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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. Cell Genom 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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King CP, Chitre AS, Leal-Gutiérrez JD, Tripi JA, Hughson AR, Horvath AP, Lamparelli AC, George A, Martin C, Pierre CLS, Sanches T, Bimschleger HV, Gao J, Cheng R, Nguyen KM, Holl KL, Polesskaya O, Ishiwari K, Chen H, Woods LCS, Palmer AA, Robinson TE, Flagel SB, Meyer PJ. Genomic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats. bioRxiv 2024:2024.03.13.584852. [PMID: 38559127 PMCID: PMC10980002 DOI: 10.1101/2024.03.13.584852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Addiction vulnerability is associated with the tendency to attribute incentive salience to reward predictive cues; both addiction and the attribution of incentive salience are influenced by environmental and genetic factors. To characterize the genetic contributions to incentive salience attribution, we performed a genome-wide association study (GWAS) in a cohort of 1,645 genetically diverse heterogeneous stock (HS) rats. We tested HS rats in a Pavlovian conditioned approach task, in which we characterized the individual responses to food-associated stimuli ("cues"). Rats exhibited either cue-directed "sign-tracking" behavior or food-cup directed "goal-tracking" behavior. We then used the conditioned reinforcement procedure to determine whether rats would perform a novel operant response for unrewarded presentations of the cue. We found that these measures were moderately heritable (SNP heritability, h2 = .189-.215). GWAS identified 14 quantitative trait loci (QTLs) for 11 of the 12 traits we examined. Interval sizes of these QTLs varied widely. 7 traits shared a QTL on chromosome 1 that contained a few genes (e.g. Tenm4, Mir708) that have been associated with substance use disorders and other mental health traits in humans. Other candidate genes (e.g. Wnt11, Pak1) in this region had coding variants and expression-QTLs in mesocorticolimbic regions of the brain. We also conducted a Phenome-Wide Association Study (PheWAS) on other behavioral measures in HS rats and found that regions containing QTLs on chromosome 1 were also associated with nicotine self-administration in a separate cohort of HS rats. These results provide a starting point for the molecular genetic dissection of incentive salience and provide further support for a relationship between attribution of incentive salience and drug abuse-related traits.
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Affiliation(s)
- Christopher P. King
- Department of Psychology, University at Buffalo, Buffalo, USA
- Clinical and Research Institute on Addictions, Buffalo, USA
| | - Apurva S. Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | | | - Jordan A. Tripi
- Department of Psychology, University at Buffalo, Buffalo, USA
| | - Alesa R. Hughson
- Department of Psychology, University of Michigan, Ann Arbor, USA
| | - Aidan P. Horvath
- Department of Psychology, University of Michigan, Ann Arbor, USA
| | | | - Anthony George
- Clinical and Research Institute on Addictions, Buffalo, USA
| | - Connor Martin
- Clinical and Research Institute on Addictions, Buffalo, USA
| | | | - Thiago Sanches
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | | | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Katie L. Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, Buffalo, USA
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, USA
| | - Leah C. Solberg Woods
- Department of Internal Medicine, Molecular Medicine, Center on Diabetes, Obesity and Metabolism, Wake Forest School of Medicine, Winston-Salem, USA
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, USA
| | | | - Shelly B. Flagel
- Department of Psychiatry, University of Michigan, Ann Arbor, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
| | - Paul J. Meyer
- Department of Psychology, University at Buffalo, Buffalo, USA
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3
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Batista S, Madar VS, Freda PJ, Bhandary P, Ghosh A, Matsumoto N, Chitre AS, Palmer AA, Moore JH. Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis. BioData Min 2024; 17:7. [PMID: 38419006 PMCID: PMC10900690 DOI: 10.1186/s13040-024-00358-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE Epistasis, the interaction between two or more genes, is integral to the study of genetics and is present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects, partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Furthermore, existing methods for epistasis detection only consider a Cartesian (multiplicative) model for interaction terms. This is likely limiting as epistatic interactions can evolve to produce varied relationships between genetic loci, some complex and not linearly separable. METHODS We present new algorithms for the interaction coefficients for standard regression models for epistasis that permit many varied models for the interaction terms for loci and efficient memory usage. The algorithms are given for two-way and three-way epistasis and may be generalized to higher order epistasis. Statistical tests for the interaction coefficients are also provided. We also present an efficient matrix based algorithm for permutation testing for two-way epistasis. We offer a proof and experimental evidence that methods that look for epistasis only at loci that have main effects may not be justified. Given the computational efficiency of the algorithm, we applied the method to a rat data set and mouse data set, with at least 10,000 loci and 1,000 samples each, using the standard Cartesian model and the XOR model to explore body mass index. RESULTS This study reveals that although many of the loci found to exhibit significant statistical epistasis overlap between models in rats, the pairs are mostly distinct. Further, the XOR model found greater evidence for statistical epistasis in many more pairs of loci in both data sets with almost all significant epistasis in mice identified using XOR. In the rat data set, loci involved in epistasis under the XOR model are enriched for biologically relevant pathways. CONCLUSION Our results in both species show that many biologically relevant epistatic relationships would have been undetected if only one interaction model was applied, providing evidence that varied interaction models should be implemented to explore epistatic interactions that occur in living systems.
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Affiliation(s)
- Sandra Batista
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA.
| | | | - Philip J Freda
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Priyanka Bhandary
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Attri Ghosh
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Nicholas Matsumoto
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
- Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA.
