cell-type-specific association of predicted genes with early pathology of AD. Third, by interrogating proteomic data in the Religious Orders Study and Memory and Aging Project and Baltimore Longitudinal Study of Aging studies, we observed a significant association of protein expression level with cognitive function and AD clinical severity. The network, method and predictions could become a valuable resource to advance the identification of risk genes for AD.
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Affiliation(s)
- Cui-Xiang Lin
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Chao Deng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Weisheng Liu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
| | - Shannon Erhardt
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Fang-Xiang Wu
- Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SKS7N5A9, Canada
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States
| | - Jun Wang
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics and Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Bin Hu
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P. R. China
- Hunan Provincial Key Lab of Bioinformatics, Central South University, Changsha, Hunan 410083, P. R. China
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8
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Beierle JA, Yao EJ, Goldstein SI, Scotellaro JL, Sena KD, Linnertz CA, Willits AB, Kader L, Young EE, Peltz G, Emili A, Ferris MT, Bryant CD. Genetic basis of thermal nociceptive sensitivity and brain weight in a BALB/c reduced complexity cross. Mol Pain 2022; 18:17448069221079540. [PMID: 35088629 PMCID: PMC8891926 DOI: 10.1177/17448069221079540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 11/30/2022] Open
Abstract
Thermal nociception involves the transmission of temperature-related noxious information from the periphery to the CNS and is a heritable trait that could predict transition to persistent pain. Rodent forward genetics complement human studies by controlling genetic complexity and environmental factors, analysis of end point tissue, and validation of variants on appropriate genetic backgrounds. Reduced complexity crosses between nearly identical inbred substrains with robust trait differences can greatly facilitate unbiased discovery of novel genes and variants. We found BALB/cByJ mice showed enhanced sensitivity on the 53.5°C hot plate and mechanical stimulation in the von Frey test compared to BALB/cJ mice and replicated decreased gross brain weight in BALB/cByJ versus BALB/cJ. We then identified a quantitative trait locus (QTL) on chromosome 13 for hot plate sensitivity (LOD = 10.7; p < 0.001; peak = 56 Mb) and a QTL for brain weight on chromosome 5 (LOD = 8.7; p < 0.001). Expression QTL mapping of brain tissues identified H2afy (56.07 Mb) as the top transcript with the strongest association at the hot plate locus (FDR = 0.0002) and spliceome analysis identified differential exon usage within H2afy associated with the same locus. Whole brain proteomics further supported decreased H2AFY expression could underlie enhanced hot plate sensitivity, and identified ACADS as a candidate for reduced brain weight. To summarize, a BALB/c reduced complexity cross combined with multiple-omics approaches facilitated identification of candidate genes underlying thermal nociception and brain weight. These substrains provide a powerful, reciprocal platform for future validation of candidate variants.
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Affiliation(s)
- Jacob A Beierle
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Emily J Yao
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Stanley I Goldstein
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
| | - Julia L Scotellaro
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
- Undergraduate Research Opportunity Program, Boston University, Boston, MA, USA
| | - Katherine D Sena
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
- Undergraduate Research Opportunity Program, Boston University, Boston, MA, USA
| | - Colton A Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam B Willits
- Neuroscience Program, University of Kansas Medical Center, Kansas City, KS, USA
| | - Leena Kader
- Neuroscience Program, University of Kansas Medical Center, Kansas City, KS, USA
| | - Erin E Young
- Department of Anesthesiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Gary Peltz
- Department of Anesthesiology, Pain, and Preoperative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Emili
- Department of Biology and Biochemistry, Center for Network Systems Biology, Boston University School of Medicine, Boston, MA, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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9
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Lin CX, Li HD, Deng C, Guan Y, Wang J. TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. Nucleic Acids Res 2021; 50:D710-D718. [PMID: 34850130 PMCID: PMC8728275 DOI: 10.1093/nar/gkab1133] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/10/2021] [Accepted: 11/18/2021] [Indexed: 01/02/2023] Open
Abstract
Mapping gene interactions within tissues/cell types plays a crucial role in understanding the genetic basis of human physiology and disease. Tissue functional gene networks (FGNs) are essential models for mapping complex gene interactions. We present TissueNexus, a database of 49 human tissue/cell line FGNs constructed by integrating heterogeneous genomic data. We adopted an advanced machine learning approach for data integration because Bayesian classifiers, which is the main approach used for constructing existing tissue gene networks, cannot capture the interaction and nonlinearity of genomic features well. A total of 1,341 RNA-seq datasets containing 52,087 samples were integrated for all of these networks. Because the tissue label for RNA-seq data may be annotated with different names or be missing, we performed intensive hand-curation to improve quality. We further developed a user-friendly database for network search, visualization, and functional analysis. We illustrate the application of TissueNexus in prioritizing disease genes. The database is publicly available at https://www.diseaselinks.com/TissueNexus/.
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Affiliation(s)
- Cui-Xiang Lin
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China.,Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China.,Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China
| | - Chao Deng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China.,Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China.,Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China
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10
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Keenan BT, Galante RJ, Lian J, Zhang L, Guo X, Veatch OJ, Chesler EJ, O'Brien WT, Svenson KL, Churchill GA, Pack AI. The dihydropyrimidine dehydrogenase gene contributes to heritable differences in sleep in mice. Curr Biol 2021; 31:5238-5248.e7. [PMID: 34653361 DOI: 10.1016/j.cub.2021.09.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/25/2021] [Accepted: 09/17/2021] [Indexed: 12/27/2022]
Abstract
Many aspects of sleep are heritable, but only a few sleep-regulating genes have been reported. Here, we leverage mouse models to identify and confirm a previously unreported gene affecting sleep duration-dihydropyrimidine dehydrogenase (Dpyd). Using activity patterns to quantify sleep in 325 Diversity Outbred (DO) mice-a population with high genetic and phenotypic heterogeneity-a linkage peak for total sleep in the active lights off period was identified on chromosome 3 (LOD score = 7.14). Mice with the PWK/PhJ ancestral haplotype at this location demonstrated markedly reduced sleep. Among the genes within the linkage region, available RNA sequencing data in an independent sample of DO mice supported a highly significant expression quantitative trait locus for Dpyd, wherein reduced expression was associated with the PWK/PhJ allele. Validation studies were performed using activity monitoring and EEG/EMG recording in Collaborative Cross mouse strains with and without the PWK/PhJ haplotype at this location, as well as EEG and EMG recording of sleep and wake in Dpyd knockout mice and wild-type littermate controls. Mice lacking Dpyd had 78.4 min less sleep during the lights-off period than wild-type mice (p = 0.007; Cohen's d = -0.94). There was no difference in other measured behaviors in knockout mice, including assays evaluating cognitive-, social-, and affective-disorder-related behaviors. Dpyd encodes the rate-limiting enzyme in the metabolic pathway that catabolizes uracil and thymidine to β-alanine, an inhibitory neurotransmitter. Thus, data support β-alanine as a neurotransmitter that promotes sleep in mice.
