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Chen PB, Chen R, LaPierre N, Chen Z, Mefford J, Marcus E, Heffel MG, Soto DC, Ernst J, Luo C, Flint J. Complementation testing identifies genes mediating effects at quantitative trait loci underlying fear-related behavior. CELL GENOMICS 2024; 4:100545. [PMID: 38697120 PMCID: PMC11099346 DOI: 10.1016/j.xgen.2024.100545] [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: 01/03/2024] [Revised: 02/23/2024] [Accepted: 04/04/2024] [Indexed: 05/04/2024]
Abstract
Knowing the genes involved in quantitative traits provides an entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six quantitative trait loci (QTLs) by quantitative complementation, and identified six genes. Four genes, Lamp, Ptprd, Nptx2, and Sh3gl, have known roles in synapse function; the fifth, Psip1, was not previously implicated in behavior; and the sixth is a long non-coding RNA, 4933413L06Rik, of unknown function. Variation in transcriptome and epigenetic modalities occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results relieve a bottleneck in using genetic mapping of QTLs to uncover biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.
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Affiliation(s)
- Patrick B Chen
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Rachel Chen
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zeyuan Chen
- Department of Computer Science, Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joel Mefford
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emilie Marcus
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Matthew G Heffel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniela C Soto
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jason Ernst
- Department of Computer Science, Samueli School of Engineering, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonathan Flint
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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2
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Ninoyu Y, Friedman RA. The genetic landscape of age-related hearing loss. Trends Genet 2024; 40:228-237. [PMID: 38161109 DOI: 10.1016/j.tig.2023.12.001] [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: 09/16/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Age-related hearing loss (ARHL) is a prevalent concern in the elderly population. Recent genome-wide and phenome-wide association studies (GWASs and PheWASs) have delved into the identification of causative variants and the understanding of pleiotropy, highlighting the polygenic intricacies of this complex condition. While recent large-scale GWASs have pinpointed significant SNPs and risk variants associated with ARHL, the detailed mechanisms, encompassing both genetic and epigenetic modifications, remain to be fully elucidated. This review presents the latest advances in association studies, integrating findings from both human studies and model organisms. By juxtaposing historical perspectives with contemporary genomics, we aim to catalyze innovative research and foster the development of novel therapeutic strategies for ARHL.
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Affiliation(s)
- Yuzuru Ninoyu
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rick A Friedman
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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3
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Yosief RHS, Lone IM, Nachshon A, Himmelbauer H, Gat‐Viks I, Iraqi FA. Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach. Animal Model Exp Med 2024; 7:36-47. [PMID: 38356021 PMCID: PMC10961901 DOI: 10.1002/ame2.12386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/15/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Aspergillus fumigatus (Af) is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic background. The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus (Af) using an RNAseq approach in CC lines and hepatic gene expression. METHODS We studied 31 male mice from 25 CC lines at 8 weeks old; the mice were infected with Af. Liver tissues were extracted from these mice 5 days post-infection, and next-generation RNA-sequencing (RNAseq) was performed. The GENE-E analysis platform was used to generate a clustered heat map matrix. RESULTS Significant variation in body weight changes between CC lines was observed. Hepatic gene expression revealed 12 top prioritized candidate genes differentially expressed in resistant versus susceptible mice based on body weight changes. Interestingly, three candidate genes are located within genomic intervals of the previously mapped quantitative trait loci (QTL), including Gm16270 and Stox1 on chromosome 10 and Gm11033 on chromosome 8. CONCLUSIONS Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af. As a next step, eQTL analysis will be performed for our RNA-Seq data. Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.
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Affiliation(s)
- Roa'a H. S. Yosief
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
| | - Iqbal M. Lone
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
| | - Aharon Nachshon
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 181190 ViennaAustria
| | - Irit Gat‐Viks
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel‐Aviv UniversityTel‐AvivIsrael
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4
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Chen PB, Chen R, LaPierre N, Chen Z, Mefford J, Marcus E, Heffel MG, Soto DC, Ernst J, Luo C, Flint J. Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574060. [PMID: 38260483 PMCID: PMC10802323 DOI: 10.1101/2024.01.03.574060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. Four genes, Lsamp, Ptprd, Nptx2 and Sh3gl, have known roles in synapse function; the fifth gene, Psip1, is a transcriptional co-activator not previously implicated in behavior; the sixth is a long non-coding RNA 4933413L06Rik with no known function. Single nucleus transcriptomic and epigenetic analyses implicated excitatory neurons as likely mediating the genetic effects. Surprisingly, variation in transcriptome and epigenetic modalities between inbred strains occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results open a bottleneck in using genetic mapping of QTLs to find novel biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.
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5
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He Q, Li Z, Liu Y, Yang H, Liu L, Ren Y, Zheng J, Xu R, Wang S, Zhan Q. Chromosome-scale assembly and analysis of Melilotus officinalis genome for SSR development and nodulation genes analysis. THE PLANT GENOME 2023; 16:e20345. [PMID: 37259688 DOI: 10.1002/tpg2.20345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 06/02/2023]
Abstract
Melilotus officinalis is an important legume crop with forage and Chinese medicinal value. The unknown genome of M. officinalis restricted the domestication and utilization of the species and its germplasm resource diversity. A chromosome-scale assembly of the M. officinalis genome was assembled and analysed. The 976.27 Mb of genome was divided into eight chromosomes covering 99.16% of the whole genome. A total of 50022 genes were predicted in the genome. M. officinalis and Melilotus albus shared a common ancestor 0.5-5.65 million years ago (MYA). A genome-wide doubling event occurred 68.93 MYA according to the synonymous nucleotide-substitution values. A total of 552102 tandem repeats were predicted, and 46004 SSR primers of TRs with 10 or more base pairs were developed and designed. The elucidation of the M. officinalis genome provides a compelling model system for studying the genetic, evolutionary and biosynthesis of this legume.
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Affiliation(s)
- Qinguan He
- Life and Health Science College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Zhengpeng Li
- Life and Health Science College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Yanlong Liu
- Agricultural College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Hao Yang
- Agricultural College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Li Liu
- Agricultural College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Yi Ren
- Agricultural College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Jiacheng Zheng
- Agricultural College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Ronghua Xu
- Life and Health Science College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Songhua Wang
- Life and Health Science College of Anhui Science and Technology University, Fengyang Auhui, China
| | - Qiuwen Zhan
- Agricultural College of Anhui Science and Technology University, Fengyang Auhui, China
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6
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Clahsen T, Hadrian K, Notara M, Schlereth SL, Howaldt A, Prokosch V, Volatier T, Hos D, Schroedl F, Kaser-Eichberger A, Heindl LM, Steven P, Bosch JJ, Steinkasserer A, Rokohl AC, Liu H, Mestanoglu M, Kashkar H, Schumacher B, Kiefer F, Schulte-Merker S, Matthaei M, Hou Y, Fassbender S, Jantsch J, Zhang W, Enders P, Bachmann B, Bock F, Cursiefen C. The novel role of lymphatic vessels in the pathogenesis of ocular diseases. Prog Retin Eye Res 2023; 96:101157. [PMID: 36759312 DOI: 10.1016/j.preteyeres.2022.101157] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 02/10/2023]
Abstract
Historically, the eye has been considered as an organ free of lymphatic vessels. In recent years, however, it became evident, that lymphatic vessels or lymphatic-like vessels contribute to several ocular pathologies at various peri- and intraocular locations. The aim of this review is to outline the pathogenetic role of ocular lymphatics, the respective molecular mechanisms and to discuss current and future therapeutic options based thereon. We will give an overview on the vascular anatomy of the healthy ocular surface and the molecular mechanisms contributing to corneal (lymph)angiogenic privilege. In addition, we present (i) current insights into the cellular and molecular mechanisms occurring during pathological neovascularization of the cornea triggered e.g. by inflammation or trauma, (ii) the role of lymphatic vessels in different ocular surface pathologies such as dry eye disease, corneal graft rejection, ocular graft versus host disease, allergy, and pterygium, (iii) the involvement of lymphatic vessels in ocular tumors and metastasis, and (iv) the novel role of the lymphatic-like structure of Schlemm's canal in glaucoma. Identification of the underlying molecular mechanisms and of novel modulators of lymphangiogenesis will contribute to the development of new therapeutic targets for the treatment of ocular diseases associated with pathological lymphangiogenesis in the future. The preclinical data presented here outline novel therapeutic concepts for promoting transplant survival, inhibiting metastasis of ocular tumors, reducing inflammation of the ocular surface, and treating glaucoma. Initial data from clinical trials suggest first success of novel treatment strategies to promote transplant survival based on pretransplant corneal lymphangioregression.
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Affiliation(s)
- Thomas Clahsen
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Karina Hadrian
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Maria Notara
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Simona L Schlereth
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Antonia Howaldt
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Verena Prokosch
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thomas Volatier
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Deniz Hos
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Falk Schroedl
- Center for Anatomy and Cell Biology, Institute of Anatomy and Cell Biology - Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Alexandra Kaser-Eichberger
- Center for Anatomy and Cell Biology, Institute of Anatomy and Cell Biology - Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Ludwig M Heindl
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Philipp Steven
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Cluster of Excellence: Cellular Stress Responses in Ageing-Associated Diseases, CECAD, University of Cologne, Cologne, Germany
| | - Jacobus J Bosch
- Centre for Human Drug Research and Leiden University Medical Center, Leiden, the Netherlands
| | | | - Alexander C Rokohl
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hanhan Liu
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Mert Mestanoglu
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hamid Kashkar
- Institute for Molecular Immunology, Center for Molecular Medicine Cologne (CMMC), CECAD Research Center, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence: Cellular Stress Responses in Ageing-Associated Diseases, CECAD, University of Cologne, Cologne, Germany
| | - Friedemann Kiefer
- European Institute for Molecular Imaging (EIMI), University of Münster, 48149, Münster, Germany
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU Münster, Münster, Germany
| | - Mario Matthaei
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Yanhong Hou
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Xuhui District, Shanghai, China
| | - Sonja Fassbender
- IUF‒Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany; Immunology and Environment, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonathan Jantsch
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Wei Zhang
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Philip Enders
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Björn Bachmann
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Felix Bock
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Claus Cursiefen
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence: Cellular Stress Responses in Ageing-Associated Diseases, CECAD, University of Cologne, Cologne, Germany.