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4
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Ishiwari K, King CP, Martin CD, Tripi JA, George AM, Lamparelli AC, Chitre AS, Polesskaya O, Richards JB, Solberg Woods LC, Gancarz AM, Palmer AA, Dietz DM, Mitchell SH, Meyer PJ. Environmental enrichment promotes adaptive responding during tests of behavioral regulation in male heterogeneous stock rats. Sci Rep 2024; 14:4182. [PMID: 38378969 PMCID: PMC10879139 DOI: 10.1038/s41598-024-53943-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Organisms must regulate their behavior flexibly in the face of environmental challenges. Failure can lead to a host of maladaptive behavioral traits associated with a range of neuropsychiatric disorders, including attention deficit hyperactivity disorder, autism, and substance use disorders. This maladaptive dysregulation of behavior is influenced by genetic and environmental factors. For example, environmental enrichment produces beneficial neurobehavioral effects in animal models of such disorders. The present study determined the effects of environmental enrichment on a range of measures related to behavioral regulation using a large cohort of male, outbred heterogeneous stock (HS) rats as subjects. Subjects were reared from late adolescence onwards either in pairs in standard housing with minimal enrichment (n = 200) or in groups of 16 in a highly enriched environment consisting of a large multi-level cage filled with toys, running wheels, and shelters (n = 64). Rats were subjected to a battery of tests, including: (i) locomotor response to novelty, (ii) light reinforcement, (iii) social reinforcement, (iv) reaction time, (v) a patch-depletion foraging test, (vi) Pavlovian conditioned approach, (vii) conditioned reinforcement, and (viii) cocaine conditioned cue preference. Results indicated that rats housed in the enriched environment were able to filter out irrelevant stimuli more effectively and thereby regulate their behavior more efficiently than standard-housing rats. The dramatic impact of environmental enrichment suggests that behavioral studies using standard housing conditions may not generalize to more complex environments that may be more ethologically relevant.
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Affiliation(s)
- Keita Ishiwari
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY, USA
| | - Christopher P King
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA
- Department of Psychology, University at Buffalo, Buffalo, NY, 14260, USA
| | - Connor D Martin
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA
| | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, NY, 14260, USA
| | - Anthony M George
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA
| | | | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jerry B Richards
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Molecular Medicine, Center on Diabetes, Obesity and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Amy M Gancarz
- Department of Psychology, California State University, Bakersfield, CA, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - David M Dietz
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY, USA
| | - Suzanne H Mitchell
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
- Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA
- Oregon Institute for Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Paul J Meyer
- Department of Psychology, University at Buffalo, Buffalo, NY, 14260, USA.
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Lara MK, Chitre AS, Chen D, Johnson BB, Nguyen KM, Cohen KA, Muckadam SA, Lin B, Ziegler S, Beeson A, Sanches T, Solberg Woods LC, Polesskaya O, Palmer AA, Mitchell SH. Genome-wide association study of delay discounting in Heterogenous Stock rats. bioRxiv 2023:2023.12.12.570851. [PMID: 38168347 PMCID: PMC10760013 DOI: 10.1101/2023.12.12.570851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Delay discounting refers to the behavioral tendency to devalue rewards as a function of their delay in receipt. Heightened delay discounting has been associated with substance use disorders, as well as multiple co-occurring psychopathologies. Genetic studies in humans and animal models have established that delay discounting is a heritable trait, but only a few specific genes have been associated with delay discounting. Here, we aimed to identify novel genetic loci associated with delay discounting through a genome-wide association study (GWAS) using Heterogenous Stock rats, a genetically diverse outbred population derived from eight inbred founder strains. We assessed delay discounting in 650 male and female rats using an adjusting amount procedure in which rats chose between smaller immediate sucrose rewards or a larger reward at variable delays. Preference switch points were calculated for each rat and both exponential and hyperbolic functions were fitted to these indifference points. Area under the curve (AUC) and the discounting parameter k of both functions were used as delay discounting measures. GWAS for AUC, exponential k, and indifference points for a short delay identified significant loci on chromosomes 20 and 14. The gene Slc35f1, which encodes a member of the solute carrier family of nucleoside sugar transporters, was the only gene within the chromosome 20 locus. That locus also contained an eQTL for Slc35f1, suggesting that heritable differences in the expression of that gene might be responsible for the association with behavior. The gene Adgrl3, which encodes a member of the latrophilin family of G-protein coupled receptors, was the only gene within the chromosome 14 locus. These findings implicate novel genes in delay discounting and highlight the need for further exploration.
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Affiliation(s)
- Montana Kay Lara
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Apurva S. Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Benjamin B. Johnson
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Katarina A. Cohen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sakina A. Muckadam
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bonnie Lin
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shae Ziegler
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Angela Beeson
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Thiago Sanches
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Leah C. Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Suzanne H. Mitchell
- Departments of Behavioral Neuroscience, Psychiatry, the Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239 USA
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6
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Okamoto F, Chitre AS, Missfeldt Sanches T, Chen D, Munro D, Polesskaya O, Palmer AA. Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population. bioRxiv 2023:2023.11.29.566473. [PMID: 38076923 PMCID: PMC10705385 DOI: 10.1101/2023.11.29.566473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Genome-wide association studies typically evaluate the autosomes and sometimes the X Chromosome, but seldom consider the Y or mitochondrial Chromosomes. We genotyped the Y and mitochondrial chromosomes in heterogeneous stock rats (Rattus norvegicus), which were created in 1984 by intercrossing eight inbred strains and have subsequently been maintained as an outbred population for 100 generations. As the Y and mitochondrial Chromosomes do not recombine, we determined which founder had contributed these chromosomes for each rat, and then performed association analysis for all complex traits (n=12,055; intersection of 12,116 phenotyped and 15,042 haplotyped rats). We found the eight founders had 8 distinct Y and 4 distinct mitochondrial Chromosomes, however only two of each were observed in our modern heterogeneous stock rat population (Generations 81-97). Despite the unusually large sample size, the p-value distribution did not deviate from expectations; there were no significant associations for behavioral, physiological, metabolome, or microbiome traits after correcting for multiple comparisons. However, both Y and mitochondrial Chromosomes were strongly associated with expression of a few genes located on those chromosomes, which provided a positive control. Our results suggest that within modern heterogeneous stock rats there are no Y and mitochondrial Chromosomes differences that strongly influence behavioral or physiological traits. These results do not address other ancestral Y and mitochondrial Chromosomes that do not appear in modern heterogeneous stock rats, nor do they address effects that may exist in other rat populations, or in other species.