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Affiliation(s)
- Brendan T Keenan
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Raymond J Galante
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jie Lian
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lin Zhang
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Xiaofeng Guo
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Olivia J Veatch
- Department of Psychiatry & Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - W Timothy O'Brien
- Neurobehavior Testing Core, Institute for Translational and Therapeutic Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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11
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Gould RL, Craig SW, McClatchy S, Churchill GA, Pazdro R. Genetic mapping of renal glutathione suggests a novel regulatory locus on the murine X chromosome and overlap with hepatic glutathione regulation. Free Radic Biol Med 2021; 174:28-39. [PMID: 34324982 PMCID: PMC8597656 DOI: 10.1016/j.freeradbiomed.2021.07.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/14/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Glutathione (GSH) is a critical cellular antioxidant that protects against byproducts of aerobic metabolism and other reactive electrophiles to prevent oxidative stress and cell death. Proper maintenance of its reduced form, GSH, in excess of its oxidized form, GSSG, prevents oxidative stress in the kidney and protects against the development of chronic kidney disease. Evidence has indicated that renal concentrations of GSH and GSSG, as well as their ratio GSH/GSSG, are moderately heritable, and past research has identified polymorphisms and candidate genes associated with these phenotypes in mice. Yet those discoveries were made with in silico mapping methods that are prone to false positives and power limitations, so the true loci and candidate genes that control renal glutathione remain unknown. The present study utilized high-resolution gene mapping with the Diversity Outbred mouse stock to identify causal loci underlying variation in renal GSH levels and redox status. Mapping output identified a suggestive locus associated with renal GSH on murine chromosome X at 51.602 Mbp, and bioinformatic analyses identified apoptosis-inducing factor mitochondria-associated 1 (Aifm1) as the most plausible candidate. Then, mapping outputs were compiled and compared against the genetic architecture of the hepatic GSH system, and we discovered a locus on murine chromosome 14 that overlaps between hepatic GSH concentrations and renal GSH redox potential. Overall, the results support our previously proposed model that the GSH redox system is regulated by both global and tissue-specific loci, vastly improving our understanding of GSH and its regulation and proposing new candidate genes for future mechanistic studies.
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Affiliation(s)
- Rebecca L Gould
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Steven W Craig
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Susan McClatchy
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Gary A Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA.
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12
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Gould RL, Craig SW, McClatchy S, Churchill GA, Pazdro R. Quantitative trait mapping in Diversity Outbred mice identifies novel genomic regions associated with the hepatic glutathione redox system. Redox Biol 2021; 46:102093. [PMID: 34418604 PMCID: PMC8385155 DOI: 10.1016/j.redox.2021.102093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/24/2021] [Accepted: 08/04/2021] [Indexed: 11/01/2022] Open
Abstract
The tripeptide glutathione (GSH) is instrumental to antioxidant protection and xenobiotic metabolism, and the ratio of its reduced and oxidized forms (GSH/GSSG) indicates the cellular redox environment and maintains key aspects of cellular signaling. Disruptions in GSH levels and GSH/GSSG have long been tied to various chronic diseases, and many studies have examined whether variant alleles in genes responsible for GSH synthesis and metabolism are associated with increased disease risk. However, past studies have been limited to established, canonical GSH genes, though emerging evidence suggests that novel loci and genes influence the GSH redox system in specific tissues. The present study marks the most comprehensive effort to date to directly identify genetic loci associated with the GSH redox system. We employed the Diversity Outbred (DO) mouse population, a model of human genetics, and measured GSH and the essential redox cofactor NADPH in liver, the organ with the highest levels of GSH in the body. Under normal physiological conditions, we observed substantial variation in hepatic GSH and NADPH levels and their redox balances, and discovered a novel, significant quantitative trait locus (QTL) on murine chromosome 16 underlying GSH/GSSG; bioinformatics analyses revealed Socs1 to be the most likely candidate gene. We also discovered novel QTL associated with hepatic NADP+ levels and NADP+/NADPH, as well as unique candidate genes behind each trait. Overall, these findings transform our understanding of the GSH redox system, revealing genetic loci that govern it and proposing new candidate genes to investigate in future mechanistic endeavors.
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Affiliation(s)
- Rebecca L Gould
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Steven W Craig
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Susan McClatchy
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Gary A Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA.
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13
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Abstract
Pain is an immense clinical and societal challenge, and the key to understanding and treating it is variability. Robust interindividual differences are consistently observed in pain sensitivity, susceptibility to developing painful disorders, and response to analgesic manipulations. This review examines the causes of this variability, including both organismic and environmental sources. Chronic pain development is a textbook example of a gene-environment interaction, requiring both chance initiating events (e.g., trauma, infection) and more immutable risk factors. The focus is on genetic factors, since twin studies have determined that a plurality of the variance likely derives from inherited genetic variants, but sex, age, ethnicity, personality variables, and environmental factors are also considered.
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Affiliation(s)
- Jeffrey S Mogil
- Departments of Psychology and Anesthesia, Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec H3A 1B1, Canada;
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14
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Keenan BT, Webster JC, Wiemken AS, Lavi-Romer N, Nguyen T, Svenson KL, Galante RJ, Churchill GA, Pickup S, Pack AI, Schwab RJ. Heritability of fat distributions in male mice from the founder strains of the Diversity Outbred mouse population. G3-GENES GENOMES GENETICS 2021; 11:6171186. [PMID: 33720343 PMCID: PMC8104956 DOI: 10.1093/g3journal/jkab079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Specific fat distributions are risk factors for complex diseases, including coronary heart disease and obstructive sleep apnea. To demonstrate the utility of high-diversity mouse models for elucidating genetic associations, we describe the phenotyping and heritability of fat distributions within the five classical inbred and three wild-derived founder mouse strains of the Collaborative Cross and Diversity Outbred mice. Measurements of subcutaneous and internal fat volumes in the abdomen, thorax and neck, and fat volumes in the tongue and pericardium were obtained using magnetic resonance imaging in male mice from the A/J (n = 12), C57BL/6J (n = 17), 129S1/SvlmJ (n = 12), NOD/LtJ (n = 14), NZO/HILtJ (n = 12), CAST/EiJ (n = 14), PWK/PhJ (n = 12), and WSB/EiJ (n = 15) strains. Phenotypes were compared across strains using analysis of variance and heritability estimated as the proportion of phenotypic variability attributable to strain. Heritability ranged from 44 to 91% across traits, including >70% heritability of tongue fat. A majority of heritability estimates remained significant controlling for body weight, suggesting genetic influences independent of general obesity. Principal components analysis supports genetic influences on overall obesity and specific to increased pericardial and intra-neck fat. Thus, among the founder strains of the Collaborative Cross and Diversity Outbred mice, we observed significant heritability of subcutaneous and internal fat volumes in the neck, thorax and abdomen, pericardial fat volume and tongue fat volume, consistent with genetic architecture playing an important role in explaining trait variability. Findings pave the way for studies utilizing high-diversity mouse models to identify genes affecting fat distributions and, in turn, influencing risk for associated complex disorders.