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Larson DR, Kimber AJ, Meyer KJ, Anderson MG. Anterior chamber depth in mice is controlled by several quantitative trait loci. PLoS One 2023; 18:e0286897. [PMID: 37624784 PMCID: PMC10456175 DOI: 10.1371/journal.pone.0286897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Anterior chamber depth (ACD) is a quantitative trait associated with primary angle closure glaucoma (PACG). Although ACD is highly heritable, known genetic variations explain a small fraction of the phenotypic variability. The purpose of this study was to identify additional ACD-influencing loci using strains of mice. Cohorts of 86 N2 and 111 F2 mice were generated from crosses between recombinant inbred BXD24/TyJ and wild-derived CAST/EiJ mice. Using anterior chamber optical coherence tomography, mice were phenotyped at 10-12 weeks of age, genotyped based on 93 genome-wide SNPs, and subjected to quantitative trait locus (QTL) analysis. In an analysis of ACD among all mice, six loci passed the significance threshold of p = 0.05 and persisted after multiple regression analysis. These were on chromosomes 6, 7, 11, 12, 15 and 17 (named Acdq6, Acdq7, Acdq11, Acdq12, Acdq15, and Acdq17, respectively). Our findings demonstrate a quantitative multi-genic pattern of ACD inheritance in mice and identify six previously unrecognized ACD-influencing loci. We have taken a unique approach to studying the anterior chamber depth phenotype by using mice as genetic tool to examine this continuously distributed trait.
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Affiliation(s)
- Demelza R. Larson
- Department of Biology, College of Saint Benedict & Saint John’s University, Collegeville, Minnesota, United States of America
| | - Allysa J. Kimber
- Department of Biology, College of Saint Benedict & Saint John’s University, Collegeville, Minnesota, United States of America
| | - Kacie J. Meyer
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, Iowa, United States of America
| | - Michael G. Anderson
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, Iowa, United States of America
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, Iowa, United States of America
- Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, Iowa, United States of America
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8
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Ramos A, Granzotto N, Kremer R, Boeder AM, de Araújo JFP, Pereira AG, Izídio GS. Hunting for Genes Underlying Emotionality in the Laboratory Rat: Maps, Tools and Traps. Curr Neuropharmacol 2023; 21:1840-1863. [PMID: 36056863 PMCID: PMC10514530 DOI: 10.2174/1570159x20666220901154034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/13/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
Scientists have systematically investigated the hereditary bases of behaviors since the 19th century, moved by either evolutionary questions or clinically-motivated purposes. The pioneer studies on the genetic selection of laboratory animals had already indicated, one hundred years ago, the immense complexity of analyzing behaviors that were influenced by a large number of small-effect genes and an incalculable amount of environmental factors. Merging Mendelian, quantitative and molecular approaches in the 1990s made it possible to map specific rodent behaviors to known chromosome regions. From that point on, Quantitative Trait Locus (QTL) analyses coupled with behavioral and molecular techniques, which involved in vivo isolation of relevant blocks of genes, opened new avenues for gene mapping and characterization. This review examines the QTL strategy applied to the behavioral study of emotionality, with a focus on the laboratory rat. We discuss the challenges, advances and limitations of the search for Quantitative Trait Genes (QTG) playing a role in regulating emotionality. For the past 25 years, we have marched the long journey from emotionality-related behaviors to genes. In this context, our experiences are used to illustrate why and how one should move forward in the molecular understanding of complex psychiatric illnesses. The promise of exploring genetic links between immunological and emotional responses are also discussed. New strategies based on humans, rodents and other animals (such as zebrafish) are also acknowledged, as they are likely to allow substantial progress to be made in the near future.
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Affiliation(s)
- André Ramos
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Natalli Granzotto
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rafael Kremer
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Ariela Maína Boeder
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Julia Fernandez Puñal de Araújo
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Aline Guimarães Pereira
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Geison Souza Izídio
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
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9
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Du EY, Boussaty EC, La Monte OA, Dixon PR, Zhou TY, Friedman RA. Large-scale phenotyping and characterization of age-related hearing loss in outbred CFW mice. Hear Res 2022; 424:108605. [PMID: 36088865 DOI: 10.1016/j.heares.2022.108605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/27/2022] [Accepted: 09/03/2022] [Indexed: 11/18/2022]
Abstract
Age-related hearing loss (ARHL), or presbycusis, is one of the most prevalent conditions affecting the global population. A substantial fraction of patients with ARHL have no identifiable mutation despite over a hundred having been discovered, suggesting unidentified monogenic or polygenic causes. In this study, we investigated the hearing function of the aging outbred CFW mice through auditory brainstem response (ABR) thresholds. Through the characterization of 1,132 ABRs, we observed significant variation in both absolute thresholds and the effect of aging. We identify eight distinct patterns of hearing loss and were able to categorize nearly all data within these eight categories. Proportions within each category varied immensely between aging timepoints. We observe a small but consistent hearing deficit in female CFW mice. The resulting phenotypic data are a necessity for ARHL association mapping at a higher resolution than has previously been achieved and provides a new resource for studying ARHL.
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Affiliation(s)
- Eric Y Du
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Ely C Boussaty
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Olivia A La Monte
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA; University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Peter R Dixon
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Thomas Y Zhou
- University of California, San Diego, La Jolla, CA, USA
| | - Rick A Friedman
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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10
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Zhang XY, Gong H, Fang Q, Zhu X, Jiang L, Wu R. A Holling Functional Response Model for Mapping QTLs Governing Interspecific Interactions. Front Genet 2021; 12:766372. [PMID: 34721549 PMCID: PMC8554200 DOI: 10.3389/fgene.2021.766372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Genes play an important role in community ecology and evolution, but how to identify the genes that affect community dynamics at the whole genome level is very challenging. Here, we develop a Holling type II functional response model for mapping quantitative trait loci (QTLs) that govern interspecific interactions. The model, integrated with generalized Lotka-Volterra differential dynamic equations, shows a better capacity to reveal the dynamic complexity of inter-species interactions than classic competition models. By applying the new model to a published mapping data from a competition experiment of two microbial species, we identify a set of previously uncharacterized QTLs that are specifically responsible for microbial cooperation and competition. The model can not only characterize how these QTLs affect microbial interactions, but also address how change in ecological interactions activates the genetic effects of the QTLs. This model provides a quantitative means of predicting the genetic architecture that shapes the dynamic behavior of ecological communities.
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Affiliation(s)
- Xiao-Yu Zhang
- College of Science, Beijing Forestry University, Beijing, China
| | - Huiying Gong
- College of Science, Beijing Forestry University, Beijing, China
| | - Qing Fang
- Faculty of Science, Yamagata University, Yamagata, Japan
| | - Xuli Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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11
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Borrelli KN, Langan CR, Dubinsky KR, Szumlinski KK, Carlezon WA, Chartoff EH, Bryant CD. Intracranial self-stimulation and concomitant behaviors following systemic methamphetamine administration in Hnrnph1 mutant mice. Psychopharmacology (Berl) 2021; 238:2031-2041. [PMID: 33758972 PMCID: PMC8715365 DOI: 10.1007/s00213-021-05829-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 03/15/2021] [Indexed: 11/30/2022]
Abstract
RATIONALE Methamphetamine (MA) addiction is a major public health issue in the USA, with a poorly understood genetic component. We previously identified heterogeneous nuclear ribonucleoprotein H1 (Hnrnph1; H1) as a quantitative trait gene underlying sensitivity to MA-induced behavioral sensitivity. Mice heterozygous for a frameshift deletion in the first coding exon of H1 (H1+/-) showed reduced MA phenotypes including oral self-administration, locomotor activity, dopamine release, and dose-dependent differences in MA conditioned place preference. However, the effects of H1+/- on innate and MA-modulated reward sensitivity are not known. OBJECTIVES We examined innate reward sensitivity and facilitation by MA in H1+/- mice via intracranial self-stimulation (ICSS). METHODS We used intracranial self-stimulation (ICSS) of the medial forebrain bundle to assess shifts in reward sensitivity following acute, ascending doses of MA (0.5-4.0 mg/kg, i.p.) using a within-subjects design. We also assessed video-recorded behaviors during ICSS testing sessions. RESULTS H1+/- mice displayed reduced normalized maximum response rates in response to MA. H1+/- females had lower normalized M50 values compared to wild-type females, suggesting enhanced reward facilitation by MA. Finally, regardless of genotype, there was a dose-dependent reduction in distance to the response wheel following MA administration, providing an additional measure of MA-induced reward-driven behavior. CONCLUSIONS H1+/- mice displayed a complex ICSS phenotype following MA, displaying indications of both blunted reward magnitude (lower normalized maximum response rates) and enhanced reward sensitivity specific to H1+/- females (lower normalized M50 values).
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Affiliation(s)
- Kristyn N Borrelli
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, 72 E. Concord St, L-606C, Boston, MA, 02118, USA
- Ph.D. Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA, USA
- Graduate Program for Neuroscience, Boston University, Boston, MA, USA
- Transformative Training Program in Addiction Science, Boston University, Boston, MA, USA
| | - Carly R Langan
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, 72 E. Concord St, L-606C, Boston, MA, 02118, USA
| | - Kyra R Dubinsky
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, 72 E. Concord St, L-606C, Boston, MA, 02118, USA
| | - Karen K Szumlinski
- Department of Psychological and Brain Sciences; Department of Molecular, Cellular and Developmental Biology; and the Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - William A Carlezon
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Elena H Chartoff
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, 72 E. Concord St, L-606C, Boston, MA, 02118, USA.
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12
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Regional Variation in Genetic Control of Atherosclerosis in Hyperlipidemic Mice. G3-GENES GENOMES GENETICS 2020; 10:4679-4689. [PMID: 33109727 PMCID: PMC7718748 DOI: 10.1534/g3.120.401856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atherosclerosis is a polygenic disorder that often affects multiple arteries. Carotid arteries are common sites for evaluating subclinical atherosclerosis, and aortic root is the standard site for quantifying atherosclerosis in mice. We compared genetic control of atherosclerosis between the two sites in the same cohort derived from two phenotypically divergent Apoe-null (Apoe -/-) mouse strains. Female F2 mice were generated from C57BL/6 (B6) and C3H/He (C3H) Apoe -/- mice and fed 12 weeks of Western diet. Atherosclerotic lesions in carotid bifurcation and aortic root and plasma levels of fasting lipids and glucose were measured. 153 genetic markers across the genome were typed. All F2 mice developed aortic atherosclerosis, while 1/5 formed no or little carotid lesions. Genome-wide scans revealed 3 significant loci on chromosome (Chr) 1, Chr15, 6 suggestive loci for aortic atherosclerosis, 2 significant loci on Chr6, Chr12, and 6 suggestive loci for carotid atherosclerosis. Only 2 loci for aortic lesions showed colocalization with loci for carotid lesions. Carotid lesion sizes were moderately correlated with aortic lesion sizes (r = 0.303; P = 4.6E-6), but they showed slight or no association with plasma HDL, non-HDL cholesterol, triglyceride, or glucose levels among F2 mice. Bioinformatics analyses prioritized Cryge as a likely causal gene for Ath30, Cdh6 and Dnah5 as causal genes for Ath22 Our data demonstrate vascular site-specific effects of genetic factors on atherosclerosis in the same animals and highlight the need to extend studies of atherosclerosis to sites beyond aortas of mice.
