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Han ZP, Yang RZ, Zhou W, Zhang LL, Wang JR, Liu CJ, Liu SD. Population structure and selection signal analysis of indigenous sheep from the southern edge of the Taklamakan Desert. BMC Genomics 2024; 25:681. [PMID: 38982349 PMCID: PMC11232224 DOI: 10.1186/s12864-024-10581-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Analyzing the genetic diversity and selection characteristics of sheep (Ovis aries) holds significant value in understanding their environmental adaptability, enhancing breeding efficiency, and achieving effective conservation and rational utilization of genetic resources. In this study, we utilized Illumina Ovine SNP 50 K BeadChip data from four indigenous sheep breeds from the southern margin of the Taklamakan Desert (Duolang sheep: n = 36, Hetian sheep: n = 74, Kunlun sheep: n = 27, Qira black sheep: n = 178) and three foreign meat sheep breeds (Poll Dorset sheep: n = 105, Suffolk sheep: n = 153, Texel sheep: n = 150) to investigate the population structure, genetic diversity, and genomic signals of positive selection within the indigenous sheep. According to the Principal component analysis (PCA), the Neighbor-Joining tree (NJ tree), and Admixture, we revealed distinct clustering patterns of these seven sheep breeds based on their geographical distribution. Then used Cross Population Extended Haplotype Homozygosity (XP-EHH), Fixation Index (FST), and Integrated Haplotype Score (iHS), we identified a collective set of 32 overlapping genes under positive selection across four indigenous sheep breeds. These genes are associated with wool follicle development and wool traits, desert environmental adaptability, disease resistance, reproduction, and high-altitude adaptability. This study reveals the population structure and genomic selection characteristics in the extreme desert environments of native sheep breeds from the southern edge of the Taklimakan Desert, providing new insights into the conservation and sustainable use of indigenous sheep genetic resources in extreme environments. Additionally, these findings offer valuable genetic resources for sheep and other mammals to adapt to global climate change.
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Affiliation(s)
- Zhi-Peng Han
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Rui-Zhi Yang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Lu-Lu Zhang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Jie-Ru Wang
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Chun-Jie Liu
- College of Animal Science and Technology, Tarim University, Alar, 843300, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China
| | - Shu-Dong Liu
- College of Animal Science and Technology, Tarim University, Alar, 843300, China.
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, 843300, China.
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Fitzpatrick M, Szalanczy A, Beeson A, Vora A, Scott C, Grzybowski M, Klotz J, Der N, Chen R, Geurts AM, Woods LCS. Protein-coding mutation in Adcy3 increases adiposity and alters emotional behaviors sex-dependently in rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.598846. [PMID: 38916175 PMCID: PMC11195162 DOI: 10.1101/2024.06.16.598846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Objective Adenylate cyclase 3 (Adcy3) has been linked to both obesity and major depressive disorder (MDD). Our lab identified a protein-coding variant in the 2nd transmembrane (TM) helix of Adcy3 in rats, and similar obesity variants have been identified in humans. The current study investigates the role of a TM variant in adiposity and behavior. Methods We used CRISPR-SpCas9 to mutate the TM domain of Adcy3 in WKY rats (Adcy3mut/mut). We also created a heterozygous knockout rat in the same strain (Adcy3+/-). Wild-type (WT), Adcy3+/-, and Adcy3mut/mut rats were fed a high-fat diet for 12 weeks. We measured body weight, fat mass, glucose tolerance, food intake, metabolism, emotion-like behaviors, and memory. Results Adcy3+/- and Adcy3mut/mut rats weighed more than WT rats due to increased fat mass. There were key sex differences: adiposity was driven by increased food intake in males but by decreased energy expenditure in females. Adcy3mut/mut males displayed increased passive coping and decreased memory while Adcy3mut/mut females displayed increased anxiety-like behavior. Conclusions These studies show that the ADCY3 TM domain plays a role in protein function, that Adcy3 may contribute to the relationship between obesity and MDD, and that sex influences the relationships between Adcy3, metabolism, and behavior.
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Affiliation(s)
- Mackenzie Fitzpatrick
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem NC, USA
| | - Alexandria Szalanczy
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem NC, USA
| | - Angela Beeson
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem NC, USA
| | - Anusha Vora
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem NC, USA
| | - Christina Scott
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem NC, USA
| | - Michael Grzybowski
- Department of Physiology, Medical College of Wisconsin, Milwaukee WI, USA
| | - Jason Klotz
- Department of Physiology, Medical College of Wisconsin, Milwaukee WI, USA
| | - Nataley Der
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem NC, USA
| | - Rong Chen
- Department of Translational Neuroscience, Wake Forest University School of Medicine, Winston-Salem NC, USA
| | - Aron M Geurts
- Department of Physiology, 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
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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 GENOMICS 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] [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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Nielsen DE, Adise S, Davis XS. Editorial: Unravelling complex biobehavioural contributors to obesity: omics, neural, and environmental considerations. Front Genet 2024; 15:1371642. [PMID: 38380427 PMCID: PMC10876997 DOI: 10.3389/fgene.2024.1371642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Affiliation(s)
- Daiva E. Nielsen
- School of Human Nutrition, McGill University, Montreal, QC, Canada
| | - Shana Adise
- Division of Endocrinology, Diabetes and Metabolism, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Xue Sun Davis
- Yale School of Medicine, New Haven, CT, United States
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Szalanczy AM, Fitzpatrick M, Beeson A, Bui T, Dyson C, Eller S, Landry J, Scott C, Grzybowski M, Klotz J, Geurts AM, Weiner JL, Redei EE, Solberg Woods LC. Chronic stress from adolescence to adulthood increases adiposity and anxiety in rats with decreased expression of Krtcap3. Front Genet 2024; 14:1247232. [PMID: 38323241 PMCID: PMC10844407 DOI: 10.3389/fgene.2023.1247232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024] Open
Abstract
We previously identified Keratinocyte-associated protein 3, Krtcap3, as a novel adiposity gene, but subsequently found that its impact on adiposity may depend on environmental stress. To more thoroughly understand the connection between Krtcap3, adiposity, and stress, we exposed wild-type (WT) and Krtcap3 knock-out (KO) rats to chronic stress then measured adiposity and behavioral outcomes. We found that KO rats displayed lower basal stress than WT rats under control conditions and exhibited metabolic and behavioral responses to chronic stress exposure. Specifically, stress-exposed KO rats gained more weight, consumed more food when socially isolated, and displayed more anxiety-like behaviors relative to control KO rats. Meanwhile, there were minimal differences between control and stressed WT rats. At study conclusion stress-exposed KO rats had increased corticosterone (CORT) relative to control KO rats with no differences between WT rats. In addition, KO rats, independent of prior stress exposure, had an increased CORT response to removal of their cage-mate (psychosocial stress), which was only seen in WT rats when exposed to chronic stress. Finally, we found differences in expression of the glucocorticoid receptor, Nr3c1, in the pituitary and colon between control and stress-exposed KO rats that were not present in WT rats. These data support that Krtcap3 expression affects stress response, potentially via interactions with Nr3c1, with downstream effects on adiposity and behavior. Future work is necessary to more thoroughly understand the role of Krtcap3 in the stress response.
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Affiliation(s)
- Alexandria M. Szalanczy
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Mackenzie Fitzpatrick
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Angela Beeson
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Trangdai Bui
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Christina Dyson
- Department of Physiology and Pharmacology, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Seth Eller
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Julia Landry
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Christina Scott
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Michael Grzybowski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jason Klotz
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Aron M. Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jeff L. Weiner
- Department of Physiology and Pharmacology, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Eva E. Redei
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Leah C. Solberg Woods
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
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Fitzpatrick M, Solberg Woods LC. Adenylate cyclase 3: a potential genetic link between obesity and major depressive disorder. Physiol Genomics 2024; 56:1-8. [PMID: 37955134 PMCID: PMC11281808 DOI: 10.1152/physiolgenomics.00056.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023] Open
Abstract
Obesity and major depressive disorder (MDD) are both significant health issues that have been increasing in prevalence and are associated with multiple comorbidities. Obesity and MDD have been shown to be bidirectionally associated, and they are both influenced by genetics and environmental factors. However, the molecular mechanisms that link these two diseases are not yet fully understood. It is possible that these diseases are connected through the actions of the cAMP/protein kinase A (PKA) pathway. Within this pathway, adenylate cyclase 3 (Adcy3) has emerged as a key player in both obesity and MDD. Numerous genetic variants in Adcy3 have been identified in humans in association with obesity. Rodent knockout studies have also validated the importance of this gene for energy homeostasis. Furthermore, Adcy3 has been identified as a top candidate gene and even a potential blood biomarker for MDD. Adcy3 and the cAMP/PKA pathway may therefore serve as an important genetic and functional link between these two diseases. In this mini-review, we discuss the role of both Adcy3 and the cAMP/PKA pathway, including specific genetic mutations, in both diseases. Understanding the role that Adcy3 mutations play in obesity and MDD could open the door for precision medicine approaches and treatments for both diseases that target this gene.