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Affiliation(s)
- Brendan T Keenan
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeanette C Webster
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew S Wiemken
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nir Lavi-Romer
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Teresa Nguyen
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Raymond J Galante
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Stephen Pickup
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Richard J Schwab
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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15
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Keenan BT, Galante RJ, Lian J, Simecek P, Gatti DM, Zhang L, Lim DC, Svenson KL, Churchill GA, Pack AI. High-throughput sleep phenotyping produces robust and heritable traits in Diversity Outbred mice and their founder strains. Sleep 2021; 43:5740842. [PMID: 32074270 DOI: 10.1093/sleep/zsz278] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/25/2019] [Indexed: 12/14/2022] Open
Abstract
STUDY OBJECTIVES This study describes high-throughput phenotyping strategies for sleep and circadian behavior in mice, including examinations of robustness, reliability, and heritability among Diversity Outbred (DO) mice and their eight founder strains. METHODS We performed high-throughput sleep and circadian phenotyping in male mice from the DO population (n = 338) and their eight founder strains: A/J (n = 6), C57BL/6J (n = 14), 129S1/SvlmJ (n = 6), NOD/LtJ (n = 6), NZO/H1LtJ (n = 6), CAST/EiJ (n = 8), PWK/PhJ (n = 8), and WSB/EiJ (n = 6). Using infrared beam break systems, we defined sleep as at least 40 s of continuous inactivity and quantified sleep-wake amounts and bout characteristics. We developed assays to measure sleep latency in a new environment and during a modified Murine Multiple Sleep Latency Test, and estimated circadian period from wheel-running experiments. For each trait, broad-sense heritability (proportion of variability explained by all genetic factors) was derived in founder strains, while narrow-sense heritability (proportion of variability explained by additive genetic effects) was calculated in DO mice. RESULTS Phenotypes were robust to different inactivity durations to define sleep. Differences across founder strains and moderate/high broad-sense heritability were observed for most traits. There was large phenotypic variability among DO mice, and phenotypes were reliable, although estimates of heritability were lower than in founder mice. This likely reflects important nonadditive genetic effects. CONCLUSIONS A high-throughput phenotyping strategy in mice, based primarily on monitoring of activity patterns, provides reliable and heritable estimates of sleep and circadian traits. This approach is suitable for discovery analyses in DO mice, where genetic factors explain some proportion of phenotypic variation.
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Affiliation(s)
- Brendan T Keenan
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Raymond J Galante
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jie Lian
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Petr Simecek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Jackson Laboratory, Bar Harbor, ME
| | | | - Lin Zhang
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Diane C Lim
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | | | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA
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16
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Patterson AM, Plett PA, Chua HL, Sampson CH, Fisher A, Feng H, Unthank JL, Miller SJ, Katz BP, MacVittie TJ, Orschell CM. Development of a Model of the Acute and Delayed Effects of High Dose Radiation Exposure in Jackson Diversity Outbred Mice; Comparison to Inbred C57BL/6 Mice. HEALTH PHYSICS 2020; 119:633-646. [PMID: 32932286 PMCID: PMC9374540 DOI: 10.1097/hp.0000000000001344] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Development of medical countermeasures against radiation relies on robust animal models for efficacy testing. Mouse models have advantages over larger species due to economics, ease of conducting aging studies, existence of historical databases, and research tools allowing for sophisticated mechanistic studies. However, the radiation dose-response relationship of inbred strains is inherently steep and sensitive to experimental variables, and inbred models have been criticized for lacking genetic diversity. Jackson Diversity Outbred (JDO) mice are the most genetically diverse strain available, developed by the Collaborative Cross Consortium using eight founder strains, and may represent a more accurate model of humans than inbred strains. Herein, models of the Hematopoietic-Acute Radiation Syndrome and the Delayed Effects of Acute Radiation Exposure were developed in JDO mice and compared to inbred C57BL/6. The dose response relationship curve in JDO mice mirrored the more shallow curves of primates and humans, characteristic of genetic diversity. JDO mice were more radioresistant than C57BL/6 and differed in sensitivity to antibiotic countermeasures. The model was validated with pegylated-G-CSF, which provided significantly enhanced 30-d survival and accelerated blood recovery. Long-term JDO survivors exhibited increased recovery of blood cells and functional bone marrow hematopoietic progenitors compared to C57BL/6. While JDO hematopoietic stem cells declined more in number, they maintained a greater degree of quiescence compared to C57BL/6, which is essential for maintaining function. These JDO radiation models offer many of the advantages of small animals with the genetic diversity of large animals, providing an attractive alternative to currently available radiation animal models.
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Affiliation(s)
- Andrea M. Patterson
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - P. Artur Plett
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Hui Lin Chua
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Carol H. Sampson
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Alexa Fisher
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Hailin Feng
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Joseph L. Unthank
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Steve J. Miller
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Barry P. Katz
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Thomas J. MacVittie
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD
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17
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Bubier JA, He H, Philip VM, Roy T, Hernandez CM, Bernat R, Donohue KD, O'Hara BF, Chesler EJ. Genetic variation regulates opioid-induced respiratory depression in mice. Sci Rep 2020; 10:14970. [PMID: 32917924 PMCID: PMC7486296 DOI: 10.1038/s41598-020-71804-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
In the U.S., opioid prescription for treatment of pain nearly quadrupled from 1999 to 2014. The diversion and misuse of prescription opioids along with increased use of drugs like heroin and fentanyl, has led to an epidemic in addiction and overdose deaths. The most common cause of opioid overdose and death is opioid-induced respiratory depression (OIRD), a life-threatening depression in respiratory rate thought to be caused by stimulation of opioid receptors in the inspiratory-generating regions of the brain. Studies in mice have revealed that variation in opiate lethality is associated with strain differences, suggesting that sensitivity to OIRD is genetically determined. We first tested the hypothesis that genetic variation in inbred strains of mice influences the innate variability in opioid-induced responses in respiratory depression, recovery time and survival time. Using the founders of the advanced, high-diversity mouse population, the Diversity Outbred (DO), we found substantial sex and genetic effects on respiratory sensitivity and opiate lethality. We used DO mice treated with morphine to map quantitative trait loci for respiratory depression, recovery time and survival time. Trait mapping and integrative functional genomic analysis in GeneWeaver has allowed us to implicate Galnt11, an N-acetylgalactosaminyltransferase, as a gene that regulates OIRD.
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Affiliation(s)
| | - Hao He
- The Jackson Laboratory, Bar Harbor, ME, 04605, USA
| | | | - Tyler Roy
- The Jackson Laboratory, Bar Harbor, ME, 04605, USA
| | | | | | - Kevin D Donohue
- Signal Solutions, LLC, Lexington, KY, USA
- Electrical and Computer Engineering Department, University of Kentucky, Lexington, KY, USA
| | - Bruce F O'Hara
- Signal Solutions, LLC, Lexington, KY, USA
- Department of Biology, University of Kentucky, Lexington, KY, USA
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18
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Strillacci MG, Marelli SP, Martinez-Velazquez G. Hybrid Versus Autochthonous Turkey Populations: Homozygous Genomic Regions Occurrences Due to Artificial and Natural Selection. Animals (Basel) 2020; 10:ani10081318. [PMID: 32751760 PMCID: PMC7460020 DOI: 10.3390/ani10081318] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary In this study we investigate the genomic differentiation of traditional Mexican turkey breeds and commercial hybrid strains. The analysis aimed to identify the effects of different types of selection on the birds’ genome structure. Mexican turkeys are characterized by an adaptive selection to their specific original environment; on the other hand, commercial hybrid strains are directionally selected to maximize productive traits and to reduce production costs. The Mexican turkeys were grouped in two geographic subpopulations, while high genomic homogeneity was found in hybrid birds. Traditional breeds and commercial strains are clearly differentiated from a genetic point of view. Inbreeding coefficients were here calculated with different approaches. A clear effect of selection for productive traits was recorded. Abstract The Mexican turkey population is considered to be the descendant of the original domesticated wild turkey and it is distinct from hybrid strains obtained by the intense artificial selection activity that has occurred during the last 40 years. In this study 30 Mexican turkeys were genomically compared to 38 commercial hybrids using 327,342 SNP markers in order to elucidate the differences in genome variability resulting from different types of selection, i.e., only adaptive for Mexican turkey, and strongly directional for hybrids. Runs of homozygosity (ROH) were detected and the two inbreeding coefficients (F and FROH) based on genomic information were calculated. Principal component and admixture analyses revealed two different clusters for Mexican turkeys (MEX_cl_1 and MEX_cl_2) showing genetic differentiation from hybrids (HYB) (FST equal 0.168 and 0.167, respectively). A total of 3602 ROH were found in the genome of the all turkeys populations. ROH resulted mainly short in length and the ROH_island identified in HYB (n = 9), MEX_cl_1 (n = 1), and MEX_cl_2 (n = 2) include annotated genes related to production traits: abdominal fat (percentage and weight) and egg characteristics (egg shell color and yolk weight). F and FROH resulted correlated to each other only for Mexican populations. Mexican turkey genomic variability allows us to separate the birds into two subgroups according to the geographical origin of samples, while the genomic homogeneity of hybrid birds reflected the strong directional selection occurring in this population.