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Affiliation(s)
- Faith Okamoto
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Apurva S Chitre
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Thiago Missfeldt Sanches
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Denghui Chen
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | | | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
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7
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Zhou JL, de Guglielmo G, Ho AJ, Kallupi M, Pokhrel N, Li HR, Chitre AS, Munro D, Mohammadi P, Carrette LLG, George O, Palmer AA, McVicker G, Telese F. Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition. Nat Neurosci 2023; 26:1868-1879. [PMID: 37798411 PMCID: PMC10620093 DOI: 10.1038/s41593-023-01452-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The amygdala processes positive and negative valence and contributes to addiction, but the cell-type-specific gene regulatory programs involved are unknown. We generated an atlas of single-nucleus gene expression and chromatin accessibility in the amygdala of outbred rats with high and low cocaine addiction-like behaviors following prolonged abstinence. Differentially expressed genes between the high and low groups were enriched for energy metabolism across cell types. Rats with high addiction index (AI) showed increased relapse-like behaviors and GABAergic transmission in the amygdala. Both phenotypes were reversed by pharmacological inhibition of the glyoxalase 1 enzyme, which metabolizes methylglyoxal-a GABAA receptor agonist produced by glycolysis. Differences in chromatin accessibility between high and low AI rats implicated pioneer transcription factors in the basic helix-loop-helix, FOX, SOX and activator protein 1 families. We observed opposite regulation of chromatin accessibility across many cell types. Most notably, excitatory neurons had greater accessibility in high AI rats and inhibitory neurons had greater accessibility in low AI rats.
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Affiliation(s)
- Jessica L Zhou
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Aaron J Ho
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marsida Kallupi
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Narayan Pokhrel
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Hai-Ri Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Munro
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Olivier George
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Graham McVicker
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Francesca Telese
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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8
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Zhou JL, de Guglielmo G, Ho AJ, Kallupi M, Pokhrel N, Li HR, Chitre AS, Munro D, Mohammadi P, Carrette LLG, George O, Palmer AA, McVicker G, Telese F. Author Correction: Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition. Nat Neurosci 2023; 26:2035. [PMID: 37845545 PMCID: PMC10620070 DOI: 10.1038/s41593-023-01489-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Affiliation(s)
- Jessica L Zhou
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Aaron J Ho
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marsida Kallupi
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Narayan Pokhrel
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Hai-Ri Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Munro
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Olivier George
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Graham McVicker
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Francesca Telese
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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9
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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. bioRxiv 2023:2023.04.13.536694. [PMID: 37214860 PMCID: PMC10197727 DOI: 10.1101/2023.04.13.536694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics; The American Genome Center, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center For Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC Groningen, The Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
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10
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Xu J, Casanave R, Chitre AS, Wang Q, Nguyen KM, Blake C, Wagle M, Cheng R, Polesskaya O, Palmer AA, Guo S. Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes. bioRxiv 2023:2023.09.06.556529. [PMID: 37732200 PMCID: PMC10508786 DOI: 10.1101/2023.09.06.556529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Behavioral diversity is critical for population fitness. Individual differences in risk-taking are observed across species, but underlying genetic mechanisms and conservation are largely unknown. We examined dark avoidance in larval zebrafish, a motivated behavior reflecting an approach-avoidance conflict. Brain-wide calcium imaging revealed significant neural activity differences between approach-inclined versus avoidance-inclined individuals. We used a population of ∼6,000 to perform the first genome-wide association study (GWAS) in zebrafish, which identified 34 genomic regions harboring many genes that are involved in synaptic transmission and human psychiatric diseases. We used CRISPR to study several causal genes: serotonin receptor-1b ( htr1b ), nitric oxide synthase-1 ( nos1 ), and stress-induced phosphoprotein-1 ( stip1 ). We further identified 52 conserved elements containing 66 GWAS significant variants. One encoded an exonic regulatory element that influenced tissue-specific nos1 expression. Together, these findings reveal new genetic loci and establish a powerful, scalable animal system to probe mechanisms underlying motivation, a critical dimension of psychiatric diseases.
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11
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Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Rep 2023; 42:112873. [PMID: 37527041 PMCID: PMC10546330 DOI: 10.1016/j.celrep.2023.112873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
A vexing observation in genome-wide association studies (GWASs) is that parallel analyses in different species may not identify orthologous genes. Here, we demonstrate that cross-species translation of GWASs can be greatly improved by an analysis of co-localization within molecular networks. Using body mass index (BMI) as an example, we show that the genes associated with BMI in humans lack significant agreement with those identified in rats. However, the networks interconnecting these genes show substantial overlap, highlighting common mechanisms including synaptic signaling, epigenetic modification, and hormonal regulation. Genetic perturbations within these networks cause abnormal BMI phenotypes in mice, too, supporting their broad conservation across mammals. Other mechanisms appear species specific, including carbohydrate biosynthesis (humans) and glycerolipid metabolism (rodents). Finally, network co-localization also identifies cross-species convergence for height/body length. This study advances a general paradigm for determining whether and how phenotypes measured in model species recapitulate human biology.
