1
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Strosahl J, Ye K, Pazdro R. Novel insights into the pleiotropic health effects of growth differentiation factor 11 gained from genome-wide association studies in population biobanks. BMC Genomics 2024; 25:837. [PMID: 39237910 PMCID: PMC11378601 DOI: 10.1186/s12864-024-10710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/14/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Growth differentiation factor 11 (GDF11) is a member of the transforming growth factor-β (TGF-β) superfamily that has gained considerable attention over the last decade for its observed ability to reverse age-related deterioration of multiple tissues, including the heart. Yet as many researchers have struggled to confirm the cardioprotective and anti-aging effects of GDF11, the topic has grown increasingly controversial, and the field has reached an impasse. We postulated that a clearer understanding of GDF11 could be gained by investigating its health effects at the population level. METHODS AND RESULTS We employed a comprehensive strategy to interrogate results from genome-wide association studies in population Biobanks. Interestingly, phenome-wide association studies (PheWAS) of GDF11 tissue-specific cis-eQTLs revealed associations with asthma, immune function, lung function, and thyroid phenotypes. Furthermore, PheWAS of GDF11 genetic variants confirmed these results, revealing similar associations with asthma, immune function, lung function, and thyroid health. To complement these findings, we mined results from transcriptome-wide association studies, which uncovered associations between predicted tissue-specific GDF11 expression and the same health effects identified from PheWAS analyses. CONCLUSIONS In this study, we report novel relationships between GDF11 and disease, namely asthma and hypothyroidism, in contrast to its formerly assumed role as a rejuvenating factor in basic aging and cardiovascular health. We propose that these associations are mediated through the involvement of GDF11 in inflammatory signaling pathways. Taken together, these findings provide new insights into the health effects of GDF11 at the population level and warrant future studies investigating the role of GDF11 in these specific health conditions.
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Affiliation(s)
- Jessica Strosahl
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Robert Pazdro
- Department of Nutritional Sciences, University of Georgia, 305 Sanford Drive, Athens, GA, 30602, USA.
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2
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Dubovik T, Lukačišin M, Starosvetsky E, LeRoy B, Normand R, Admon Y, Alpert A, Ofran Y, G'Sell M, Shen-Orr SS. Interactions between immune cell types facilitate the evolution of immune traits. Nature 2024; 632:350-356. [PMID: 38866051 PMCID: PMC11306095 DOI: 10.1038/s41586-024-07661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
An essential prerequisite for evolution by natural selection is variation among individuals in traits that affect fitness1. The ability of a system to produce selectable variation, known as evolvability2, thus markedly affects the rate of evolution. Although the immune system is among the fastest-evolving components in mammals3, the sources of variation in immune traits remain largely unknown4,5. Here we show that an important determinant of the immune system's evolvability is its organization into interacting modules represented by different immune cell types. By profiling immune cell variation in bone marrow of 54 genetically diverse mouse strains from the Collaborative Cross6, we found that variation in immune cell frequencies is polygenic and that many associated genes are involved in homeostatic balance through cell-intrinsic functions of proliferation, migration and cell death. However, we also found genes associated with the frequency of a particular cell type that are expressed in a different cell type, exerting their effect in what we term cyto-trans. The vertebrate evolutionary record shows that genes associated in cyto-trans have faced weaker negative selection, thus increasing the robustness and hence evolvability2,7,8 of the immune system. This phenomenon is similarly observable in human blood. Our findings suggest that interactions between different components of the immune system provide a phenotypic space in which mutations can produce variation with little detriment, underscoring the role of modularity in the evolution of complex systems9.
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Affiliation(s)
- Tania Dubovik
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Martin Lukačišin
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Elina Starosvetsky
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Benjamin LeRoy
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
- Nike, Beaverton, OR, USA
| | - Rachelly Normand
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Massachusetts General Hospital, Boston, MA, USA
| | - Yasmin Admon
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Ayelet Alpert
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Yishai Ofran
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Haematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
- Haematology and Bone Marrow Transplantation Department and the Eisenberg R&D Authority, Shaare Zedek Medical Centre, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Max G'Sell
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shai S Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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3
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Parikh C, Glenn RA, Shi Y, Chatterjee K, Swanzey EE, Singer S, Do SC, Zhan Y, Furuta Y, Tahiliani M, Apostolou E, Polyzos A, Koche R, Mezey JG, Vierbuchen T, Stadtfeld M. Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naïve pluripotent stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600805. [PMID: 38979237 PMCID: PMC11230387 DOI: 10.1101/2024.06.26.600805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Naïve pluripotent stem cells (nPSC) frequently undergo pathological and not readily reversible loss of DNA methylation marks at imprinted gene loci. This abnormality poses a hurdle for using pluripotent cell lines in biomedical applications and underscores the need to identify the causes of imprint instability in these cells. We show that nPSCs from inbred mouse strains exhibit pronounced strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming to pluripotency and upon culture with MAP kinase inhibitors, a common approach to maintain naïve pluripotency. Analysis of genetically highly diverse nPSCs from the Diversity Outbred (DO) stock confirms that genetic variation is a major determinant of epigenome stability in pluripotent cells. We leverage the variable DNA hypomethylation in DO lines to identify several trans-acting quantitative trait loci (QTLs) that determine epigenome stability at either specific target loci or genome-wide. Candidate factors encoded by two multi-target QTLs on chromosomes 4 and 17 suggest specific transcriptional regulators that contribute to DNA methylation maintenance in nPSCs. We propose that genetic variants represent candidate biomarkers to identify pluripotent cell lines with desirable properties and might serve as entry points for the targeted engineering of nPSCs with stable epigenomes. Highlights Naïve pluripotent stem cells from distinct inbred mouse strains exhibit variable DNA methylation levels at imprinted gene loci.The vulnerability of pluripotent stem cells to loss of genomic imprinting caused by MAP kinase inhibition strongly differs between inbred mouse strains.Genetically diverse pluripotent stem cell lines from Diversity Outbred mouse stock allow the identification of quantitative trait loci controlling DNA methylation stability.Genetic variants may serve as biomarkers to identify naïve pluripotent stem cell lines that are epigenetically stable in specific culture conditions.
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4
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Mignogna KM, Tatom Z, Macleod L, Sergi Z, Nguyen A, Michenkova M, Smith ML, Miles MF. Identification of novel genetic loci and candidate genes for progressive ethanol consumption in diversity outbred mice. Neuropsychopharmacology 2024:10.1038/s41386-024-01902-6. [PMID: 38951586 DOI: 10.1038/s41386-024-01902-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 07/03/2024]
Abstract
Mouse behavioral genetic mapping studies can identify genomic intervals modulating complex traits under well-controlled environmental conditions and have been used to study ethanol behaviors to aid in understanding genetic risk and the neurobiology of alcohol use disorder (AUD). However, historically such studies have produced large confidence intervals, thus complicating identification of potential causal candidate genes. Diversity Outbred (DO) mice offer the ability to perform high-resolution quantitative trait loci (QTL) mapping on a very genetically diverse background, thus facilitating identification of candidate genes. Here, we studied a population of 636 male DO mice with four weeks of intermittent ethanol access via a three-bottle choice procedure, producing a progressive ethanol consumption phenotype. QTL analysis identified 3 significant (Chrs 3, 4, and 12) and 13 suggestive loci for ethanol-drinking behaviors with narrow confidence intervals (1-4 Mbp for significant QTLs). Results suggested that genetic influences on initial versus progressive ethanol consumption were localized to different genomic intervals. A defined set of positional candidate genes were prioritized using haplotype analysis, identified coding polymorphisms, prefrontal cortex transcriptomics data, human GWAS data and prior rodent gene set data for ethanol or other misused substances. These candidates included Car8, the lone gene with a significant cis-eQTL within a Chr 4 QTL for week four ethanol consumption. These results represent the highest-resolution genetic mapping of ethanol consumption behaviors in mice to date, providing identification of novel loci and candidate genes for study in relation to the neurobiology of AUD.
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Affiliation(s)
- Kristin M Mignogna
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Zachary Tatom
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Lorna Macleod
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Zachary Sergi
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Angel Nguyen
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Marie Michenkova
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Maren L Smith
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael F Miles
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA.
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA.
- Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA.
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, USA.
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5
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Oliveira TY, Merkenschlager J, Eisenreich T, Bortolatto J, Yao KH, Gatti DM, Churchill GA, Nussenzweig MC, Breton G. Quantitative trait loci mapping provides insights into the genetic regulation of dendritic cell numbers in mouse tissues. Cell Rep 2024; 43:114296. [PMID: 38823019 DOI: 10.1016/j.celrep.2024.114296] [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: 12/07/2023] [Revised: 04/02/2024] [Accepted: 05/14/2024] [Indexed: 06/03/2024] Open
Abstract
To explore the influence of genetics on homeostatic regulation of dendritic cell (DC) numbers, we present a screen of DCs and their progenitors in lymphoid and non-lymphoid tissues in Collaborative Cross (CC) and Diversity Outbred (DO) mice. We report 30 and 71 loci with logarithm of the odds (LOD) scores >8.18 and ranging from 6.67 to 8.19, respectively. The analysis reveals the highly polygenic and pleiotropic architecture of this complex trait, including many of the previously identified genetic regulators of DC development and maturation. Two SNPs in genes potentially underlying variation in DC homeostasis, a splice variant in Gramd4 (rs235532740) and a missense variant in Orai3 (rs216659754), are confirmed by gene editing using CRISPR-Cas9. Gramd4 is a central regulator of DC homeostasis that impacts the entire DC lineage, and Orai3 regulates cDC2 numbers in tissues. Overall, the data reveal a large number of candidate genes regulating DC homeostasis in vivo.
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Affiliation(s)
- Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Julia Merkenschlager
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Eisenreich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Juliana Bortolatto
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY 10065, USA
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | | | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute (HHMI), The Rockefeller University, New York, NY 10065, USA.
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.