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13
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Wang Y, Bu L, Cao X, Qu H, Zhang C, Ren J, Huang Z, Zhao Y, Luo C, Hu X, Shu D, Li N. Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line. Front Genet 2020; 11:894. [PMID: 33033489 PMCID: PMC7509424 DOI: 10.3389/fgene.2020.00894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
The advanced intercross line (AIL) that is created by successive generations of pseudo-random mating after the F2 generation is a valuable resource, especially in agricultural livestock and poultry species, because it improves the precision of quantitative trait loci (QTL) mapping compared with traditional association populations by introducing more recombination events. The growth traits of broilers have significant economic value in the chicken industry, and many QTLs affecting growth traits have been identified, especially on chromosomes 1, 4, and 27, albeit with large confidence intervals that potentially contain dozens of genes. To promote a better understanding of the underlying genetic architecture of growth trait differences, specifically body weight and bone development, in this study, we report a nine-generation AIL derived from two divergent outbred lines: High Quality chicken Line A (HQLA) and Huiyang Bearded (HB) chicken. We evaluate the genetic architecture of the F0, F2, F8, and F9 generations of AIL and demonstrate that the population of the F9 generation sufficiently randomized the founder genomes and has the characteristics of rapid linkage disequilibrium decay, limited allele frequency decline, and abundant nucleotide diversity. This AIL yielded a much narrower QTL than the F2 generations, especially the QTL on chromosome 27, which was reduced to 120 Kb. An ancestral haplotype association analysis showed that most of the dominant haplotypes are inherited from HQLA but with fluctuation of the effects between them. We highlight the important role of four candidate genes (PHOSPHO1, IGF2BP1, ZNF652, and GIP) in bone growth. We also retrieved a missing QTL from AIL on chromosome 4 by identifying the founder selection signatures, which are explained by the loss of association power that results from rare alleles. Our study provides a reasonable resource for detecting quantitative trait genes and tracking ancestor history and will facilitate our understanding of the genetic mechanisms underlying chicken bone growth.
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Affiliation(s)
- Yuzhe Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lina Bu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xuemin Cao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hao Qu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunyuan Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangli Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhuolin Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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14
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Jupp B, Pitzoi S, Petretto E, Mar AC, Oliver YP, Jordan ER, Taylor S, Atanur SS, Srivastava PK, Saar K, Hubner N, Sommer WH, Staehlin O, Spanagel R, Robinson ES, Schumann G, Moreno M, Everitt BJ, Robbins TW, Aitman TJ, Dalley JW. Impulsivity is a heritable trait in rodents and associated with a novel quantitative trait locus on chromosome 1. Sci Rep 2020; 10:6684. [PMID: 32317713 PMCID: PMC7174407 DOI: 10.1038/s41598-020-63646-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/01/2020] [Indexed: 12/30/2022] Open
Abstract
Impulsivity describes the tendency to act prematurely without appropriate foresight and is symptomatic of a number of neuropsychiatric disorders. Although a number of genes for impulsivity have been identified, no study to date has carried out an unbiased, genome-wide approach to identify genetic markers associated with impulsivity in experimental animals. Herein we report a linkage study of a six-generational pedigree of adult rats phenotyped for one dimension of impulsivity, namely premature responding on the five-choice serial reaction time task, combined with genome wide sequencing and transcriptome analysis to identify candidate genes associated with the expression of the impulsivity trait. Premature responding was found to be heritable (h2 = 13-16%), with significant linkage (LOD 5.2) identified on chromosome 1. Fine mapping of this locus identified a number of polymorphic candidate genes, however only one, beta haemoglobin, was differentially expressed in both the founder strain and F6 generation. These findings provide novel insights into the genetic substrates and putative neurobiological mechanisms of impulsivity with broader translational relevance for impulsivity-related disorders in humans.
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Affiliation(s)
- Bianca Jupp
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Silvia Pitzoi
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK
| | - Enrico Petretto
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK ,0000 0004 0385 0924grid.428397.3Duke-NUS Medical School, Singapore, Singapore
| | - Adam C. Mar
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK ,0000 0004 1936 8753grid.137628.9NYU School of Medicine, New York, USA
| | - Yolanda Pena Oliver
- 0000 0004 1936 7590grid.12082.39School of Psychology, University of Sussex, Brighton, UK
| | - Emily R. Jordan
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Stephanie Taylor
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Santosh S. Atanur
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK
| | - Prashant K. Srivastava
- 0000 0001 2113 8111grid.7445.2MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, UK
| | - Kathrin Saar
- 0000 0001 1014 0849grid.419491.0Max Delbruck Centre for Molecular Medicine, Berlin, Germany
| | - Norbert Hubner
- 0000 0001 1014 0849grid.419491.0Max Delbruck Centre for Molecular Medicine, Berlin, Germany
| | - Wolfgang H. Sommer
- 0000 0004 0477 2235grid.413757.3Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Oliver Staehlin
- 0000 0004 0477 2235grid.413757.3Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Rainer Spanagel
- 0000 0004 0477 2235grid.413757.3Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine Mannheim, University of Heidelberg, Mannheim, Germany
| | - Emma S. Robinson
- 0000 0004 1936 7603grid.5337.2School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Gunter Schumann
- 0000 0001 2322 6764grid.13097.3cCentre for Population Neuroscience and Stratified Medicine, Institute of Psychiatry, Psychology and Neuroscience, King¹s College, London, UK
| | - Margarita Moreno
- 0000000101969356grid.28020.38Department of Psychology & Health Research Centre (CEINSA), University of Almería, Almería, Spain
| | - Barry J. Everitt
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Trevor W. Robbins
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
| | - Timothy J. Aitman
- 0000 0004 1936 7988grid.4305.2Centre for Genomics and Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jeffrey W. Dalley
- 0000000121885934grid.5335.0Department of Psychology and Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK ,0000000121885934grid.5335.0Department of Psychiatry, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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15
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Macdonald SJ, Highfill CA. A naturally-occurring 22-bp coding deletion in Ugt86Dd reduces nicotine resistance in Drosophila melanogaster. BMC Res Notes 2020; 13:188. [PMID: 32228671 PMCID: PMC7106894 DOI: 10.1186/s13104-020-05035-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 03/19/2020] [Indexed: 11/10/2022] Open
Abstract
Objective Segregating genetic variants contribute to the response to toxic, xenobiotic compounds, and identifying these causative sites can help describe the mechanisms underlying metabolism of toxic compounds. In previous work we implicated the detoxification gene Ugt86Dd in the genetic control of larval nicotine resistance in Drosophila melanogaster. Furthermore, we suggested that a naturally-occurring 22-bp deletion that leads to a stop codon in exon 2 of the gene markedly reduces resistance. Here we use homology directed CRISPR/Cas9 gene editing to specifically test this hypothesis. Results We edited chromosome three from an inbred strain named A4 which carries the insertion allele at Ugt86Dd, successfully generated four alleles carrying the 22-bp Ugt86Dd deletion, and substituted edited chromosomes back into the A4 background. The original A4 strain, and an un-edited control strain in the same A4 background, show no significant difference in egg-to-adult or larva-to-adult viability on either control media or nicotine-supplemented media, and only slightly delayed development in nicotine media. However, strains carrying the 22-bp deletion showed reduced viability in nicotine conditions, and significantly longer development. Our data strongly suggest that the naturally-occurring 22-bp insertion/deletion event in Ugt86Dd directly impacts variation in nicotine resistance in D. melanogaster.
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Affiliation(s)
- Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, 4043 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA. .,Center for Computational Biology, University of Kansas, Lawrence, KS, 66047, USA.
| | - Chad A Highfill
- Department of Molecular Biosciences, University of Kansas, 4043 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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16
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Gpr63 is a modifier of microcephaly in Ttc21b mouse mutants. PLoS Genet 2019; 15:e1008467. [PMID: 31730647 PMCID: PMC6881074 DOI: 10.1371/journal.pgen.1008467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2019] [Accepted: 10/08/2019] [Indexed: 11/19/2022] Open
Abstract
The primary cilium is a signaling center critical for proper embryonic development. Previous studies have demonstrated that mice lacking Ttc21b have impaired retrograde trafficking within the cilium and multiple organogenesis phenotypes, including microcephaly. Interestingly, the severity of the microcephaly in Ttc21baln/aln homozygous null mutants is considerably affected by the genetic background and mutants on an FVB/NJ (FVB) background develop a forebrain significantly smaller than mutants on a C57BL/6J (B6) background. We performed a Quantitative Trait Locus (QTL) analysis to identify potential genetic modifiers and identified two regions linked to differential forebrain size: modifier of alien QTL1 (Moaq1) on chromosome 4 at 27.8 Mb and Moaq2 on chromosome 6 at 93.6 Mb. These QTLs were validated by constructing congenic strains. Further analysis of Moaq1 identified an orphan G-protein coupled receptor (GPCR), Gpr63, as a candidate gene. We identified a SNP that is polymorphic between the FVB and B6 strains in Gpr63 and creates a missense mutation predicted to be deleterious in the FVB protein. We used CRISPR-Cas9 genome editing to create two lines of FVB congenic mice: one with the B6 sequence of Gpr63 and the other with a deletion allele leading to a truncation of the GPR63 C-terminal tail. We then demonstrated that Gpr63 can localize to the cilium in vitro. These alleles affect ciliary localization of GPR63 in vitro and genetically interact with Ttc21baln/aln as Gpr63;Ttc21b double mutants show unique phenotypes including spina bifida aperta and earlier embryonic lethality. This validated Gpr63 as a modifier of multiple Ttc21b neural phenotypes and strongly supports Gpr63 as a causal gene (i.e., a quantitative trait gene, QTG) within the Moaq1 QTL. TTC21B in humans is a known ciliopathy gene and contributes to the pathophysiology of a number of ciliopathies. Mice homozygous for a null allele of Ttc21b also have a spectrum of ciliopathy phenotypes, including microcephaly (small brain). Further work has shown that the severity of the microcephaly significantly depends on the genetic background of the mouse model. The genetic mechanisms of the Ttc21b pathophysiology and the interacting gene network remain far from understood. As an initial attempt to understand the underlying mechanism(s) underlying the variable effects on brain size, we performed a quantitative trait locus (QTL) analysis and found two regions of genomic significance that correlated with smaller brain size. We confirmed both QTLs with congenic lines. One of the two regions was small enough that we considered candidate genes and hypothesized Gpr63 might be a contributing locus for a number of reasons. We evaluated this hypothesis directly with precise variant creation using genome editing and provide evidence that Ttc21b and Gpr63 do indeed genetically interact. Thus, we have been able to combine classical QTL analysis and genome editing to directly test the resulting hypothesis.