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Affiliation(s)
- Sarah N Wright
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Brittany S Leger
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA; Program in Biomedical Sciences, University of California San Diego, La Jolla, CA 93093, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sophie N Liu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Tongqiu Jia
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Katie Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Anthony George
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA
| | - Alexander F Gileta
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Wenyan Han
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Alesa H Netzley
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher P King
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA; Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | | | - Connor Martin
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA; Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | | | - Tengfei Wang
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Hannah Bimschleger
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA
| | - Jerry Richards
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY 14203, USA; Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY 14203, USA
| | - Hao Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Shelly B Flagel
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul Meyer
- Department of Psychology, University at Buffalo, Buffalo, NY 14260, USA
| | - Terry E Robinson
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 93093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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12
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Chitre AS, Polesskaya O, Munro D, Cheng R, Mohammadi P, Holl K, Gao J, Bimschleger H, Martinez AG, George AM, Gileta AF, Han W, Horvath A, Hughson A, Ishiwari K, King CP, Lamparelli A, Versaggi CL, Martin CD, St. Pierre CL, Tripi JA, Richards JB, Wang T, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Palmer AA. An exponential increase in QTL detection with an increased sample size. Genetics 2023; 224:iyad054. [PMID: 36974931 PMCID: PMC10213487 DOI: 10.1093/genetics/iyad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Power analyses are often used to determine the number of animals required for a genome-wide association study (GWAS). These analyses are typically intended to estimate the sample size needed for at least 1 locus to exceed a genome-wide significance threshold. A related question that is less commonly considered is the number of significant loci that will be discovered with a given sample size. We used simulations based on a real data set that consisted of 3,173 male and female adult N/NIH heterogeneous stock rats to explore the relationship between sample size and the number of significant loci discovered. Our simulations examined the number of loci identified in subsamples of the full data set. The subsampling analysis was conducted for 4 traits with low (0.15 ± 0.03), medium (0.31 ± 0.03 and 0.36 ± 0.03), and high (0.46 ± 0.03) SNP-based heritabilities. For each trait, we subsampled the data 100 times at different sample sizes (500, 1,000, 1,500, 2,000, and 2,500). We observed an exponential increase in the number of significant loci with larger sample sizes. Our results are consistent with similar observations in human GWAS and imply that future rodent GWAS should use sample sizes that are significantly larger than those needed to obtain a single significant result.
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Affiliation(s)
- Apurva S Chitre
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
- Department of Integrative Structural and Computational Biology, The Scripps
Research Institute, La Jolla, CA 92037, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps
Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, The Scripps Research
Institute, La Jolla, CA 92037, USA
| | - Katie Holl
- Department of Physiology, Medical College of Wisconsin,
Milwaukee, WI 53226, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
| | - Hannah Bimschleger
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, University of Tennessee Health Science
Center, Memphis, TN 38163, USA
| | - Anthony M George
- Clinical and Research Institute on Addictions, State University of New York
at Buffalo, Buffalo, NY 14203, USA
| | - Alexander F Gileta
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
- Department of Human Genetics, University of Chicago,
Chicago, IL 60637, USA
| | - Wenyan Han
- Department of Pharmacology, University of Tennessee Health Science
Center, Memphis, TN 38163, USA
| | - Aidan Horvath
- Department of Psychiatry, University of Michigan,
Ann Arbor, MI 48109, USA
| | - Alesa Hughson
- Department of Psychiatry, University of Michigan,
Ann Arbor, MI 48109, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, State University of New York
at Buffalo, Buffalo, NY 14203, USA
- Department of Pharmacology and Toxicology, State University of New York at
Buffalo, Buffalo, NY 14203, USA
| | - Christopher P King
- Department of Psychology, State University of New York at
Buffalo, Buffalo, NY 14260, USA
| | - Alexander Lamparelli
- Department of Psychology, State University of New York at
Buffalo, Buffalo, NY 14260, USA
| | - Cassandra L Versaggi
- Department of Psychology, State University of New York at
Buffalo, Buffalo, NY 14260, USA
| | - Connor D Martin
- Clinical and Research Institute on Addictions, State University of New York
at Buffalo, Buffalo, NY 14203, USA
- Department of Pharmacology and Toxicology, State University of New York at
Buffalo, Buffalo, NY 14203, USA
| | - Celine L St. Pierre
- Department of Genetics, Washington University in St Louis,
St Louis, MO 63110, USA
| | - Jordan A Tripi
- Department of Psychology, State University of New York at
Buffalo, Buffalo, NY 14260, USA
| | - Jerry B Richards
- Clinical and Research Institute on Addictions, State University of New York
at Buffalo, Buffalo, NY 14203, USA
- Department of Pharmacology and Toxicology, State University of New York at
Buffalo, Buffalo, NY 14203, USA
| | - Tengfei Wang
- Department of Pharmacology, University of Tennessee Health Science
Center, Memphis, TN 38163, USA
| | - Hao Chen
- Department of Pharmacology, University of Tennessee Health Science
Center, Memphis, TN 38163, USA
| | - Shelly B Flagel
- Department of Psychiatry, University of Michigan,
Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute, University of Michigan,
Ann Arbor, MI 48109, USA
| | - Paul Meyer
- Department of Psychology, State University of New York at
Buffalo, Buffalo, NY 14260, USA
| | - Terry E Robinson
- Department of Psychology, University of Michigan,
Ann Arbor, MI 48109, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of
Medicine, Winston-Salem, NC 27101, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego,
La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San
Diego, La Jolla, CA 92093, USA
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13
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Freda PJ, Ghosh A, Zhang E, Luo T, Chitre AS, Polesskaya O, St Pierre CL, Gao J, Martin CD, Chen H, Garcia-Martinez AG, Wang T, Han W, Ishiwari K, Meyer P, Lamparelli A, King CP, Palmer AA, Li R, Moore JH. Automated quantitative trait locus analysis (AutoQTL). BioData Min 2023; 16:14. [PMID: 37038201 PMCID: PMC10088184 DOI: 10.1186/s13040-023-00331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/31/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Quantitative Trait Locus (QTL) analysis and Genome-Wide Association Studies (GWAS) have the power to identify variants that capture significant levels of phenotypic variance in complex traits. However, effort and time are required to select the best methods and optimize parameters and pre-processing steps. Although machine learning approaches have been shown to greatly assist in optimization and data processing, applying them to QTL analysis and GWAS is challenging due to the complexity of large, heterogenous datasets. Here, we describe proof-of-concept for an automated machine learning approach, AutoQTL, with the ability to automate many complicated decisions related to analysis of complex traits and generate solutions to describe relationships that exist in genetic data. RESULTS Using a publicly available dataset of 18 putative QTL from a large-scale GWAS of body mass index in the laboratory rat, Rattus norvegicus, AutoQTL captures the phenotypic variance explained under a standard additive model. AutoQTL also detects evidence of non-additive effects including deviations from additivity and 2-way epistatic interactions in simulated data via multiple optimal solutions. Additionally, feature importance metrics provide different insights into the inheritance models and predictive power of multiple GWAS-derived putative QTL. CONCLUSIONS This proof-of-concept illustrates that automated machine learning techniques can complement standard approaches and have the potential to detect both additive and non-additive effects via various optimal solutions and feature importance metrics. In the future, we aim to expand AutoQTL to accommodate omics-level datasets with intelligent feature selection and feature engineering strategies.