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Affiliation(s)
- Mackenzie Fitzpatrick
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States
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Wagner VA, Holl KL, Clark KC, Reho JJ, Lehmler HJ, Wang K, Grobe JL, Dwinell MR, Raff H, Kwitek AE. The Power of the Heterogeneous Stock Rat Founder Strains in Modeling Metabolic Disease. Endocrinology 2023; 164:bqad157. [PMID: 37882530 PMCID: PMC10637104 DOI: 10.1210/endocr/bqad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/04/2023] [Accepted: 10/24/2023] [Indexed: 10/27/2023]
Abstract
Metabolic diseases are a host of complex conditions, including obesity, diabetes mellitus, and metabolic syndrome. Endocrine control systems (eg, adrenals, thyroid, gonads) are causally linked to metabolic health outcomes. N/NIH Heterogeneous Stock (HS) rats are a genetically heterogeneous outbred population developed for genetic studies of complex traits. Genetic mapping studies in adult HS rats identified loci associated with cardiometabolic risks, such as glucose intolerance, insulin resistance, and increased body mass index. This study determined underappreciated metabolic health traits and the associated endocrine glands within available substrains of the HS rat founders. We hypothesize that the genetic diversity of the HS rat founder strains causes a range of endocrine health conditions contributing to the diversity of cardiometabolic disease risks. ACI/EurMcwi, BN/NHsdMcwi, BUF/MnaMcwi, F344/StmMcwi, M520/NRrrcMcwi, and WKY/NCrl rats of both sexes were studied from birth until 13 weeks of age. Birth weight was recorded, body weight was measured weekly, metabolic characteristics were assessed, and blood and tissues were collected. Our data show wide variation in endocrine traits and metabolic health states in ACI, BN, BUF, F344, M520, and WKY rat strains. This is the first report to compare birth weight, resting metabolic rate, endocrine gland weight, hypothalamic-pituitary-thyroid axis hormones, and brown adipose tissue weight in these rat strains. Importantly, this work unveils new potential for the HS rat population to model early life adversity and adrenal and thyroid pathophysiology. The HS population likely inherited risk alleles for these strain-specific traits, making the HS rat a powerful model to investigate interventions on endocrine and metabolic health.
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Affiliation(s)
- Valerie A Wagner
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Katie L Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Karen C Clark
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - John J Reho
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA 52242, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Justin L Grobe
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hershel Raff
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Endocrine Research Laboratory, Aurora St. Luke's Medical Center, Advocate Aurora Research Institute, Milwaukee, WI 53233, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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8
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Szalanczy AM, Giorgio G, Goff E, Seshie O, Grzybowski M, Klotz J, Geurts AM, Redei EE, Solberg Woods LC. Changes in environmental stress over COVID-19 pandemic likely contributed to failure to replicate adiposity phenotype associated with Krtcap3. Physiol Genomics 2023; 55:452-467. [PMID: 37458463 PMCID: PMC10642928 DOI: 10.1152/physiolgenomics.00019.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/25/2023] [Accepted: 07/09/2023] [Indexed: 07/28/2023] Open
Abstract
We previously identified keratinocyte-associated protein 3, Krtcap3, as an obesity-related gene in female rats where a whole body Krtcap3 knockout (KO) led to increased adiposity compared to wild-type (WT) controls when fed a high-fat diet (HFD). We sought to replicate this work to better understand the function of Krtcap3 but were unable to reproduce the adiposity phenotype. In the current work, WT female rats ate more compared to WT in the prior study, with corresponding increases in body weight and fat mass, while there were no changes in these measures in KO females between the studies. The prior study was conducted before the COVID-19 pandemic, while the current study started after initial lockdown orders and was completed during the pandemic in a generally less stressful environment. We hypothesize that the environmental changes impacted stress levels and may explain the failure to replicate our results. Analysis of corticosterone (CORT) at euthanasia showed a significant study-by-genotype interaction where WT had significantly higher CORT relative to KO in study 1, with no differences in study 2. These data suggest that decreasing Krtcap3 expression may alter the environmental stress response to influence adiposity. We also found that KO rats in both studies, but not WT, experienced a dramatic increase in CORT after their cage mate was removed, suggesting a separate connection to social behavioral stress. Future work is necessary to confirm and elucidate the finer mechanisms of these relationships, but these data indicate the possibility of Krtcap3 as a novel stress gene.NEW & NOTEWORTHY Obesity is linked to both genetics and environmental factors such as stress. Krtcap3 has previously been identified as a gene associated with adiposity, and our work here demonstrates that environmental stress may influence the role of Krtcap3 on both food intake and adiposity. Obesity is strongly influenced by stress in humans, so the identification of novel genes that link stress and obesity will greatly advance our understanding of the disease.
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Affiliation(s)
- Alexandria M Szalanczy
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, North Carolina, United States
| | - Gina Giorgio
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, North Carolina, United States
| | - Emily Goff
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, North Carolina, United States
| | - Osborne Seshie
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, North Carolina, United States
| | - Michael Grzybowski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Jason Klotz
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Eva E Redei
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Leah C Solberg Woods
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, North Carolina, United States
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9
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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: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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10
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Wagner VA, Holl KL, Clark KC, Reho JJ, Dwinell MR, Lehmler HJ, Raff H, Grobe JL, Kwitek AE. Genetic background in the rat affects endocrine and metabolic outcomes of bisphenol F exposure. Toxicol Sci 2023; 194:84-100. [PMID: 37191987 PMCID: PMC10306406 DOI: 10.1093/toxsci/kfad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Environmental bisphenol compounds like bisphenol F (BPF) are endocrine-disrupting chemicals (EDCs) affecting adipose and classical endocrine systems. Genetic factors that influence EDC exposure outcomes are poorly understood and are unaccounted variables that may contribute to the large range of reported outcomes in the human population. We previously demonstrated that BPF exposure increased body growth and adiposity in male N/NIH heterogeneous stock (HS) rats, a genetically heterogeneous outbred population. We hypothesize that the founder strains of the HS rat exhibit EDC effects that were strain- and sex-dependent. Weanling littermate pairs of male and female ACI, BN, BUF, F344, M520, and WKY rats randomly received either vehicle (0.1% EtOH) or 1.125 mg BPF/l in 0.1% EtOH for 10 weeks in drinking water. Body weight and fluid intake were measured weekly, metabolic parameters were assessed, and blood and tissues were collected. BPF increased thyroid weight in ACI males, thymus and kidney weight in BUF females, adrenal weight in WKY males, and possibly increased pituitary weight in BN males. BUF females also developed a disruption in activity and metabolic rate with BPF exposure. These sex- and strain-specific exposure outcomes illustrate that HS rat founders possess diverse bisphenol-exposure risk alleles and suggest that BPF exposure may intensify inherent organ system dysfunction existing in the HS rat founders. We propose that the HS rat will be an invaluable model for dissecting gene EDC interactions on health.
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Affiliation(s)
- Valerie A Wagner
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Katie L Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Karen C Clark
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - John J Reho
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa 52246, USA
| | - Hershel Raff
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Endocrine Research Laboratory, Aurora St. Luke’s Medical Center, Advocate Aurora Research Institute, Milwaukee, Wisconsin 53233, USA
| | - Justin L Grobe
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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11
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Szalanczy AM, Giorgio G, Goff E, Seshie O, Grzybowski M, Klotz J, Geurts AM, Redei EE, Solberg Woods LC. Changes in Environmental Stress over COVID-19 Pandemic Likely Contributed to Failure to Replicate Adiposity Phenotype Associated with Krtcap3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532439. [PMID: 36993361 PMCID: PMC10055176 DOI: 10.1101/2023.03.15.532439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
We previously identified Keratinocyte-associated protein 3, Krtcap3, as an obesity-related gene in female rats where a whole-body Krtcap3 knock-out (KO) led to increased adiposity compared to wild-type (WT) controls when fed a high-fat diet (HFD). We sought to replicate this work to better understand the function of Krtcap3 but were unable to reproduce the adiposity phenotype. In the current work, WT female rats ate more compared to WT in the prior study, with corresponding increases in body weight and fat mass, while there were no changes in these measures in KO females between the studies. The prior study was conducted before the COVID-19 pandemic, while the current study started after initial lock-down orders and was completed during the pandemic with a generally less stressful environment. We hypothesize that the environmental changes impacted stress levels and may explain the failure to replicate our results. Analysis of corticosterone (CORT) at euthanasia showed a significant study by genotype interaction where WT had significantly higher CORT relative to KO in Study 1, with no differences in Study 2. These data suggest that decreasing Krtcap3 expression may alter the environmental stress response to influence adiposity. We also found that KO rats in both studies, but not WT, experienced a dramatic increase in CORT after their cage mate was removed, suggesting a separate connection to social behavioral stress. Future work is necessary to confirm and elucidate the finer mechanisms of these relationships, but these data indicate the possibility of Krtcap3 as a novel stress gene.
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Affiliation(s)
- Alexandria M Szalanczy
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC USA
| | - Gina Giorgio
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC USA
| | - Emily Goff
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC USA
| | - Osborne Seshie
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC USA
| | - Michael Grzybowski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jason Klotz
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Eva E Redei
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC USA
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12
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Vedi M, Smith JR, Thomas Hayman G, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. 2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource. Genetics 2023; 224:iyad042. [PMID: 36930729 PMCID: PMC10474928 DOI: 10.1093/genetics/iyad042] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types and extensive disease and phenotype annotations and developing tools to effectively mine, analyze, and visualize the available data, to empower investigators in their hypothesis-driven research. Leveraging its robust and flexible infrastructure, RGD has added data for human and eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) besides rat to enhance its translational aspect. This article presents an overview of the database with the most recent additions to RGD's genome, variant, and quantitative phenotype data. We also briefly introduce Virtual Comparative Map (VCMap), an updated tool that explores synteny between species as an improvement to RGD's suite of tools, followed by a discussion regarding the refinements to the existing PhenoMiner tool that assists researchers in finding and comparing quantitative data across rat strains. Collectively, RGD focuses on providing a continuously improving, consistent, and high-quality data resource for researchers while advancing data reproducibility and fulfilling Findable, Accessible, Interoperable, and Reusable (FAIR) data principles.