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17
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Lustyk D, Kinský S, Ullrich KK, Yancoskie M, Kašíková L, Gergelits V, Sedlacek R, Chan YF, Odenthal-Hesse L, Forejt J, Jansa P. Genomic Structure of Hstx2 Modifier of Prdm9-Dependent Hybrid Male Sterility in Mice. Genetics 2019; 213:1047-1063. [PMID: 31562180 PMCID: PMC6827376 DOI: 10.1534/genetics.119.302554] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023] Open
Abstract
F1 hybrids between mouse inbred strains PWD and C57BL/6 represent the most thoroughly genetically defined model of hybrid sterility in vertebrates. Hybrid male sterility can be fully reconstituted from three components of this model, the Prdm9 gene, intersubspecific homeology of Mus musculus musculus and Mus musculus domesticus autosomes, and the X-linked Hstx2 locus. Hstx2 modulates the extent of Prdm9-dependent meiotic arrest and harbors two additional factors responsible for intersubspecific introgression-induced oligospermia (Hstx1) and meiotic recombination rate (Meir1). To facilitate positional cloning and to overcome the recombination suppression within the 4.3 Mb encompassing the Hstx2 locus, we designed Hstx2-CRISPR and SPO11/Cas9 transgenes aimed to induce DNA double-strand breaks specifically within the Hstx2 locus. The resulting recombinant reduced the Hstx2 locus to 2.70 Mb (chromosome X: 66.51-69.21 Mb). The newly defined Hstx2 locus still operates as the major X-linked factor of the F1 hybrid sterility, and controls meiotic chromosome synapsis and meiotic recombination rate. Despite extensive further crosses, the 2.70 Mb Hstx2 interval behaved as a recombination cold spot with reduced PRDM9-mediated H3K4me3 hotspots and absence of DMC1-defined DNA double-strand-break hotspots. To search for structural anomalies as a possible cause of recombination suppression, we used optical mapping and observed high incidence of subspecies-specific structural variants along the X chromosome, with a striking copy number polymorphism of the microRNA Mir465 cluster. This observation together with the absence of a strong sterility phenotype in Fmr1 neighbor (Fmr1nb) null mutants support the role of microRNA as a likely candidate for Hstx2.
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Affiliation(s)
- Diana Lustyk
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
- Faculty of Science, Charles University, Prague CZ-12000, Czech Republic
| | - Slavomír Kinský
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Kristian Karsten Ullrich
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Michelle Yancoskie
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Lenka Kašíková
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Vaclav Gergelits
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Radislav Sedlacek
- The Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Yingguang Frank Chan
- Molecular Basis and Evolution of Complex Traits Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen 72076, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Petr Jansa
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
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18
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Pascale RM, Simile MM, Peitta G, Seddaiu MA, Feo F, Calvisi DF. Experimental Models to Define the Genetic Predisposition to Liver Cancer. Cancers (Basel) 2019; 11:cancers11101450. [PMID: 31569678 PMCID: PMC6826893 DOI: 10.3390/cancers11101450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/24/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a frequent human cancer and the most frequent liver tumor. The study of genetic mechanisms of the inherited predisposition to HCC, implicating gene-gene and gene-environment interaction, led to the discovery of multiple gene loci regulating the growth and multiplicity of liver preneoplastic and neoplastic lesions, thus uncovering the action of multiple genes and epistatic interactions in the regulation of the individual susceptibility to HCC. The comparative evaluation of the molecular pathways involved in HCC development in mouse and rat strains differently predisposed to HCC indicates that the genes responsible for HCC susceptibility control the amplification and/or overexpression of c-Myc, the expression of cell cycle regulatory genes, and the activity of Ras/Erk, AKT/mTOR, and of the pro-apoptotic Rassf1A/Nore1A and Dab2IP/Ask1 pathways, the methionine cycle, and DNA repair pathways in mice and rats. Comparative functional genetic studies, in rats and mice differently susceptible to HCC, showed that preneoplastic and neoplastic lesions of resistant mouse and rat strains cluster with human HCC with better prognosis, while the lesions of susceptible mouse and rats cluster with HCC with poorer prognosis, confirming the validity of the studies on the influence of the genetic predisposition to hepatocarinogenesis on HCC prognosis in mouse and rat models. Recently, the hydrodynamic gene transfection in mice provided new opportunities for the recognition of genes implicated in the molecular mechanisms involved in HCC pathogenesis and prognosis. This method appears to be highly promising to further study the genetic background of the predisposition to this cancer.
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Affiliation(s)
- Rosa M Pascale
- Department of Medical, Surgical and Experimental Sciences, Via P. Manzella 4, 07100 Sassari, Italy.
| | - Maria M Simile
- Department of Medical, Surgical and Experimental Sciences, Via P. Manzella 4, 07100 Sassari, Italy.
| | - Graziella Peitta
- Department of Medical, Surgical and Experimental Sciences, Via P. Manzella 4, 07100 Sassari, Italy.
| | - Maria A Seddaiu
- Department of Medical, Surgical and Experimental Sciences, Via P. Manzella 4, 07100 Sassari, Italy.
| | - Francesco Feo
- Department of Medical, Surgical and Experimental Sciences, Via P. Manzella 4, 07100 Sassari, Italy.
| | - Diego F Calvisi
- Department of Medical, Surgical and Experimental Sciences, Via P. Manzella 4, 07100 Sassari, Italy.
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Akinola LS, Mckiver B, Toma W, Zhu AZX, Tyndale RF, Kumar V, Damaj MI. C57BL/6 Substrain Differences in Pharmacological Effects after Acute and Repeated Nicotine Administration. Brain Sci 2019; 9:brainsci9100244. [PMID: 31546627 PMCID: PMC6827359 DOI: 10.3390/brainsci9100244] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 01/16/2023] Open
Abstract
Tobacco smoking is the major cause of disability and death in the United States and around the world. In addition, tobacco dependence and addiction express themselves as complex behaviors involving an interplay of genetics, environment, and psychological state. Mouse genetic studies could potentially elucidate the novel genes and/or gene networks regulating various aspects of nicotine dependence. Using the closely related C57BL/6 (B6) mice substrains, recent reports have noted phenotypic differences within C57BL/6J (B6J) and C57BL/6N (B6N) mice for some drugs of abuse: alcohol, opiates, and cocaine. However, the differences in nicotine’s effects have not yet been described in these substrains. We examined the phenotypic differences in these substrains following the acute and repeated administration of nicotine in several pharmacological measures, including locomotion (after acute and repeated exposure), body temperature, nociception, and anxiety-like behaviors. We report substrain differences in the pharmacological effects of acute and repeated nicotine administration in the B6 substrains. Overall, we show enhanced nicotine sensitivity to locomotion, hypothermia, antinociception, and anxiety-like behaviors in the B6J mouse substrain compared to B6N. In the repeated administration paradigm, both the B6N and B6J substrains showed no sensitized locomotor responses after repeated exposure to nicotine at the two doses tested. This study thus provides evidence that the B6 mouse substrains may be useful for genetic studies to elucidate some of the genetic variants involved in tobacco dependence and addiction.
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Affiliation(s)
- Lois S Akinola
- Department of Pharmacology and Toxicology, and Translational Research Initiative for Pain and Neuropathy, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298, USA.
| | - Bryan Mckiver
- Department of Pharmacology and Toxicology, and Translational Research Initiative for Pain and Neuropathy, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298, USA.
| | - Wisam Toma
- Department of Pharmacology and Toxicology, and Translational Research Initiative for Pain and Neuropathy, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298, USA.
| | - Andy Z X Zhu
- Takeda Pharmaceutical Company Limited, Cambridge, MA 02139, USA.
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Department of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, ON, Canada.
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.
| | - M Imad Damaj
- Department of Pharmacology and Toxicology, and Translational Research Initiative for Pain and Neuropathy, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298, USA.
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20
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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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21
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Abu‐Toamih Atamni HJ, Iraqi FA. Efficient protocols and methods for high-throughput utilization of the Collaborative Cross mouse model for dissecting the genetic basis of complex traits. Animal Model Exp Med 2019; 2:137-149. [PMID: 31773089 PMCID: PMC6762040 DOI: 10.1002/ame2.12074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
The Collaborative Cross (CC) mouse model is a next-generation mouse genetic reference population (GRP) designated for a high-resolution quantitative trait loci (QTL) mapping of complex traits during health and disease. The CC lines were generated from reciprocal crosses of eight divergent mouse founder strains composed of five classical and three wild-derived strains. Complex traits are defined to be controlled by variations within multiple genes and the gene/environment interactions. In this article, we introduce and present variety of protocols and results of studying the host response to infectious and chronic diseases, including type 2 diabetes and metabolic diseases, body composition, immune response, colorectal cancer, susceptibility to Aspergillus fumigatus, Klebsiella pneumoniae, Pseudomonas aeruginosa, sepsis, and mixed infections of Porphyromonas gingivalis and Fusobacterium nucleatum, which were conducted at our laboratory using the CC mouse population. These traits are observed at multiple levels of the body systems, including metabolism, body weight, immune profile, susceptibility or resistance to the development and progress of infectious or chronic diseases. Herein, we present full protocols and step-by-step methods, implemented in our laboratory for the phenotypic and genotypic characterization of the different CC lines, mapping the gene underlying the host response to these infections and chronic diseases. The CC mouse model is a unique and powerful GRP for dissecting the host genetic architectures underlying complex traits, including chronic and infectious diseases.
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Affiliation(s)
- Hanifa J. Abu‐Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel AvivRamat AvivIsrael
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of MedicineTel Aviv UniversityTel AvivRamat AvivIsrael
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22
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Li F, Shi J, Lu HS, Zhang H. Functional Genomics and CRISPR Applied to Cardiovascular Research and Medicine. Arterioscler Thromb Vasc Biol 2019; 39:e188-e194. [PMID: 31433696 DOI: 10.1161/atvbaha.119.312579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Fang Li
- From the Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York (F.L., J.S., H.Z.)
| | - Jianting Shi
- From the Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York (F.L., J.S., H.Z.)
| | - Hong S Lu
- Department of Physiology, Saha Cardiovascular Research Center, University of Kentucky, Lexington (H.S.L.)
| | - Hanrui Zhang
- From the Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York (F.L., J.S., H.Z.)