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Affiliation(s)
- Maria Giuseppina Strillacci
- Department of Veterinary Medicine, University of Milan, Via Festa del Perdono, 7, 20122 Milano, Italy;
- Correspondence: ; Tel.: +39-025-033-4582
| | - Stefano Paolo Marelli
- Department of Veterinary Medicine, University of Milan, Via Festa del Perdono, 7, 20122 Milano, Italy;
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19
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Li HD, Bai T, Sandford E, Burmeister M, Guan Y. BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets. Bioinformatics 2020; 35:2486-2488. [PMID: 30521009 DOI: 10.1093/bioinformatics/bty1001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Functional gene networks, representing how likely two genes work in the same biological process, are important models for studying gene interactions in complex tissues. However, a limitation of the current network-building scheme is the lack of leveraging evidence from multiple model organisms as well as the lack of expert curation and quality control of the input genomic data. RESULTS Here, we present BaiHui, a brain-specific functional gene network built by probabilistically integrating expertly-hand-curated (by reading original publications) heterogeneous and multi-species genomic data in human, mouse and rat brains. To facilitate the use of this network, we deployed a web server through which users can query their genes of interest, visualize the network, gain functional insight from enrichment analysis and download network data. We also illustrated how this network could be used to generate testable hypotheses on disease gene prioritization of brain disorders. AVAILABILITY AND IMPLEMENTATION BaiHui is freely available at: http://guanlab.ccmb.med.umich.edu/BaiHui/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hong-Dong Li
- Center for Bioinformatics, School of Information Science and Engineering, Central South University, Changsha, People's Republic of China.,Department of Computational Medicine and Bioinformatics
| | - Tianjian Bai
- Department of Computational Medicine and Bioinformatics
| | - Erin Sandford
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Margit Burmeister
- Department of Computational Medicine and Bioinformatics.,Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics
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20
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Smith JC. A Review of Strain and Sex Differences in Response to Pain and Analgesia in Mice. Comp Med 2019; 69:490-500. [PMID: 31822324 DOI: 10.30802/aalas-cm-19-000066] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pain and its alleviation are currently a highly studied issue in human health. Research on pain and response to analgesia has evolved to include the effects of genetics, heritability, and sex as important components in both humans and animals. The laboratory mouse is the major animal studied in the field of pain and analgesia. Studying the inbred mouse to understand how genetic heritable traits and/or sex influence pain and analgesia has added valuable information to the complex nature of pain as a human disease. In the context of biomedical research, identifying pain and ensuring its control through analgesia in research animals remains one of the hallmark responsibilities of the research community. Advancements in both human and mouse genomic research shed light not only on the need to understand how both strain and sex affect the mouse pain response but also on how these research achievements can be used to improve the humane use of all research animal species. A better understanding of how strain and sex affect the response to pain may allow researchers to improve study design and thereby the reproducibility of animal research studies. The need to use both sexes, along with an improved understanding of how genetic heritability affects nociception and analgesic sensitivity, remains a key priority for pain researchers working with mice. This review summarizes the current literature on how strain and sex alter the response to pain and analgesia in the modern research mouse, and highlights the importance of both strain and sex selection in pain research.
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Affiliation(s)
- Jennifer C Smith
- Department of Bioresources, Henry Ford Health System, Detroit, Michigan;,
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21
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Abstract
In this chapter we will review both the rationale and experimental design for using Heterogeneous Stock (HS) populations for fine-mapping of complex traits in mice and rats. We define an HS as an outbred population derived from an intercross between two or more inbred strains. HS have been used to perform genome-wide association studies (GWAS) for multiple behavioral, physiological, and gene expression traits. GWAS using HS require four key steps, which we review: selection of an appropriate HS population, phenotyping, genotyping, and statistical analysis. We provide advice on the selection of an HS, comment on key issues related to phenotyping, discuss genotyping methods relevant to these populations, and describe statistical genetic analyses that are applicable to genetic analyses that use HS.
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22
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Recla JM, Bubier JA, Gatti DM, Ryan JL, Long KH, Robledo RF, Glidden NC, Hou G, Churchill GA, Maser RS, Zhang ZW, Young EE, Chesler EJ, Bult CJ. Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response. Pain 2019; 160:1740-1753. [PMID: 31335644 PMCID: PMC6668363 DOI: 10.1097/j.pain.0000000000001571] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Identification of genetic variants that influence susceptibility to pain is key to identifying molecular mechanisms and targets for effective and safe therapeutic alternatives to opioids. To identify genes and variants associated with persistent pain, we measured late-phase response to formalin injection in 275 male and female Diversity Outbred mice genotyped for over 70,000 single nucleotide polymorphisms. One quantitative trait locus reached genome-wide significance on chromosome 1 with a support interval of 3.1 Mb. This locus, Nociq4 (nociceptive sensitivity quantitative trait locus 4; MGI: 5661503), harbors the well-known pain gene Trpa1 (transient receptor potential cation channel, subfamily A, member 1). Trpa1 is a cation channel known to play an important role in acute and chronic pain in both humans and mice. Analysis of Diversity Outbred founder strain allele effects revealed a significant effect of the CAST/EiJ allele at Trpa1, with CAST/EiJ carrier mice showing an early, but not late, response to formalin relative to carriers of the 7 other inbred founder alleles (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ). We characterized possible functional consequences of sequence variants in Trpa1 by assessing channel conductance, TRPA1-TRPV1 interactions, and isoform expression. The phenotypic differences observed in CAST/EiJ relative to C57BL/6J carriers were best explained by Trpa1 isoform expression differences, implicating a splice junction variant as the causal functional variant. This study demonstrates the utility of advanced, high-precision genetic mapping populations in resolving specific molecular mechanisms of variation in pain sensitivity.
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Affiliation(s)
- Jill M. Recla
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- IGERT Program in Functional Genomics, Graduate School of Biomedical Sciences and Engineering, The University of Maine, Orono, ME 04469, USA
| | - Jason A. Bubier
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jennifer L. Ryan
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Katie H. Long
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Nicole C. Glidden
- Department of Genetics and Genome Sciences, UCONN Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Guoqiang Hou
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Richard S. Maser
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Zhong-wei Zhang
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Erin E. Young
- Department of Genetics and Genome Sciences, UCONN Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
- School of Nursing, University of Connecticut, 231 Glenbrook Rd, Unit 4026, Storrs, CT 06269-4026, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269-4026, USA
| | | | - Carol J. Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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23
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Abstract
The high mapping resolution of multiparental populations, combined with technology to measure tens of thousands of phenotypes, presents a need for quantitative methods to enhance understanding of the genetic architecture of complex traits. When multiple traits map to a common genomic region, knowledge of the number of distinct loci provides important insight into the underlying mechanism and can assist planning for subsequent experiments. We extend the method of Jiang and Zeng (1995), for testing pleiotropy with a pair of traits, to the case of more than two alleles. We also incorporate polygenic random effects to account for population structure. We use a parametric bootstrap to determine statistical significance. We apply our methods to a behavioral genetics data set from Diversity Outbred mice. Our methods have been incorporated into the R package qtl2pleio.