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6
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Gatti DM, Tyler AL, Mahoney JM, Churchill GA, Yener B, Koyuncu D, Gurcan MN, Niazi MKK, Tavolara T, Gower A, Dayao D, McGlone E, Ginese ML, Specht A, Alsharaydeh A, Tessier PA, Kurtz SL, Elkins KL, Kramnik I, Beamer G. Systems genetics uncover new loci containing functional gene candidates in Mycobacterium tuberculosis-infected Diversity Outbred mice. PLoS Pathog 2024; 20:e1011915. [PMID: 38861581 PMCID: PMC11195971 DOI: 10.1371/journal.ppat.1011915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/24/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
Mycobacterium tuberculosis infects two billion people across the globe, and results in 8-9 million new tuberculosis (TB) cases and 1-1.5 million deaths each year. Most patients have no known genetic basis that predisposes them to disease. Here, we investigate the complex genetic basis of pulmonary TB by modelling human genetic diversity with the Diversity Outbred mouse population. When infected with M. tuberculosis, one-third develop early onset, rapidly progressive, necrotizing granulomas and succumb within 60 days. The remaining develop non-necrotizing granulomas and survive longer than 60 days. Genetic mapping using immune and inflammatory mediators; and clinical, microbiological, and granuloma correlates of disease identified five new loci on mouse chromosomes 1, 2, 4, 16; and three known loci on chromosomes 3 and 17. Further, multiple positively correlated traits shared loci on chromosomes 1, 16, and 17 and had similar patterns of allele effects, suggesting these loci contain critical genetic regulators of inflammatory responses to M. tuberculosis. To narrow the list of candidate genes, we used a machine learning strategy that integrated gene expression signatures from lungs of M. tuberculosis-infected Diversity Outbred mice with gene interaction networks to generate scores representing functional relationships. The scores were used to rank candidates for each mapped trait, resulting in 11 candidate genes: Ncf2, Fam20b, S100a8, S100a9, Itgb5, Fstl1, Zbtb20, Ddr1, Ier3, Vegfa, and Zfp318. Although all candidates have roles in infection, inflammation, cell migration, extracellular matrix remodeling, or intracellular signaling, and all contain single nucleotide polymorphisms (SNPs), SNPs in only four genes (S100a8, Itgb5, Fstl1, Zfp318) are predicted to have deleterious effects on protein functions. We performed methodological and candidate validations to (i) assess biological relevance of predicted allele effects by showing that Diversity Outbred mice carrying PWK/PhJ alleles at the H-2 locus on chromosome 17 QTL have shorter survival; (ii) confirm accuracy of predicted allele effects by quantifying S100A8 protein in inbred founder strains; and (iii) infection of C57BL/6 mice deficient for the S100a8 gene. Overall, this body of work demonstrates that systems genetics using Diversity Outbred mice can identify new (and known) QTLs and functionally relevant gene candidates that may be major regulators of complex host-pathogens interactions contributing to granuloma necrosis and acute inflammation in pulmonary TB.
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Affiliation(s)
- Daniel M. Gatti
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Anna L. Tyler
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | | | - Bulent Yener
- Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Deniz Koyuncu
- Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Metin N. Gurcan
- Wake Forest University School of Medicine, Winston Salem, North Carolina, United States of America
| | - MK Khalid Niazi
- Wake Forest University School of Medicine, Winston Salem, North Carolina, United States of America
| | - Thomas Tavolara
- Wake Forest University School of Medicine, Winston Salem, North Carolina, United States of America
| | - Adam Gower
- Clinical and Translational Science Institute, Boston University, Boston, Massachusetts, United States of America
| | - Denise Dayao
- Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Emily McGlone
- Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Melanie L. Ginese
- Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Aubrey Specht
- Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, United States of America
| | - Anas Alsharaydeh
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Philipe A. Tessier
- Department of Microbiology and Immunology, Laval University School of Medicine, Quebec, Canada
| | - Sherry L. Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Karen L. Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Igor Kramnik
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Gillian Beamer
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
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7
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Schäfer A, Gralinski LE, Leist SR, Hampton BK, Mooney MA, Jensen KL, Graham RL, Agnihothram S, Jeng S, Chamberlin S, Bell TA, Scobey DT, Linnertz CL, VanBlargan LA, Thackray LB, Hock P, Miller DR, Shaw GD, Diamond MS, de Villena FPM, McWeeney SK, Heise MT, Menachery VD, Ferris MT, Baric RS. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans. Virus Res 2024; 344:199357. [PMID: 38508400 PMCID: PMC10981091 DOI: 10.1016/j.virusres.2024.199357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Mooney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Kara L Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steven Chamberlin
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology2, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology3, Washington University School of Medicine, St. Louis, MO, USA
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA; Department of Pathology and Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA.
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8
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Schäfer A, Marzi A, Furuyama W, Catanzaro NJ, Nguyen C, Haddock E, Feldmann F, Meade-White K, Thomas T, Hubbard ML, Gully KL, Leist SR, Hock P, Bell TA, De la Cruz GE, Midkiff BR, Martinez DR, Shaw GD, Miller DR, Vernon MJ, Graham RL, Cowley DO, Montgomery SA, Schughart K, de Villena FPM, Wilkerson GK, Ferris MT, Feldmann H, Baric RS. Mapping of susceptibility loci for Ebola virus pathogenesis in mice. Cell Rep 2024; 43:114127. [PMID: 38652660 PMCID: PMC11348656 DOI: 10.1016/j.celrep.2024.114127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Ebola virus (EBOV), a major global health concern, causes severe, often fatal EBOV disease (EVD) in humans. Host genetic variation plays a critical role, yet the identity of host susceptibility loci in mammals remains unknown. Using genetic reference populations, we generate an F2 mapping cohort to identify host susceptibility loci that regulate EVD. While disease-resistant mice display minimal pathogenesis, susceptible mice display severe liver pathology consistent with EVD-like disease and transcriptional signatures associated with inflammatory and liver metabolic processes. A significant quantitative trait locus (QTL) for virus RNA load in blood is identified in chromosome (chr)8, and a severe clinical disease and mortality QTL is mapped to chr7, which includes the Trim5 locus. Using knockout mice, we validate the Trim5 locus as one potential driver of liver failure and mortality after infection. The identification of susceptibility loci provides insight into molecular genetic mechanisms regulating EVD progression and severity, potentially informing therapeutics and vaccination strategies.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA.
| | - Wakako Furuyama
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Cameron Nguyen
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elaine Haddock
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Tina Thomas
- Rocky Mountain Veterinary Branch, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Miranda L Hubbard
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kendra L Gully
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gabriela E De la Cruz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Bentley R Midkiff
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael J Vernon
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Animal Models Core Facility, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephanie A Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Klaus Schughart
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Institute of Virology, University of Muenster, 48149 Muenster, Germany
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gregory K Wilkerson
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, NIAID, NIH, Hamilton, MT 59840, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA.
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9
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O’Connor C, Keele GR, Martin W, Stodola T, Gatti D, Hoffman BR, Korstanje R, Churchill GA, Reinholdt LG. Unraveling the genetics of arsenic toxicity with cellular morphology QTL. PLoS Genet 2024; 20:e1011248. [PMID: 38662777 PMCID: PMC11075906 DOI: 10.1371/journal.pgen.1011248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/07/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024] Open
Abstract
The health risks that arise from environmental exposures vary widely within and across human populations, and these differences are largely determined by genetic variation and gene-by-environment (gene-environment) interactions. However, risk assessment in laboratory mice typically involves isogenic strains and therefore, does not account for these known genetic effects. In this context, genetically heterogenous cell lines from laboratory mice are promising tools for population-based screening because they provide a way to introduce genetic variation in risk assessment without increasing animal use. Cell lines from genetic reference populations of laboratory mice offer genetic diversity, power for genetic mapping, and potentially, predictive value for in vivo experimentation in genetically matched individuals. To explore this further, we derived a panel of fibroblast lines from a genetic reference population of laboratory mice (the Diversity Outbred, DO). We then used high-content imaging to capture hundreds of cell morphology traits in cells exposed to the oxidative stress-inducing arsenic metabolite monomethylarsonous acid (MMAIII). We employed dose-response modeling to capture latent parameters of response and we then used these parameters to identify several hundred cell morphology quantitative trait loci (cmQTL). Response cmQTL encompass genes with established associations with cellular responses to arsenic exposure, including Abcc4 and Txnrd1, as well as novel gene candidates like Xrcc2. Moreover, baseline trait cmQTL highlight the influence of natural variation on fundamental aspects of nuclear morphology. We show that the natural variants influencing response include both coding and non-coding variation, and that cmQTL haplotypes can be used to predict response in orthogonal cell lines. Our study sheds light on the major molecular initiating events of oxidative stress that are under genetic regulation, including the NRF2-mediated antioxidant response, cellular detoxification pathways, DNA damage repair response, and cell death trajectories.
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Affiliation(s)
- Callan O’Connor
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Gregory R. Keele
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- RTI International, Research Triangle Park, Durham, North Carolina, United States of America
| | - Whitney Martin
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Timothy Stodola
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Daniel Gatti
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Brian R. Hoffman
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Ron Korstanje
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Gary A. Churchill
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Laura G. Reinholdt
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
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10
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Kurtz SL, Baker RE, Boehm FJ, Lehman CC, Mittereder LR, Khan H, Rossi AP, Gatti DM, Beamer G, Sassetti CM, Elkins KL. Multiple genetic loci influence vaccine-induced protection against Mycobacterium tuberculosis in genetically diverse mice. PLoS Pathog 2024; 20:e1012069. [PMID: 38452145 PMCID: PMC10950258 DOI: 10.1371/journal.ppat.1012069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/19/2024] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Mycobacterium tuberculosis (M.tb.) infection leads to over 1.5 million deaths annually, despite widespread vaccination with BCG at birth. Causes for the ongoing tuberculosis endemic are complex and include the failure of BCG to protect many against progressive pulmonary disease. Host genetics is one of the known factors implicated in susceptibility to primary tuberculosis, but less is known about the role that host genetics plays in controlling host responses to vaccination against M.tb. Here, we addressed this gap by utilizing Diversity Outbred (DO) mice as a small animal model to query genetic drivers of vaccine-induced protection against M.tb. DO mice are a highly genetically and phenotypically diverse outbred population that is well suited for fine genetic mapping. Similar to outcomes in people, our previous studies demonstrated that DO mice have a wide range of disease outcomes following BCG vaccination and M.tb. challenge. In the current study, we used a large population of BCG-vaccinated/M.tb.-challenged mice to perform quantitative trait loci mapping of complex infection traits; these included lung and spleen M.tb. burdens, as well as lung cytokines measured at necropsy. We found sixteen chromosomal loci associated with complex infection traits and cytokine production. QTL associated with bacterial burdens included a region encoding major histocompatibility antigens that are known to affect susceptibility to tuberculosis, supporting validity of the approach. Most of the other QTL represent novel associations with immune responses to M.tb. and novel pathways of cytokine regulation. Most importantly, we discovered that protection induced by BCG is a multigenic trait, in which genetic loci harboring functionally-distinct candidate genes influence different aspects of immune responses that are crucial collectively for successful protection. These data provide exciting new avenues to explore and exploit in developing new vaccines against M.tb.
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Affiliation(s)
- Sherry L. Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Richard E. Baker
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Frederick J. Boehm
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Chelsea C. Lehman
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Lara R. Mittereder
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Hamda Khan
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Amy P. Rossi
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- College of Medicine, University of Cincinatti, Cincinatti, Ohio, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Gillian Beamer
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Karen L. Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
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11
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Kleiman NJ, Edmondson EF, Weil MM, Fallgren CM, King A, Schmidt C, Hall EJ. Radiation cataract in Heterogeneous Stock mice after γ-ray or HZE ion exposure. LIFE SCIENCES IN SPACE RESEARCH 2024; 40:97-105. [PMID: 38245354 PMCID: PMC10800003 DOI: 10.1016/j.lssr.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 01/22/2024]
Abstract
Health effects of space radiation are a serious concern for astronauts on long-duration missions. The lens of the eye is one of the most radiosensitive tissues in the body and, therefore, ocular health risks for astronauts is a significant concern. Studies in humans and animals indicate that ionizing radiation exposure to the eye produces characteristic lens changes, termed "radiation cataract," that can affect visual function. Animal models of radiation cataractogenesis have previously utilized inbred mouse or rat strains. These studies were essential for determining morphological changes and dose-response relationships between radiation exposure and cataract. However, the relevance of these studies to human radiosensitivity is limited by the narrow phenotypic range of genetically homogeneous animal models. To model radiation cataract in genetically diverse populations, longitudinal cataract phenotyping was nested within a lifetime carcinogenesis study in male and female heterogeneous stock (HS/Npt) mice exposed to 0.4 Gy HZE ions (n = 609) or 3.0 Gy γ-rays (n = 602) and in unirradiated controls (n = 603). Cataractous change was quantified in each eye for up to 2 years using Merriam-Focht grading criteria by dilated slit lamp examination. Virtual Optomotry™ measurement of visual acuity and contrast sensitivity was utilized to assess visual function in a subgroup of mice. Prevalence and severity of posterior lens opacifications were 2.6-fold higher in HZE ion and 2.3-fold higher in γ-ray irradiated mice compared to unirradiated controls. Male mice were at greater risk for spontaneous and radiation associated cataracts. Risk for cataractogenesis was associated with family structure, demonstrating that HS/Npt mice are well-suited to evaluate genetic determinants of ocular radiosensitivity. Last, mice were extensively evaluated for cataract and tumor formation, which revealed an overlap between individual susceptibility to both cancer and cataract.