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Affiliation(s)
- Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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13
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Keele GR. Which mouse multiparental population is right for your study? The Collaborative Cross inbred strains, their F1 hybrids, or the Diversity Outbred population. G3 (BETHESDA, MD.) 2023; 13:jkad027. [PMID: 36735601 PMCID: PMC10085760 DOI: 10.1093/g3journal/jkad027] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 12/30/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023]
Abstract
Multiparental populations (MPPs) encompass greater genetic diversity than traditional experimental crosses of two inbred strains, enabling broader surveys of genetic variation underlying complex traits. Two such mouse MPPs are the Collaborative Cross (CC) inbred panel and the Diversity Outbred (DO) population, which are descended from the same eight inbred strains. Additionally, the F1 intercrosses of CC strains (CC-RIX) have been used and enable study designs with replicate outbred mice. Genetic analyses commonly used by researchers to investigate complex traits in these populations include characterizing how heritable a trait is, i.e. its heritability, and mapping its underlying genetic loci, i.e. its quantitative trait loci (QTLs). Here we evaluate the relative merits of these populations for these tasks through simulation, as well as provide recommendations for performing the quantitative genetic analyses. We find that sample populations that include replicate animals, as possible with the CC and CC-RIX, provide more efficient and precise estimates of heritability. We report QTL mapping power curves for the CC, CC-RIX, and DO across a range of QTL effect sizes and polygenic backgrounds for samples of 174 and 500 mice. The utility of replicate animals in the CC and CC-RIX for mapping QTLs rapidly decreased as traits became more polygenic. Only large sample populations of 500 DO mice were well-powered to detect smaller effect loci (7.5-10%) for highly complex traits (80% polygenic background). All results were generated with our R package musppr, which we developed to simulate data from these MPPs and evaluate genetic analyses from user-provided genotypes.
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Affiliation(s)
- Gregory R Keele
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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14
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Hong-Le T, Crouse WL, Keele GR, Holl K, Seshie O, Tschannen M, Craddock A, Das SK, Szalanczy AM, McDonald B, Grzybowski M, Klotz J, Sharma NK, Geurts AM, Key CCC, Hawkins G, Valdar W, Mott R, Solberg Woods LC. Genetic Mapping of Multiple Traits Identifies Novel Genes for Adiposity, Lipids, and Insulin Secretory Capacity in Outbred Rats. Diabetes 2023; 72:135-148. [PMID: 36219827 PMCID: PMC9797320 DOI: 10.2337/db22-0252] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 10/04/2022] [Indexed: 01/21/2023]
Abstract
Despite the successes of human genome-wide association studies, the causal genes underlying most metabolic traits remain unclear. We used outbred heterogeneous stock (HS) rats, coupled with expression data and mediation analysis, to identify quantitative trait loci (QTLs) and candidate gene mediators for adiposity, glucose tolerance, serum lipids, and other metabolic traits. Physiological traits were measured in 1,519 male HS rats, with liver and adipose transcriptomes measured in >410 rats. Genotypes were imputed from low-coverage whole-genome sequencing. Linear mixed models were used to detect physiological and expression QTLs (pQTLs and eQTLs, respectively), using both single nucleotide polymorphism (SNP)- and haplotype-based models for pQTL mapping. Genes with cis-eQTLs that overlapped pQTLs were assessed as causal candidates through mediation analysis. We identified 14 SNP-based pQTLs and 19 haplotype-based pQTLs, of which 10 were in common. Using mediation, we identified the following genes as candidate mediators of pQTLs: Grk5 for fat pad weight and serum triglyceride pQTLs on Chr1, Krtcap3 for fat pad weight and serum triglyceride pQTLs on Chr6, Ilrun for a fat pad weight pQTL on Chr20, and Rfx6 for a whole pancreatic insulin content pQTL on Chr20. Furthermore, we verified Grk5 and Ktrcap3 using gene knockdown/out models, thereby shedding light on novel regulators of obesity.
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Affiliation(s)
- Thu Hong-Le
- Genetics Institute, University College London, London, U.K
| | - Wesley L. Crouse
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Katie Holl
- Medical College of Wisconsin, Milwaukee, WI
| | - Osborne Seshie
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | | | - Ann Craddock
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Swapan K. Das
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Alexandria M. Szalanczy
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Bailey McDonald
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | | | | | - Neeraj K. Sharma
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | | | - Chia-Chi Chuang Key
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Gregory Hawkins
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Richard Mott
- Genetics Institute, University College London, London, U.K
| | - Leah C. Solberg Woods
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC
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15
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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] [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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16
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Szalanczy AM, Goff E, Seshie O, Deal A, Grzybowski M, Klotz J, Chuang Key CC, Geurts AM, Solberg Woods LC. Keratinocyte-associated protein 3 plays a role in body weight and adiposity with differential effects in males and females. Front Genet 2022; 13:942574. [PMID: 36212147 PMCID: PMC9535360 DOI: 10.3389/fgene.2022.942574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Despite the obesity crisis in the United States, the underlying genetics are poorly understood. Our lab previously identified Keratinocyte-associated protein 3, Krtcap3, as a candidate gene for adiposity through a genome-wide association study in outbred rats, where increased liver expression of Krtcap3 correlated with decreased fat mass. Here we seek to confirm that Krtcap3 expression affects adiposity traits. To do so, we developed an in vivo whole-body Krtcap3 knock-out (KO) rat model. Wild-type (WT) and KO rats were placed onto a high-fat (HFD) or low-fat diet (LFD) at 6 weeks of age and were maintained on diet for 13 weeks, followed by assessments of metabolic health. We hypothesized that Krtcap3-KO rats will have increased adiposity and a worsened metabolic phenotype relative to WT. We found that KO male and female rats have significantly increased body weight versus WT, with the largest effect in females on a HFD. KO females also ate more and had greater adiposity, but were more insulin sensitive than WT regardless of diet condition. Although KO males weighed more than WT under both diet conditions, there were no differences in eating behavior or fat mass. Interestingly, KO males on a HFD were more insulin resistant than WT. This study confirms that Krtcap3 plays a role in body weight regulation and demonstrates genotype- and sex-specific effects on food intake, adiposity, and insulin sensitivity. Future studies will seek to better understand these sex differences, the role of diet, and establish a mechanism for Krtcap3 in obesity.
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Affiliation(s)
- Alexandria M. Szalanczy
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Emily Goff
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Osborne Seshie
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Aaron Deal
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Michael Grzybowski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jason Klotz
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Chia-Chi Chuang Key
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
| | - Aron M. Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Leah C. Solberg Woods
- Department of Internal Medicine, School of Medicine, Wake Forest University, Winston Salem, NC, United States
- *Correspondence: Leah C. Solberg Woods,
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17
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Hu L, Zhang L, Li Q, Liu H, Xu T, Zhao N, Han X, Xu S, Zhao X, Zhang C. Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing. Front Genet 2022; 13:971464. [PMID: 36160022 PMCID: PMC9490000 DOI: 10.3389/fgene.2022.971464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.
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Affiliation(s)
- Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qi Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hongjin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tianwei Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Na Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xueping Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Technology Extension Service of Animal Husbandry of Qinghai, Xining, China
| | - Shixiao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- *Correspondence: Cunfang Zhang,
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Martins TF, Braga Magalhães AF, Verardo LL, Santos GC, Silva Fernandes AA, Gomes Vieira JI, Irano N, dos Santos DB. Functional analysis of litter size and number of teats in pigs: From GWAS to post-GWAS. Theriogenology 2022; 193:157-166. [DOI: 10.1016/j.theriogenology.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 10/31/2022]
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19
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de Jong TV, Chen H, Brashear WA, Kochan KJ, Hillhouse AE, Zhu Y, Dhande IS, Hudson EA, Sumlut MH, Smith ML, Kalbfleisch TS, Doris PA. mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly. Physiol Genomics 2022; 54:251-260. [PMID: 35543507 PMCID: PMC9236863 DOI: 10.1152/physiolgenomics.00017.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Rat genomic tools have been slower to emerge than for those of humans and mice and have remained less thorough and comprehensive. The arrival of a new and improved rat reference genome, mRatBN7.2, in late 2020 is a welcome event. This assembly, like predecessor rat reference assemblies, is derived from an inbred Brown Norway rat. In this "user" survey we hope to provide other users of this assembly some insight into its characteristics and some assessment of its improvements as well as a few caveats that arise from the unique aspects of this assembly. mRatBN7.2 was generated by the Wellcome Sanger Institute as part of the large Vertebrate Genomes Project. This rat assembly has now joined human, mouse, chicken, and zebrafish in the National Center for Biotechnology Information (NCBI)'s Genome Reference Consortium, which provides ongoing curation of the assembly. Here we examine the technical procedures by which the assembly was created and assess how this assembly constitutes an improvement over its predecessor. We also indicate the technical limitations affecting the assembly, providing illustrations of how these limitations arise and the impact that results for this reference assembly.
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Affiliation(s)
- Tristan V. de Jong
- 1Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Hao Chen
- 1Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Wesley A. Brashear
- 2Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas
| | - Kelli J. Kochan
- 2Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas
| | - Andrew E. Hillhouse
- 2Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas
| | - Yaming Zhu
- 3Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, Texas
| | - Isha S. Dhande
- 3Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, Texas
| | - Elizabeth A. Hudson
- 4Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky
| | - Mary H. Sumlut
- 4Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky
| | - Melissa L. Smith
- 4Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky
| | - Theodore S. Kalbfleisch
- 5Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, Kentucky
| | - Peter A. Doris
- 3Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, Texas
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Crouse WL, Das SK, Le T, Keele G, Holl K, Seshie O, Craddock A, Sharma NK, Comeau ME, Langefeld C, Hawkins GA, Mott R, Valdar W, Solberg Woods LC. Transcriptome-wide analyses of adipose tissue in outbred rats reveal genetic regulatory mechanisms relevant for human obesity. Physiol Genomics 2022; 54:206-219. [PMID: 35467982 DOI: 10.1152/physiolgenomics.00172.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transcriptomic analysis in metabolically active tissues allows a systems genetics approach to identify causal genes and networks involved in metabolic disease. Outbred heterogeneous stock (HS) rats are used for genetic mapping of complex traits, but to-date, a systems genetics analysis of metabolic tissues has not been done. We investigated whether adiposity-associated genes and gene co-expression networks in outbred heterogeneous stock (HS) rats overlap those found in humans. We analyzed RNAseq data from adipose tissue of 415 male HS rats, correlated these transcripts with body weight (BW) and compared transcriptome signatures to two human cohorts: the "African American Genetics of Metabolism and Expression" and "Metabolic Syndrome in Men". We used weighted gene co-expression network analysis to identify adiposity-associated gene networks and mediation analysis to identify genes under genetic control whose expression drives adiposity. We identified 554 orthologous "consensus genes" whose expression correlates with BW in the rat and with body mass index (BMI) in both human cohorts. Consensus genes fell within eight co-expressed networks and were enriched for genes involved in immune system function, cell growth, extracellular matrix organization and lipid metabolic processes. We identified 19 consensus genes for which genetic variation may influence BW via their expression, including those involved in lipolysis (e.g., Hcar1), inflammation (e.g., Rgs1), adipogenesis (e.g., Tmem120b) or no previously known role in obesity (e.g., St14, Msa4a6). Strong concordance between HS rat and human BW/BMI associated transcripts demonstrates translational utility of the rat model, while identification of novel genes expands our knowledge of the genetics underlying obesity.
