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Meijsen J, Hu K, Krebs MD, Athanasiadis G, Washbrook S, Zetterberg R, E Silva RNA, Shorter JR, Gådin JR, Bergstedt J, Howard DM, Ye W, Lu Y, Valdimarsdóttir UA, Ingason A, Mikkelsen DH, Plana-Ripoll O, McGrath JJ, Micali N, Andreassen OA, Werge TM, Fang F, Buil A. Quantifying the Relative Importance of Genetics and Environment on the Comorbidity between Mental- and Cardiometabolic Disorders: A Comprehensive Analysis of National Register Data from 17 million Scandinavians. medRxiv 2024:2024.02.29.24303530. [PMID: 38464139 PMCID: PMC10925466 DOI: 10.1101/2024.02.29.24303530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mental disorders (MDs) are leading causes of disability and premature death worldwide, partly due to high comorbidity with cardiometabolic disorders (CMDs). Reasons for this comorbidity are still poorly understood. We leverage nation-wide health records and complete genealogies of Denmark and Sweden (n=17 million) to reveal the genetic and environmental contributions underlying the observed comorbidity between six MDs and 14 CMDs. Genetic factors contributed about 50% to the comorbidity of schizophrenia, affective disorders, and autism spectrum disorder with CMDs, whereas the comorbidity of attention-deficit/hyperactivity disorder and anorexia with CMDs was mainly or fully driven by environmental factors. These findings provide causal insight to guide clinical and scientific initiatives directed at achieving mechanistic understanding as well as preventing and alleviating the consequences of these disorders.
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2
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Pasman JA, Meijsen JJ, Haram M, Kowalec K, Harder A, Xiong Y, Nguyen TD, Jangmo A, Shorter JR, Bergstedt J, Das U, Zetterberg R, Tate A, Lichtenstein P, Larsson H, Odsbu I, Werge T, Reichborn-Kjennerud T, Andreassen OA, Sullivan PF, Buil A, Tesli M, Lu Y. Epidemiological overview of major depressive disorder in Scandinavia using nationwide registers. Lancet Reg Health Eur 2023. [DOI: 10.1016/j.lanepe.2023.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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Shorter JR, Meijsen J, Nudel R, Krebs M, Gådin J, Mikkelsen DH, Nogueira Avelar E Silva R, Benros ME, Thompson WK, Ingason A, Werge T. Infection Polygenic Factors Account for a Small Proportion of the Relationship Between Infections and Mental Disorders. Biol Psychiatry 2022; 92:283-290. [PMID: 35305821 DOI: 10.1016/j.biopsych.2022.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/07/2022] [Accepted: 01/07/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Several recent studies have suggested a role for infections in the development of mental disorders; however, the genetic contribution to this association is understudied. METHODS We use the iPSYCH case-cohort genotyped sample (n = 65,534) and Danish health care registry data to study the genetic association between infections and mental disorders. To test the hypothesis that these associations are due to genetic pleiotropy, we estimated the genetic correlation between infection and mental disorders. Polygenic risk scores (PRSs) were used to assess whether genetic pleiotropy of infections and mental disorders was mediated by actual infection diagnoses. RESULTS We observed that schizophrenia, attention-deficit/hyperactivity disorder, major depressive disorder, bipolar disorder, and posttraumatic stress disorder (rg ranging between 0.18 and 0.83), but not autism spectrum disorder and anorexia nervosa, were significantly genetically correlated with infection diagnoses. PRSs for infections were associated with modest increase in risk of attention-deficit/hyperactivity disorder, major depressive disorder, and schizophrenia in the iPSYCH case-cohort (hazard ratios = 1.04 to 1.10) but was not associated with risk of anorexia, autism, or bipolar disorder. Using mediation analysis, we show that infection diagnoses account for only a small proportion (6%-14%) of the risk for mental disorders conferred by infection PRSs. CONCLUSIONS Infections and mental disorders share a modest genetic architecture. Infection PRSs can predict risk of certain mental disorders; however, this effect is moderate. Finally, recorded infections partially explain the relationship between infection PRSs and mental disorders.