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23
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Mesner LD, Calabrese GM, Al-Barghouthi B, Gatti DM, Sundberg JP, Churchill GA, Godfrey DA, Ackert-Bicknell CL, Farber CR. Mouse genome-wide association and systems genetics identifies Lhfp as a regulator of bone mass. PLoS Genet 2019; 15:e1008123. [PMID: 31042701 PMCID: PMC6513102 DOI: 10.1371/journal.pgen.1008123] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 05/13/2019] [Accepted: 04/03/2019] [Indexed: 11/19/2022] Open
Abstract
Bone mineral density (BMD) is a strong predictor of osteoporotic fracture. It is also one of the most heritable disease-associated quantitative traits. As a result, there has been considerable effort focused on dissecting its genetic basis. Here, we performed a genome-wide association study (GWAS) in a panel of inbred strains to identify associations influencing BMD. This analysis identified a significant (P = 3.1 x 10−12) BMD locus on Chromosome 3@52.5 Mbp that replicated in two separate inbred strain panels and overlapped a BMD quantitative trait locus (QTL) previously identified in a F2 intercross. The association mapped to a 300 Kbp region containing four genes; Gm2447, Gm20750, Cog6, and Lhfp. Further analysis found that Lipoma HMGIC Fusion Partner (Lhfp) was highly expressed in bone and osteoblasts. Furthermore, its expression was regulated by a local expression QTL (eQTL), which overlapped the BMD association. A co-expression network analysis revealed that Lhfp was strongly connected to genes involved in osteoblast differentiation. To directly evaluate its role in bone, Lhfp deficient mice (Lhfp-/-) were created using CRISPR/Cas9. Consistent with genetic and network predictions, bone marrow stromal cells (BMSCs) from Lhfp-/- mice displayed increased osteogenic differentiation. Lhfp-/- mice also had elevated BMD due to increased cortical bone mass. Lastly, we identified SNPs in human LHFP that were associated (P = 1.2 x 10−5) with heel BMD. In conclusion, we used GWAS and systems genetics to identify Lhfp as a regulator of osteoblast activity and bone mass. Osteoporosis is a common, chronic disease characterized by low bone mineral density (BMD) that puts millions of Americans at high risk of fracture. Variation in BMD in the general population is, in large part, determined by genetic factors. To identify novel genes influencing BMD, we performed a genome-wide association study in a panel of inbred mouse strains. We identified a locus on Chromosome 3 strongly associated with BMD. Using a combination of systems genetics approaches, we connected the expression of the Lhfp gene with BMD-associated genetic variants and predicted it influenced BMD by altering the activity of bone-forming osteoblasts. Using mice deficient in Lhfp, we demonstrated that Lhfp negatively regulates bone formation and BMD. These data suggest that inhibiting Lhfp may represent a novel therapeutic strategy to increase BMD and decrease the risk of fracture.
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Affiliation(s)
- Larry D. Mesner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States of America
| | - Gina M. Calabrese
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Basel Al-Barghouthi
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - John P. Sundberg
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | | | - Dana. A. Godfrey
- Center for Musculoskeletal Research, University of Rochester, Rochester, NY, United States of America
| | - Cheryl L. Ackert-Bicknell
- Center for Musculoskeletal Research, University of Rochester, Rochester, NY, United States of America
| | - Charles R. Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States of America
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
- * E-mail:
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24
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Pamir N, Pan C, Plubell DL, Hutchins PM, Tang C, Wimberger J, Irwin A, Vallim TQDA, Heinecke JW, Lusis AJ. Genetic control of the mouse HDL proteome defines HDL traits, function, and heterogeneity. J Lipid Res 2019; 60:594-608. [PMID: 30622162 PMCID: PMC6399512 DOI: 10.1194/jlr.m090555] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/10/2018] [Indexed: 12/30/2022] Open
Abstract
HDLs are nanoparticles with more than 80 associated proteins, phospholipids, cholesterol, and cholesteryl esters. The potential inverse relation of HDL to coronary artery disease (CAD) and the effects of HDL on myriad other inflammatory conditions warrant a better understanding of the genetic basis of the HDL proteome. We conducted a comprehensive genetic analysis of the regulation of the proteome of HDL isolated from a panel of 100 diverse inbred strains of mice (the hybrid mouse diversity panel) and examined protein composition and efflux capacity to identify novel factors that affect the HDL proteome. Genetic analysis revealed widely varied HDL protein levels across the strains. Some of this variation was explained by local cis-acting regulation, termed cis-protein quantitative trait loci (QTLs). Variations in apoA-II and apoC-3 affected the abundance of multiple HDL proteins, indicating a coordinated regulation. We identified modules of covarying proteins and defined a protein-protein interaction network that describes the protein composition of the naturally occurring subspecies of HDL in mice. Sterol efflux capacity varied up to 3-fold across the strains, and HDL proteins displayed distinct correlation patterns with macrophage and ABCA1-specific cholesterol efflux capacity and cholesterol exchange, suggesting that subspecies of HDL participate in discrete functions. The baseline and stimulated sterol efflux capacity phenotypes were associated with distinct QTLs with smaller effect size, suggesting a multigenetic regulation. Our results highlight the complexity of HDL particles by revealing the high degree of heterogeneity and intercorrelation, some of which is associated with functional variation, and support the concept that HDL-cholesterol alone is not an accurate measure of HDL’s properties, such as protection against CAD.
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Affiliation(s)
- Nathalie Pamir
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR
| | - Calvin Pan
- Departments of Genetics University of California at Los Angeles, Los Angeles, CA
| | - Deanna L Plubell
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR
| | | | - Chongren Tang
- Department of Medicine University of Washington, Seattle, WA
| | - Jake Wimberger
- Department of Medicine University of Washington, Seattle, WA
| | - Angela Irwin
- Department of Medicine University of Washington, Seattle, WA
| | | | - Jay W Heinecke
- Department of Medicine University of Washington, Seattle, WA
| | - Aldons J Lusis
- Departments of Genetics University of California at Los Angeles, Los Angeles, CA
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25
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Genetic Factors in Cannabinoid Use and Dependence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1162:129-150. [DOI: 10.1007/978-3-030-21737-2_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Makino K, Ishikawa A. Genetic identification of Ly75 as a novel quantitative trait gene for resistance to obesity in mice. Sci Rep 2018; 8:17658. [PMID: 30518881 PMCID: PMC6281609 DOI: 10.1038/s41598-018-36073-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/12/2018] [Indexed: 01/02/2023] Open
Abstract
Identification of causal quantitative trait genes (QTGs) governing obesity is challenging. We previously revealed that the lymphocyte antigen 75 (Ly75) gene with an immune function is a putative QTG for Pbwg1.5, a quantitative trait locus (QTL) for resistance to obesity found from wild mice (Mus musculus castaneus). The objective of this study was to identify a true QTG for Pbwg1.5 by a combined approach of a quantitative complementation test, qualitative phenotypic analyses and causal analysis using segregating populations. In a four-way cross population among an Ly75 knockout strain, a subcongenic strain carrying Pbwg1.5 and their background strains, the quantitative complementation test showed genetic evidence that the Ly75 locus is identical to Pbwg1.5. Qualitative phenotypic analyses in two intercross populations between knockout and background strains and between subcongenic and background strains suggested that Ly75 may have pleiotropic effects on weights of white fat pads and organs. Causal analysis in the intercross population between knockout and background strains revealed that only variation in fat pad weight is caused by the genotypic difference via the difference in liver Ly75 expression. The results showed that Ly75 is a true Pbwg1.5 QTG for resistance to obesity. The finding provides a novel insight for obesity biology.
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Affiliation(s)
- Keita Makino
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Akira Ishikawa
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan.
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27
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Knoll AT, Jiang K, Levitt P. Quantitative trait locus mapping and analysis of heritable variation in affiliative social behavior and co-occurring traits. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12431. [PMID: 29052939 PMCID: PMC5910301 DOI: 10.1111/gbb.12431] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/04/2017] [Accepted: 10/14/2017] [Indexed: 02/06/2023]
Abstract
Humans exhibit broad heterogeneity in affiliative social behavior. Twin and family studies show that individual differences in core dimensions of social behavior are heritable, yet there are knowledge gaps in understanding the underlying genetic and neurobiological mechanisms. Animal genetic reference panels (GRPs) provide a tractable strategy for examining the behavioral and genetic architecture of complex traits. Here, using males from 50 mouse strains from the BXD GRP, 4 domains of affiliative social behavior-social approach, social recognition, direct social interaction (DSI) (partner sniffing) and vocal communication-were examined in 2 widely used behavioral tasks-the 3-chamber and DSI tasks. There was continuous and broad variation in social and nonsocial traits, with moderate to high heritability of social approach sniff preference (0.31), ultrasonic vocalization (USV) count (0.39), partner sniffing (0.51), locomotor activity (0.54-0.66) and anxiety-like behavior (0.36). Principal component analysis shows that variation in social and nonsocial traits are attributable to 5 independent factors. Genome-wide mapping identified significant quantitative trait loci for USV count on chromosome (Chr) 18 and locomotor activity on Chr X, with suggestive loci and candidate quantitative trait genes identified for all traits with one notable exception-partner sniffing in the DSI task. The results show heritable variation in sociability, which is independent of variation in activity and anxiety-like traits. In addition, a highly heritable and ethological domain of affiliative sociability-partner sniffing-appears highly polygenic. These findings establish a basis for identifying functional natural variants, leading to a new understanding typical and atypical sociability.