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Affiliation(s)
- Norman J Kleiman
- Department of Environmental Health Sciences, Eye Radiation and Environmental Research Laboratory, Columbia University, Mailman School of Public Health, 722 West 168th St., 11th Floor, New York, NY, 10032, United States.
| | - Elijah F Edmondson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, United States; Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, United States
| | - Michael M Weil
- Department of Environment and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, United States
| | - Christina M Fallgren
- Department of Environment and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, United States
| | - Adam King
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, 80523, United States; MedVet Chicago, Chicago, IL, 60618, United States
| | - Catherine Schmidt
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, 80523, United States; Veterinary Eye Specialists, Thornwood, NY, 10594, , United States
| | - Eric J Hall
- Center for Radiological Research, Columbia University, College of Physicians and Surgeons, 630W. 168th St., New York, NY,10032, , United States
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12
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Gatti DM, Tyler AL, Mahoney JM, Churchill GA, Yener B, Koyuncu D, Gurcan MN, Niazi M, Tavolara T, Gower AC, Dayao D, McGlone E, Ginese ML, Specht A, Alsharaydeh A, Tessier PA, Kurtz SL, Elkins K, Kramnik I, Beamer G. Systems genetics uncover new loci containing functional gene candidates in Mycobacterium tuberculosis-infected Diversity Outbred mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572738. [PMID: 38187647 PMCID: PMC10769337 DOI: 10.1101/2023.12.21.572738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mycobacterium tuberculosis, the bacillus that causes tuberculosis (TB), infects 2 billion people across the globe, and results in 8-9 million new TB cases and 1-1.5 million deaths each year. Most patients have no known genetic basis that predisposes them to disease. We investigated the complex genetic basis of pulmonary TB by modelling human genetic diversity with the Diversity Outbred mouse population. When infected with M. tuberculosis, one-third develop early onset, rapidly progressive, necrotizing granulomas and succumb within 60 days. The remaining develop non-necrotizing granulomas and survive longer than 60 days. Genetic mapping using clinical indicators of disease, granuloma histopathological features, and immune response traits identified five new loci on mouse chromosomes 1, 2, 4, 16 and three previously identified loci on chromosomes 3 and 17. Quantitative trait loci (QTLs) on chromosomes 1, 16, and 17, associated with multiple correlated traits and had similar patterns of allele effects, suggesting these QTLs contain important genetic regulators of responses to M. tuberculosis. To narrow the list of candidate genes in QTLs, we used a machine learning strategy that integrated gene expression signatures from lungs of M. tuberculosis-infected Diversity Outbred mice with gene interaction networks, generating functional scores. The scores were then used to rank candidates for each mapped trait in each locus, resulting in 11 candidates: Ncf2, Fam20b, S100a8, S100a9, Itgb5, Fstl1, Zbtb20, Ddr1, Ier3, Vegfa, and Zfp318. Importantly, all 11 candidates have roles in infection, inflammation, cell migration, extracellular matrix remodeling, or intracellular signaling. Further, all candidates contain single nucleotide polymorphisms (SNPs), and some but not all SNPs were predicted to have deleterious consequences on protein functions. Multiple methods were used for validation including (i) a statistical method that showed Diversity Outbred mice carrying PWH/PhJ alleles on chromosome 17 QTL have shorter survival; (ii) quantification of S100A8 protein levels, confirming predicted allele effects; and (iii) infection of C57BL/6 mice deficient for the S100a8 gene. Overall, this work demonstrates that systems genetics using Diversity Outbred mice can identify new (and known) QTLs and new functionally relevant gene candidates that may be major regulators of granuloma necrosis and acute inflammation in pulmonary TB.
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Affiliation(s)
- D M Gatti
- The Jackson Laboratory, Bar Harbor, ME
| | - A L Tyler
- The Jackson Laboratory, Bar Harbor, ME
| | | | | | - B Yener
- Rensselaer Polytechnic Institute, Troy, NY
| | - D Koyuncu
- Rensselaer Polytechnic Institute, Troy, NY
| | - M N Gurcan
- Wake Forest University School of Medicine, Winston Salem, NC
| | - Mkk Niazi
- Wake Forest University School of Medicine, Winston Salem, NC
| | - T Tavolara
- Wake Forest University School of Medicine, Winston Salem, NC
| | - A C Gower
- Clinical and Translational Science Institute, Boston University, Boston, MA
| | - D Dayao
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - E McGlone
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - M L Ginese
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - A Specht
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA
| | - A Alsharaydeh
- Texas Biomedical Research Institute, San Antonio, TX
| | - P A Tessier
- Department of Microbiology and Immunology, Laval University School of Medicine, Quebec, Canada
| | - S L Kurtz
- Center for Biologics, Food and Drug Administration, Bethesda, MD
| | - K Elkins
- Center for Biologics, Food and Drug Administration, Bethesda, MD
| | - I Kramnik
- NIEDL, Boston University, Boston, MA
| | - G Beamer
- Texas Biomedical Research Institute, San Antonio, TX
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13
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Kenny J, Mullin BH, Tomlinson W, Robertson B, Yuan J, Chen W, Zhao J, Pavlos NJ, Walsh JP, Wilson SG, Tickner J, Morahan G, Xu J. Age-dependent genetic regulation of osteoarthritis: independent effects of immune system genes. Arthritis Res Ther 2023; 25:232. [PMID: 38041181 PMCID: PMC10691153 DOI: 10.1186/s13075-023-03216-2] [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: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023] Open
Abstract
OBJECTIVES Osteoarthritis (OA) is a joint disease with a heritable component. Genetic loci identified via genome-wide association studies (GWAS) account for an estimated 26.3% of the disease trait variance in humans. Currently, there is no method for predicting the onset or progression of OA. We describe the first use of the Collaborative Cross (CC), a powerful genetic resource, to investigate knee OA in mice, with follow-up targeted multi-omics analysis of homologous regions of the human genome. METHODS We histologically screened 275 mice for knee OA and conducted quantitative trait locus (QTL) mapping in the complete cohort (> 8 months) and the younger onset sub-cohort (8-12 months). Multi-omic analysis of human genetic datasets was conducted to investigate significant loci. RESULTS We observed a range of OA phenotypes. QTL mapping identified a genome-wide significant locus on mouse chromosome 19 containing Glis3, the human equivalent of which has been identified as associated with OA in recent GWAS. Mapping the younger onset sub-cohort identified a genome-wide significant locus on chromosome 17. Multi-omic analysis of the homologous region of the human genome (6p21.32) indicated the presence of pleiotropic effects on the expression of the HLA - DPB2 gene and knee OA development risk, potentially mediated through the effects on DNA methylation. CONCLUSIONS The significant associations at the 6p21.32 locus in human datasets highlight the value of the CC model of spontaneous OA that we have developed and lend support for an immune role in the disease. Our results in mice also add to the accumulating evidence of a role for Glis3 in OA.
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Affiliation(s)
- Jacob Kenny
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia.
| | - Benjamin H Mullin
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - William Tomlinson
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Brett Robertson
- Australian Institute of Robotic Orthopaedics, Crawley, WA, Australia
| | - Jinbo Yuan
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Weiwei Chen
- Research Centre for Regenerative Medicine, and Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Guangxi, China
| | - Jinmin Zhao
- Research Centre for Regenerative Medicine, and Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Guangxi, China
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- Medical School, University of Western Australia, Crawley, WA, Australia
| | - Scott G Wilson
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jennifer Tickner
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute for Medical Research, Nedlands, WA, Australia.
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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14
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O'Connor C, Keele GR, Martin W, Stodola T, Gatti D, Hoffman BR, Korstanje R, Churchill GA, Reinholdt LG. Cell morphology QTL reveal gene by environment interactions in a genetically diverse cell population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567597. [PMID: 38014303 PMCID: PMC10680806 DOI: 10.1101/2023.11.18.567597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Genetically heterogenous cell lines from laboratory mice are promising tools for population-based screening as they offer power for genetic mapping, and potentially, predictive value for in vivo experimentation in genetically matched individuals. To explore this further, we derived a panel of fibroblast lines from a genetic reference population of laboratory mice (the Diversity Outbred, DO). We then used high-content imaging to capture hundreds of cell morphology traits in cells exposed to the oxidative stress-inducing arsenic metabolite monomethylarsonous acid (MMAIII). We employed dose-response modeling to capture latent parameters of response and we then used these parameters to identify several hundred cell morphology quantitative trait loci (cmQTL). Response cmQTL encompass genes with established associations with cellular responses to arsenic exposure, including Abcc4 and Txnrd1, as well as novel gene candidates like Xrcc2. Moreover, baseline trait cmQTL highlight the influence of natural variation on fundamental aspects of nuclear morphology. We show that the natural variants influencing response include both coding and non-coding variation, and that cmQTL haplotypes can be used to predict response in orthogonal cell lines. Our study sheds light on the major molecular initiating events of oxidative stress that are under genetic regulation, including the NRF2-mediated antioxidant response, cellular detoxification pathways, DNA damage repair response, and cell death trajectories.
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Affiliation(s)
- Callan O'Connor
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Gregory R Keele
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- RTI International, RTP, NC 27709, USA
| | | | | | - Daniel Gatti
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | | | - Laura G Reinholdt
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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15
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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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16
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Masson SWC, Madsen S, Cooke KC, Potter M, Vegas AD, Carroll L, Thillainadesan S, Cutler HB, Walder KR, Cooney GJ, Morahan G, Stöckli J, James DE. Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance. eLife 2023; 12:RP86961. [PMID: 37494090 PMCID: PMC10371229 DOI: 10.7554/elife.86961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Systems genetics has begun to tackle the complexity of insulin resistance by capitalising on computational advances to study high-diversity populations. 'Diversity Outbred in Australia (DOz)' is a population of genetically unique mice with profound metabolic heterogeneity. We leveraged this variance to explore skeletal muscle's contribution to whole-body insulin action through metabolic phenotyping and skeletal muscle proteomics of 215 DOz mice. Linear modelling identified 553 proteins that associated with whole-body insulin sensitivity (Matsuda Index) including regulators of endocytosis and muscle proteostasis. To enrich for causality, we refined this network by focusing on negatively associated, genetically regulated proteins, resulting in a 76-protein fingerprint of insulin resistance. We sought to perturb this network and restore insulin action with small molecules by integrating the Broad Institute Connectivity Map platform and in vitro assays of insulin action using the Prestwick chemical library. These complementary approaches identified the antibiotic thiostrepton as an insulin resistance reversal agent. Subsequent validation in ex vivo insulin-resistant mouse muscle and palmitate-induced insulin-resistant myotubes demonstrated potent insulin action restoration, potentially via upregulation of glycolysis. This work demonstrates the value of a drug-centric framework to validate systems-level analysis by identifying potential therapeutics for insulin resistance.