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24
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Saul MC, Philip VM, Reinholdt LG, Chesler EJ. High-Diversity Mouse Populations for Complex Traits. Trends Genet 2019; 35:501-514. [PMID: 31133439 DOI: 10.1016/j.tig.2019.04.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/21/2022]
Abstract
Contemporary mouse genetic reference populations are a powerful platform to discover complex disease mechanisms. Advanced high-diversity mouse populations include the Collaborative Cross (CC) strains, Diversity Outbred (DO) stock, and their isogenic founder strains. When used in systems genetics and integrative genomics analyses, these populations efficiently harnesses known genetic variation for precise and contextualized identification of complex disease mechanisms. Extensive genetic, genomic, and phenotypic data are already available for these high-diversity mouse populations and a growing suite of data analysis tools have been developed to support research on diverse mice. This integrated resource can be used to discover and evaluate disease mechanisms relevant across species.
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Affiliation(s)
- Michael C Saul
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
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- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA; UNC Chapel Hill, Chapel Hill, NC, USA; SUNY Binghamton, Binghamton, NY, USA; Pittsburgh University, Pittsburgh, PA, USA
| | - Elissa J Chesler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA.
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25
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Sundberg JP, Boyd K, Hogenesch H, Nikitin AY, Treuting PM, Ward JM. Training mouse pathologists: 16 th annual workshop on the pathology of mouse models of human disease. Lab Anim (NY) 2018; 47:38-40. [PMID: 29384517 DOI: 10.1038/laban.1399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Kelli Boyd
- Departments of Comparative Medicine and Pathology, Vanderbilt University, Nashville, TN
| | - Harm Hogenesch
- Purdue University College of Veterinary Medicine, West Lafayette, IN
| | | | - Piper M Treuting
- Departments of Comparative Medicine and Pathology, University of Washington, Seattle, WA
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26
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Manet C, Roth C, Tawfik A, Cantaert T, Sakuntabhai A, Montagutelli X. Host genetic control of mosquito-borne Flavivirus infections. Mamm Genome 2018; 29:384-407. [PMID: 30167843 PMCID: PMC7614898 DOI: 10.1007/s00335-018-9775-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
Abstract
Flaviviruses are arthropod-borne viruses, several of which represent emerging or re-emerging pathogens responsible for widespread infections with consequences ranging from asymptomatic seroconversion to severe clinical diseases and congenital developmental deficits. This variability is due to multiple factors including host genetic determinants, the role of which has been investigated in mouse models and human genetic studies. In this review, we provide an overview of the host genes and variants which modify susceptibility or resistance to major mosquito-borne flaviviruses infections in mice and humans.
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Affiliation(s)
- Caroline Manet
- Mouse Genetics Laboratory, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Claude Roth
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- CNRS, UMR 2000-Génomique Evolutive, Modélisation et Santé, Institut Pasteur, 75015, Paris, France
| | - Ahmed Tawfik
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- CNRS, UMR 2000-Génomique Evolutive, Modélisation et Santé, Institut Pasteur, 75015, Paris, France
| | - Tineke Cantaert
- Immunology Group, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, Phnom Penh, 12201, Cambodia
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
- CNRS, UMR 2000-Génomique Evolutive, Modélisation et Santé, Institut Pasteur, 75015, Paris, France.
| | - Xavier Montagutelli
- Mouse Genetics Laboratory, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
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27
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Yuan JT, Gatti DM, Philip VM, Kasparek S, Kreuzman AM, Mansky B, Sharif K, Taterra D, Taylor WM, Thomas M, Ward JO, Holmes A, Chesler EJ, Parker CC. Genome-wide association for testis weight in the diversity outbred mouse population. Mamm Genome 2018; 29:310-324. [PMID: 29691636 DOI: 10.1007/s00335-018-9745-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/16/2018] [Indexed: 12/28/2022]
Abstract
Testis weight is a genetically mediated trait associated with reproductive efficiency across numerous species. We sought to evaluate the genetically diverse, highly recombinant Diversity Outbred (DO) mouse population as a tool to identify and map quantitative trait loci (QTLs) associated with testis weight. Testis weights were recorded for 502 male DO mice and the mice were genotyped on the GIGAMuga array at ~ 143,000 SNPs. We performed a genome-wide association analysis and identified one significant and two suggestive QTLs associated with testis weight. Using bioinformatic approaches, we developed a list of candidate genes and identified those with known roles in testicular size and development. Candidates of particular interest include the RNA demethylase gene Alkbh5, the cyclin-dependent kinase inhibitor gene Cdkn2c, the dynein axonemal heavy chain gene Dnah11, the phospholipase D gene Pld6, the trans-acting transcription factor gene Sp4, and the spermatogenesis-associated gene Spata6, each of which has a human ortholog. Our results demonstrate the utility of DO mice in high-resolution genetic mapping of complex traits, enabling us to identify developmentally important genes in adult mice. Understanding how genetic variation in these genes influence testis weight could aid in the understanding of mechanisms of mammalian reproductive function.
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Affiliation(s)
- Joshua T Yuan
- Department of Computer Science, Program in Molecular Biology & Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Daniel M Gatti
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME, 04609, USA
| | - Vivek M Philip
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME, 04609, USA
| | - Steven Kasparek
- Department of Psychology, Middlebury College, Middlebury, VT, 05753, USA
| | - Andrew M Kreuzman
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Benjamin Mansky
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Kayvon Sharif
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Dominik Taterra
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Walter M Taylor
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Mary Thomas
- Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA
| | - Jeremy O Ward
- Department of Biology, Program in Molecular Biology & Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcoholism and Alcohol Abuse (NIAAA), US National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elissa J Chesler
- The Jackson Laboratory, 610 Main Street, Bar Harbor, ME, 04609, USA
| | - Clarissa C Parker
- Department of Psychology, Middlebury College, Middlebury, VT, 05753, USA. .,Program in Neuroscience, Middlebury College, Middlebury, VT, 05753, USA.
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28
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Shorter JR, Huang W, Beak JY, Hua K, Gatti DM, de Villena FPM, Pomp D, Jensen BC. Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size. Mamm Genome 2018; 29:80-89. [PMID: 29279960 PMCID: PMC6340297 DOI: 10.1007/s00335-017-9730-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/11/2017] [Indexed: 01/19/2023]
Abstract
Heart size is an important factor in cardiac health and disease. In particular, increased heart weight is predictive of adverse cardiovascular outcomes in multiple large community-based studies. We use two cohorts of Diversity Outbred (DO) mice to investigate the role of genetics, sex, age, and diet on heart size. DO mice (n = 289) of both sexes from generation 10 were fed a standard chow diet, and analyzed at 12-15 weeks of age. Another cohort of female DO mice (n = 258) from generation 11 were fed either a high-fat, cholesterol-containing (HFC) diet or a low-fat, high-protein diet, and analyzed at 24-25 weeks. We did not observe an effect of diet on body or heart weight in generation 11 mice, although we previously reported an effect on other cardiovascular risk factors, including cholesterol, triglycerides, and insulin. We do observe a significant genetic effect on heart weight in this population. We identified two quantitative trait loci for heart weight, one (Hwtf1) at a genome-wide significance level of p ≤ 0.05 on MMU15 and one (Hwtf2) at a genome-wide suggestive level of p ≤ 0.1 on MMU10, that together explain 13.3% of the phenotypic variance. Hwtf1 contained collagen type XXII alpha 1 chain (Col22a1), and the NZO/HlLtJ and WSB/EiJ haplotypes were associated with larger hearts. This is consistent with heart tissue Col22a1 expression in DO founders and SNP patterns within Hwtf1 for Col22a1. Col22a1 has been previously associated with cardiac fibrosis in mice, suggesting that Col22a1 may be involved in pathological cardiac hypertrophy.