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Affiliation(s)
- John R Shorter
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.
| | - Joeri Meijsen
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Ron Nudel
- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Morten Krebs
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Jesper Gådin
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Dorte H Mikkelsen
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Raquel Nogueira Avelar E Silva
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Michael E Benros
- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Wesley K Thompson
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark; Population Neuroscience and Genetics Lab, University of California San Diego, San Diego, California; Division of Biostatistics and Department of Radiology, University of California San Diego, San Diego, California
| | - Andrés Ingason
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
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4
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Sigmon JS, Blanchard MW, Baric RS, Bell TA, Brennan J, Brockmann GA, Burks AW, Calabrese JM, Caron KM, Cheney RE, Ciavatta D, Conlon F, Darr DB, Faber J, Franklin C, Gershon TR, Gralinski L, Gu B, Gaines CH, Hagan RS, Heimsath EG, Heise MT, Hock P, Ideraabdullah F, Jennette JC, Kafri T, Kashfeen A, Kulis M, Kumar V, Linnertz C, Livraghi-Butrico A, Lloyd KCK, Lutz C, Lynch RM, Magnuson T, Matsushima GK, McMullan R, Miller DR, Mohlke KL, Moy SS, Murphy CEY, Najarian M, O'Brien L, Palmer AA, Philpot BD, Randell SH, Reinholdt L, Ren Y, Rockwood S, Rogala AR, Saraswatula A, Sassetti CM, Schisler JC, Schoenrock SA, Shaw GD, Shorter JR, Smith CM, St Pierre CL, Tarantino LM, Threadgill DW, Valdar W, Vilen BJ, Wardwell K, Whitmire JK, Williams L, Zylka MJ, Ferris MT, McMillan L, Manuel de Villena FP. Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research. Genetics 2020; 216:905-930. [PMID: 33067325 PMCID: PMC7768238 DOI: 10.1534/genetics.120.303596] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.
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Affiliation(s)
- John Sebastian Sigmon
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Matthew W Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jennifer Brennan
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - A Wesley Burks
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Kathleen M Caron
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Richard E Cheney
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dominic Ciavatta
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Frank Conlon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - James Faber
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Craig Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri 65211
| | - Timothy R Gershon
- Department of Neurology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lisa Gralinski
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Bin Gu
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christiann H Gaines
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Robert S Hagan
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ernest G Heimsath
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Folami Ideraabdullah
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Charles Jennette
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Tal Kafri
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Anwica Kashfeen
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mike Kulis
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Colton Linnertz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Alessandra Livraghi-Butrico
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - K C Kent Lloyd
- Department of Surgery, University of California Davis, Davis, California 95616
- School of Medicine, University of California Davis, California 95616
- Mouse Biology Program, University of California Davis, California 95616
| | | | - Rachel M Lynch
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Glenn K Matsushima
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Rachel McMullan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Caroline E Y Murphy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Maya Najarian
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lori O'Brien
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Benjamin D Philpot
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Scott H Randell
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Yuyu Ren
- University of California San Diego, La Jolla, California 92093
| | | | - Allison R Rogala
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Avani Saraswatula
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Jonathan C Schisler
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah A Schoenrock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R Shorter
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Clare M Smith
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | | | - Lisa M Tarantino
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David W Threadgill
- University of California San Diego, La Jolla, California 92093
- Department of Biochemistry and Biophysics, Texas A&M University, Texas 77843
| | - William Valdar
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Barbara J Vilen
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Jason K Whitmire
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lucy Williams
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark J Zylka
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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5
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Gu B, Shorter JR, Williams LH, Bell TA, Hock P, Dalton KA, Pan Y, Miller DR, Shaw GD, Philpot BD, Pardo-Manuel de Villena F. Collaborative Cross mice reveal extreme epilepsy phenotypes and genetic loci for seizure susceptibility. Epilepsia 2020; 61:2010-2021. [PMID: 32852103 DOI: 10.1111/epi.16617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Animal studies remain essential for understanding mechanisms of epilepsy and identifying new therapeutic targets. However, existing animal models of epilepsy do not reflect the high level of genetic diversity found in the human population. The Collaborative Cross (CC) population is a genetically diverse recombinant inbred panel of mice. The CC offers large genotypic and phenotypic diversity, inbred strains with stable genomes that allow for repeated phenotypic measurements, and genomic tools including whole genome sequence to identify candidate genes and candidate variants. METHODS We evaluated multiple complex epileptic traits in a sampling of 35 CC inbred strains using the flurothyl-induced seizure and kindling paradigm. We created an F2 population of 297 mice with extreme seizure susceptibility and performed quantitative trait loci (QTL) mapping to identify genomic regions associated with seizure sensitivity. We used quantitative RNA sequencing from CC hippocampal tissue to identify candidate genes and whole genome sequence to identify genetic variants likely affecting gene expression. RESULTS We identified new mouse models with extreme seizure susceptibility, seizure propagation, epileptogenesis, and SUDEP (sudden unexpected death in epilepsy). We performed QTL mapping and identified one known and seven novel loci associated with seizure sensitivity. We combined whole genome sequencing and hippocampal gene expression to pinpoint biologically plausible candidate genes (eg, Gabra2) and variants associated with seizure sensitivity. SIGNIFICANCE New mouse models of epilepsy are needed to better understand the complex genetic architecture of seizures and to identify therapeutics. We performed a phenotypic screen utilizing a novel genetic reference population of CC mice. The data we provide enable the identification of protective/risk genes and novel molecular mechanisms linked to complex seizure traits that are currently challenging to study and treat.