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Affiliation(s)
- A. T. Knoll
- Program in Developmental NeurogeneticsInstitute for the Developing Mind, The Saban Research Institute, Children’s Hospital Los AngelesLos AngelesCA
- Department of PediatricsKeck School of Medicine of the University of Southern CaliforniaLos AngelesCA
| | - K. Jiang
- Department of PediatricsKeck School of Medicine of the University of Southern CaliforniaLos AngelesCA
| | - P. Levitt
- Program in Developmental NeurogeneticsInstitute for the Developing Mind, The Saban Research Institute, Children’s Hospital Los AngelesLos AngelesCA
- Department of PediatricsKeck School of Medicine of the University of Southern CaliforniaLos AngelesCA
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28
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Zhang J, Malo D, Mott R, Panthier JJ, Montagutelli X, Jaubert J. Identification of new loci involved in the host susceptibility to Salmonella Typhimurium in collaborative cross mice. BMC Genomics 2018; 19:303. [PMID: 29703142 PMCID: PMC5923191 DOI: 10.1186/s12864-018-4667-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 04/12/2018] [Indexed: 12/31/2022] Open
Abstract
Background Salmonella is a Gram-negative bacterium causing a wide range of clinical syndromes ranging from typhoid fever to diarrheic disease. Non-typhoidal Salmonella (NTS) serovars infect humans and animals, causing important health burden in the world. Susceptibility to salmonellosis varies between individuals under the control of host genes, as demonstrated by the identification of over 20 genetic loci in various mouse crosses. We have investigated the host response to S. Typhimurium infection in 35 Collaborative Cross (CC) strains, a genetic population which involves wild-derived strains that had not been previously assessed. Results One hundred and forty-eight mice from 35 CC strains were challenged intravenously with 1000 colony-forming units (CFUs) of S. Typhimurium. Bacterial load was measured in spleen and liver at day 4 post-infection. CC strains differed significantly (P < 0.0001) in spleen and liver bacterial loads, while sex and age had no effect. Two significant quantitative trait loci (QTLs) on chromosomes 8 and 10 and one suggestive QTL on chromosome 1 were found for spleen bacterial load, while two suggestive QTLs on chromosomes 6 and 17 were found for liver bacterial load. These QTLs are caused by distinct allelic patterns, principally involving alleles originating from the wild-derived founders. Using sequence variations between the eight CC founder strains combined with database mining for expression in target organs and known immune phenotypes, we were able to refine the QTLs intervals and establish a list of the most promising candidate genes. Furthermore, we identified one strain, CC042/GeniUnc (CC042), as highly susceptible to S. Typhimurium infection. Conclusions By exploring a broader genetic variation, the Collaborative Cross population has revealed novel loci of resistance to Salmonella Typhimurium. It also led to the identification of CC042 as an extremely susceptible strain. Electronic supplementary material The online version of this article (10.1186/s12864-018-4667-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Zhang
- Institut Pasteur, Department of Development & Stem Cell Biology, Mouse Functional Genetics, F-75015, Paris, France.,Centre National de la Recherche Scientifique, CNRS UMR 3738, F-75015, Paris, France
| | - Danielle Malo
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Richard Mott
- University College London, UCL Genetics Institute, London, UK
| | - Jean-Jacques Panthier
- Institut Pasteur, Department of Development & Stem Cell Biology, Mouse Functional Genetics, F-75015, Paris, France.,Centre National de la Recherche Scientifique, CNRS UMR 3738, F-75015, Paris, France
| | - Xavier Montagutelli
- Institut Pasteur, Department of Development & Stem Cell Biology, Mouse Functional Genetics, F-75015, Paris, France.,Centre National de la Recherche Scientifique, CNRS UMR 3738, F-75015, Paris, France
| | - Jean Jaubert
- Institut Pasteur, Department of Development & Stem Cell Biology, Mouse Functional Genetics, F-75015, Paris, France. .,Centre National de la Recherche Scientifique, CNRS UMR 3738, F-75015, Paris, France.
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29
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Škrabar N, Turner LM, Pallares LF, Harr B, Tautz D. Using the
Mus musculus
hybrid zone to assess covariation and genetic architecture of limb bone lengths. Mol Ecol Resour 2018. [DOI: 10.1111/1755-0998.12776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Neva Škrabar
- Max‐Planck Institute for Evolutionary Biology Plön Germany
| | - Leslie M. Turner
- Max‐Planck Institute for Evolutionary Biology Plön Germany
- Department of Biology and Biochemistry Milner Centre for Evolution University of Bath Bath UK
| | - Luisa F. Pallares
- Max‐Planck Institute for Evolutionary Biology Plön Germany
- Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton NJ USA
| | - Bettina Harr
- Max‐Planck Institute for Evolutionary Biology Plön Germany
| | - Diethard Tautz
- Max‐Planck Institute for Evolutionary Biology Plön Germany
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30
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She R, Jarosz DF. Mapping Causal Variants with Single-Nucleotide Resolution Reveals Biochemical Drivers of Phenotypic Change. Cell 2018; 172:478-490.e15. [PMID: 29373829 PMCID: PMC5788306 DOI: 10.1016/j.cell.2017.12.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/21/2017] [Accepted: 12/06/2017] [Indexed: 12/13/2022]
Abstract
Understanding the sequence determinants that give rise to diversity among individuals and species is the central challenge of genetics. However, despite ever greater numbers of sequenced genomes, most genome-wide association studies cannot distinguish causal variants from linked passenger mutations spanning many genes. We report that this inherent challenge can be overcome in model organisms. By pushing the advantages of inbred crossing to its practical limit in Saccharomyces cerevisiae, we improved the statistical resolution of linkage analysis to single nucleotides. This "super-resolution" approach allowed us to map 370 causal variants across 26 quantitative traits. Missense, synonymous, and cis-regulatory mutations collectively gave rise to phenotypic diversity, providing mechanistic insight into the basis of evolutionary divergence. Our data also systematically unmasked complex genetic architectures, revealing that multiple closely linked driver mutations frequently act on the same quantitative trait. Single-nucleotide mapping thus complements traditional deletion and overexpression screening paradigms and opens new frontiers in quantitative genetics.
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Affiliation(s)
- Richard She
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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31
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Genome-Wide Exome Analysis of Cmv5-Disparate Mouse Strains that Differ in Host Resistance to Murine Cytomegalovirus Infection. G3-GENES GENOMES GENETICS 2017; 7:1979-1984. [PMID: 28450376 PMCID: PMC5473773 DOI: 10.1534/g3.117.042531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Host resistance to murine cytomegalovirus (MCMV) varies in different strains of laboratory mice due to differences in expression of determinants that control and clear viral infection. The major histocompatibility complex class I Dk molecule is one such determinant that controls MCMV through the action of natural killer (NK) cells. However, the extent of NK cell–mediated Dk-dependent resistance to infection varies in different mouse strains. The molecular genetic basis of this variation remains unclear. Previous work to examine the Dk effect on MCMV resistance in MA/My × C57L offspring discovered multiple quantitative trait loci (QTL) that may serve to modify NK cells or their capacity to respond during MCMV infection. One QTL in particular, Cmv5, was found to regulate the frequency of NK cells and secondary lymphoid organ structure in spleen during MCMV infection. Cmv5 alleles, however, have not been identified. We therefore sequenced and analyzed genome-wide exome (GWE) variants, including those aligned to the critical genetic interval, in Cmv5-disparate mouse strains. Their GWE variant profiles were compared to assess strain-specific sequence data integrity and to analyze mouse strain relatedness across the genome. GWE content was further compared against data from the Mouse Genomes Project. This approach was developed as a platform for using GWE variants to define genomic regions of divergence and similarity in different mouse strains while also validating the overall quality of GWE sequence data. Moreover, the analysis provides a framework for the selection of novel QTL candidate sequences, including at the Cmv5 critical region.
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32
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Abstract
Identifying genes and pathways that contribute to differences in neurobehavioural traits is a key goal in psychiatric research. Despite considerable success in identifying quantitative trait loci (QTLs) associated with behaviour in laboratory rodents, pinpointing the causal variants and genes is more challenging. For a long time, the main obstacle was the size of QTLs, which could encompass tens if not hundreds of genes. However, recent studies have exploited mouse and rat resources that allow mapping of phenotypes to narrow intervals, encompassing only a few genes. Here, we review these studies, showcase the rodent resources they have used and highlight the insights into neurobehavioural traits provided to date. We discuss what we see as the biggest challenge in the field - translating QTLs into biological knowledge by experimentally validating and functionally characterizing candidate genes - and propose that the CRISPR/Cas genome-editing system holds the key to overcoming this obstacle. Finally, we challenge traditional views on inbred versus outbred resources in the light of recent resource and technology developments.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095-1761, USA
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Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice. Sci Rep 2017; 7:41204. [PMID: 28145470 PMCID: PMC5286500 DOI: 10.1038/srep41204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 12/16/2016] [Indexed: 12/30/2022] Open
Abstract
Although the search for quantitative trait loci for behaviour remains a considerable challenge, the complicated genetic architecture of quantitative traits is beginning to be understood. The current project utilised heterogeneous stock (HS) male mice (n = 580) to investigate the genetic basis for brain weights, activity, anxiety and cognitive phenotypes. We identified 126 single nucleotide polymorphisms (SNPs) in genes involved in regulation of neurotransmitter systems, nerve growth/death and gene expression, and subsequently investigated their associations with changes in behaviour and/or brain weights in our sample. We found significant associations between four SNP-phenotype pairs, after controlling for multiple testing. Specificity protein 2 (Sp2, rs3708840), tryptophan hydroxylase 1 (Tph1, rs262731280) and serotonin receptor 3A (Htr3a, rs50670893) were associated with activity/anxiety behaviours, and microtubule-associated protein 2 (Map2, rs13475902) was associated with cognitive performance. All these genes except for Tph1 were expressed in the brain above the array median, and remained significantly associated with relevant behaviours after controlling for the family structure. Additionally, we found evidence for a correlation between Htr3a expression and activity. We discuss our findings in the light of the advantages and limitations of currently available mouse genetic tools, suggesting further directions for association studies in rodents.
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Ishikawa A. Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests. PLoS One 2017; 12:e0170652. [PMID: 28114323 PMCID: PMC5256930 DOI: 10.1371/journal.pone.0170652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/09/2017] [Indexed: 11/19/2022] Open
Abstract
It is still challenging to identify causal genes governing obesity. Pbwg1.5, a quantitative trait locus (QTL) for resistance to obesity, was previously discovered from wild Mus musculus castaneus mice and was fine-mapped to a 2.1-Mb genomic region of mouse chromosome 2, where no known gene with an effect on white adipose tissue (WAT) has been reported. The aim of this study was to identify a strong candidate gene for Pbwg1.5 by an integration approach of transcriptome analysis (RNA-sequencing followed by real-time PCR analysis) and the causal inference test (CIT), a statistical method to infer causal relationships between diplotypes, gene expression and trait values. Body weight, body composition and biochemical traits were measured in F2 mice obtained from an intercross between the C57BL/6JJcl strain and a congenic strain carrying Pbwg1.5 on the C57BL/6JJcl background. The F2 mice showed significant diplotype differences in 12 traits including body weight, WAT weight and serum cholesterol/triglyceride levels. The transcriptome analysis revealed that Ly75, Pla2r1, Fap and Gca genes were differentially expressed in the liver and that Fap, Ifih1 and Grb14 were differentially expressed in WAT. However, CITs indicated statistical evidence that only the liver Ly75 gene mediated between genotype and WAT. Ly75 expression was negatively associated with WAT weight. The results suggested that Ly75 is a putative quantitative trait gene for the obesity-resistant Pbwg1.5 QTL discovered from the wild M. m. castaneus mouse. The finding provides a novel insight into a better understanding of the genetic basis for prevention of obesity.