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Affiliation(s)
- Wesley L Crouse
- University of North Carolina at Chapel Hill, Department of Genetics, Chapel Hill, NC, United States
| | - Swapan Kumar Das
- Wake Forest University School of Medicine, Department of Internal Medicine, Winston Salem, NC, United States
| | - Thu Le
- University College London, Department of Genetics, Evolution and Environment, Division of Biosciences, London, United Kingdom
| | - Gregory Keele
- Jackson Laboratories, Roux Center for Genomics and Computational Biology, Bar Harbor, ME, United States
| | - Katie Holl
- Medical College of Wisconsin, Department of Pediatrics, Milwaukee, WI, United States
| | - Osborne Seshie
- Wake Forest University School of Medicine, Department of Internal Medicine, Winston Salem, NC, United States
| | - Ann Craddock
- Wake Forest University School of Medicine, Department of Biochemistry, Winston Salem, NC, United States
| | - Neeraj Kumar Sharma
- Wake Forest University School of Medicine, Department of Internal Medicine, Winston Salem, NC, United States
| | - Mary Elizabeth Comeau
- Wake Forest University School of Medicine, Department of Biostatistics and Data Sciences, Winston Salem, NC, United States
| | - Carl Langefeld
- Wake Forest University School of Medicine, Department of Biostatistics and Data Sciences, Winston Salem, NC, United States
| | - Gregory A Hawkins
- Wake Forest University School of Medicine, Department of Biochemistry, Winston Salem, NC, United States
| | - Richard Mott
- University College London, Department of Genetics, Evolution and Environment, Division of Biosciences, London, United Kingdom
| | - William Valdar
- University of North Carolina at Chapel Hill, Department of Genetics, Chapel Hill, NC, United States
| | - Leah C Solberg Woods
- Wake Forest University School of Medicine, Department of Internal Medicine, Winston Salem, NC, United States
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21
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Szalanczy AM, Key CCC, Woods LCS. Genetic variation in satiety signaling and hypothalamic inflammation: merging fields for the study of obesity. J Nutr Biochem 2022; 101:108928. [PMID: 34936921 PMCID: PMC8959400 DOI: 10.1016/j.jnutbio.2021.108928] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/08/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023]
Abstract
Although obesity has been a longstanding health crisis, the genetic architecture of the disease remains poorly understood. Genome-wide association studies have identified many genomic loci associated with obesity, with genes being enriched in the brain, particularly in the hypothalamus. This points to the role of the central nervous system (CNS) in predisposition to obesity, and we emphasize here several key genes along the satiety signaling pathway involved in genetic susceptibility. Interest has also risen regarding the chronic, low-grade obesity-associated inflammation, with a growing concern toward inflammation in the hypothalamus as a precursor to obesity. Recent studies have found that genetic variation in inflammatory genes play a role in obesity susceptibility, and we highlight here several key genes. Despite the interest in the genetic variants of these pathways individually, there is a lack of research that investigates the relationship between the two. Understanding the interplay between genetic variation in obesity genes enriched in the CNS and inflammation genes will advance our understanding of obesity etiology and heterogeneity, improve genetic risk prediction analyses, and highlight new drug targets for the treatment of obesity. Additionally, this increased knowledge will assist in physician's ability to develop personalized nutrition and medication strategies for combating the obesity epidemic. Though it often seems to present universally, obesity is a highly individual disease, and there remains a need in the field to develop methods to treat at the individual level.
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22
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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] [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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23
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Clark KC, Kwitek AE. Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome. Compr Physiol 2021; 12:3045-3084. [PMID: 34964118 PMCID: PMC9373910 DOI: 10.1002/cphy.c210010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Metabolic syndrome (MetS) is a highly heritable disease and a major public health burden worldwide. MetS diagnosis criteria are met by the simultaneous presence of any three of the following: high triglycerides, low HDL/high LDL cholesterol, insulin resistance, hypertension, and central obesity. These diseases act synergistically in people suffering from MetS and dramatically increase risk of morbidity and mortality due to stroke and cardiovascular disease, as well as certain cancers. Each of these component features is itself a complex disease, as is MetS. As a genetically complex disease, genetic risk factors for MetS are numerous, but not very powerful individually, often requiring specific environmental stressors for the disease to manifest. When taken together, all sequence variants that contribute to MetS disease risk explain only a fraction of the heritable variance, suggesting additional, novel loci have yet to be discovered. In this article, we will give a brief overview on the genetic concepts needed to interpret genome-wide association studies (GWAS) and quantitative trait locus (QTL) data, summarize the state of the field of MetS physiological genomics, and to introduce tools and resources that can be used by the physiologist to integrate genomics into their own research on MetS and any of its component features. There is a wealth of phenotypic and molecular data in animal models and humans that can be leveraged as outlined in this article. Integrating these multi-omic QTL data for complex diseases such as MetS provides a means to unravel the pathways and mechanisms leading to complex disease and promise for novel treatments. © 2022 American Physiological Society. Compr Physiol 12:1-40, 2022.
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Affiliation(s)
- Karen C Clark
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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24
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Iglesias-Carres L, Neilson AP. Utilizing preclinical models of genetic diversity to improve translation of phytochemical activities from rodents to humans and inform personalized nutrition. Food Funct 2021; 12:11077-11105. [PMID: 34672309 DOI: 10.1039/d1fo02782d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mouse models are an essential tool in different areas of research, including nutrition and phytochemical research. Traditional inbred mouse models have allowed the discovery of therapeutical targets and mechanisms of action and expanded our knowledge of health and disease. However, these models lack the genetic variability typically found in human populations, which hinders the translatability of the results found in mice to humans. The development of genetically diverse mouse models, such as the collaborative cross (CC) or the diversity outbred (DO) models, has been a useful tool to overcome this obstacle in many fields, such as cancer, immunology and toxicology. However, these tools have not yet been widely adopted in the field of phytochemical research. As demonstrated in other disciplines, use of CC and DO models has the potential to provide invaluable insights for translation of phytochemicals from rodents to humans, which are desperately needed given the challenges and numerous failed clinical trials in this field. These models may prove informative for personalized use of phytochemicals in humans, including: predicting interindividual variability in phytochemical bioavailability and efficacy, identifying genetic loci or genes governing response to phytochemicals, identifying phytochemical mechanisms of action and therapeutic targets, and understanding the impact of genetic variability on individual response to phytochemicals. Such insights would prove invaluable for personalized implementation of phytochemicals in humans. This review will focus on the current work performed with genetically diverse mouse populations, and the research opportunities and advantages that these models can offer to phytochemical research.
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Affiliation(s)
- Lisard Iglesias-Carres
- Plants for Human Health Institute, Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Kannapolis, NC, USA.
| | - Andrew P Neilson
- Plants for Human Health Institute, Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Kannapolis, NC, USA.
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25
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The Cocaine and Oxycodone Biobanks, Two Repositories from Genetically Diverse and Behaviorally Characterized Rats for the Study of Addiction. eNeuro 2021; 8:ENEURO.0033-21.2021. [PMID: 33875455 PMCID: PMC8213442 DOI: 10.1523/eneuro.0033-21.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 11/21/2022] Open
Abstract
The rat oxycodone and cocaine biobanks contain samples that vary by genotypes (by using genetically diverse genotyped HS rats), phenotypes (by measuring addiction-like behaviors in an advanced SA model), timepoints (samples are collected longitudinally before, during, and after SA, and terminally at three different timepoints in the addiction cycle: intoxication, withdrawal, and abstinence or without exposure to drugs through age-matched naive rats), samples collected (organs, cells, biofluids, feces), preservation (paraformaldehyde-fixed, snap-frozen, or cryopreserved) and application (proteomics, transcriptomics, microbiomics, metabolomics, epigenetics, anatomy, circuitry analysis, biomarker discovery, etc.Substance use disorders (SUDs) are pervasive in our society and have substantial personal and socioeconomical costs. A critical hurdle in identifying biomarkers and novel targets for medication development is the lack of resources for obtaining biological samples with a detailed behavioral characterization of SUD. Moreover, it is nearly impossible to find longitudinal samples. As part of two ongoing large-scale behavioral genetic studies in heterogeneous stock (HS) rats, we have created two preclinical biobanks using well-validated long access (LgA) models of intravenous cocaine and oxycodone self-administration (SA) and comprehensive characterization of addiction-related behaviors. The genetic diversity in HS rats mimics diversity in the human population and includes individuals that are vulnerable or resilient to compulsive-like responding for cocaine or oxycodone. Longitudinal samples are collected throughout the experiment, before exposure to the drug, during intoxication, acute withdrawal, and protracted abstinence, and include naive, age-matched controls. Samples include, but are not limited to, blood plasma, feces and urine, whole brains, brain slices and punches, kidney, liver, spleen, ovary, testis, and adrenal glands. Three preservation methods (fixed in formaldehyde, snap-frozen, or cryopreserved) are used to facilitate diverse downstream applications such as proteomics, metabolomics, transcriptomics, epigenomics, microbiomics, neuroanatomy, biomarker discovery, and other cellular and molecular approaches. To date, >20,000 samples have been collected from over 1000 unique animals and made available free of charge to non-profit institutions through https://www.cocainebiobank.org/ and https://www.oxycodonebiobank.org/.