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Affiliation(s)
- John R Shorter
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA.
| | - Wei Huang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ju Youn Beak
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kunjie Hua
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel Pomp
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA
| | - Brian C Jensen
- Division of Cardiology, Department of Medicine, University of North Carolina, 6012 Burnett-Womack Building, Chapel Hill, NC, 27599, USA.
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA.
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA.
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29
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Harrill AH, McAllister KA. New Rodent Population Models May Inform Human Health Risk Assessment and Identification of Genetic Susceptibility to Environmental Exposures. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:086002. [PMID: 28886592 PMCID: PMC5783628 DOI: 10.1289/ehp1274] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 04/19/2017] [Accepted: 04/27/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND This paper provides an introduction for environmental health scientists to emerging population-based rodent resources. Mouse reference populations provide an opportunity to model environmental exposures and gene-environment interactions in human disease and to inform human health risk assessment. OBJECTIVES This review will describe several mouse populations for toxicity assessment, including older models such as the Mouse Diversity Panel (MDP), and newer models that include the Collaborative Cross (CC) and Diversity Outbred (DO) models. METHODS This review will outline the features of the MDP, CC, and DO mouse models and will discuss published case studies investigating the use of these mouse population resources in each step of the risk assessment paradigm. DISCUSSION These unique resources have the potential to be powerful tools for generating hypotheses related to gene-environment interplay in human disease, performing controlled exposure studies to understand the differential responses in humans for susceptibility or resistance to environmental exposures, and identifying gene variants that influence sensitivity to toxicity and disease states. CONCLUSIONS These new resources offer substantial advances to classical toxicity testing paradigms by including genetically sensitive individuals that may inform toxicity risks for sensitive subpopulations. Both in vivo and complementary in vitro resources provide platforms with which to reduce uncertainty by providing population-level data around biological variability. https://doi.org/10.1289/EHP1274.
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Affiliation(s)
- Alison H Harrill
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , Research Triangle Park, North Carolina, USA
| | - Kimberly A McAllister
- Genes, Environment, and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , Research Triangle Park, North Carolina, USA
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30
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Young EE, Bryant CD, Lee SE, Peng X, Cook B, Nair HK, Dreher KJ, Zhang X, Palmer AA, Chung JM, Mogil JS, Chesler EJ, Lariviere WR. Systems genetic and pharmacological analysis identifies candidate genes underlying mechanosensation in the von Frey test. GENES BRAIN AND BEHAVIOR 2017; 15:604-15. [PMID: 27231153 DOI: 10.1111/gbb.12302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/05/2016] [Accepted: 05/24/2016] [Indexed: 12/22/2022]
Abstract
Mechanical sensitivity is commonly affected in chronic pain and other neurological disorders. To discover mechanisms of individual differences in punctate mechanosensation, we performed quantitative trait locus (QTL) mapping of the response to von Frey monofilament stimulation in BXD recombinant inbred (BXD) mice. Significant loci were detected on mouse chromosome (Chr) 5 and 15, indicating the location of underlying polymorphisms that cause heritable variation in von Frey response. Convergent evidence from public gene expression data implicates candidate genes within the loci: von Frey thresholds were strongly correlated with baseline expression of Cacna2d1, Ift27 and Csnk1e in multiple brain regions of BXD strains. Systemic gabapentin and PF-670462, which target the protein products of Cacna2d1 and Csnk1e, respectively, significantly increased von Frey thresholds in a genotype-dependent manner in progenitors and BXD strains. Real-time polymerase chain reaction confirmed differential expression of Cacna2d1 and Csnk1e in multiple brain regions in progenitors and showed differential expression of Cacna2d1 and Csnk1e in the dorsal root ganglia of the progenitors and BXD strains grouped by QTL genotype. Thus, linkage mapping, transcript covariance and pharmacological testing suggest that genetic variation affecting Cacna2d1 and Csnk1e may contribute to individual differences in von Frey filament response. This study implicates Cacna2d1 and Ift27 in basal mechanosensation in line with their previously suspected role in mechanical hypersensitivity. Csnk1e is implicated for von Frey response for the first time. Further investigation is warranted to identify the specific polymorphisms involved and assess the relevance of these findings to clinical conditions of disturbed mechanosensation.
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Affiliation(s)
- E E Young
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,School of Nursing, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - C D Bryant
- Department of Pharmacology and Experimental Therapeutics and Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - S E Lee
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - X Peng
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - B Cook
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - H K Nair
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - K J Dreher
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - X Zhang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - A A Palmer
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA.,Department of Human Genetics, University of Chicago, Chicago, IL, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - J M Chung
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - J S Mogil
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - E J Chesler
- Mammalian Genetics & Genomics, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,The Jackson Laboratory, Bar Harbor, ME, USA
| | - W R Lariviere
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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31
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Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection. G3-GENES GENOMES GENETICS 2016; 6:3893-3902. [PMID: 27694113 PMCID: PMC5144960 DOI: 10.1534/g3.116.035527] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility.
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32
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Abstract
The laboratory mouse is the primary mammalian species used for studying alternative splicing events. Recent studies have generated computational models to predict functions for splice isoforms in the mouse. However, the functional relationship network, describing the probability of splice isoforms participating in the same biological process or pathway, has not yet been studied in the mouse. Here we describe a rich genome-wide resource of mouse networks at the isoform level, which was generated using a unique framework that was originally developed to infer isoform functions. This network was built through integrating heterogeneous genomic and protein data, including RNA-seq, exon array, protein docking and pseudo-amino acid composition. Through simulation and cross-validation studies, we demonstrated the accuracy of the algorithm in predicting isoform-level functional relationships. We showed that this network enables the users to reveal functional differences of the isoforms of the same gene, as illustrated by literature evidence with Anxa6 (annexin a6) as an example. We expect this work will become a useful resource for the mouse genetics community to understand gene functions. The network is publicly available at: http://guanlab.ccmb.med.umich.edu/isoformnetwork.