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Affiliation(s)
- Stewart W C Masson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Søren Madsen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Meg Potter
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Alexis Diaz Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Luke Carroll
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, Australia
| | - Senthil Thillainadesan
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Harry B Cutler
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Ken R Walder
- School of Medicine, Deakin University, Geelong, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Murdoch, Australia
| | - Jacqueline Stöckli
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
- School of Medical Sciences University of Sydney, Sydney, Australia
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17
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Kim M, Huda MN, Evans LW, Que E, Gertz ER, Maeda-Smithies N, Bennett BJ. Integrative analysis of hepatic transcriptional profiles reveals genetic regulation of atherosclerosis in hyperlipidemic Diversity Outbred-F1 mice. Sci Rep 2023; 13:9475. [PMID: 37301941 PMCID: PMC10257719 DOI: 10.1038/s41598-023-35917-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Atherogenesis is an insipidus but precipitating process leading to serious consequences of many cardiovascular diseases (CVD). Numerous genetic loci contributing to atherosclerosis have been identified in human genome-wide association studies, but these studies have limitations in the ability to control environmental factors and to decipher cause/effect relationships. To assess the power of hyperlipidemic Diversity Outbred (DO) mice in facilitating quantitative trait loci (QTL) analysis of complex traits, we generated a high-resolution genetic panel of atherosclerosis susceptible (DO-F1) mouse cohort by crossing 200 DO females with C57BL/6J males carrying two human genes: encoding apolipoprotein E3-Leiden and cholesterol ester transfer protein. We examined atherosclerotic traits including plasma lipids and glucose in the 235 female and 226 male progeny before and after 16 weeks of a high-fat/cholesterol diet, and aortic plaque size at 24 weeks. We also assessed the liver transcriptome using RNA-sequencing. Our QTL mapping for atherosclerotic traits identified one previously reported female-specific QTL on Chr10 with a narrower interval of 22.73 to 30.80 Mb, and one novel male-specific QTL at 31.89 to 40.25 Mb on Chr19. Liver transcription levels of several genes within each QTL were highly correlated with the atherogenic traits. A majority of these candidates have already known atherogenic potential in humans and/or mice, but integrative QTL, eQTL, and correlation analyses further pointed Ptprk as a major candidate of the Chr10 QTL, while Pten and Cyp2c67 of the Chr19 QTL in our DO-F1 cohort. Finally, through additional analyses of RNA-seq data we identified genetic regulation of hepatic transcription factors, including Nr1h3, contributes to atherogenesis in this cohort. Thus, an integrative approach using DO-F1 mice effectively validates the influence of genetic factors on atherosclerosis in DO mice and suggests an opportunity to discover therapeutics in the setting of hyperlipidemia.
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Affiliation(s)
- Myungsuk Kim
- Department of Nutrition, University of California, Davis, CA, USA
- Korea Institute of Science and Technology (KIST), Gangneung, Gangwon-Do, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - M Nazmul Huda
- Department of Nutrition, University of California, Davis, CA, USA
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Levi W Evans
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Excel Que
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Erik R Gertz
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Nobuyo Maeda-Smithies
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brian J Bennett
- Department of Nutrition, University of California, Davis, CA, USA.
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA.
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18
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Chung CJ, Hermes BM, Gupta Y, Ibrahim S, Belheouane M, Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Anim Microbiome 2023; 5:31. [PMID: 37264412 DOI: 10.1186/s42523-023-00250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung. RESULTS Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice. CONCLUSIONS Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.
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Affiliation(s)
- C J Chung
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - B M Hermes
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Y Gupta
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - S Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Meriem Belheouane
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
- Research Center Borstel, Evolution of the Resistome, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
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19
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Tyler AL, Spruce C, Kursawe R, Haber A, Ball RL, Pitman WA, Fine AD, Raghupathy N, Walker M, Philip VM, Baker CL, Mahoney JM, Churchill GA, Trowbridge JJ, Stitzel ML, Paigen K, Petkov PM, Carter GW. Variation in histone configurations correlates with gene expression across nine inbred strains of mice. Genome Res 2023; 33:857-871. [PMID: 37217254 PMCID: PMC10519406 DOI: 10.1101/gr.277467.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
The Diversity Outbred (DO) mice and their inbred founders are widely used models of human disease. However, although the genetic diversity of these mice has been well documented, their epigenetic diversity has not. Epigenetic modifications, such as histone modifications and DNA methylation, are important regulators of gene expression and, as such, are a critical mechanistic link between genotype and phenotype. Therefore, creating a map of epigenetic modifications in the DO mice and their founders is an important step toward understanding mechanisms of gene regulation and the link to disease in this widely used resource. To this end, we performed a strain survey of epigenetic modifications in hepatocytes of the DO founders. We surveyed four histone modifications (H3K4me1, H3K4me3, H3K27me3, and H3K27ac), as well as DNA methylation. We used ChromHMM to identify 14 chromatin states, each of which represents a distinct combination of the four histone modifications. We found that the epigenetic landscape is highly variable across the DO founders and is associated with variation in gene expression across strains. We found that epigenetic state imputed into a population of DO mice recapitulated the association with gene expression seen in the founders, suggesting that both histone modifications and DNA methylation are highly heritable mechanisms of gene expression regulation. We illustrate how DO gene expression can be aligned with inbred epigenetic states to identify putative cis-regulatory regions. Finally, we provide a data resource that documents strain-specific variation in the chromatin state and DNA methylation in hepatocytes across nine widely used strains of laboratory mice.
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Affiliation(s)
- Anna L Tyler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Catrina Spruce
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Annat Haber
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Robyn L Ball
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Wendy A Pitman
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Alexander D Fine
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael Walker
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - J Matthew Mahoney
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Gary A Churchill
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Kenneth Paigen
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Petko M Petkov
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA;
| | - Gregory W Carter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
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20
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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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21
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Gastonguay MS, Keele GR, Churchill GA. The trouble with triples: Examining the impact of measurement error in mediation analysis. Genetics 2023; 224:iyad045. [PMID: 36932658 PMCID: PMC10158839 DOI: 10.1093/genetics/iyad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/03/2023] [Accepted: 02/11/2023] [Indexed: 03/19/2023] Open
Abstract
Mediation analysis is used in genetic mapping studies to identify candidate gene mediators of quantitative trait loci (QTL). We consider genetic mediation analysis of triplets-sets of three variables consisting of a target trait, the genotype at a QTL for the target trait, and a candidate mediator that is the abundance of a transcript or protein whose coding gene co-locates with the QTL. We show that, in the presence of measurement error, mediation analysis can infer partial mediation even in the absence of a causal relationship between the candidate mediator and the target. We describe a measurement error model and a corresponding latent variable model with estimable parameters that are combinations of the causal effects and measurement errors across all three variables. The relative magnitudes of the latent variable correlations determine whether or not mediation analysis will tend to infer the correct causal relationship in large samples. We examine case studies that illustrate the common failure modes of genetic mediation analysis and demonstrate how to evaluate the effects of measurement error. While genetic mediation analysis is a powerful tool for identifying candidate genes, we recommend caution when interpreting mediation analysis findings.
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22
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Aydin S, Pham DT, Zhang T, Keele GR, Skelly DA, Paulo JA, Pankratz M, Choi T, Gygi SP, Reinholdt LG, Baker CL, Churchill GA, Munger SC. Genetic dissection of the pluripotent proteome through multi-omics data integration. CELL GENOMICS 2023; 3:100283. [PMID: 37082146 PMCID: PMC10112288 DOI: 10.1016/j.xgen.2023.100283] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/12/2022] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
Genetic background drives phenotypic variability in pluripotent stem cells (PSCs). Most studies to date have used transcript abundance as the primary molecular readout of cell state in PSCs. We performed a comprehensive proteogenomics analysis of 190 genetically diverse mouse embryonic stem cell (mESC) lines. The quantitative proteome is highly variable across lines, and we identified pluripotency-associated pathways that were differentially activated in the proteomics data that were not evident in transcriptome data from the same lines. Integration of protein abundance to transcript levels and chromatin accessibility revealed broad co-variation across molecular layers as well as shared and unique drivers of quantitative variation in pluripotency-associated pathways. Quantitative trait locus (QTL) mapping localized the drivers of these multi-omic signatures to genomic hotspots. This study reveals post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome and provides a regulatory map for mESCs that can provide a basis for future mechanistic studies.
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Affiliation(s)
- Selcan Aydin
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Duy T. Pham
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Tian Zhang
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | - Ted Choi
- Predictive Biology, Inc., Carlsbad, CA 92010, USA
| | | | - Laura G. Reinholdt
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Christopher L. Baker
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Gary A. Churchill
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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23
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Keele GR. Which mouse multiparental population is right for your study? The Collaborative Cross inbred strains, their F1 hybrids, or the Diversity Outbred population. G3 (BETHESDA, MD.) 2023; 13:jkad027. [PMID: 36735601 PMCID: PMC10085760 DOI: 10.1093/g3journal/jkad027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 12/30/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023]
Abstract
Multiparental populations (MPPs) encompass greater genetic diversity than traditional experimental crosses of two inbred strains, enabling broader surveys of genetic variation underlying complex traits. Two such mouse MPPs are the Collaborative Cross (CC) inbred panel and the Diversity Outbred (DO) population, which are descended from the same eight inbred strains. Additionally, the F1 intercrosses of CC strains (CC-RIX) have been used and enable study designs with replicate outbred mice. Genetic analyses commonly used by researchers to investigate complex traits in these populations include characterizing how heritable a trait is, i.e. its heritability, and mapping its underlying genetic loci, i.e. its quantitative trait loci (QTLs). Here we evaluate the relative merits of these populations for these tasks through simulation, as well as provide recommendations for performing the quantitative genetic analyses. We find that sample populations that include replicate animals, as possible with the CC and CC-RIX, provide more efficient and precise estimates of heritability. We report QTL mapping power curves for the CC, CC-RIX, and DO across a range of QTL effect sizes and polygenic backgrounds for samples of 174 and 500 mice. The utility of replicate animals in the CC and CC-RIX for mapping QTLs rapidly decreased as traits became more polygenic. Only large sample populations of 500 DO mice were well-powered to detect smaller effect loci (7.5-10%) for highly complex traits (80% polygenic background). All results were generated with our R package musppr, which we developed to simulate data from these MPPs and evaluate genetic analyses from user-provided genotypes.
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Affiliation(s)
- Gregory R Keele
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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24
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Cornes BK, Paisie C, Swanzey E, Fields PD, Schile A, Brackett K, Reinholdt LG, Srivastava A. Protein coding variation in the J:ARC and J:DO outbred laboratory mouse stocks provides a molecular basis for distinct research applications. G3 (BETHESDA, MD.) 2023; 13:jkad015. [PMID: 36649207 PMCID: PMC10085793 DOI: 10.1093/g3journal/jkad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/02/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023]
Abstract
Outbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice in biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that enhances research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein-coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for the on-going genetic quality control. We also compared these data to protein-coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss-derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. The fact that individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability.