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Affiliation(s)
- Philip J Freda
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G540, West Hollywood, CA, 90069, USA
| | - Attri Ghosh
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G540, West Hollywood, CA, 90069, USA
| | - Elizabeth Zhang
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G540, West Hollywood, CA, 90069, USA
| | - Tianhao Luo
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G540, West Hollywood, CA, 90069, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr., Mail Code: 0667, La Jolla, CA, 92093-0667, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr., Mail Code: 0667, La Jolla, CA, 92093-0667, USA
| | - Celine L St Pierre
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr., Mail Code: 0667, La Jolla, CA, 92093-0667, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr., Mail Code: 0667, La Jolla, CA, 92093-0667, USA
| | - Connor D Martin
- Department of Pharmacology & Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 955 Main Street, Suite 3102, Buffalo, NY, 14203, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Translational Research Building, 71 South Manassas, Memphis, TN, 38163, USA
| | - Angel G Garcia-Martinez
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Translational Research Building, 71 South Manassas, Memphis, TN, 38163, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Translational Research Building, 71 South Manassas, Memphis, TN, 38163, USA
| | - Wenyan Han
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Translational Research Building, 71 South Manassas, Memphis, TN, 38163, USA
| | - Keita Ishiwari
- Department of Pharmacology & Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 955 Main Street, Suite 3102, Buffalo, NY, 14203, USA
- Clinical and Research Institute on Addictions, University at Buffalo, 1021 Main Street, Buffalo, NY, 14203-1016, USA
| | - Paul Meyer
- Department of Psychology, University at Buffalo, 204 Park Hall, North Campus, Buffalo, NY, 14260-4110, USA
| | - Alexander Lamparelli
- Department of Psychology, University at Buffalo, 204 Park Hall, North Campus, Buffalo, NY, 14260-4110, USA
| | - Christopher P King
- Department of Psychology, University at Buffalo, 204 Park Hall, North Campus, Buffalo, NY, 14260-4110, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr., Mail Code: 0667, La Jolla, CA, 92093-0667, USA
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr., Mail Code: 0667, La Jolla, CA, 92093-0667, USA
| | - Ruowang Li
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G540, West Hollywood, CA, 90069, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N. San Vicente Blvd., Pacific Design Center, Suite G540, West Hollywood, CA, 90069, USA.
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14
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Fowler S, Wang T, Munro D, Kumar A, Chitre AS, Hollingsworth TJ, Garcia Martinez A, St. Pierre CL, Bimschleger H, Gao J, Cheng R, Mohammadi P, Chen H, Palmer AA, Polesskaya O, Jablonski MM. Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats. Front Genet 2023; 13:1029058. [PMID: 36793389 PMCID: PMC9922724 DOI: 10.3389/fgene.2022.1029058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/28/2022] [Indexed: 02/03/2023] Open
Abstract
Elevated intraocular pressure (IOP) is influenced by environmental and genetic factors. Increased IOP is a major risk factor for most types of glaucoma, including primary open angle glaucoma (POAG). Investigating the genetic basis of IOP may lead to a better understanding of the molecular mechanisms of POAG. The goal of this study was to identify genetic loci involved in regulating IOP using outbred heterogeneous stock (HS) rats. HS rats are a multigenerational outbred population derived from eight inbred strains that have been fully sequenced. This population is ideal for a genome-wide association study (GWAS) owing to the accumulated recombinations among well-defined haplotypes, the relatively high allele frequencies, the accessibility to a large collection of tissue samples, and the large allelic effect size compared to human studies. Both male and female HS rats (N = 1,812) were used in the study. Genotyping-by-sequencing was used to obtain ∼3.5 million single nucleotide polymorphisms (SNP) from each individual. SNP heritability for IOP in HS rats was 0.32, which agrees with other studies. We performed a GWAS for the IOP phenotype using a linear mixed model and used permutation to determine a genome-wide significance threshold. We identified three genome-wide significant loci for IOP on chromosomes 1, 5, and 16. Next, we sequenced the mRNA of 51 whole eye samples to find cis-eQTLs to aid in identification of candidate genes. We report 5 candidate genes within those loci: Tyr, Ctsc, Plekhf2, Ndufaf6 and Angpt2. Tyr, Ndufaf6 and Angpt2 genes have been previously implicated by human GWAS of IOP-related conditions. Ctsc and Plekhf2 genes represent novel findings that may provide new insight into the molecular basis of IOP. This study highlights the efficacy of HS rats for investigating the genetics of elevated IOP and identifying potential candidate genes for future functional testing.