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33
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Mouse models of human TB pathology: roles in the analysis of necrosis and the development of host-directed therapies. Semin Immunopathol 2015; 38:221-37. [PMID: 26542392 PMCID: PMC4779126 DOI: 10.1007/s00281-015-0538-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/22/2015] [Indexed: 12/28/2022]
Abstract
A key aspect of TB pathogenesis that maintains Mycobacterium tuberculosis in the human population is the ability to cause necrosis in pulmonary lesions. As co-evolution shaped M. tuberculosis (M.tb) and human responses, the complete TB disease profile and lesion manifestation are not fully reproduced by any animal model. However, animal models are absolutely critical to understand how infection with virulent M.tb generates outcomes necessary for the pathogen transmission and evolutionary success. In humans, a wide spectrum of TB outcomes has been recognized based on clinical and epidemiological data. In mice, there is clear genetic basis for susceptibility. Although the spectra of human and mouse TB do not completely overlap, comparison of human TB with mouse lesions across genetically diverse strains firmly establishes points of convergence. By embracing the genetic heterogeneity of the mouse population, we gain tremendous advantage in the quest for suitable in vivo models. Below, we review genetically defined mouse models that recapitulate a key element of M.tb pathogenesis—induction of necrotic TB lesions in the lungs—and discuss how these models may reflect TB stratification and pathogenesis in humans. The approach ensures that roles that mouse models play in basic and translational TB research will continue to increase allowing researchers to address fundamental questions of TB pathogenesis and bacterial physiology in vivo using this well-defined, reproducible, and cost-efficient system. Combination of the new generation mouse models with advanced imaging technologies will also allow rapid and inexpensive assessment of experimental vaccines and therapies prior to testing in larger animals and clinical trials.
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Collaborative Cross and Diversity Outbred data resources in the Mouse Phenome Database. Mamm Genome 2015; 26:511-20. [PMID: 26286858 PMCID: PMC4602074 DOI: 10.1007/s00335-015-9595-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/10/2015] [Indexed: 10/27/2022]
Abstract
The Mouse Phenome Database was originally conceived as a platform for the integration of phenotype data collected on a defined collection of 40 inbred mouse strains--the "phenome panel." This model provided an impetus for community data sharing, and integration was readily achieved through the reproducible genotypes of the phenome panel strains. Advances in the development of mouse populations lead to an expanded role of the Mouse Phenome Database to encompass new strain panels and inbred strain crosses. The recent introduction of the Collaborative Cross and Diversity Outbred mice, which share an extensive pool of genetic variation from eight founder inbred strains, presents new opportunities and challenges for community data resources. A wide variety of molecular and clinical phenotypes are being collected across genotypes, tissues, ages, environmental exposures, interventions, and treatments. The Mouse Phenome Database provides a framework for retrieval, integration, analysis, and display of these data, enabling them to be evaluated in the context of existing data from standard inbred strains. Primary data in the Mouse Phenome Database are supported by extensive metadata on protocols and procedures. These are centrally curated to ensure accuracy and reproducibility and to provide data in consistent formats. The Mouse Phenome Database represents an established and growing community data resource for mouse phenotype data and encourages submissions from new mouse resources, enabling investigators to integrate existing data into their studies of the phenotypic consequences of genetic variation.
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35
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Niazi MKK, Dhulekar N, Schmidt D, Major S, Cooper R, Abeijon C, Gatti DM, Kramnik I, Yener B, Gurcan M, Beamer G. Lung necrosis and neutrophils reflect common pathways of susceptibility to Mycobacterium tuberculosis in genetically diverse, immune-competent mice. Dis Model Mech 2015. [PMID: 26204894 PMCID: PMC4582107 DOI: 10.1242/dmm.020867] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pulmonary tuberculosis (TB) is caused by Mycobacterium tuberculosis in susceptible humans. Here, we infected Diversity Outbred (DO) mice with ∼100 bacilli by aerosol to model responses in a highly heterogeneous population. Following infection, ‘supersusceptible’, ‘susceptible’ and ‘resistant’ phenotypes emerged. TB disease (reduced survival, weight loss, high bacterial load) correlated strongly with neutrophils, neutrophil chemokines, tumor necrosis factor (TNF) and cell death. By contrast, immune cytokines were weak correlates of disease. We next applied statistical and machine learning approaches to our dataset of cytokines and chemokines from lungs and blood. Six molecules from the lung: TNF, CXCL1, CXCL2, CXCL5, interferon-γ (IFN-γ), interleukin 12 (IL-12); and two molecules from blood – IL-2 and TNF – were identified as being important by applying both statistical and machine learning methods. Using molecular features to generate tree classifiers, CXCL1, CXCL2 and CXCL5 distinguished four classes (supersusceptible, susceptible, resistant and non-infected) from each other with approximately 77% accuracy using completely independent experimental data. By contrast, models based on other molecules were less accurate. Low to no IFN-γ, IL-12, IL-2 and IL-10 successfully discriminated non-infected mice from infected mice but failed to discriminate disease status amongst supersusceptible, susceptible and resistant M.-tuberculosis-infected DO mice. Additional analyses identified CXCL1 as a promising peripheral biomarker of disease and of CXCL1 production in the lungs. From these results, we conclude that: (1) DO mice respond variably to M. tuberculosis infection and will be useful to identify pathways involving necrosis and neutrophils; (2) data from DO mice is suited for machine learning methods to build, validate and test models with independent data based solely on molecular biomarkers; (3) low levels of immunological cytokines best indicate a lack of exposure to M. tuberculosis but cannot distinguish infection from disease. Summary: Molecular biomarkers of tuberculosis are identified and used to classify disease status of Diversity Outbred mice that have been infected with Mycobacterium tuberculosis.
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Affiliation(s)
- Muhammad K K Niazi
- Department of Biomedical Informatics, The Ohio State University, Columbus, 43210 OH, USA
| | - Nimit Dhulekar
- Department of Computer Science and Department of Electrical, Computer and Systems Engineering, Rensselaer Polytechnic Institute, Troy, 12810 NY, USA
| | - Diane Schmidt
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, 01536 MA, USA
| | - Samuel Major
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, 01536 MA, USA
| | - Rachel Cooper
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, 01536 MA, USA
| | - Claudia Abeijon
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, 01536 MA, USA
| | | | - Igor Kramnik
- Department of Medicine, Boston University School of Medicine, Boston, 02215 MA, USA
| | - Bulent Yener
- Department of Computer Science and Department of Electrical, Computer and Systems Engineering, Rensselaer Polytechnic Institute, Troy, 12810 NY, USA
| | - Metin Gurcan
- Department of Biomedical Informatics, The Ohio State University, Columbus, 43210 OH, USA
| | - Gillian Beamer
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, 01536 MA, USA
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36
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Bello SM, Smith CL, Eppig JT. Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis. Mamm Genome 2015; 26:285-94. [PMID: 26162703 PMCID: PMC4534497 DOI: 10.1007/s00335-015-9582-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 11/16/2022]
Abstract
A core part of the Mouse Genome Informatics (MGI) resource is the collection of mouse mutations and the annotation phenotypes and diseases displayed by mice carrying these mutations. These data are integrated with the rest of data in MGI and exported to numerous other resources. The use of mouse phenotype data to drive translational research into human disease has expanded rapidly with the improvements in sequencing technology. MGI has implemented many improvements in allele and phenotype data annotation, search, and display to facilitate access to these data through multiple avenues. For example, the description of alleles has been modified to include more detailed categories of allele attributes. This allows improved discrimination between mutation types. Further, connections have been created between mutations involving multiple genes and each of the genes overlapping the mutation. This allows users to readily find all mutations affecting a gene and see all genes affected by a mutation. In a similar manner, the genes expressed by transgenic or knock-in alleles are now connected to these alleles. The advanced search forms and public reports have been updated to take advantage of these improvements. These search forms and reports are used by an expanding number of researchers to identify novel human disease genes and mouse models of human disease.