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Affiliation(s)
- Belinda K Cornes
- Mammalian Genetics, The Jackson Laboratory, 600 Main Street, USA
| | - Carolyn Paisie
- Mammalian Genetics, The Jackson Laboratory, 600 Main Street, USA
| | - Emily Swanzey
- Mammalian Genetics, The Jackson Laboratory, 600 Main Street, USA
| | - Peter D Fields
- Mammalian Genetics, The Jackson Laboratory, 600 Main Street, USA
| | - Andrew Schile
- Mammalian Genetics, The Jackson Laboratory, 600 Main Street, USA
| | - Kelly Brackett
- Mammalian Genetics, The Jackson Laboratory, 600 Main Street, USA
| | | | - Anuj Srivastava
- Mammalian Genetics, The Jackson Laboratory, 600 Main Street, USA
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25
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Ackert-Bicknell C, Karasik D. Proceedings of the Post-Genome Analysis for Musculoskeletal Biology Workshop. Curr Osteoporos Rep 2023; 21:184-192. [PMID: 36869984 DOI: 10.1007/s11914-023-00781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2023] [Indexed: 03/05/2023]
Abstract
PURPOSE OF THE REVIEW Herein, we report on the proceedings of the workshop entitled "Post-Genome analysis for musculoskeletal biology" that was held in July of 2022 in Safed, Galilee, Israel. Supported by the Israel Science Foundation, the goal of this workshop was to bring together established investigators and their trainees who were interested in understanding the etiology of musculoskeletal disease, from Israel and from around the world. RECENT FINDINGS Presentations at this workshop spanned the spectrum from basic science to clinical studies. A major emphasis of the discussion centered on genetic studies in humans, and the limitations and advantages of such studies. The power of coupling studies using human data with functional follow-up studies in pre-clinical models such as mice, rats, and zebrafish was discussed in depth. The advantages and limitations of mice and zebrafish for faithfully modelling aspects of human disease were debated, specifically in the context of age-related diseases such as osteoporosis, osteoarthritis, adult-onset auto-immune disease, and osteosarcopenia. There remain significant gaps in our understanding of the nature and etiology of human musculoskeletal disease. While therapies and medications exist, much work is still needed to find safe and effective interventions for all patients suffering from diseases associated with age-related deterioration of musculoskeletal tissues. The potential of forward and reverse genetic studies has not been exhausted for diseases of muscles, joints, and bones.
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Affiliation(s)
- Cheryl Ackert-Bicknell
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado, Anschutz Medical Campus, 12800 E 19th Ave, Aurora, CO, 80045, USA.
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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26
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Li G, Zhou YH, Li HF, Zhang YM. A multi-locus linear mixed model methodology for detecting small-effect QTLs for quantitative traits in MAGIC, NAM, and ROAM populations. Comput Struct Biotechnol J 2023; 21:2241-2252. [PMID: 37035553 PMCID: PMC10073995 DOI: 10.1016/j.csbj.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Although multi-parent populations (MPPs) integrate the advantages of linkage and association mapping populations in the genetic dissection of complex traits and especially combine genetic analysis with crop breeding, it is difficult to detect small-effect quantitative trait loci (QTL) for complex traits in multiparent advanced generation intercross (MAGIC), nested association mapping (NAM), and random-open-parent association mapping (ROAM) populations. To address this issue, here we proposed a multi-locus linear mixed model method, namely mppQTL, to detect QTLs, especially small-effect QTLs, in these MPPs. The new method includes two steps. The first is genome-wide scanning based on a single-locus linear mixed model; the P-values are obtained from likelihood-ratio test, the peaks of negative logarithm P-value curve are selected by group-lasso, and all the selected peaks are regarded as potential QTLs. In the second step, all the potential QTLs are placed on a multi-locus linear mixed model, all the effects are estimated using expectation-maximization empirical Bayes algorithm, and all the non-zero effect vectors are further evaluated via likelihood-ratio test for significant QTLs. In Monte Carlo simulation studies, the new method has higher power in QTL detection, lower false positive rate, lower mean absolute deviation for QTL position estimate, and lower mean squared error for the estimate of QTL size (r2) than existing methods because the new method increases the power of detecting small-effect QTLs. In real dataset analysis, the new method (19) identified five more known genes than the existing three methods (14). This study provides an effective method for detecting small-effect QTLs in any MPPs.
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27
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Gupta Y, Ernst AL, Vorobyev A, Beltsiou F, Zillikens D, Bieber K, Sanna-Cherchi S, Christiano AM, Sadik CD, Ludwig RJ, Sezin T. Impact of diet and host genetics on the murine intestinal mycobiome. Nat Commun 2023; 14:834. [PMID: 36788222 PMCID: PMC9929102 DOI: 10.1038/s41467-023-36479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its' interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.
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Affiliation(s)
- Yask Gupta
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna Lara Ernst
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Artem Vorobyev
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Foteini Beltsiou
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Angela M Christiano
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
- Department of Dermatology, University of Lübeck, Lübeck, Germany.
| | - Tanya Sezin
- Department of Dermatology, University of Lübeck, Lübeck, Germany.
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA.
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Yu Q, Liu X, Keller MP, Navarrete-Perea J, Zhang T, Fu S, Vaites LP, Shuken SR, Schmid E, Keele GR, Li J, Huttlin EL, Rashan EH, Simcox J, Churchill GA, Schweppe DK, Attie AD, Paulo JA, Gygi SP. Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. Nat Commun 2023; 14:555. [PMID: 36732331 PMCID: PMC9894840 DOI: 10.1038/s41467-023-36269-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Targeted proteomics enables hypothesis-driven research by measuring the cellular expression of protein cohorts related by function, disease, or class after perturbation. Here, we present a pathway-centric approach and an assay builder resource for targeting entire pathways of up to 200 proteins selected from >10,000 expressed proteins to directly measure their abundances, exploiting sample multiplexing to increase throughput by 16-fold. The strategy, termed GoDig, requires only a single-shot LC-MS analysis, ~1 µg combined peptide material, a list of up to 200 proteins, and real-time analytics to trigger simultaneous quantification of up to 16 samples for hundreds of analytes. We apply GoDig to quantify the impact of genetic variation on protein expression in mice fed a high-fat diet. We create several GoDig assays to quantify the expression of multiple protein families (kinases, lipid metabolism- and lipid droplet-associated proteins) across 480 fully-genotyped Diversity Outbred mice, revealing protein quantitative trait loci and establishing potential linkages between specific proteins and lipid homeostasis.
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Affiliation(s)
- Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sipei Fu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Laura P Vaites
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven R Shuken
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ernst Schmid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Edrees H Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Judith Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joao A Paulo
- 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.
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Bagley JR, Bailey LS, Gagnon LH, He H, Philip VM, Reinholdt LG, Tarantino LM, Chesler EJ, Jentsch JD. Behavioral phenotypes revealed during reversal learning are linked with novel genetic loci in diversity outbred mice. ADDICTION NEUROSCIENCE 2022; 4:100045. [PMID: 36714272 PMCID: PMC9879139 DOI: 10.1016/j.addicn.2022.100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Impulsive behavior and impulsivity are heritable phenotypes that are strongly associated with risk for substance use disorders. Identifying the neurogenetic mechanisms that influence impulsivity may also reveal novel biological insights into addiction vulnerability. Our past studies using the BXD and Collaborative Cross (CC) recombinant inbred mouse panels have revealed that behavioral indicators of impulsivity measured in a reversal-learning task are heritable and are genetically correlated with aspects of intravenous cocaine self-administration. Genome-wide linkage studies in the BXD panel revealed a quantitative trait locus (QTL) on chromosome 10, but we expect to identify additional QTL by testing in a population with more genetic diversity. To this end, we turned to Diversity Outbred (DO) mice; 392 DO mice (156 males, 236 females) were phenotyped using the same reversal learning test utilized previously. Our primary indicator of impulsive responding, a measure that isolates the relative difficulty mice have with reaching performance criteria under reversal conditions, revealed a genome-wide significant QTL on chromosome 7 (max LOD score = 8.73, genome-wide corrected p<0.05). A measure of premature responding akin to that implemented in the 5-choice serial reaction time task yielded a suggestive QTL on chromosome 17 (max LOD score = 9.14, genome-wide corrected <0.1). Candidate genes were prioritized (2900076A07Rik, Wdr73 and Zscan2) based upon expression QTL data we collected in DO and CC mice and analyses using publicly available gene expression and phenotype databases. These findings may advance understanding of the genetics that drive impulsive behavior and enhance risk for substance use disorders.
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Affiliation(s)
- Jared R. Bagley
- Department of Psychology, Binghamton University, Binghamton, NY, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
| | - Lauren S. Bailey
- Department of Psychology, Binghamton University, Binghamton, NY, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
| | - Leona H. Gagnon
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Hao He
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Vivek M. Philip
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Laura G. Reinholdt
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Lisa M. Tarantino
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Elissa J. Chesler
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - James D. Jentsch
- Department of Psychology, Binghamton University, Binghamton, NY, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
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Hampton BK, Plante KS, Whitmore AC, Linnertz CL, Madden EA, Noll KE, Boyson SP, Parotti B, Xenakis JG, Bell TA, Hock P, Shaw GD, de Villena FPM, Ferris MT, Heise MT. Forward genetic screen of homeostatic antibody levels in the Collaborative Cross identifies MBD1 as a novel regulator of B cell homeostasis. PLoS Genet 2022; 18:e1010548. [PMID: 36574452 PMCID: PMC9829176 DOI: 10.1371/journal.pgen.1010548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/09/2023] [Accepted: 11/28/2022] [Indexed: 12/28/2022] Open
Abstract
Variation in immune homeostasis, the state in which the immune system is maintained in the absence of stimulation, is highly variable across populations. This variation is attributed to both genetic and environmental factors. However, the identity and function of specific regulators have been difficult to identify in humans. We evaluated homeostatic antibody levels in the serum of the Collaborative Cross (CC) mouse genetic reference population. We found heritable variation in all antibody isotypes and subtypes measured. We identified 4 quantitative trait loci (QTL) associated with 3 IgG subtypes: IgG1, IgG2b, and IgG2c. While 3 of these QTL map to genome regions of known immunological significance (major histocompatibility and immunoglobulin heavy chain locus), Qih1 (associated with variation in IgG1) mapped to a novel locus on Chromosome 18. We further associated this locus with B cell proportions in the spleen and identify Methyl-CpG binding domain protein 1 under this locus as a novel regulator of homeostatic IgG1 levels in the serum and marginal zone B cells (MZB) in the spleen, consistent with a role in MZB differentiation to antibody secreting cells.