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Affiliation(s)
- Bin Gu
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.,Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - John R Shorter
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA.,Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services, Copenhagen, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Lucy H Williams
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Katherine A Dalton
- Neuroscience Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Yiyun Pan
- Neuroscience Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Benjamin D Philpot
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.,Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA.,Neuroscience Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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6
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Shorter JR, Najarian ML, Bell TA, Blanchard M, Ferris MT, Hock P, Kashfeen A, Kirchoff KE, Linnertz CL, Sigmon JS, Miller DR, McMillan L, Pardo-Manuel de Villena F. Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population. G3 (Bethesda) 2019; 9:1303-1311. [PMID: 30858237 PMCID: PMC6505143 DOI: 10.1534/g3.119.400039] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022]
Abstract
Two key features of recombinant inbred panels are well-characterized genomes and reproducibility. Here we report on the sequenced genomes of six additional Collaborative Cross (CC) strains and on inbreeding progress of 72 CC strains. We have previously reported on the sequences of 69 CC strains that were publicly available, bringing the total of CC strains with whole genome sequence up to 75. The sequencing of these six CC strains updates the efforts toward inbreeding undertaken by the UNC Systems Genetics Core. The timing reflects our competing mandates to release to the public as many CC strains as possible while achieving an acceptable level of inbreeding. The new six strains have a higher than average founder contribution from non-domesticus strains than the previously released CC strains. Five of the six strains also have high residual heterozygosity (>14%), which may be related to non-domesticus founder contributions. Finally, we report on updated estimates on residual heterozygosity across the entire CC population using a novel, simple and cost effective genotyping platform on three mice from each strain. We observe a reduction in residual heterozygosity across all previously released CC strains. We discuss the optimal use of different genetic resources available for the CC population.
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Affiliation(s)
| | | | - Timothy A Bell
- Department of Genetics
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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7
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Shorter JR, Huang W, Beak JY, Hua K, Gatti DM, de Villena FPM, Pomp D, Jensen BC. Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size. Mamm Genome 2017; 29:80-89. [PMID: 29279960 DOI: 10.1007/s00335-017-9730-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/11/2017] [Indexed: 01/19/2023]
Abstract
Heart size is an important factor in cardiac health and disease. In particular, increased heart weight is predictive of adverse cardiovascular outcomes in multiple large community-based studies. We use two cohorts of Diversity Outbred (DO) mice to investigate the role of genetics, sex, age, and diet on heart size. DO mice (n = 289) of both sexes from generation 10 were fed a standard chow diet, and analyzed at 12-15 weeks of age. Another cohort of female DO mice (n = 258) from generation 11 were fed either a high-fat, cholesterol-containing (HFC) diet or a low-fat, high-protein diet, and analyzed at 24-25 weeks. We did not observe an effect of diet on body or heart weight in generation 11 mice, although we previously reported an effect on other cardiovascular risk factors, including cholesterol, triglycerides, and insulin. We do observe a significant genetic effect on heart weight in this population. We identified two quantitative trait loci for heart weight, one (Hwtf1) at a genome-wide significance level of p ≤ 0.05 on MMU15 and one (Hwtf2) at a genome-wide suggestive level of p ≤ 0.1 on MMU10, that together explain 13.3% of the phenotypic variance. Hwtf1 contained collagen type XXII alpha 1 chain (Col22a1), and the NZO/HlLtJ and WSB/EiJ haplotypes were associated with larger hearts. This is consistent with heart tissue Col22a1 expression in DO founders and SNP patterns within Hwtf1 for Col22a1. Col22a1 has been previously associated with cardiac fibrosis in mice, suggesting that Col22a1 may be involved in pathological cardiac hypertrophy.