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Affiliation(s)
- Akira Ishikawa
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
- * E-mail:
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Abstract
A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain.
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Affiliation(s)
- Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 77 S. Manassas Street, Memphis, TN, 38163, USA.
| | - Evan G Williams
- Department of Biology, Institute for Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
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Podliesna S, Bezzina CR, Lodder EM. Complex Genetics of Cardiovascular Traits in Mice: F2-Mapping of QTLs and Their Underlying Genes. Methods Mol Biol 2017; 1488:431-454. [PMID: 27933537 DOI: 10.1007/978-1-4939-6427-7_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this chapter, we will use the example of the identification of Tnni3k as a modulator of cardiac conduction to introduce you to the use of a murine F2-generation intercross as a powerful method for the identification of novel genes relevant for cardiovascular traits. Murine F2-progeny is a genetically diverse panel of mice with differences in phenotype manifestations, e.g. cardiovascular traits such as cardiomyopathy and ECG parameters. This chapter discusses the best strategies for using F2-mice for genetic mapping. Moreover, we provide an example of the feasibility of identification of new genes modulating cardiac function utilizing the technique of mapping quantitative trait loci (QTLs) and a systems genetics integration of available genetic, gene expression, and phenotypic data.
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Affiliation(s)
- Svitlana Podliesna
- Department of Clinical and Experimental Cardiology, Academic Medical Centre (AMC), University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Academic Medical Centre (AMC), University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Elisabeth M Lodder
- Department of Clinical and Experimental Cardiology, Academic Medical Centre (AMC), University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
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Genome Sequencing of Chromosome 1 Substitution Lines Derived from Chinese Wild Mice Revealed a Unique Resource for Genetic Studies of Complex Traits. G3-GENES GENOMES GENETICS 2016; 6:3571-3580. [PMID: 27605517 PMCID: PMC5100856 DOI: 10.1534/g3.116.033902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mouse resources such as Collaborative Cross, outbred stocks, Hybrid Mouse Diversity Panel, and chromosome substitution strains have been instrumental to many progresses in the studies of complex traits genetics. We have established a population of chromosome 1 (Chr 1) substitution lines (C1SLs) in which donor chromosomes were derived from Chinese wild mice. Genome sequencing of 18 lines of this population showed that Chr 1 had been replaced by the donor chromosome. About 4.5 million unique single nucleotide polymorphisms and indels were discovered on Chr 1, of which 1.3 million were novel. Compared with sequenced classical inbred strains, Chr 1 of each C1SL had fivefold more variants, and more loss of function and potentially regulatory variants. Further haplotype analysis showed that the donor chromosome accumulated more historical recombination events, with the largest haplotype block being only 100 kb, and about 57% of the blocks were <1 kb. Subspecies origin analysis showed that these chromosomes had a mosaic genome structure that dominantly originated from Mus musculus musculus and M. m. castaneus subspecies, except for the C57BL/6J-Chr1KM line from M. m. domesticus. In addition, phenotyping four of these lines on blood biochemistry suggested that there were substantial phenotypic variations among our lines, especially line C57BL/6J-Chr1HZ and donor strain C57BL/6J. Further gene ontology enrichment revealed that the differentially expressed genes among liver-expressed genes between C57BL/6J and C57BL/6J-Chr1HZ were enriched in lipid metabolism biological processes. All these characteristics enable C1SLs to be a unique resource for identifying and fine mapping quantitative trait loci on mouse Chr 1, and carrying out systems genetics studies of complex traits.
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Dowell R, Odell A, Richmond P, Malmer D, Halper-Stromberg E, Bennett B, Larson C, Leach S, Radcliffe RA. Genome characterization of the selected long- and short-sleep mouse lines. Mamm Genome 2016; 27:574-586. [PMID: 27651241 PMCID: PMC5110614 DOI: 10.1007/s00335-016-9663-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/22/2016] [Indexed: 01/29/2023]
Abstract
The Inbred Long- and Short-Sleep (ILS, ISS) mouse lines were selected for differences in acute ethanol sensitivity using the loss of righting response (LORR) as the selection trait. The lines show an over tenfold difference in LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect the genetic underpinnings of acute ethanol sensitivity. Here we have sequenced the genomes of the ILS and ISS to investigate the DNA variants that contribute to their sensitivity difference. We identified ~2.7 million high-confidence SNPs and small indels and ~7000 structural variants between the lines; variants were found to occur in 6382 annotated genes. Using a hidden Markov model, we were able to reconstruct the genome-wide ancestry patterns of the eight inbred progenitor strains from which the ILS and ISS were derived, and found that quantitative trait loci that have been mapped for LORR were slightly enriched for DNA variants. Finally, by mapping and quantifying RNA-seq reads from the ILS and ISS to their strain-specific genomes rather than to the reference genome, we found a substantial improvement in a differential expression analysis between the lines. This work will help in identifying and characterizing the DNA sequence variants that contribute to the difference in ethanol sensitivity between the ILS and ISS and will also aid in accurate quantification of RNA-seq data generated from the LXS RIs.
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Affiliation(s)
- Robin Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309, USA. .,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA. .,Department of Computer Science, University of Colorado Boulder, Boulder, CO, 80309, USA.
| | - Aaron Odell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Phillip Richmond
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Daniel Malmer
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Eitan Halper-Stromberg
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Beth Bennett
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA
| | - Colin Larson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA
| | - Sonia Leach
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Richard A Radcliffe
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, 80045, USA.
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Quantitative trait gene Slit2 positively regulates murine hematopoietic stem cell numbers. Sci Rep 2016; 6:31412. [PMID: 27503415 PMCID: PMC4977545 DOI: 10.1038/srep31412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 07/21/2016] [Indexed: 12/30/2022] Open
Abstract
Hematopoietic stem cells (HSC) demonstrate natural variation in number and function. The genetic factors responsible for the variations (or quantitative traits) are largely unknown. We previously identified a gene whose differential expression underlies the natural variation of HSC numbers in C57BL/6 (B6) and DBA/2 (D2) mice. We now report the finding of another gene, Slit2, on chromosome 5 that also accounts for variation in HSC number. In reciprocal chromosome 5 congenic mice, introgressed D2 alleles increased HSC numbers, whereas B6 alleles had the opposite effect. Using gene array and quantitative polymerase chain reaction, we identified Slit2 as a quantitative trait gene whose expression was positively correlated with the number of HSCs. Ectopic expression of Slit2 not only increased the number of the long-term colony forming HSCs, but also enhanced their repopulation capacity upon transplantation. Therefore, Slit2 is a novel quantitative trait gene and a positive regulator of the number and function of murine HSCs. This finding suggests that Slit2 may be a potential therapeutic target for the effective in vitro and in vivo expansion of HSCs without compromising normal hematopoiesis.
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Bennett B, Larson C, Richmond PA, Odell AT, Saba LM, Tabakoff B, Dowell R, Radcliffe RA. Quantitative trait locus mapping of acute functional tolerance in the LXS recombinant inbred strains. Alcohol Clin Exp Res 2016; 39:611-20. [PMID: 25833023 DOI: 10.1111/acer.12678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/09/2015] [Indexed: 01/23/2023]
Abstract
BACKGROUND We previously reported that acute functional tolerance (AFT) to the hypnotic effects of alcohol was significantly correlated with drinking in the dark (DID) in the LXS recombinant inbred panel, but only in mice that had been pretreated with alcohol. Here, we have conducted quantitative trait locus (QTL) mapping for AFT. DNA sequencing of the progenitor ILS and ISS strains and microarray analyses were also conducted to identify candidate genes and functional correlates. METHODS LXS mice were given either saline or alcohol (5 g/kg) on day 1 and then tested for loss of righting reflex AFT on day 2. QTLs were mapped using standard procedures. Two microarray analyses from brain were conducted: (i) naïve LXS mice and (ii) an alcohol treatment time course in the ILS and ISS. The full genomes of the ILS and ISS were sequenced to a depth of approximately 30×. RESULTS A significant QTL for AFT in the alcohol pretreatment group was mapped to distal chromosome 4; numerous suggestive QTLs were also mapped. Preference drinking and DID have previously been mapped to the chromosome 4 locus. The credible interval of the significant chromosome 4 QTL spanned 23 Mb and included 716 annotated genes of which 150 had at least 1 nonsynonymous single nucleotide polymorphism or small indel that differed between the ILS and ISS; expression of 48 of the genes was cis-regulated. Enrichment analysis indicated broad functional categories underlying AFT, including proteolysis, transcription regulation, chromatin modification, protein kinase activity, and apoptosis. CONCLUSIONS The chromosome 4 QTL is a key region containing possibly pleiotropic genes for AFT and drinking behavior. Given that the region contains many viable candidates and a large number of the genes in the interval fall into 1 or more of the enriched functional categories, we postulate that many genes of varying effect size contribute to the observed QTL effect.
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Affiliation(s)
- Beth Bennett
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Ackert-Bicknell CL, Rosen CJ. Passenger Gene Mutations: Unwanted Guests in Genetically Modified Mice. J Bone Miner Res 2016; 31:270-3. [PMID: 26684928 PMCID: PMC4752421 DOI: 10.1002/jbmr.2772] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Cheryl L Ackert-Bicknell
- Center for Musculoskeletal Research, Department of Orthopaedics and Rehabilitation, University of Rochester, School of Medicine and Dentistry, Rochester, New York, 14624, USA
| | - Clifford J Rosen
- Maine Medical Center Research Institute, Scarborough, Maine, 04074
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Mattsson CM, Wheeler MT, Waggott D, Caleshu C, Ashley EA. Sports genetics moving forward: lessons learned from medical research. Physiol Genomics 2016; 48:175-82. [PMID: 26757801 DOI: 10.1152/physiolgenomics.00109.2015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Sports genetics can take advantage of lessons learned from human disease genetics. By righting past mistakes and increasing scientific rigor, we can magnify the breadth and depth of knowledge in the field. We present an outline of challenges facing sports genetics in the light of experiences from medical research. Sports performance is complex, resulting from a combination of a wide variety of different traits and attributes. Improving sports genetics will foremost require analyses based on detailed phenotyping. To find widely valid, reproducible common variants associated with athletic phenotypes, study sample sizes must be dramatically increased. One paradox is that in order to confirm relevance, replications in specific populations must be undertaken. Family studies of athletes may facilitate the discovery of rare variants with large effects on athletic phenotypes. The complexity of the human genome, combined with the complexity of athletic phenotypes, will require additional metadata and biological validation to identify a comprehensive set of genes involved. Analysis of personal genetic and multiomic profiles contribute to our conceptualization of precision medicine; the same will be the case in precision sports science. In the refinement of sports genetics it is essential to evaluate similarities and differences between sexes and among ethnicities. Sports genetics to date have been hampered by small sample sizes and biased methodology, which can lead to erroneous associations and overestimation of effect sizes. Consequently, currently available genetic tests based on these inherently limited data cannot predict athletic performance with any accuracy.