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Affiliation(s)
- Brea K. Hampton
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kenneth S. Plante
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alan C. Whitmore
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Colton L. Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Emily A. Madden
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kelsey E. Noll
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Samuel P. Boyson
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Breantie Parotti
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - James G. Xenakis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Mark T. Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Moran MM, Ko FC, Mesner LD, Calabrese GM, Al-Barghouthi BM, Farber CR, Sumner DR. Intramembranous bone regeneration in diversity outbred mice is heritable. Bone 2022; 164:116524. [PMID: 36028119 PMCID: PMC9798271 DOI: 10.1016/j.bone.2022.116524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 12/31/2022]
Abstract
There are over one million cases of failed bone repair in the U.S. annually, resulting in substantial patient morbidity and societal costs. Multiple candidate genes affecting bone traits such as bone mineral density have been identified in human subjects and animal models using genome-wide association studies (GWAS). This approach for understanding the genetic factors affecting bone repair is impractical in human subjects but could be performed in a model organism if there is sufficient variability and heritability in the bone regeneration response. Diversity Outbred (DO) mice, which have significant genetic diversity and have been used to examine multiple intact bone traits, would be an excellent possibility. Thus, we sought to evaluate the phenotypic distribution of bone regeneration, sex effects and heritability of intramembranous bone regeneration on day 7 following femoral marrow ablation in 47 12-week old DO mice (23 males, 24 females). Compared to a previous study using 4 inbred mouse strains, we found similar levels of variability in the amount of regenerated bone (coefficient of variation of 86 % v. 88 %) with approximately the same degree of heritability (0.42 v. 0.49). There was a trend toward more bone regeneration in males than females. The amount of regenerated bone was either weakly or not correlated with bone mass at intact sites, suggesting that the genetic factors responsible for bone regeneration and intact bone phenotypes are at least partially independent. In conclusion, we demonstrate that DO mice exhibit variation and heritability of intramembranous bone regeneration that will be suitable for future GWAS.
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Affiliation(s)
- Meghan M Moran
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL, USA; Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA.
| | - Frank C Ko
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL, USA; Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Larry D Mesner
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Gina M Calabrese
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Basel M Al-Barghouthi
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA; Departments of Public Health Sciences and Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - D Rick Sumner
- Department of Anatomy & Cell Biology, Rush University Medical Center, Chicago, IL, USA; Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
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32
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Schoenrock SA, Gagnon L, Olson A, Leonardo M, Philip VM, He H, Reinholdt LG, Sukoff Rizzo SJ, Jentsch JD, Chesler EJ, Tarantino LM. The collaborative cross strains and their founders vary widely in cocaine-induced behavioral sensitization. Front Behav Neurosci 2022; 16:886524. [PMID: 36275853 PMCID: PMC9580558 DOI: 10.3389/fnbeh.2022.886524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/01/2022] [Indexed: 07/25/2023] Open
Abstract
Cocaine use and overdose deaths attributed to cocaine have increased significantly in the United States in the last 10 years. Despite the prevalence of cocaine use disorder (CUD) and the personal and societal problems it presents, there are currently no approved pharmaceutical treatments. The absence of treatment options is due, in part, to our lack of knowledge about the etiology of CUDs. There is ample evidence that genetics plays a role in increasing CUD risk but thus far, very few risk genes have been identified in human studies. Genetic studies in mice have been extremely useful for identifying genetic loci and genes, but have been limited to very few genetic backgrounds, leaving substantial phenotypic, and genetic diversity unexplored. Herein we report the measurement of cocaine-induced behavioral sensitization using a 19-day protocol that captures baseline locomotor activity, initial locomotor response to an acute exposure to cocaine and locomotor sensitization across 5 exposures to the drug. These behaviors were measured in 51 genetically diverse Collaborative Cross (CC) strains along with their inbred founder strains. The CC was generated by crossing eight genetically diverse inbred strains such that each inbred CC strain has genetic contributions from each of the founder strains. Inbred CC mice are infinitely reproducible and provide a stable, yet diverse genetic platform on which to study the genetic architecture and genetic correlations among phenotypes. We have identified significant differences in cocaine locomotor sensitivity and behavioral sensitization across the panel of CC strains and their founders. We have established relationships among cocaine sensitization behaviors and identified extreme responding strains that can be used in future studies aimed at understanding the genetic, biological, and pharmacological mechanisms that drive addiction-related behaviors. Finally, we have determined that these behaviors exhibit relatively robust heritability making them amenable to future genetic mapping studies to identify addiction risk genes and genetic pathways that can be studied as potential targets for the development of novel therapeutics.
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Affiliation(s)
- Sarah A. Schoenrock
- Department of Genetics, School of Medicine, Chapel Hill, NC, United States
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
| | - Leona Gagnon
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Ashley Olson
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Michael Leonardo
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Vivek M. Philip
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Hao He
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Laura G. Reinholdt
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Stacey J. Sukoff Rizzo
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - James D. Jentsch
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- Department of Psychology, Binghamton University, Binghamton, NY, United States
| | - Elissa J. Chesler
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Lisa M. Tarantino
- Department of Genetics, School of Medicine, Chapel Hill, NC, United States
- Center for Systems Neurogenetics of Addiction, Bar Harbor, ME, United States
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Abstract
Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to severe acute respiratory syndrome coronavirus (SARS-CoV) disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6, that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2, and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species. IMPORTANCE Host genetic variation is an important determinant that predicts disease outcomes following infection. In the setting of highly pathogenic coronavirus infections genetic determinants underlying host susceptibility and mortality remain unclear. To elucidate the role of host genetic variation on sarbecovirus pathogenesis and disease outcomes, we utilized the Collaborative Cross (CC) mouse genetic reference population as a model to identify susceptibility alleles to SARS-CoV and SARS-CoV-2 infections. Our findings reveal that a multitrait loci found in chromosome 9 is an important regulator of sarbecovirus pathogenesis in mice. Within this locus, we identified and validated CCR9 and CXCR6 as important regulators of host disease outcomes. Specifically, both CCR9 and CXCR6 are protective against severe SARS-CoV, SARS-CoV-2, and SARS-related HKU3 virus disease in mice. This chromosome 9 multitrait locus may be important to help identify genes that regulate coronavirus disease outcomes in humans.
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Percival CJ, Devine J, Hassan CR, Vidal‐Garcia M, O'Connor‐Coates CJ, Zaffarini E, Roseman C, Katz D, Hallgrimsson B. The genetic basis of neurocranial size and shape across varied lab mouse populations. J Anat 2022; 241:211-229. [PMID: 35357006 PMCID: PMC9296060 DOI: 10.1111/joa.13657] [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: 07/07/2021] [Revised: 02/11/2022] [Accepted: 03/08/2022] [Indexed: 11/26/2022] Open
Abstract
Brain and skull tissues interact through molecular signalling and mechanical forces during head development, leading to a strong correlation between the neurocranium and the external brain surface. Therefore, when brain tissue is unavailable, neurocranial endocasts are often used to approximate brain size and shape. Evolutionary changes in brain morphology may have resulted in secondary changes to neurocranial morphology, but the developmental and genetic processes underlying this relationship are not well understood. Using automated phenotyping methods, we quantified the genetic basis of endocast variation across large genetically varied populations of laboratory mice in two ways: (1) to determine the contributions of various genetic factors to neurocranial form and (2) to help clarify whether a neurocranial variation is based on genetic variation that primarily impacts bone development or on genetic variation that primarily impacts brain development, leading to secondary changes in bone morphology. Our results indicate that endocast size is highly heritable and is primarily determined by additive genetic factors. In addition, a non-additive inbreeding effect led to founder strains with lower neurocranial size, but relatively large brains compared to skull size; suggesting stronger canalization of brain size and/or a general allometric effect. Within an outbred sample of mice, we identified a locus on mouse chromosome 1 that is significantly associated with variation in several positively correlated endocast size measures. Because the protein-coding genes at this locus have been previously associated with brain development and not with bone development, we propose that genetic variation at this locus leads primarily to variation in brain volume that secondarily leads to changes in neurocranial globularity. We identify a strain-specific missense mutation within Akt3 that is a strong causal candidate for this genetic effect. Whilst it is not appropriate to generalize our hypothesis for this single locus to all other loci that also contribute to the complex trait of neurocranial skull morphology, our results further reveal the genetic basis of neurocranial variation and highlight the importance of the mechanical influence of brain growth in determining skull morphology.
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Affiliation(s)
| | - Jay Devine
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | | | - Marta Vidal‐Garcia
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | | | - Eva Zaffarini
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | - Charles Roseman
- Department of Evolution, Ecology, and BehaviorUniversity of IllinoisUrbanaIllinoisUSA
| | - David Katz
- Cell Biology and AnatomyUniversity of Calgary Cumming School of MedicineCalgaryCanada
| | - Benedikt Hallgrimsson
- Cell Biology and Anatomy, Alberta Children's Hospital Research Institute, Cumming School of MedicineUniversity of CalgaryCalgaryCanada
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Vincent M, Gerdes Gyuricza I, Keele GR, Gatti DM, Keller MP, Broman KW, Churchill GA. QTLViewer: an interactive webtool for genetic analysis in the Collaborative Cross and Diversity Outbred mouse populations. G3 (BETHESDA, MD.) 2022; 12:jkac146. [PMID: 35703938 PMCID: PMC9339332 DOI: 10.1093/g3journal/jkac146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/28/2022] [Indexed: 01/10/2023]
Abstract
The Collaborative Cross and the Diversity Outbred mouse populations are related multiparental populations, derived from the same 8 isogenic founder strains. They carry >50 M known genetic variants, which makes them ideal tools for mapping genetic loci that regulate phenotypes, including physiological and molecular traits. Mapping quantitative trait loci requires statistical and computational training, which can present a barrier to access for some researchers. The QTLViewer software allows users to graphically explore Collaborative Cross and Diversity Outbred quantitative trait locus mapping and related analyses performed through the R/qtl2 package. Additionally, the QTLViewer website serves as a repository for published Collaborative Cross and Diversity Outbred studies, increasing the accessibility of these genetic resources to the broader scientific community.
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Affiliation(s)
| | | | | | | | - Mark P Keller
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706-1544, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, WI 53706-1544, USA
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Olguín V, Durán A, Las Heras M, Rubilar JC, Cubillos FA, Olguín P, Klein AD. Genetic Background Matters: Population-Based Studies in Model Organisms for Translational Research. Int J Mol Sci 2022; 23:7570. [PMID: 35886916 PMCID: PMC9316598 DOI: 10.3390/ijms23147570] [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: 05/23/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 02/01/2023] Open
Abstract
We are all similar but a bit different. These differences are partially due to variations in our genomes and are related to the heterogeneity of symptoms and responses to treatments that patients exhibit. Most animal studies are performed in one single strain with one manipulation. However, due to the lack of variability, therapies are not always reproducible when treatments are translated to humans. Panels of already sequenced organisms are valuable tools for mimicking human phenotypic heterogeneities and gene mapping. This review summarizes the current knowledge of mouse, fly, and yeast panels with insightful applications for translational research.
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Affiliation(s)
- Valeria Olguín
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Anyelo Durán
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Macarena Las Heras
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Juan Carlos Rubilar
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
| | - Francisco A. Cubillos
- Departamento de Biología, Santiago, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170022, Chile;
- Millennium Institute for Integrative Biology (iBio), Santiago 7500565, Chile
| | - Patricio Olguín
- Program in Human Genetics, Institute of Biomedical Sciences, Biomedical Neurosciences Institute, Department of Neuroscience, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Andrés D. Klein
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile; (V.O.); (A.D.); (M.L.H.); (J.C.R.)