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Affiliation(s)
- John R Shorter
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA.
| | - Wei Huang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ju Youn Beak
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kunjie Hua
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA
| | | | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel Pomp
- Department of Genetics, University of North Carolina, CB# 7264, Chapel Hill, NC, 27599, USA
| | - Brian C Jensen
- Division of Cardiology, Department of Medicine, University of North Carolina, 6012 Burnett-Womack Building, Chapel Hill, NC, 27599, USA.
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, 27599, USA.
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA.
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8
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Shorter JR, Dembeck LM, Everett LJ, Morozova TV, Arya GH, Turlapati L, St Armour GE, Schal C, Mackay TFC, Anholt RRH. Obp56h Modulates Mating Behavior in Drosophila melanogaster. G3 (Bethesda) 2016; 6:3335-3342. [PMID: 27558663 PMCID: PMC5068952 DOI: 10.1534/g3.116.034595] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/18/2016] [Indexed: 11/25/2022]
Abstract
Social interactions in insects are driven by conspecific chemical signals that are detected via olfactory and gustatory neurons. Odorant binding proteins (Obps) transport volatile odorants to chemosensory receptors, but their effects on behaviors remain poorly characterized. Here, we report that RNAi knockdown of Obp56h gene expression in Drosophila melanogaster enhances mating behavior by reducing courtship latency. The change in mating behavior that results from inhibition of Obp56h expression is accompanied by significant alterations in cuticular hydrocarbon (CHC) composition, including reduction in 5-tricosene (5-T), an inhibitory sex pheromone produced by males that increases copulation latency during courtship. Whole genome RNA sequencing confirms that expression of Obp56h is virtually abolished in Drosophila heads. Inhibition of Obp56h expression also affects expression of other chemoreception genes, including upregulation of lush in both sexes and Obp83ef in females, and reduction in expression of Obp19b and Or19b in males. In addition, several genes associated with lipid metabolism, which underlies the production of cuticular hydrocarbons, show altered transcript abundances. Our data show that modulation of mating behavior through reduction of Obp56h is accompanied by altered cuticular hydrocarbon profiles and implicate 5-T as a possible ligand for Obp56h.
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Affiliation(s)
- John R Shorter
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Lauren M Dembeck
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Logan J Everett
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Tatiana V Morozova
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Gunjan H Arya
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Lavanya Turlapati
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Genevieve E St Armour
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Coby Schal
- Department of Entomology and Plant Pathology, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Trudy F C Mackay
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
| | - Robert R H Anholt
- Department of Biological Sciences, Program in Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695
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Shorter JR, Arechavaleta-Velasco M, Robles-Rios C, Hunt GJ. A genetic analysis of the stinging and guarding behaviors of the honey bee. Behav Genet 2012; 42:663-74. [PMID: 22327626 DOI: 10.1007/s10519-012-9530-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 01/31/2012] [Indexed: 11/30/2022]
Abstract
In order to identify genes that are influencing defensive behaviors, we have taken a new approach by dissecting colony-level defensive behavior into individual behavioral measurements using two families containing backcross workers from matings involving European and Africanized bees. We removed the social context from stinging behavior by using a laboratory assay to measure the stinging response of individual bees. A mild shock was given to bees using a constant-current stimulator. The time it took bees to sting in response to this stimulus was recorded. In addition, bees that were seen performing guard behaviors at the hive entrance were collected. We performed QTL mapping in two backcross families with SNP probes within genes and identified two new QTL regions for stinging behavior and another QTL region for guarding behavior. We also identified several candidate genes involved in neural signaling, neural development and muscle development that may be influencing stinging and guarding behaviors. The lack of overlap between these regions and previous defensive behavior QTL underscores the complexity of this behavior and increases our understanding of its genetic architecture.
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Affiliation(s)
- John R Shorter
- Department of Entomology, Purdue University, 901 West State St, West Lafayette, IN 47906, USA.
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