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26
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Wagner VA, Clark KC, Carrillo-Sáenz L, Holl KA, Velez-Bermudez M, Simonsen D, Grobe JL, Wang K, Thurman A, Solberg Woods LC, Lehmler HJ, Kwitek AE. Bisphenol F Exposure in Adolescent Heterogeneous Stock Rats Affects Growth and Adiposity. Toxicol Sci 2021; 181:246-261. [PMID: 33755180 PMCID: PMC8163043 DOI: 10.1093/toxsci/kfab035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Bisphenol F (BPF) is increasingly substituting bisphenol A in manufacturing polycarbonates and consumer products. The cardiometabolic effects of BPF in either humans or model organisms are not clear, and no studies to date have investigated the role of genetic background on susceptibility to BPF-induced cardiometabolic traits. The primary goal of this project was to determine if BPF exposure influences growth and adiposity in male N:NIH heterogeneous stock (HS) rats, a genetically heterogeneous population. Littermate pairs of male HS rats were randomly exposed to either vehicle (0.1% ethanol) or 1.125 µg/ml BPF in 0.1% ethanol for 5 weeks in drinking water starting at 3 weeks-of-age. Water consumption and body weight was measured weekly, body composition was determined using nuclear magnetic resonance, urine and feces were collected in metabolic cages, and blood and tissues were collected at the end of the study. BPF-exposed rats showed significantly increased body growth and abdominal adiposity, risk factors for cardiometabolic disease. Urine output was increased in BPF-exposed rats, driving a trend in increased creatinine clearance. We also report the first relationship between a bisphenol metabolizing enzyme and a bisphenol-induced phenotype. Preliminary heritability estimates of significant phenotypes suggest that BPF exposure may alter trait variation. These findings support BPF exposure as a cardiometabolic disease risk factor and indicate that the HS rat will be a useful model for dissecting gene by BPF interactions on metabolic health.
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Affiliation(s)
- Valerie A Wagner
- Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Karen C Clark
- Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Leslie Carrillo-Sáenz
- Division of Endocrinology, Diabetes and Metabolism and Department of Physiology and Biophysics, University of Illinois at Chicago College of Medicine, Chicago, Illinois 60612, USA
| | - Katie A Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Miriam Velez-Bermudez
- Department of Psychological & Brain Sciences, University of Iowa, Iowa City, Iowa 52242, USA
| | - Derek Simonsen
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa 52242, USA
| | - Justin L Grobe
- Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew Thurman
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa 52242, USA
| | - Anne E Kwitek
- Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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27
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Converging vulnerability factors for compulsive food and drug use. Neuropharmacology 2021; 196:108556. [PMID: 33862029 DOI: 10.1016/j.neuropharm.2021.108556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/29/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
Highly palatable foods and substance of abuse have intersecting neurobiological, metabolic and behavioral effects relevant for understanding vulnerability to conditions related to food (e.g., obesity, binge eating disorder) and drug (e.g., substance use disorder) misuse. Here, we review data from animal models, clinical populations and epidemiological evidence in behavioral, genetic, pathophysiologic and therapeutic domains. Results suggest that consumption of highly palatable food and drugs of abuse both impact and conversely are regulated by metabolic hormones and metabolic status. Palatable foods high in fat and/or sugar can elicit adaptation in brain reward and withdrawal circuitry akin to substances of abuse. Intake of or withdrawal from palatable food can impact behavioral sensitivity to drugs of abuse and vice versa. A robust literature suggests common substrates and roles for negative reinforcement, negative affect, negative urgency, and impulse control deficits, with both highly palatable foods and substances of abuse. Candidate genetic risk loci shared by obesity and alcohol use disorders have been identified in molecules classically associated with both metabolic and motivational functions. Finally, certain drugs may have overlapping therapeutic potential to treat obesity, diabetes, binge-related eating disorders and substance use disorders. Taken together, data are consistent with the hypotheses that compulsive food and substance use share overlapping, interacting substrates at neurobiological and metabolic levels and that motivated behavior associated with feeding or substance use might constitute vulnerability factors for one another. This article is part of the special issue on 'Vulnerabilities to Substance Abuse'.
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Tarbeeva S, Lyamtseva E, Lisitsa A, Kozlova A, Ponomarenko E, Ilgisonis E. ScanBious: Survey for Obesity Genes Using PubMed Abstracts and DisGeNET. J Pers Med 2021; 11:246. [PMID: 33805313 PMCID: PMC8065449 DOI: 10.3390/jpm11040246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/29/2022] Open
Abstract
We used automatic text-mining of PubMed abstracts of papers related to obesity, with the aim of revealing that the information used in abstracts reflects the current understanding and key concepts of this widely explored problem. We compared expert data from DisGeNET to the results of an automated MeSH (Medical Subject Heading) search, which was performed by the ScanBious web tool. The analysis provided an overview of the obesity field, highlighting major trends such as physiological conditions, age, and diet, as well as key well-studied genes, such as adiponectin and its receptor. By intersecting the DisGeNET knowledge with the ScanBious results, we deciphered four clusters of obesity-related genes. An initial set of 100+ thousand abstracts and 622 genes was reduced to 19 genes, distributed among just a few groups: heredity, inflammation, intercellular signaling, and cancer. Rapid profiling of articles could drive personalized medicine: if the disease signs of a particular person were superimposed on a general network, then it would be possible to understand which are non-specific (observed in cohorts and, therefore, most likely have known treatment solutions) and which are less investigated, and probably represent a personalized case.
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Affiliation(s)
- Svetlana Tarbeeva
- International School “Medicine of the Future”, Sechenov University, 119991 Moscow, Russia
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (A.L.); (A.K.); (E.P.); (E.I.)
| | | | - Andrey Lisitsa
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (A.L.); (A.K.); (E.P.); (E.I.)
| | - Anna Kozlova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (A.L.); (A.K.); (E.P.); (E.I.)
- Laboratory of Molecular Design and Synthesis, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (A.L.); (A.K.); (E.P.); (E.I.)
| | - Ekaterina Ilgisonis
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (A.L.); (A.K.); (E.P.); (E.I.)
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Deal A, Cooper N, Kirse HA, Uneri A, Raab-Graham K, Weiner JL, Solberg Woods LC. Early life stress induces hyperactivity but not increased anxiety-like behavior or ethanol drinking in outbred heterogeneous stock rats. Alcohol 2021; 91:41-51. [PMID: 33321179 PMCID: PMC8767639 DOI: 10.1016/j.alcohol.2020.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/10/2020] [Accepted: 11/30/2020] [Indexed: 01/26/2023]
Abstract
Early life stress is known to impact vulnerability to psychopathological disorders in adulthood, including anxiety and alcohol use disorder (AUD), but the mechanisms underlying susceptibility to these outcomes are not fully understood. In the current study, we used adolescent social isolation (ASI) to determine whether Heterogeneous Stock (HS) rats, an outbred model used for genetic fine-mapping, could be used to study the genetics contributing to ASI-induced anxiety- and AUD-like behavior. We isolated (ASI) or group-housed (adolescent group-housed; AGH) 64 male HS rats at 4 weeks of age. After 5 weeks in these housing conditions, multiple anxiety and coping/despair-like behaviors were measured. All rats were then individually housed and assessed for voluntary ethanol self-administration. At euthanasia, synaptoneurosomes were isolated from a subset of brains to examine the expression of two proteins associated with alcohol drinking-related behaviors, GluA1 and SK2, in the dorsal (dHC) and ventral hippocampus (vHC). We found that ASI increased hyperactivity in the open field test relative to AGH, with no changes in other anxiety-like behaviors. Surprisingly, ASI rats demonstrated decreased immobility and increased climbing in the forced swim test relative to AGH. In contrast to prior studies by us and others, we found no difference in self-administration of 20% ethanol, with decreased ethanol self-administration in ASI relative to AGH rats at higher ethanol concentrations. Furthermore, while ASI in Long-Evans rats resulted in decreased SK2 expression in vHC synaptosomes, no differences were seen in vHC synaptosomes for SK2 or GluA1 in HS rats. These results demonstrate that HS rats are protected against many of the negative effects previously seen in response to ASI, namely anxiety-like behavior and increased ethanol self-administration. The current work suggests that a lack of change in SK2 and GluA1 expression levels in the vHC may play a role in conferring this protection.
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Affiliation(s)
- Aaron Deal
- Department of Internal Medicine, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, United States.
| | - Nicholas Cooper
- Department of Internal Medicine, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, United States.
| | - Haley Ann Kirse
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, United States.
| | - Ayse Uneri
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, United States.
| | - Kimberly Raab-Graham
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, United States.
| | - Jeffrey L Weiner
- Department of Physiology and Pharmacology, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, United States.
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, United States.