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37
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Schäfer A, Leist SR, Gralinski LE, Martinez DR, Winkler ES, Okuda K, Hawkins PE, Gully KL, Graham RL, Scobey DT, Bell TA, Hock P, Shaw GD, Loome JF, Madden EA, Anderson E, Baxter VK, Taft-Benz SA, Zweigart MR, May SR, Dong S, Clark M, Miller DR, Lynch RM, Heise MT, Tisch R, Boucher RC, Pardo Manuel de Villena F, Montgomery SA, Diamond MS, Ferris MT, Baric RS. A Multitrait Locus Regulates Sarbecovirus Pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35677067 DOI: 10.1101/2022.06.01.494461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to SARS-CoV disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse Chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6 that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2 and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species.
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Parker CC, Philip VM, Gatti DM, Kasparek S, Kreuzman AM, Kuffler L, Mansky B, Masneuf S, Sharif K, Sluys E, Taterra D, Taylor WM, Thomas M, Polesskaya O, Palmer AA, Holmes A, Chesler EJ. Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population. Alcohol Clin Exp Res 2022; 46:941-960. [PMID: 35383961 DOI: 10.1111/acer.14825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND A strong predictor for the development of alcohol use disorder (AUD) is altered sensitivity to the intoxicating effects of alcohol. Individual differences in the initial sensitivity to alcohol are controlled in part by genetic factors. Mice offer a powerful tool to elucidate the genetic basis of behavioral and physiological traits relevant to AUD, but conventional experimental crosses have only been able to identify large chromosomal regions rather than specific genes. Genetically diverse, highly recombinant mouse populations make it possible to observe a wider range of phenotypic variation, offer greater mapping precision, and thus increase the potential for efficient gene identification. METHODS We have taken advantage of the Diversity Outbred (DO) mouse population to identify and precisely map quantitative trait loci (QTL) associated with ethanol sensitivity. We phenotyped 798 male J:DO mice for three measures of ethanol sensitivity: ataxia, hypothermia, and loss of the righting response. We used high-density MegaMUGA and GigaMUGA to obtain genotypes ranging from 77,808 to 143,259 SNPs. We also performed RNA sequencing in striatum to map expression QTLs and identify gene expression-trait correlations. We then applied a systems genetic strategy to identify narrow QTLs and construct the network of correlations that exists between DNA sequence, gene expression values, and ethanol-related phenotypes to prioritize our list of positional candidate genes. RESULTS We observed large amounts of phenotypic variation with the DO population and identified suggestive and significant QTLs associated with ethanol sensitivity on chromosomes 1, 2, and 16. The implicated regions were narrow (4.5-6.9 Mb in size) and each QTL explained ~4-5% of the variance. CONCLUSIONS Our results can be used to identify alleles that contribute to AUD in humans, elucidate causative biological mechanisms, or assist in the development of novel therapeutic interventions.
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Affiliation(s)
- Clarissa C Parker
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Vivek M Philip
- Center for Computational Sciences, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Daniel M Gatti
- Center for Computational Sciences, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Steven Kasparek
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Andrew M Kreuzman
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Lauren Kuffler
- Center for Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Benjamin Mansky
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Sophie Masneuf
- Laboratory of Behavioral and Genomic Neuroscience, NIAAA, NIH, Rockville, MD, USA
| | - Kayvon Sharif
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Erica Sluys
- Laboratory of Behavioral and Genomic Neuroscience, NIAAA, NIH, Rockville, MD, USA
| | - Dominik Taterra
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Walter M Taylor
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Mary Thomas
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA.,Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA.,Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, NIAAA, NIH, Rockville, MD, USA
| | - Elissa J Chesler
- Center for Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine, USA
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39
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Al-Shaer AE, Pal A, Shi Q, Carson MS, Regan J, Behee M, Buddenbaum N, Drawdy C, Davis T, Virk R, Shaikh SR. Modeling human heterogeneity of obesity with diversity outbred mice reveals a fat mass-dependent therapeutic window for resolvin E1. FASEB J 2022; 36:e22354. [PMID: 35616343 PMCID: PMC10027372 DOI: 10.1096/fj.202200350r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/27/2022] [Accepted: 05/06/2022] [Indexed: 11/11/2022]
Abstract
Resolvin E1 (RvE1), a specialized pro-resolving mediator (SPM), improves glucose homeostasis in inbred mouse models of obesity. However, an impediment toward translation is that obesity is a highly heterogenous disease in which individuals will respond very differently to interventions such as RvE1. Thus, there is a need to study SPMs in the context of modeling the heterogeneity of obesity that is observed in humans. We investigated how RvE1 controls the concentration of key circulating metabolic biomarkers using diversity outbred (DO) mice, which mimic human heterogeneity. We first demonstrate that weights of DO mice can be classified into distinct distributions of fat mass (i.e., modeling differing classes of obesity) in response to a high-fat diet and in the human population when examining body composition. Next, we show RvE1 administration based on body weight for four consecutive days after giving mice a high-fat diet led to approximately half of the mice responding positively for serum total gastric inhibitory polypeptide (GIP), glucagon, insulin, glucose, leptin, and resistin. Interestingly, RvE1 improved hyperleptinemia most effectively in the lowest class of fat mass despite adjusting the dose of RvE1 with increasing adiposity. Furthermore, leptin levels after RvE1 treatment were the lowest in those mice that were also RvE1 positive responders for insulin and resistin. Collectively, these results suggest a therapeutic fat mass-dependent window for RvE1, which should be considered in future clinical trials. Moreover, the data underscore the importance of studying SPMs with heterogenous mice as a step toward precision SPM administration in humans.
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Affiliation(s)
- Abrar E Al-Shaer
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anandita Pal
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Qing Shi
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meredith S Carson
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Regan
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Madeline Behee
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nicole Buddenbaum
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catie Drawdy
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Traci Davis
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rafia Virk
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Saame Raza Shaikh
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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40
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Long PN, Cook VJ, Majumder A, Barbour AG, Long AD. The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits. Genetics 2022; 221:iyac026. [PMID: 35143664 PMCID: PMC9071557 DOI: 10.1093/genetics/iyac026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Deermice of the genus Peromyscus are well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and their ability to serve as disease vectors. Here, we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a nontraditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals and subsequently maintained for ∼40-60 generations. From 405 low-pass short-read sequenced deermice we accurate impute genotypes at 16 million single nucleotide polymorphisms. Conditional on observed genotypes simulations were conducted in which three different sized quantitative trait loci contribute to a complex trait under three different genetic models. Using a stringent significance threshold power was modest, largely a function of the percent variation attributable to the simulated quantitative trait loci, with the underlying genetic model having only a subtle impact. We additionally simulated 2,000 pseudo-individuals, whose genotypes were consistent with those observed in the genotyped cohort and carried out additional power simulations. In experiments employing more than 1,000 mice power is high to detect quantitative trait loci contributing greater than 2.5% to a complex trait, with a localization ability of ∼100 kb. We finally carried out a Genome-Wide Association Study on two demonstration traits, bleeding time and body weight, and uncovered one significant region. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice and similar colonies in other systems using easily obtained genotypes from low-pass sequencing.
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Affiliation(s)
- Phillip N Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
| | - Vanessa J Cook
- Departments of Microbiology & Molecular Genetics and Medicine, School of Medical Sciences, University of California Irvine, Irvine, CA 92687-2525, USA
| | - Arundhati Majumder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
| | - Alan G Barbour
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
- Departments of Microbiology & Molecular Genetics and Medicine, School of Medical Sciences, University of California Irvine, Irvine, CA 92687-2525, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
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41
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Gerdes Gyuricza I, Chick JM, Keele GR, Deighan AG, Munger SC, Korstanje R, Gygi SP, Churchill GA. Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart. Genome Res 2022; 32:838-852. [PMID: 35277432 PMCID: PMC9104701 DOI: 10.1101/gr.275672.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 03/09/2022] [Indexed: 11/25/2022]
Abstract
Investigation of the molecular mechanisms of aging in the human heart is challenging because of confounding factors, such as diet and medications, as well as limited access to tissues from healthy aging individuals. The laboratory mouse provides an ideal model to study aging in healthy individuals in a controlled environment. However, previous mouse studies have examined only a narrow range of the genetic variation that shapes individual differences during aging. Here, we analyze transcriptome and proteome data from 185 genetically diverse male and female mice at ages 6, 12, and 18 mo to characterize molecular changes that occur in the aging heart. Transcripts and proteins reveal activation of pathways related to exocytosis and cellular transport with age, whereas processes involved in protein folding decrease with age. Additional changes are apparent only in the protein data including reduced fatty acid oxidation and increased autophagy. For proteins that form complexes, we see a decline in correlation between their component subunits with age, suggesting age-related loss of stoichiometry. The most affected complexes are themselves involved in protein homeostasis, which potentially contributes to a cycle of progressive breakdown in protein quality control with age. Our findings highlight the important role of post-transcriptional regulation in aging. In addition, we identify genetic loci that modulate age-related changes in protein homeostasis, suggesting that genetic variation can alter the molecular aging process.
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Affiliation(s)
| | - Joel M Chick
- Vividion Therapeutics, San Diego, California 92121, USA
| | | | | | | | - Ron Korstanje
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Steven P Gygi
- Harvard Medical School, Boston, Massachusetts 02115, USA
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42
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Chen Z, Raj A, Prateek GV, Di Francesco A, Liu J, Keyes BE, Kolumam G, Jojic V, Freund A. Automated, high-dimensional evaluation of physiological aging and resilience in outbred mice. eLife 2022; 11:e72664. [PMID: 35404230 PMCID: PMC9000950 DOI: 10.7554/elife.72664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Behavior and physiology are essential readouts in many studies but have not benefited from the high-dimensional data revolution that has transformed molecular and cellular phenotyping. To address this, we developed an approach that combines commercially available automated phenotyping hardware with a systems biology analysis pipeline to generate a high-dimensional readout of mouse behavior/physiology, as well as intuitive and health-relevant summary statistics (resilience and biological age). We used this platform to longitudinally evaluate aging in hundreds of outbred mice across an age range from 3 months to 3.4 years. In contrast to the assumption that aging can only be measured at the limits of animal ability via challenge-based tasks, we observed widespread physiological and behavioral aging starting in early life. Using network connectivity analysis, we found that organism-level resilience exhibited an accelerating decline with age that was distinct from the trajectory of individual phenotypes. We developed a method, Combined Aging and Survival Prediction of Aging Rate (CASPAR), for jointly predicting chronological age and survival time and showed that the resulting model is able to predict both variables simultaneously, a behavior that is not captured by separate age and mortality prediction models. This study provides a uniquely high-resolution view of physiological aging in mice and demonstrates that systems-level analysis of physiology provides insights not captured by individual phenotypes. The approach described here allows aging, and other processes that affect behavior and physiology, to be studied with improved throughput, resolution, and phenotypic scope.