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Affiliation(s)
- Samuel Fowler
- Hamilton Eye Institute Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United states
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee, United states
| | - Daniel Munro
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states,Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, California, United states
| | - Aman Kumar
- Hamilton Eye Institute Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United states
| | - Apurva S. Chitre
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states
| | - T. J. Hollingsworth
- Hamilton Eye Institute Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United states
| | - Angel Garcia Martinez
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee, United states
| | - Celine L. St. Pierre
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states
| | - Hannah Bimschleger
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states
| | - Jianjun Gao
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states
| | - Riyan Cheng
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, California, United states,Scripps Research Translational Institute, Scripps Research, San Diego, California, United states
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee, United states
| | - Abraham A. Palmer
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states,Institute for Genomic Medicine, University of California, San Diego, San Diego, California, United states
| | - Oksana Polesskaya
- Department of Psychiatry, University of California, San Diego, San Diego, California, United states
| | - Monica M. Jablonski
- Hamilton Eye Institute Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United states,*Correspondence: Monica M. Jablonski,
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15
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Chitre AS, Hebda-Bauer EK, Blandino P, Bimschleger H, Nguyen KM, Maras P, Li F, Ozel AB, Pan Y, Polesskaya O, Cheng R, Flagel SB, Watson SJ, Li J, Akil H, Palmer AA. Genome-wide association study in a rat model of temperament identifies multiple loci for exploratory locomotion and anxiety-like traits. Front Genet 2023; 13:1003074. [PMID: 36712851 PMCID: PMC9873817 DOI: 10.3389/fgene.2022.1003074] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023] Open
Abstract
Common genetic factors likely contribute to multiple psychiatric diseases including mood and substance use disorders. Certain stable, heritable traits reflecting temperament, termed externalizing or internalizing, play a large role in modulating vulnerability to these disorders. To model these heritable tendencies, we selectively bred rats for high and low exploration in a novel environment [bred High Responders (bHR) vs. Low Responders (bLR)]. To identify genes underlying the response to selection, we phenotyped and genotyped 538 rats from an F2 cross between bHR and bLR. Several behavioral traits show high heritability, including the selection trait: exploratory locomotion (EL) in a novel environment. There were significant phenotypic and genetic correlations between tests that capture facets of EL and anxiety. There were also correlations with Pavlovian conditioned approach (PavCA) behavior despite the lower heritability of that trait. Ten significant and conditionally independent loci for six behavioral traits were identified. Five of the six traits reflect different facets of EL that were captured by three behavioral tests. Distance traveled measures from the open field and the elevated plus maze map onto different loci, thus may represent different aspects of novelty-induced locomotor activity. The sixth behavioral trait, number of fecal boli, is the only anxiety-related trait mapping to a significant locus on chromosome 18 within which the Pik3c3 gene is located. There were no significant loci for PavCA. We identified a missense variant in the Plekhf1 gene on the chromosome 1:95 Mb QTL and Fancf and Gas2 as potential candidate genes that may drive the chromosome 1:107 Mb QTL for EL traits. The identification of a locomotor activity-related QTL on chromosome 7 encompassing the Pkhd1l1 and Trhr genes is consistent with our previous finding of these genes being differentially expressed in the hippocampus of bHR vs. bLR rats. The strong heritability coupled with identification of several loci associated with exploratory locomotion and emotionality provide compelling support for this selectively bred rat model in discovering relatively large effect causal variants tied to elements of internalizing and externalizing behaviors inherent to psychiatric and substance use disorders.
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Affiliation(s)
- Apurva S. Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Elaine K. Hebda-Bauer
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Peter Blandino
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Hannah Bimschleger
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Pamela Maras
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Fei Li
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - A. Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States
| | - Shelly B. Flagel
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Stanley J. Watson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Jun Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States,Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, United States,*Correspondence: Abraham A. Palmer,
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16
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Munro D, Wang T, Chitre AS, Polesskaya O, Ehsan N, Gao J, Gusev A, Woods LS, Saba L, Chen H, Palmer A, Mohammadi P. The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats. Nucleic Acids Res 2022; 50:10882-10895. [PMID: 36263809 PMCID: PMC9638908 DOI: 10.1093/nar/gkac912] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/17/2022] [Accepted: 10/05/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous Stock (HS) rats are a genetically diverse outbred rat population that is widely used for studying genetics of behavioral and physiological traits. Mapping Quantitative Trait Loci (QTL) associated with transcriptional changes would help to identify mechanisms underlying these traits. We generated genotype and transcriptome data for five brain regions from 88 HS rats. We identified 21 392 cis-QTLs associated with expression and splicing changes across all five brain regions and validated their effects using allele specific expression data. We identified 80 cases where eQTLs were colocalized with genome-wide association study (GWAS) results from nine physiological traits. Comparing our dataset to human data from the Genotype-Tissue Expression (GTEx) project, we found that the HS rat data yields twice as many significant eQTLs as a similarly sized human dataset. We also identified a modest but highly significant correlation between genetic regulatory variation among orthologous genes. Surprisingly, we found less genetic variation in gene regulation in HS rats relative to humans, though we still found eQTLs for the orthologs of many human genes for which eQTLs had not been found. These data are available from the RatGTEx data portal (RatGTEx.org) and will enable new discoveries of the genetic influences of complex traits.
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Affiliation(s)
- Daniel Munro
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Nava Ehsan
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Leah C Solberg Woods
- Section of Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Abraham A Palmer
- Correspondence may also be addressed to Abraham A. Palmer. Tel: +1 858 534 2093;
| | - Pejman Mohammadi
- To whom correspondence should be addressed. Tel: +1 858 784 8746;
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17
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Gunturkun MH, Wang T, Chitre AS, Garcia Martinez A, Holl K, St Pierre C, Bimschleger H, Gao J, Cheng R, Polesskaya O, Solberg Woods LC, Palmer AA, Chen H. Genome-Wide Association Study on Three Behaviors Tested in an Open Field in Heterogeneous Stock Rats Identifies Multiple Loci Implicated in Psychiatric Disorders. Front Psychiatry 2022; 13:790566. [PMID: 35237186 PMCID: PMC8882588 DOI: 10.3389/fpsyt.2022.790566] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/18/2022] [Indexed: 12/05/2022] Open
Abstract
Many personality traits are influenced by genetic factors. Rodents models provide an efficient system for analyzing genetic contribution to these traits. Using 1,246 adolescent heterogeneous stock (HS) male and female rats, we conducted a genome-wide association study (GWAS) of behaviors measured in an open field, including locomotion, novel object interaction, and social interaction. We identified 30 genome-wide significant quantitative trait loci (QTL). Using multiple criteria, including the presence of high impact genomic variants and co-localization of cis-eQTL, we identified 17 candidate genes (Adarb2, Ankrd26, Cacna1c, Cacng4, Clock, Ctu2, Cyp26b1, Dnah9, Gda, Grxcr1, Eva1a, Fam114a1, Kcnj9, Mlf2, Rab27b, Sec11a, and Ube2h) for these traits. Many of these genes have been implicated by human GWAS of various psychiatric or drug abuse related traits. In addition, there are other candidate genes that likely represent novel findings that can be the catalyst for future molecular and genetic insights into human psychiatric diseases. Together, these findings provide strong support for the use of the HS population to study psychiatric disorders.