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Affiliation(s)
- Susan M Bello
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA,
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Bubier JA, Phillips CA, Langston MA, Baker EJ, Chesler EJ. GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data. Mamm Genome 2015; 26:556-66. [PMID: 26092690 PMCID: PMC4602068 DOI: 10.1007/s00335-015-9575-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/03/2015] [Indexed: 01/20/2023]
Abstract
A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions. The data, largely consisting of gene sets and putative biological networks, are mapped onto one another through gene identifiers and homology across species. A versatile suite of interactive tools enables investigators to perform a variety of set analysis operations to find consilience among these often noisy experimental results. Fast algorithms enable real-time analysis of large queries. Specific applications include prioritizing candidate genes for quantitative trait loci, identifying biologically valid mouse models and phenotypic assays for human disease, finding the common biological substrates of related diseases, classifying experiments and the biological concepts they represent from empirical data, and applying patterns of genomic evidence to implicate novel genes in disease. These results illustrate an alternative to strict emphasis on replicability, whereby researchers classify experimental results to identify the conditions that lead to their similarity.
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Affiliation(s)
| | - Charles A Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Erich J Baker
- Computer Science Department, Baylor University, Waco, TX, 76798, USA
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Dickson PE, McNaughton KA, Hou L, Anderson LC, Long KH, Chesler EJ. Sex and strain influence attribution of incentive salience to reward cues in mice. Behav Brain Res 2015; 292:305-15. [PMID: 26102561 DOI: 10.1016/j.bbr.2015.05.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 05/18/2015] [Accepted: 05/22/2015] [Indexed: 11/28/2022]
Abstract
The propensity to attribute incentive salience to reward cues, measured by Pavlovian sign-tracking, is strongly associated with addiction-related traits including cocaine self-administration, impulsivity, novelty reactivity, and novelty preference. Despite its critical role in addiction, the genetic underpinnings of incentive salience attribution and its relationship to drug addiction are unknown. Mouse genetics can be a powerful means to discover genetic mechanisms underlying this relationship. However, feasibility of genetic dissection of sign-tracking in mice is unknown as only a single study limited to male C57BL/6J mice has rigorously examined this behavior, and limited sign-tracking was observed. Highly diverse mouse populations such as the Collaborative Cross (CC) and Diversity Outbred population (DO) possess a greater range of behavioral and genetic variation than conventional laboratory strains. In the present study, we evaluated sign-tracking and the related phenotype goal-tracking in mice of both sexes from five inbred CC and DO founder strains. Male CAST/EiJ mice exhibited robust sign-tracking; male NOD, male C57BL/6J, and female A/J mice also exhibited significant sign-tracking. Male and female mice from all strains exhibited significant goal-tracking, and significant strain and sex differences were observed. Sign-tracking in males was genetically correlated with exploration of a novel environment, and heritability of sign-tracking and goal-tracking ranged from .32 to .41. These data highlight the importance of considering genetic diversity when evaluating the occurrence of specific behavioral traits in the laboratory mouse and demonstrate that the CC and DO mouse populations can be used to discover mechanisms underlying genetic relationships among sign-tracking and addiction-related behaviors.
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Affiliation(s)
- Price E Dickson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, United States
| | | | - Lingfeng Hou
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, United States
| | - Laura C Anderson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, United States
| | - Katie H Long
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, United States
| | - Elissa J Chesler
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, United States.
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39
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Buchner DA, Nadeau JH. Contrasting genetic architectures in different mouse reference populations used for studying complex traits. Genome Res 2015; 25:775-91. [PMID: 25953951 PMCID: PMC4448675 DOI: 10.1101/gr.187450.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/31/2015] [Indexed: 01/14/2023]
Abstract
Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models.
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Affiliation(s)
- David A Buchner
- Department of Genetics and Genome Sciences, Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Joseph H Nadeau
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122, USA
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40
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Dickson PE, Ndukum J, Wilcox T, Clark J, Roy B, Zhang L, Li Y, Lin DT, Chesler EJ. Association of novelty-related behaviors and intravenous cocaine self-administration in Diversity Outbred mice. Psychopharmacology (Berl) 2015; 232:1011-24. [PMID: 25238945 PMCID: PMC4774545 DOI: 10.1007/s00213-014-3737-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/28/2014] [Indexed: 01/22/2023]
Abstract
RATIONALE The preference for and reaction to novelty are strongly associated with addiction to cocaine and other drugs. However, the genetic variants and molecular mechanisms underlying these phenomena remain largely unknown. Although the relationship between novelty- and addiction-related traits has been observed in rats, studies in mice have failed to demonstrate this association. New, genetically diverse, high-precision mouse populations including Diversity Outbred (DO) mice provide an opportunity to assess an expanded range of behavioral variation enabling detection of associations of novelty- and addiction-related traits in mice. METHODS To examine the relationship between novelty- and addiction-related traits, male (n = 51) and female (n = 47) DO mice were tested on open field exploration, hole board exploration, and novelty preference followed by intravenous cocaine self-administration (IVSA; ten 2-h sessions of fixed ratio 1 and one 6-h session of progressive ratio). RESULTS We observed high variation of cocaine IVSA in DO mice with 43 % reaching and 57 % not reaching conventional acquisition criteria. As a group, mice that did not reach these criteria still demonstrated significant lever discrimination. Mice experiencing catheter occlusion or other technical issues (n = 17) were excluded from the analysis. Novelty-related behaviors were positively associated with cocaine IVSA. Multivariate analysis of associations among novelty- and addiction-related traits revealed a large degree of shared variance (45 %). CONCLUSIONS Covariation among cocaine IVSA and novelty-related phenotypes in DO mice indicates that this relationship is amenable to genetic dissection. The high genetic precision and phenotypic diversity in the DO may facilitate discovery of previously undetectable mechanisms underlying predisposition to develop addiction disorders.
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Affiliation(s)
| | - Juliet Ndukum
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - Troy Wilcox
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - James Clark
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - Brittany Roy
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
| | - Lifeng Zhang
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224
| | - Yun Li
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224
| | - Da-Ting Lin
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224
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41
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Harrison DE, Astle CM, Niazi MKK, Major S, Beamer GL. Genetically diverse mice are novel and valuable models of age-associated susceptibility to Mycobacterium tuberculosis. Immun Ageing 2014; 11:24. [PMID: 25606048 PMCID: PMC4299371 DOI: 10.1186/s12979-014-0024-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/04/2014] [Indexed: 11/19/2022]
Abstract
BACKGROUND Tuberculosis, the disease due to Mycobacterium tuberculosis, is an important cause of morbidity and mortality in the elderly. Use of mouse models may accelerate insight into the disease and tests of therapies since mice age thirty times faster than humans. However, the majority of TB research relies on inbred mouse strains, and these results might not extrapolate well to the genetically diverse human population. We report here the first tests of M. tuberculosis infection in genetically heterogeneous aging mice, testing if old mice benefit from rapamycin. FINDINGS We find that genetically diverse aging mice are much more susceptible than young mice to M. tuberculosis, as are aging human beings. We also find that rapamycin boosts immune responses during primary infection but fails to increase survival. CONCLUSIONS Genetically diverse mouse models provide a valuable resource to study how age influences responses and susceptibility to pathogens and to test interventions. Additionally, surrogate markers such as immune measures may not predict whether interventions improve survival.
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Affiliation(s)
- David E Harrison
- />The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Clinton M Astle
- />The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | | | - Samuel Major
- />Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, Grafton, MA 01536 USA
| | - Gillian L Beamer
- />Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, Grafton, MA 01536 USA
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