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Affiliation(s)
- Zhenghao Chen
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Anil Raj
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - GV Prateek
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Andrea Di Francesco
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Justin Liu
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Brice E Keyes
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Ganesh Kolumam
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
| | - Adam Freund
- Calico Life Sciences LLC, South San FranciscoSouth San FranciscoUnited States
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43
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Perez BC, Bink MCAM, Svenson KL, Churchill GA, Calus MPL. Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice. G3 (BETHESDA, MD.) 2022; 12:6528848. [PMID: 35166767 PMCID: PMC8982369 DOI: 10.1093/g3journal/jkac039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/29/2022] [Indexed: 12/14/2022]
Abstract
We compared the performance of linear (GBLUP, BayesB, and elastic net) methods to a nonparametric tree-based ensemble (gradient boosting machine) method for genomic prediction of complex traits in mice. The dataset used contained genotypes for 50,112 SNP markers and phenotypes for 835 animals from 6 generations. Traits analyzed were bone mineral density, body weight at 10, 15, and 20 weeks, fat percentage, circulating cholesterol, glucose, insulin, triglycerides, and urine creatinine. The youngest generation was used as a validation subset, and predictions were based on all older generations. Model performance was evaluated by comparing predictions for animals in the validation subset against their adjusted phenotypes. Linear models outperformed gradient boosting machine for 7 out of 10 traits. For bone mineral density, cholesterol, and glucose, the gradient boosting machine model showed better prediction accuracy and lower relative root mean squared error than the linear models. Interestingly, for these 3 traits, there is evidence of a relevant portion of phenotypic variance being explained by epistatic effects. Using a subset of top markers selected from a gradient boosting machine model helped for some of the traits to improve the accuracy of prediction when these were fitted into linear and gradient boosting machine models. Our results indicate that gradient boosting machine is more strongly affected by data size and decreased connectedness between reference and validation sets than the linear models. Although the linear models outperformed gradient boosting machine for the polygenic traits, our results suggest that gradient boosting machine is a competitive method to predict complex traits with assumed epistatic effects.
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Affiliation(s)
- Bruno C Perez
- Hendrix Genetics B.V., Research and Technology Center (RTC), 5830 AC Boxmeer, The Netherlands
| | - Marco C A M Bink
- Hendrix Genetics B.V., Research and Technology Center (RTC), 5830 AC Boxmeer, The Netherlands
| | | | | | - Mario P L Calus
- Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
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44
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Bufi R, Korstanje R. The impact of genetic background on mouse models of kidney disease. Kidney Int 2022; 102:38-44. [DOI: 10.1016/j.kint.2022.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 12/24/2022]
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45
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Macdonald SJ, Cloud-Richardson KM, Sims-West DJ, Long AD. Powerful, efficient QTL mapping in Drosophila melanogaster using bulked phenotyping and pooled sequencing. Genetics 2022; 220:iyab238. [PMID: 35100395 PMCID: PMC8893256 DOI: 10.1093/genetics/iyab238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/19/2021] [Indexed: 01/22/2024] Open
Abstract
Despite the value of recombinant inbred lines for the dissection of complex traits, large panels can be difficult to maintain, distribute, and phenotype. An attractive alternative to recombinant inbred lines for many traits leverages selecting phenotypically extreme individuals from a segregating population, and subjecting pools of selected and control individuals to sequencing. Under a bulked or extreme segregant analysis paradigm, genomic regions contributing to trait variation are revealed as frequency differences between pools. Here, we describe such an extreme quantitative trait locus, or extreme quantitative trait loci, mapping strategy that builds on an existing multiparental population, the Drosophila Synthetic Population Resource, and involves phenotyping and genotyping a population derived by mixing hundreds of Drosophila Synthetic Population Resource recombinant inbred lines. Simulations demonstrate that challenging, yet experimentally tractable extreme quantitative trait loci designs (≥4 replicates, ≥5,000 individuals/replicate, and selecting the 5-10% most extreme animals) yield at least the same power as traditional recombinant inbred line-based quantitative trait loci mapping and can localize variants with sub-centimorgan resolution. We empirically demonstrate the effectiveness of the approach using a 4-fold replicated extreme quantitative trait loci experiment that identifies 7 quantitative trait loci for caffeine resistance. Two mapped extreme quantitative trait loci factors replicate loci previously identified in recombinant inbred lines, 6/7 are associated with excellent candidate genes, and RNAi knock-downs support the involvement of 4 genes in the genetic control of trait variation. For many traits of interest to drosophilists, a bulked phenotyping/genotyping extreme quantitative trait loci design has considerable advantages.
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Affiliation(s)
- Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA
| | | | - Dylan J Sims-West
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA 92697, USA
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46
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Broman KW. A generic hidden Markov model for multiparent populations. G3 GENES|GENOMES|GENETICS 2022; 12:6429279. [PMID: 34791211 PMCID: PMC9210298 DOI: 10.1093/g3journal/jkab396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/08/2021] [Indexed: 11/12/2022]
Abstract
A common step in the analysis of multiparent populations (MPPs) is genotype reconstruction: identifying the founder origin of haplotypes from dense marker data. This process often makes use of a probability model for the pattern of founder alleles along chromosomes, including the relative frequency of founder alleles and the probability of exchanges among them, which depend on a model for meiotic recombination and on the mating design for the population. While the precise experimental design used to generate the population may be used to derive a precise characterization of the model for exchanges among founder alleles, this can be tedious, particularly given the great variety of experimental designs that have been proposed. We describe an approximate model that can be applied for a variety of MPPs. We have implemented the approach in the R/qtl2 software, and we illustrate its use in applications to publicly available data on Diversity Outbred and Collaborative Cross mice.
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Affiliation(s)
- Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison , Madison, WI 53706, USA
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47
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Zhang G, Deighan A, Raj A, Robinson L, Donato HJ, Garland G, Leland M, Martin-McNulty B, Kolumam GA, Riegler J, Freund A, Wright KM, Churchill GA. Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice. Genetics 2022; 220:iyab157. [PMID: 34791228 PMCID: PMC8733459 DOI: 10.1093/genetics/iyab157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/10/2021] [Indexed: 11/20/2022] Open
Abstract
Dietary interventions can dramatically affect physiological health and organismal lifespan. The degree to which organismal health is improved depends upon genotype and the severity of dietary intervention, but neither the effects of these factors, nor their interaction, have been quantified in an outbred population. Moreover, it is not well understood what physiological changes occur shortly after dietary change and how these may affect the health of an adult population. In this article, we investigated the effect of 6-month exposure of either caloric restriction (CR) or intermittent fasting (IF) on a broad range of physiological traits in 960 1-year old Diversity Outbred mice. We found CR and IF affected distinct aspects of physiology and neither the magnitude nor the direction (beneficial or detrimental) of effects were concordant with the severity of the intervention. In addition to the effects of diet, genetic variation significantly affected 31 of 36 traits (heritabilities ranged from 0.04 to 0.65). We observed significant covariation between many traits that was due to both diet and genetics and quantified these effects with phenotypic and genetic correlations. We genetically mapped 16 diet-independent and 2 diet-dependent significant quantitative trait loci, both of which were associated with cardiac physiology. Collectively, these results demonstrate the degree to which diet and genetics interact to shape the physiological health of adult mice following 6 months of dietary intervention.
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Affiliation(s)
- Guozhu Zhang
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | - Anil Raj
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | | - Adam Freund
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Kevin M Wright
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
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48
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Aponte JD, Katz DC, Roth DM, Vidal-García M, Liu W, Andrade F, Roseman CC, Murray SA, Cheverud J, Graf D, Marcucio RS, Hallgrímsson B. Relating multivariate shapes to genescapes using phenotype-biological process associations for craniofacial shape. eLife 2021; 10:68623. [PMID: 34779766 PMCID: PMC8631940 DOI: 10.7554/elife.68623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Realistic mappings of genes to morphology are inherently multivariate on both sides of the equation. The importance of coordinated gene effects on morphological phenotypes is clear from the intertwining of gene actions in signaling pathways, gene regulatory networks, and developmental processes underlying the development of shape and size. Yet, current approaches tend to focus on identifying and localizing the effects of individual genes and rarely leverage the information content of high-dimensional phenotypes. Here, we explicitly model the joint effects of biologically coherent collections of genes on a multivariate trait – craniofacial shape – in a sample of n = 1145 mice from the Diversity Outbred (DO) experimental line. We use biological process Gene Ontology (GO) annotations to select skeletal and facial development gene sets and solve for the axis of shape variation that maximally covaries with gene set marker variation. We use our process-centered, multivariate genotype-phenotype (process MGP) approach to determine the overall contributions to craniofacial variation of genes involved in relevant processes and how variation in different processes corresponds to multivariate axes of shape variation. Further, we compare the directions of effect in phenotype space of mutations to the primary axis of shape variation associated with broader pathways within which they are thought to function. Finally, we leverage the relationship between mutational and pathway-level effects to predict phenotypic effects beyond craniofacial shape in specific mutants. We also introduce an online application that provides users the means to customize their own process-centered craniofacial shape analyses in the DO. The process-centered approach is generally applicable to any continuously varying phenotype and thus has wide-reaching implications for complex trait genetics.
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Affiliation(s)
- Jose D Aponte
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - David C Katz
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Daniela M Roth
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Marta Vidal-García
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Wei Liu
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Fernando Andrade
- Department of Biology, Loyola University Chicago, Chicago, United States
| | - Charles C Roseman
- Department of Biology, Loyola University Chicago, Chicago, United States
| | | | - James Cheverud
- Department of Biology, Loyola University Chicago, Chicago, United States
| | - Daniel Graf
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, School of Medicine, University of California, San Francisco, San Francisco, United States
| | - Benedikt Hallgrímsson
- Department of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Department of Animal Biology, University of Illinois Urbana Champaign, Urbana, United States
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49
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Burny C, Nolte V, Dolezal M, Schlötterer C. Highly Parallel Genomic Selection Response in Replicated Drosophila melanogaster Populations with Reduced Genetic Variation. Genome Biol Evol 2021; 13:6409861. [PMID: 34694407 PMCID: PMC8599828 DOI: 10.1093/gbe/evab239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
Many adaptive traits are polygenic and frequently more loci contributing to the phenotype are segregating than needed to express the phenotypic optimum. Experimental evolution with replicated populations adapting to a new controlled environment provides a powerful approach to study polygenic adaptation. Because genetic redundancy often results in nonparallel selection responses among replicates, we propose a modified evolve and resequence (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29 °C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Because two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.
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Affiliation(s)
- Claire Burny
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Wien, Austria
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50
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Keele GR, Zhang T, Pham DT, Vincent M, Bell TA, Hock P, Shaw GD, Paulo JA, Munger SC, Pardo-Manuel de Villena F, Ferris MT, Gygi SP, Churchill GA. Regulation of protein abundance in genetically diverse mouse populations. CELL GENOMICS 2021; 1:100003. [PMID: 36212994 PMCID: PMC9536773 DOI: 10.1016/j.xgen.2021.100003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022]
Abstract
Genetically diverse mouse populations are powerful tools for characterizing the regulation of the proteome and its relationship to whole-organism phenotypes. We used mass spectrometry to profile and quantify the abundance of 6,798 proteins in liver tissue from mice of both sexes across 58 Collaborative Cross (CC) inbred strains. We previously collected liver proteomics data from the related Diversity Outbred (DO) mice and their founder strains. We show concordance across the proteomics datasets despite being generated from separate experiments, allowing comparative analysis. We map protein abundance quantitative trait loci (pQTLs), identifying 1,087 local and 285 distal in the CC mice and 1,706 local and 414 distal in the DO mice. We find that regulatory effects on individual proteins are conserved across the mouse populations, in particular for local genetic variation and sex differences. In comparison, proteins that form complexes are often co-regulated, displaying varying genetic architectures, and overall show lower heritability and map fewer pQTLs. We have made this resource publicly available to enable quantitative analyses of the regulation of the proteome.
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Affiliation(s)
| | - Tian Zhang
- Harvard Medical School, Boston, MA 02115, USA
| | - Duy T. Pham
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ginger D. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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