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Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal AW, Kim Y, Kyle PB, Attipoe E, Johnson AC, Uhl KL, Sirpilla OL, Jahanbakhsh S, Robinson M, Levy S, Valdar W, Garrett MR, Solberg Woods LC. Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model. Sci Rep 2021; 11:2071. [PMID: 33483609 PMCID: PMC7822875 DOI: 10.1038/s41598-021-81550-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/05/2021] [Indexed: 01/29/2023] Open
Abstract
Chronic kidney disease (CKD), which can ultimately progress to kidney failure, is influenced by genetics and the environment. Genes identified in human genome wide association studies (GWAS) explain only a small proportion of the heritable variation and lack functional validation, indicating the need for additional model systems. Outbred heterogeneous stock (HS) rats have been used for genetic fine-mapping of complex traits, but have not previously been used for CKD traits. We performed GWAS for urinary protein excretion (UPE) and CKD related serum biochemistries in 245 male HS rats. Quantitative trait loci (QTL) were identified using a linear mixed effect model that tested for association with imputed genotypes. Candidate genes were identified using bioinformatics tools and targeted RNAseq followed by testing in a novel in vitro model of human tubule, hypoxia-induced damage. We identified two QTL for UPE and five for serum biochemistries. Protein modeling identified a missense variant within Septin 8 (Sept8) as a candidate for UPE. Sept8/SEPTIN8 expression increased in HS rats with elevated UPE and tubulointerstitial injury and in the in vitro hypoxia model. SEPTIN8 is detected within proximal tubule cells in human kidney samples and localizes with acetyl-alpha tubulin in the culture system. After hypoxia, SEPTIN8 staining becomes diffuse and appears to relocalize with actin. These data suggest a role of SEPTIN8 in cellular organization and structure in response to environmental stress. This study demonstrates that integration of a rat genetic model with an environmentally induced tubule damage system identifies Sept8/SEPTIN8 and informs novel aspects of the complex gene by environmental interactions contributing to CKD risk.
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Affiliation(s)
| | - Jeremy W Prokop
- HudsonAlpha Institute, Huntsville, AL, USA
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Hong He
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Katie Holl
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - John Littrell
- Departments of Pediatrics and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aaron W Deal
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yunjung Kim
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick B Kyle
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Esinam Attipoe
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Ashley C Johnson
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Katie L Uhl
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Olivia L Sirpilla
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | - Seyedehameneh Jahanbakhsh
- Department of Pediatrics and Human Development, Department of Pharmacology, Michigan State University, Grand Rapids, MI, USA
| | | | - Shawn Levy
- HudsonAlpha Institute, Huntsville, AL, USA
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael R Garrett
- Department of Pharmacology, Medicine (Nephrology), Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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Zinski AL, Carrion S, Michal JJ, Gartstein MA, Quock RM, Davis JF, Jiang Z. Genome-to-phenome research in rats: progress and perspectives. Int J Biol Sci 2021; 17:119-133. [PMID: 33390838 PMCID: PMC7757052 DOI: 10.7150/ijbs.51628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/06/2020] [Indexed: 01/07/2023] Open
Abstract
Because of their relatively short lifespan (<4 years), rats have become the second most used model organism to study health and diseases in humans who may live for up to 120 years. First-, second- and third-generation sequencing technologies and platforms have produced increasingly greater sequencing depth and accurate reads, leading to significant advancements in the rat genome assembly during the last 20 years. In fact, whole genome sequencing (WGS) of 47 strains have been completed. This has led to the discovery of genome variants in rats, which have been widely used to detect quantitative trait loci underlying complex phenotypes based on gene, haplotype, and sweep association analyses. DNA variants can also reveal strain, chromosome and gene functional evolutions. In parallel, phenome programs have advanced significantly in rats during the last 15 years and more than 10 databases host genome and/or phenome information. In order to discover the bridges between genome and phenome, systems genetics and integrative genomics approaches have been developed. On the other hand, multiple level information transfers from genome to phenome are executed by differential usage of alternative transcriptional start (ATS) and polyadenylation (APA) sites per gene. We used our own experiments to demonstrate how alternative transcriptome analysis can lead to enrichment of phenome-related causal pathways in rats. Development of advanced genome-to-phenome assays will certainly enhance rats as models for human biomedical research.
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Affiliation(s)
- Amy L. Zinski
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
| | - Shane Carrion
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
| | - Maria A. Gartstein
- Department of Psychology, Washington State University, Pullman, WA 99164-4820
| | - Raymond M. Quock
- Department of Psychology, Washington State University, Pullman, WA 99164-4820
| | - Jon F. Davis
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164-7620
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-7620
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Parker CC, Lusk R, Saba LM. Alcohol Sensitivity as an Endophenotype of Alcohol Use Disorder: Exploring Its Translational Utility between Rodents and Humans. Brain Sci 2020; 10:E725. [PMID: 33066036 PMCID: PMC7600833 DOI: 10.3390/brainsci10100725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/21/2022] Open
Abstract
Alcohol use disorder (AUD) is a complex, chronic, relapsing disorder with multiple interacting genetic and environmental influences. Numerous studies have verified the influence of genetics on AUD, yet the underlying biological pathways remain unknown. One strategy to interrogate complex diseases is the use of endophenotypes, which deconstruct current diagnostic categories into component traits that may be more amenable to genetic research. In this review, we explore how an endophenotype such as sensitivity to alcohol can be used in conjunction with rodent models to provide mechanistic insights into AUD. We evaluate three alcohol sensitivity endophenotypes (stimulation, intoxication, and aversion) for their translatability across human and rodent research by examining the underlying neurobiology and its relationship to consumption and AUD. We show examples in which results gleaned from rodents are successfully integrated with information from human studies to gain insight in the genetic underpinnings of AUD and AUD-related endophenotypes. Finally, we identify areas for future translational research that could greatly expand our knowledge of the biological and molecular aspects of the transition to AUD with the broad hope of finding better ways to treat this devastating disorder.
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Affiliation(s)
- Clarissa C. Parker
- Department of Psychology and Program in Neuroscience, Middlebury College, Middlebury, VT 05753, USA
| | - Ryan Lusk
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
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33
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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: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [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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Schumann T, König J, Henke C, Willmes DM, Bornstein SR, Jordan J, Fromm MF, Birkenfeld AL. Solute Carrier Transporters as Potential Targets for the Treatment of Metabolic Disease. Pharmacol Rev 2020; 72:343-379. [PMID: 31882442 DOI: 10.1124/pr.118.015735] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily comprises more than 400 transport proteins mediating the influx and efflux of substances such as ions, nucleotides, and sugars across biological membranes. Over 80 SLC transporters have been linked to human diseases, including obesity and type 2 diabetes (T2D). This observation highlights the importance of SLCs for human (patho)physiology. Yet, only a small number of SLC proteins are validated drug targets. The most recent drug class approved for the treatment of T2D targets sodium-glucose cotransporter 2, product of the SLC5A2 gene. There is great interest in identifying other SLC transporters as potential targets for the treatment of metabolic diseases. Finding better treatments will prove essential in future years, given the enormous personal and socioeconomic burden posed by more than 500 million patients with T2D by 2040 worldwide. In this review, we summarize the evidence for SLC transporters as target structures in metabolic disease. To this end, we identified SLC13A5/sodium-coupled citrate transporter, and recent proof-of-concept studies confirm its therapeutic potential in T2D and nonalcoholic fatty liver disease. Further SLC transporters were linked in multiple genome-wide association studies to T2D or related metabolic disorders. In addition to presenting better-characterized potential therapeutic targets, we discuss the likely unnoticed link between other SLC transporters and metabolic disease. Recognition of their potential may promote research on these proteins for future medical management of human metabolic diseases such as obesity, fatty liver disease, and T2D. SIGNIFICANCE STATEMENT: Given the fact that the prevalence of human metabolic diseases such as obesity and type 2 diabetes has dramatically risen, pharmacological intervention will be a key future approach to managing their burden and reducing mortality. In this review, we present the evidence for solute carrier (SLC) genes associated with human metabolic diseases and discuss the potential of SLC transporters as therapeutic target structures.
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Affiliation(s)
- Tina Schumann
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
| | - Jörg König
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
| | - Christine Henke
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
| | - Diana M Willmes
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
| | - Stefan R Bornstein
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
| | - Jens Jordan
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
| | - Martin F Fromm
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
| | - Andreas L Birkenfeld
- Section of Metabolic and Vascular Medicine, Medical Clinic III, Dresden University School of Medicine (T.S., C.H., D.M.W., S.R.B.), and Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine (T.S., C.H., D.M.W.), Technische Universität Dresden, Dresden, Germany; Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany (T.S., C.H., D.M.W., A.L.B.); Clinical Pharmacology and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany (J.K., M.F.F.); Institute for Aerospace Medicine, German Aerospace Center and Chair for Aerospace Medicine, University of Cologne, Cologne, Germany (J.J.); Diabetes and Nutritional Sciences, King's College London, London, United Kingdom (S.R.B., A.L.B.); Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tübingen, Tübingen, Germany (A.L.B.); and Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, Eberhard Karls University Tübingen, Tübingen, Germany (A.L.B.)
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Deal AW, Seshie O, Lenzo A, Cooper N, Ozimek N, Solberg Woods LC. High-fat diet negatively impacts both metabolic and behavioral health in outbred heterogeneous stock rats. Physiol Genomics 2020; 52:379-390. [PMID: 32687430 PMCID: PMC7509248 DOI: 10.1152/physiolgenomics.00018.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Obesity is influenced by genetics and diet and has wide ranging comorbidities, including anxiety and depressive disorders. Outbred heterogeneous stock (HS) rats are used for fine-genetic mapping of complex traits and may be useful for understanding gene by diet interactions. In this study, HS rats were fed diets containing 60% kcal from fat (high-fat diet, HFD) or 10% kcal from fat (low-fat diet, LFD) and tested for metabolic (study 1) and behavioral (study 2) outcomes. In study 1, we measured glucose tolerance, fasting glucose and insulin, fat pad weights and despair-like behavior in the forced swim test (FST). In study 2, we assessed anxiety-like (elevated plus maze, EPM; open field test, OFT) and despair-like/coping (splash test, SpT; and FST) behaviors. Body weight and food intake were measured weekly in both studies. We found negative effects of HFD on metabolic outcomes, including increased body weight and fat pad weights, decreased glucose tolerance, and increased fasting insulin. We also found negative effects of HFD on despair-like/coping and anxiety-like behaviors. These include increased immobility in the FST, decreased open arm time in the EPM, and increased movement and rest episodes and decreased rearing in the OFT. The diet-induced changes in EPM and OFT were independent of overall locomotion. Additionally, diet-induced changes in OFT behaviors were independent of adiposity, while adiposity was a confounding factor for EPM and FST behavior. This work establishes the HS as a model to study gene by diet interactions affecting metabolic and behavioral health.