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Affiliation(s)
- Mustafa Hakan Gunturkun
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Angel Garcia Martinez
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Katie Holl
- Department of Internal Medicine, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Celine St Pierre
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Hannah Bimschleger
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Jianjun Gao
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Riyan Cheng
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Oksana Polesskaya
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, United States
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18
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King CP, Tripi JA, Hughson AR, Horvath AP, Lamparelli AC, Holl KL, Chitre AS, Polesskaya O, Ishiwari K, Solberg Woods LC, Palmer AA, Robinson TE, Flagel SB, Meyer PJ. Sensitivity to food and cocaine cues are independent traits in a large sample of heterogeneous stock rats. Sci Rep 2021; 11:2223. [PMID: 33500444 PMCID: PMC7838206 DOI: 10.1038/s41598-020-80798-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/18/2020] [Accepted: 12/15/2020] [Indexed: 11/09/2022] Open
Abstract
Sensitivity to cocaine and its associated stimuli ("cues") are important factors in the development and maintenance of addiction. Rodent studies suggest that this sensitivity is related, in part, to the propensity to attribute incentive salience to food cues, which, in turn, contributes to the maintenance of cocaine self-administration, and cue-induced relapse of drug-seeking. Whereas each of these traits has established links to drug use, the relatedness between the individual traits themselves has not been well characterized in preclinical models. To this end, the propensity to attribute incentive salience to a food cue was first assessed in two distinct cohorts of 2716 outbred heterogeneous stock rats (HS; formerly N:NIH). We then determined whether each cohort was associated with performance in one of two paradigms (cocaine conditioned cue preference and cocaine contextual conditioning). These measure the unconditioned locomotor effects of cocaine, as well as conditioned approach and the locomotor response to a cocaine-paired floor or context. There was large individual variability and sex differences among all traits, but they were largely independent of one another in both males and females. These findings suggest that these traits may contribute to drug-use via independent underlying neuropsychological processes.
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Affiliation(s)
- Christopher P King
- Behavioral Neuroscience Program, Department of Psychology, University At Buffalo, Park Hall B72, Buffalo, NY, 14260, USA
| | - Jordan A Tripi
- Behavioral Neuroscience Program, Department of Psychology, University At Buffalo, Park Hall B72, Buffalo, NY, 14260, USA
| | - Alesa R Hughson
- Department of Psychology, University of Michigan, Ann Arbor, USA
| | - Aidan P Horvath
- Department of Psychology, University of Michigan, Ann Arbor, USA
| | - Alexander C Lamparelli
- Behavioral Neuroscience Program, Department of Psychology, University At Buffalo, Park Hall B72, Buffalo, NY, 14260, USA
| | - Katie L Holl
- Department of Pediatrics, Human and Molecular Genetics Center and Children's Research Institute, Medical College of Wisconsin, Milwaukee, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, USA
| | - Keita Ishiwari
- Clinical and Research Institute On Addictions, Buffalo, USA
- Department of Pharmacology and Toxicology, University At Buffalo, Buffalo, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Molecular Medicine, Center on Diabetes, Obesity and Metabolism, Wake Forest School of Medicine, Winston-Salem, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, USA
| | - Terry E Robinson
- Department of Psychology, University of Michigan, Ann Arbor, USA
| | - Shelly B Flagel
- Department of Psychiatry, University of Michigan, Ann Arbor, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
| | - Paul J Meyer
- Behavioral Neuroscience Program, Department of Psychology, University At Buffalo, Park Hall B72, Buffalo, NY, 14260, USA.
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19
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Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Bimschleger H, Garcia Martinez A, George T, Gileta AF, Han W, Horvath A, Hughson A, Ishiwari K, King CP, Lamparelli A, Versaggi CL, Martin C, St Pierre CL, Tripi JA, Wang T, Chen H, Flagel SB, Meyer P, Richards J, Robinson TE, Palmer AA, Solberg Woods LC. Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. Obesity (Silver Spring) 2020; 28:1964-1973. [PMID: 32860487 PMCID: PMC7511439 DOI: 10.1002/oby.22927] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Obesity is influenced by genetic and environmental factors. Despite the success of human genome-wide association studies, the specific genes that confer obesity remain largely unknown. The objective of this study was to use outbred rats to identify the genetic loci underlying obesity and related morphometric and metabolic traits. METHODS This study measured obesity-relevant traits, including body weight, body length, BMI, fasting glucose, and retroperitoneal, epididymal, and parametrial fat pad weight in 3,173 male and female adult N/NIH heterogeneous stock (HS) rats across three institutions, providing data for the largest rat genome-wide association study to date. Genetic loci were identified using a linear mixed model to account for the complex family relationships of the HS and using covariates to account for differences among the three phenotyping centers. RESULTS This study identified 32 independent loci, several of which contained only a single gene (e.g., Epha5, Nrg1, Klhl14) or obvious candidate genes (e.g., Adcy3, Prlhr). There were strong phenotypic and genetic correlations among obesity-related traits, and there was extensive pleiotropy at individual loci. CONCLUSIONS This study demonstrates the utility of HS rats for investigating the genetics of obesity-related traits across institutions and identify several candidate genes for future functional testing.