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Affiliation(s)
- Aaron W Deal
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Osborne Seshie
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Anne Lenzo
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Nicholas Cooper
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Noelle Ozimek
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
| | - Leah C Solberg Woods
- Wake Forest School of Medicine, Department of Internal Medicine, Winston Salem, North Carolina
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36
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Sazzini M, Abondio P, Sarno S, Gnecchi-Ruscone GA, Ragno M, Giuliani C, De Fanti S, Ojeda-Granados C, Boattini A, Marquis J, Valsesia A, Carayol J, Raymond F, Pirazzini C, Marasco E, Ferrarini A, Xumerle L, Collino S, Mari D, Arosio B, Monti D, Passarino G, D'Aquila P, Pettener D, Luiselli D, Castellani G, Delledonne M, Descombes P, Franceschi C, Garagnani P. Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans. BMC Biol 2020; 18:51. [PMID: 32438927 PMCID: PMC7243322 DOI: 10.1186/s12915-020-00778-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/01/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes. RESULTS We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition. CONCLUSIONS We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.
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Affiliation(s)
- Marco Sazzini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.
| | - Paolo Abondio
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Matteo Ragno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Claudia Ojeda-Granados
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara "Fray Antonio Alcalde" and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Alessio Boattini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Julien Marquis
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
- Current Address: Lausanne Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland
| | - Armand Valsesia
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Jerome Carayol
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Chiara Pirazzini
- IRCCS Bologna Institute of Neurological Sciences, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Alberto Ferrarini
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
- Current Address: Menarini Silicon Biosystems SpA, Castel Maggiore, Bologna, Italy
| | - Luciano Xumerle
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Daniela Mari
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Beatrice Arosio
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Davide Pettener
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Gastone Castellani
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Massimo Delledonne
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Claudio Franceschi
- Department of Applied Mathematics, Institute of Information Technology, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Paolo Garagnani
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy.
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden.
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37
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Garrett MR, Korstanje R. Using Genetic and Species Diversity to Tackle Kidney Disease. Trends Genet 2020; 36:499-509. [PMID: 32362446 DOI: 10.1016/j.tig.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/26/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
Abstract
Progress in the identification of causal genes and understanding of the mechanism underlying kidney disease is hindered by the almost exclusive use of a few animal models with restrictive monogenic backgrounds that may be more resistant to kidney disease compared with humans and, therefore, poor models. Exploring the large genetic diversity in classical animal models, such as mice and rats, and leveraging species diversity will allow us to use the genetic advantages of zebrafish, Drosophila, and other species, to develop both new animal models that are more relevant to the study of human kidney disease and potential therapies.
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Affiliation(s)
- Michael R Garrett
- Department of Pharmacology, University of Mississippi Medical Center, Jackson, MS, USA; Department of Medicine (Nephrology), University of Mississippi Medical Center, Jackson, MS, USA; Department of Pediatrics (Genetics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Ron Korstanje
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, ME, USA; Mount Desert Island Biological Laboratory, Bar Harbor, Maine, ME, USA.
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38
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Keele GR, Quach BC, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W, Rusyn I, Furey TS. Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. PLoS Genet 2020; 16:e1008537. [PMID: 31961859 PMCID: PMC7010298 DOI: 10.1371/journal.pgen.1008537] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 02/10/2020] [Accepted: 11/23/2019] [Indexed: 01/08/2023] Open
Abstract
Gene transcription profiles across tissues are largely defined by the activity of regulatory elements, most of which correspond to regions of accessible chromatin. Regulatory element activity is in turn modulated by genetic variation, resulting in variable transcription rates across individuals. The interplay of these factors, however, is poorly understood. Here we characterize expression and chromatin state dynamics across three tissues-liver, lung, and kidney-in 47 strains of the Collaborative Cross (CC) mouse population, examining the regulation of these dynamics by expression quantitative trait loci (eQTL) and chromatin QTL (cQTL). QTL whose allelic effects were consistent across tissues were detected for 1,101 genes and 133 chromatin regions. Also detected were eQTL and cQTL whose allelic effects differed across tissues, including local-eQTL for Pik3c2g detected in all three tissues but with distinct allelic effects. Leveraging overlapping measurements of gene expression and chromatin accessibility on the same mice from multiple tissues, we used mediation analysis to identify chromatin and gene expression intermediates of eQTL effects. Based on QTL and mediation analyses over multiple tissues, we propose a causal model for the distal genetic regulation of Akr1e1, a gene involved in glycogen metabolism, through the zinc finger transcription factor Zfp985 and chromatin intermediates. This analysis demonstrates the complexity of transcriptional and chromatin dynamics and their regulation over multiple tissues, as well as the value of the CC and related genetic resource populations for identifying specific regulatory mechanisms within cells and tissues.
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Affiliation(s)
- Gregory R. Keele
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Bryan C. Quach
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Center for Omics Discovery and Epidemiology, Research Triangle Institute (RTI) International, Research Triangle Park, North Carolina, United States of America
| | - Jennifer W. Israel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Grace A. Chappell
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Lauren Lewis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Alexias Safi
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Paul Cotney
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gregory E. Crawford
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Terrence S. Furey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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39
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Showmaker KC, Cobb MB, Johnson AC, Yang W, Garrett MR. Whole genome sequencing and novel candidate genes for CAKUT and altered nephrogenesis in the HSRA rat. Physiol Genomics 2020; 52:56-70. [PMID: 31841396 PMCID: PMC6985787 DOI: 10.1152/physiolgenomics.00112.2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022] Open
Abstract
The HSRA rat is a model of congenital abnormalities of the kidney and urogenital tract (CAKUT). Our laboratory has used this model to investigate the role of nephron number (functional unit of the kidney) in susceptibility to develop kidney disease as 50-75% offspring are born with a single kidney (HSRA-S), while 25-50% are born with two kidneys (HSRA-C). HSRA-S rats develop increased kidney injury and hypertension with age compared with nephrectomized two-kidney animals (HSRA-UNX), suggesting that even slight differences in nephron number can be an important driver in decline in kidney function. The HSRA rat was selected and inbred from a family of outbred heterogeneous stock (NIH-HS) rats that exhibited a high incidence of CAKUT. The HS model was originally developed from eight inbred strains (ACI, BN, BUF, F344, M520, MR, WKY, and WN). The genetic make-up of the HSRA is therefore a mosaic of these eight inbred strains. Interestingly, the ACI progenitor of the HS model exhibits CAKUT in 10-15% of offspring with the genetic cause being attributed to the presence of a long-term repeat (LTR) within exon 1 of the c-Kit gene. Our hypothesis is that the HSRA and ACI share this common genetic cause, but other alleles in the HSRA genome contribute to the increased penetrance of CAKUT (75% HSRA vs. 15% in ACI). To facilitate genetic studies and better characterize the model, we sequenced the whole genome of the HSRA to a depth of ~50×. A genome-wide variant analysis of high-impact variants identified a number of novel genes that could be linked to CAKUT in the HSRA model. In summary, the identification of new genes/modifiers that lead to CAKUT/loss of one kidney in the HSRA model will provide greater insight into association between kidney development and susceptibility to develop cardiovascular disease later in life.
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Affiliation(s)
- Kurt C Showmaker
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Meredith B Cobb
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Ashley C Johnson
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Wenyu Yang
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Michael R Garrett
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, Mississippi
- Department of Medicine (Nephrology), University of Mississippi Medical Center, Jackson, Mississippi
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40
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Abstract
In this chapter we will review both the rationale and experimental design for using Heterogeneous Stock (HS) populations for fine-mapping of complex traits in mice and rats. We define an HS as an outbred population derived from an intercross between two or more inbred strains. HS have been used to perform genome-wide association studies (GWAS) for multiple behavioral, physiological, and gene expression traits. GWAS using HS require four key steps, which we review: selection of an appropriate HS population, phenotyping, genotyping, and statistical analysis. We provide advice on the selection of an HS, comment on key issues related to phenotyping, discuss genotyping methods relevant to these populations, and describe statistical genetic analyses that are applicable to genetic analyses that use HS.
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41
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Rapp JP, Joe B. Dissecting Epistatic QTL for Blood Pressure in Rats: Congenic Strains versus Heterogeneous Stocks, a Reality Check. Compr Physiol 2019; 9:1305-1337. [PMID: 31688958 DOI: 10.1002/cphy.c180038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Advances in molecular genetics have provided well-defined physical genetic maps and large numbers of genetic markers for both model organisms and humans. It is now possible to gain a fundamental understanding of the genetic architecture underlying quantitative traits, of which blood pressure (BP) is an important example. This review emphasizes analytical techniques and results obtained using the Dahl salt-sensitive (S) rat as a model of hypertension by presenting results in detail for three specific chromosomal regions harboring genetic elements of increasing complexity controlling BP. These results highlight the critical importance of genetic interactions (epistasis) on BP at all levels of structure, intragenic, intergenic, intrachromosomal, interchromosomal, and across whole genomes. In two of the three examples presented, specific DNA structural variations leading to biochemical, physiological, and pathological mechanisms are well defined. This proves the usefulness of the techniques involving interval mapping followed by substitution mapping using congenic strains. These classic techniques are compared to newer approaches using sophisticated statistical analysis on various segregating or outbred model-organism populations, which in some cases are uniquely useful in demonstrating the existence of higher-order interactions. It is speculated that hypertension as an outlier quantitative phenotype is dependent on higher-order genetic interactions. The obstacle to the identification of genetic elements and the biochemical/physiological mechanisms involved in higher-order interactions is not theoretical or technical but the lack of future resources to finish the job of identifying the individual genetic elements underlying the quantitative trait loci for BP and ascertaining their molecular functions. © 2019 American Physiological Society. Compr Physiol 9:1305-1337, 2019.