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Affiliation(s)
- Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Katie Holl
- Human and Molecular Genetic Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Hannah Bimschleger
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Tony George
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | - Alexander F Gileta
- Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Wenyan Han
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Aidan Horvath
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Alesa Hughson
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Keita Ishiwari
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | | | | | | | - Connor Martin
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | | | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, New York, USA
| | - Tengfei Wang
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Hao Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Shelly B Flagel
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul Meyer
- Department of Psychology, University at Buffalo, Buffalo, New York, USA
| | - Jerry Richards
- Clinical and Research Institute on Addictions, University at Buffalo, Buffalo, New York, USA
| | - Terry E Robinson
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, 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
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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20
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Gileta AF, Gao J, Chitre AS, Bimschleger HV, St Pierre CL, Gopalakrishnan S, Palmer AA. Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats. G3 (Bethesda) 2020; 10:2195-2205. [PMID: 32398234 PMCID: PMC7341140 DOI: 10.1534/g3.120.401325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 07/23/2019] [Accepted: 05/01/2020] [Indexed: 02/06/2023]
Abstract
The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.
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Affiliation(s)
- Alexander F Gileta
- Department of Psychiatry
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, 92093
| | | | | | | | | | - Shyam Gopalakrishnan
- Department of Human Genetics, University of Chicago, Chicago, Illinois, 60637, and
| | - Abraham A Palmer
- Department of Psychiatry,
- Natural History Museum of Denmark, University of Copenhagen, 2200 København N, Denmark
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21
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Peterson VL, Richards JB, Meyer PJ, Cabrera-Rubio R, Tripi JA, King CP, Polesskaya O, Baud A, Chitre AS, Bastiaanssen TFS, Woods LS, Crispie F, Dinan TG, Cotter PD, Palmer AA, Cryan JF. Sex-dependent associations between addiction-related behaviors and the microbiome in outbred rats. EBioMedicine 2020; 55:102769. [PMID: 32403084 PMCID: PMC7218262 DOI: 10.1016/j.ebiom.2020.102769] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 12/11/2018] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Multiple factors contribute to the etiology of addiction, including genetics, sex, and a number of addiction-related behavioral traits. One behavioral trait where individuals assign incentive salience to food stimuli ("sign-trackers", ST) are more impulsive compared to those that do not ("goal-trackers", GT), as well as more sensitive to drugs and drug stimuli. Furthermore, this GT/ST phenotype predicts differences in other behavioral measures. Recent studies have implicated the gut microbiota as a key regulator of brain and behavior, and have shown that many microbiota-associated changes occur in a sex-dependent manner. However, few studies have examined how the microbiome might influence addiction-related behaviors. To this end, we sought to determine if gut microbiome composition was correlated with addiction-related behaviors determined by the GT/ST phenotype. METHODS Outbred male (N=101) and female (N=101) heterogeneous stock rats underwent a series of behavioral tests measuring impulsivity, attention, reward-learning, incentive salience, and locomotor response. Cecal microbiome composition was estimated using 16S rRNA gene amplicon sequencing. Behavior and microbiome were characterized and correlated with behavioral phenotypes. Robust sex differences were observed in both behavior and microbiome; further analyses were conducted within sex using the pre-established goal/sign-tracking (GT/ST) phenotype and partial least squares differential analysis (PLS-DA) clustered behavioral phenotype. RESULTS Overall microbiome composition was not associated to the GT/ST phenotype. However, microbial alpha diversity was significantly decreased in female STs. On the other hand, a measure of impulsivity had many significant correlations to microbiome in both males and females. Several measures of impulsivity were correlated with the genus Barnesiella in females. Female STs had notable correlations between microbiome and attentional deficient. In both males and females, many measures were correlated with the bacterial families Ruminocococcaceae and Lachnospiraceae. CONCLUSIONS These data demonstrate correlations between several addiction-related behaviors and the microbiome specific to sex.
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Affiliation(s)
- Veronica L Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland
| | - Jerry B Richards
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY, USA
| | - Paul J Meyer
- Department of Psychology, University at Buffalo, Buffalo, NY, USA
| | - Raul Cabrera-Rubio
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, NY, USA
| | | | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Amelie Baud
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland
| | | | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, CA, USA; Center for Microbiome Innovation, University of California San Diego, CA, USA
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland.
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22
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Zhou X, St Pierre CL, Gonzales NM, Zou J, Cheng R, Chitre AS, Sokoloff G, Palmer AA. Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity. G3 (Bethesda) 2020; 10:951-965. [PMID: 31974095 PMCID: PMC7056977 DOI: 10.1534/g3.119.400763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
There has been extensive discussion of the "Replication Crisis" in many fields, including genome-wide association studies (GWAS). We explored replication in a mouse model using an advanced intercross line (AIL), which is a multigenerational intercross between two inbred strains. We re-genotyped a previously published cohort of LG/J x SM/J AIL mice (F34; n = 428) using a denser marker set and genotyped a new cohort of AIL mice (F39-43; n = 600) for the first time. We identified 36 novel genome-wide significant loci in the F34 and 25 novel loci in the F39-43 cohort. The subset of traits that were measured in both cohorts (locomotor activity, body weight, and coat color) showed high genetic correlations, although the SNP heritabilities were slightly lower in the F39-43 cohort. For this subset of traits, we attempted to replicate loci identified in either F34 or F39-43 in the other cohort. Coat color was robustly replicated; locomotor activity and body weight were only partially replicated, which was inconsistent with our power simulations. We used a random effects model to show that the partial replications could not be explained by Winner's Curse but could be explained by study-specific heterogeneity. Despite this heterogeneity, we performed a mega-analysis by combining F34 and F39-43 cohorts (n = 1,028), which identified four novel loci associated with locomotor activity and body weight. These results illustrate that even with the high degree of genetic and environmental control possible in our experimental system, replication was hindered by study-specific heterogeneity, which has broad implications for ongoing concerns about reproducibility.
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Affiliation(s)
- Xinzhu Zhou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92092
| | - Celine L St Pierre
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110
| | | | - Jennifer Zou
- Department of Computer Science, University of California, Los Angeles, CA, 90095
| | | | | | - Greta Sokoloff
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, IO, 52242
| | - Abraham A Palmer
- Department of Psychiatry,
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92037 and
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