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Affiliation(s)
- John P Rapp
- Physiological Genomics Laboratory, Department of Physiology and Pharmacology, Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Bina Joe
- Physiological Genomics Laboratory, Department of Physiology and Pharmacology, Center for Hypertension and Precision Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
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42
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Abstract
The Collaborative Cross (CC) is a mouse genetic reference population whose range of applications includes quantitative trait loci (QTL) mapping. The design of a CC QTL mapping study involves multiple decisions, including which and how many strains to use, and how many replicates per strain to phenotype, all viewed within the context of hypothesized QTL architecture. Until now, these decisions have been informed largely by early power analyses that were based on simulated, hypothetical CC genomes. Now that more than 50 CC strains are available and more than 70 CC genomes have been observed, it is possible to characterize power based on realized CC genomes. We report power analyses from extensive simulations and examine several key considerations: 1) the number of strains and biological replicates, 2) the QTL effect size, 3) the presence of population structure, and 4) the distribution of functionally distinct alleles among the founder strains at the QTL. We also provide general power estimates to aide in the design of future experiments. All analyses were conducted with our R package, SPARCC (Simulated Power Analysis in the Realized Collaborative Cross), developed for performing either large scale power analyses or those tailored to particular CC experiments.
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Ramdas S, Ozel AB, Treutelaar MK, Holl K, Mandel M, Woods LCS, Li JZ. Extended regions of suspected mis-assembly in the rat reference genome. Sci Data 2019; 6:39. [PMID: 31015470 PMCID: PMC6478900 DOI: 10.1038/s41597-019-0041-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/22/2019] [Indexed: 11/09/2022] Open
Abstract
We performed whole-genome sequencing for eight inbred rat strains commonly used in genetic mapping studies. They are the founders of the NIH heterogeneous stock (HS) outbred colony. We provide their sequences and variant calls to the rat genomics community. When analyzing the variant calls we identified regions with unusually high levels of heterozygosity. These regions are consistent across the eight inbred strains, including Brown Norway, which is the basis of the rat reference genome. These regions show higher read depths than other regions in the genome and contain higher rates of apparent tri-allelic variant sites. The evidence suggests that these regions may correspond to duplicated segments that were incorrectly overlaid as a single segment in the reference genome. We provide masks for these regions of suspected mis-assembly as a resource for the community to flag potentially false interpretations of mapping or functional results.
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Affiliation(s)
- Shweta Ramdas
- Program in Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Mary K Treutelaar
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Katie Holl
- Department of Pediatrics, Human and Molecular Genetics Center and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Myrna Mandel
- National Institutes of Health, Bethesda, Maryland, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA. .,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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45
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Abstract
Metabolic syndrome is a complex disorder that comprises several other complex disorders, including obesity, hypertension, dyslipidemia, and diabetes. There are several rat models that encompass component features of MetS. Some models are inbred strains selected for one or more traits underlying MetS; others are population models with genetic risk for MetS traits, are induced by environmental stressors such as diet, are spontaneous monogenic mutant models, or are congenic strains derived from a combination of these models. Together they can be studied to identify the genetic and physiological underpinnings of MetS to identify candidate genes or mechanisms for study in human MetS subjects.
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Affiliation(s)
- Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
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46
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Social and anxiety-like behaviors contribute to nicotine self-administration in adolescent outbred rats. Sci Rep 2018; 8:18069. [PMID: 30584246 PMCID: PMC6305389 DOI: 10.1038/s41598-018-36263-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 11/19/2018] [Indexed: 01/06/2023] Open
Abstract
Both emotional and social traits interact with genetic factors to influence smoking behavior. We previously established a socially acquired nicotine intravenous self-administration model where social learning of a nicotine-associated odor cue reversed conditioned flavor aversion and promoted nicotine intake. In this study, we first phenotyped ~800 adolescent heterogeneous stock rats in open field, novel object interaction, social interaction, elevated plus maze, and marble burying behaviors. These rats were then phenotyped on socially acquired nicotine self-administration. We found 243 significant correlations between different behavioral tests. Principal component regression analysis found that ~10-20% of the variance in nicotine-related measures, such as intake during the first or the last three fixed-ratio sessions, the progressive ratio session, and reinstatement behavior, can be explained by variations in behavioral traits. Factors corresponding to social behavior and anxiety were among the strongest predictors of nicotine intake and reinstatement of nicotine-seeking behavior. We also found many sex differences in behavioral measures. These data indicated that the genetic diversity of this population, in combination with social behaviour and anxiety, are significant contributors to the divergent nicotine self-administration behavior and indicated a high probability of discovering sex-specific genetic mechanisms for nicotine intake in future genome-wide association studies.
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Andersen MK, Hansen T. Genetics of metabolic traits in Greenlanders: lessons from an isolated population. J Intern Med 2018; 284:464-477. [PMID: 30101502 DOI: 10.1111/joim.12814] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, we describe the extraordinary population of Greenland, which differs from large outbred populations of Europe and Asia, both in terms of population history and living conditions. Many years in isolation, small population size and an extreme environment have shaped the genetic composition of the Greenlandic population. The unique genetic background combined with the transition from a traditional Inuit lifestyle and diet, to a more Westernized lifestyle, has led to an increase in the prevalence of metabolic conditions like obesity, where the prevalence from 1993 to 2010 has increased from 16.4% to 19.4% among men, and from 13.0% to 25.4% among women, type 2 diabetes and cardiovascular diseases. The genetic susceptibility to metabolic conditions has been explored in Greenlanders, as well as other isolated populations, taking advantage of population-genetic properties of these populations. During the last 10 years, these studies have provided examples of loci showing evidence of positive selection, due to adaption to Arctic climate and Inuit diet, including TBC1D4 and FADS/CPT1A, and have facilitated the discovery of several loci associated with metabolic phenotypes. Most recently, the c.2433-1G>A loss-of-function variant in ADCY3 associated with obesity and type 2 diabetes was described. This locus has provided novel biological insights, as it has been shown that reduced ADCY3 function causes obesity through disrupted function in primary cilia. Future studies of isolated populations will likely provide further genetic as well as biological insights.
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Affiliation(s)
- M K Andersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - T Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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He H, Holl K, DeBehnke S, Yeo CT, Hansen P, Gebre AK, Leone-Kabler S, Ruas M, Parks JS, Parrington J, Solberg Woods LC. Tpcn2 knockout mice have improved insulin sensitivity and are protected against high-fat diet-induced weight gain. Physiol Genomics 2018; 50:605-614. [PMID: 29750602 DOI: 10.1152/physiolgenomics.00135.2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Type 2 diabetes is a complex disorder affected by multiple genes and the environment. Our laboratory has shown that in response to a glucose challenge, two-pore channel 2 ( Tpcn2) knockout mice exhibit a decreased insulin response but normal glucose clearance, suggesting they have improved insulin sensitivity compared with wild-type mice. We tested the hypothesis that improved insulin sensitivity in Tpcn2 knockout mice would protect against the negative effects of a high fat diet. Male and female Tpcn2 knockout (KO), heterozygous (Het), and wild-type (WT) mice were fed a low-fat (LF) or high-fat (HF) diet for 24 wk. HF diet significantly increases body weight in WT mice relative to those on the LF diet; this HF diet-induced increase in body weight is blunted in the Het and KO mice. Despite the protection against diet-induced weight gain, however, Tpcn2 KO mice are not protected against HF-diet-induced changes in glucose or insulin area under the curve during glucose tolerance tests in female mice, while HF diet has no significant effect on glucose tolerance in the male mice, regardless of genotype. Glucose disappearance during an insulin tolerance test is augmented in male KO mice, consistent with our previous findings suggesting enhanced insulin sensitivity in these mice. Male KO mice exhibit increased fasting plasma total cholesterol and triglyceride concentrations relative to WT mice on the LF diet, but this difference disappears in HF diet-fed mice where there is increased cholesterol and triglycerides across all genotypes. These data demonstrate that knockout of Tpcn2 may increase insulin action in male, but not female, mice. In addition, both male and female KO mice are protected against diet-induced weight gain, but this protection is likely independent from glucose tolerance, insulin sensitivity, and plasma lipid levels.
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Affiliation(s)
- Hong He
- Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Katie Holl
- Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Sarah DeBehnke
- Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Chay Teng Yeo
- Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Polly Hansen
- Department of Pediatrics, Medical College of Wisconsin , Milwaukee, Wisconsin
| | - Abraham K Gebre
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine , Winston Salem, North Carolina
| | - Sandra Leone-Kabler
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine , Winston Salem, North Carolina
| | - Margarida Ruas
- Department of Pharmacology, University of Oxford , Oxford , United Kingdom
| | - John S Parks
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine , Winston Salem, North Carolina
| | - John Parrington
- Department of Pharmacology, University of Oxford , Oxford , United Kingdom
| | - Leah C Solberg Woods
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine , Winston Salem, North Carolina
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Abstract
An accurate and high-resolution genetic map is critical for mapping complex traits, yet the resolution of the current rat genetic map is far lower than human and mouse, and has not been updated since the original Jensen-Seaman map in 2004. For the first time, we have refined the rat genetic map to sub-centimorgan (cM) resolution (<0.02 cM) by using 95,769 genetic markers and 870 informative meioses from a cohort of 528 heterogeneous stock (HS) rats. Global recombination rates in the revised sex-averaged map (0.66 cM/Mb) did not differ compared to the historical map (0.65 cM/Mb); however, substantial refinement was made to the localization of highly recombinant regions within the revised map. Also for the first time, sex-specific rat genetic maps were generated, which revealed both genomewide and fine-scale variation in recombination rates between male and female rats. Reanalysis of multiple quantitative trait loci (QTL) using the historical and refined rat genetic maps demonstrated marked changes to QTL localization, shape, and effect size. As a resource to the rat research community, we have provided revised centimorgan positions for all physical positions within the rat genome and commonly used genetic markers for trait mapping, including 44,828 SSLP markers and the RATDIV genotyping array. Collectively, this study provides a substantial improvement to the rat genetic map and an unprecedented resource for analysis of complex traits and recombination in the rat.
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