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Affiliation(s)
- C Mikael Mattsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California; Åstrand Laboratory of Work Physiology, The Swedish School of Sport and Health Sciences, Stockholm, Sweden;
| | - Matthew T Wheeler
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California; Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California
| | - Daryl Waggott
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California; Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California
| | - Colleen Caleshu
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California; Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California; Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, California; and
| | - Euan A Ashley
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California; Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, California; Department of Genetics, Stanford University, Stanford, California
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Atamni HJAT, Mott R, Soller M, Iraqi FA. High-fat-diet induced development of increased fasting glucose levels and impaired response to intraperitoneal glucose challenge in the collaborative cross mouse genetic reference population. BMC Genet 2016; 17:10. [PMID: 26728312 PMCID: PMC4700737 DOI: 10.1186/s12863-015-0321-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/20/2015] [Indexed: 12/17/2022] Open
Abstract
Background The prevalence of Type 2 Diabetes (T2D) mellitus in the past decades, has reached epidemic proportions. Several lines of evidence support the role of genetic variation in the pathogenesis of T2D and insulin resistance. Elucidating these factors could contribute to developing new medical treatments and tools to identify those most at risk. The aim of this study was to characterize the phenotypic response of the Collaborative Cross (CC) mouse genetic resource population to high-fat diet (HFD) induced T2D-like disease to evluate its suitability for this purpose. Results We studied 683 mice of 21 different lines of the CC population. Of these, 265 mice (149 males and 116 females) were challenged by HFD (42 % fat); and 384 mice (239 males and145 females) of 17 of the 21 lines were reared as control group on standard Chow diet (18 % fat). Briefly, 8 week old mice were maintained on HFD until 20 weeks of age, and subsequently assessed by intraperitoneal glucose tolerance test (IPGTT). Biweekly body weight (BW), body length (BL), waist circumstance (WC), and body mass index (BMI) were measured. On statistical analysis, trait measurements taken at 20 weeks of age showed significant sex by diet interaction across the different lines and traits. Consequently, males and females were analyzed, separately. Differences among lines were analyzed by ANOVA and shown to be significant (P <0.05), for BW, WC, BMI, fasting blood glucose, and IPGTT-AUC. We use these data to infer broad sense heritability adjusted for number of mice tested in each line; coefficient of genetic variation; genetic correlations between the same trait in the two sexes, and phenotypic correlations between different traits in the same sex. Conclusions These results are consistent with the hypothesis that host susceptibility to HFD-induced T2D is a complex trait and controlled by multiple genetic factors and sex, and that the CC population can be a powerful tool for genetic dissection of this trait. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0321-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hanifa J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
| | | | | | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, Tel-Aviv, 69978, Israel.
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Burrows EL, Hannan AJ. Cognitive endophenotypes, gene-environment interactions and experience-dependent plasticity in animal models of schizophrenia. Biol Psychol 2015; 116:82-9. [PMID: 26687973 DOI: 10.1016/j.biopsycho.2015.11.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 11/26/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022]
Abstract
Schizophrenia is a devastating brain disorder caused by a complex and heterogeneous combination of genetic and environmental factors. In order to develop effective new strategies to prevent and treat schizophrenia, valid animal models are required which accurately model the disorder, and ideally provide construct, face and predictive validity. The cognitive deficits in schizophrenia represent some of the most debilitating symptoms and are also currently the most poorly treated. Therefore it is crucial that animal models are able to capture the cognitive dysfunction that characterizes schizophrenia, as well as the negative and psychotic symptoms. The genomes of mice have, prior to the recent gene-editing revolution, proven the most easily manipulable of mammalian laboratory species, and hence most genetic targeting has been performed using mouse models. Importantly, when key environmental factors of relevance to schizophrenia are experimentally manipulated, dramatic changes in the phenotypes of these animal models are often observed. We will review recent studies in rodent models which provide insight into gene-environment interactions in schizophrenia. We will focus specifically on environmental factors which modulate levels of experience-dependent plasticity, including environmental enrichment, cognitive stimulation, physical activity and stress. The insights provided by this research will not only help refine the establishment of optimally valid animal models which facilitate development of novel therapeutics, but will also provide insight into the pathogenesis of schizophrenia, thus identifying molecular and cellular targets for future preclinical and clinical investigations.
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Affiliation(s)
- Emma L Burrows
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Parkville, VIC 3010, Australia; Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia.
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Logunova N, Korotetskaya M, Polshakov V, Apt A. The QTL within the H2 Complex Involved in the Control of Tuberculosis Infection in Mice Is the Classical Class II H2-Ab1 Gene. PLoS Genet 2015; 11:e1005672. [PMID: 26618355 PMCID: PMC4664271 DOI: 10.1371/journal.pgen.1005672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
The level of susceptibility to tuberculosis (TB) infection depends upon allelic variations in numerous interacting genes. In our mouse model system, the whole-genome quantitative trait loci (QTLs) scan revealed three QTLs involved in TB control on chromosomes 3, 9, and in the vicinity of the H2 complex on chromosome 17. For the present study, we have established a panel of new congenic, MHC-recombinant mouse strains bearing differential small segments of chromosome 17 transferred from the TB-susceptible I/St (H2j) strain onto the genetic background of TB-resistant C57BL/6 (B6) mice (H2b). This allowed narrowing the QTL interval to 17Ch: 33, 77–34, 34 Mb, containing 36 protein-encoding genes. Cloning and sequencing of the H2j allelic variants of these genes demonstrated profound polymorphic variations compare to the H2b haplotype. In two recombinant strains, B6.I-249.1.15.100 and B6.I-249.1.15.139, recombination breakpoints occurred in different sites of the H2-Aβ 1 gene (beta-chain of the Class II heterodimer H2-A), providing polymorphic variations in the domain β1 of the Aβ-chain. These variations were sufficient to produce different TB-relevant phenotypes: the more susceptible B6.I-249.1.15.100 strain demonstrated shorter survival time, more rapid body weight loss, higher mycobacterial loads in the lungs and more severe lung histopathology compared to the more resistant B6.I-249.1.15.139 strain. CD4+ T cells recognized mycobacterial antigens exclusively in the context of the H2-A Class II molecule, and the level of IFN-γ-producing CD4+ T cells in the lungs was significantly higher in the resistant strain. Thus, we directly demonstrated for the first time that the classical H2- Ab1 Class II gene is involved in TB control. Molecular modeling of the H2-Aj product predicts that amino acid (AA) substitutions in the Aβ-chain modify the motif of the peptide–MHC binding groove. Moreover, unique AA substitutions in both α- and β-chains of the H2-Aj molecule might affect its interactions with the T-cell receptor (TCR). Many genes of the host regulate interactions with Mycobacterium tuberculosis and determine the level of susceptibility to, and severity of, tuberculosis (TB). Identification of these genes and their alleles is continuing and contributes new knowledge about the host-pathogen interactions. So far, forward genetic approaches (from phenotype to gene) have identified several chromosomal segments involved in genetic control of TB in mice (quantitative trait loci—QTL), but only one particular gene, Ipr1, has been identified. Here, we report the identification of a second TB-controlling gene. On the basis of a pair of mouse inbred strains with polar susceptibility to TB infection (susceptible I/St and more resistant C57BL/6) we established a panel of recombinant strains carrying small segments of Chromosome 17 from I/St on the genetic background of C57BL/6. A combination of genetic mapping, gene sequencing, TB phenotypes assessment and immunological approaches demonstrates that the H2-Ab1 gene encoding the beta-chain of the Class II heterodimer H2-A determines susceptibility to TB infection. The importance of allelic polymorphisms in Class II genes encoding antigen-presenting molecules in susceptibility to infection has been suspected. This is the first prove of this role obtained by the methods of classical forward genetics.
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Affiliation(s)
- Nadezhda Logunova
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
- * E-mail: (NL); (AA)
| | - Maria Korotetskaya
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
| | - Vladimir Polshakov
- Center for Magnetic Tomography & Spectroscopy, School of Fundamental Medicine, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Apt
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
- Department of Immunology, School of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (NL); (AA)
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Koehn DR, Meyer KJ, Anderson MG. Genetic Evidence for Differential Regulation of Corneal Epithelial and Stromal Thickness. Invest Ophthalmol Vis Sci 2015; 56:5599-607. [PMID: 26305532 DOI: 10.1167/iovs.15-17179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Central corneal thickness (CCT) is a quantitative trait associated with keratoconus and primary open-angle glaucoma. Although CCT is highly heritable, known genetic variations explain only a fraction of the phenotypic variability. The purpose of this study was to identify additional CCT-influencing loci using inbred strains of mice. METHODS Cohorts of 82 backcrossed (N2) and 99 intercrossed (F2) mice were generated from crosses between recombinant inbred BXD24/TyJ and wild-derived CAST/EiJ mice. Using anterior chamber optical coherence tomography, mice were phenotyped at 10 to 12 weeks of age, genotyped based on 96 genome-wide single nucleotide polymorphisms (SNPs), and subjected to quantitative trait locus (QTL) analysis. RESULTS In an analysis of total CCT among all mice, two loci passed the significance threshold of P = 0.05. These were on Chr 3 and Chr 11 (Cctq4 and Cctq5, respectively). A third locus of interest was identified in a two-dimensional pairwise analysis; this locus on Chr 14 (Cctq6) exhibited a significant additive effect with Cctq5. Independent analyses of the dataset for epithelial and stromal thickness revealed that Cctq4 is specific to the epithelial layer and that Cctq5 and Cctq6 are specific to the stromal layer. CONCLUSIONS Our findings demonstrate a quantitative multigenic pattern of CCT inheritance in mice and identify three previously unrecognized CCT-influencing loci: Cctq4, Cctq5, and Cctq6. This is the first demonstration that distinct layers of the cornea are under differential genetic control and highlights the need to refine the design of future genome-wide association studies of CCT.
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Affiliation(s)
- Demelza R Koehn
- Department of Molecular Physiology and Biophysics University of Iowa, Iowa City, Iowa, United States
| | - Kacie J Meyer
- Department of Molecular Physiology and Biophysics University of Iowa, Iowa City, Iowa, United States
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics University of Iowa, Iowa City, Iowa, United States 2Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States 3Center for the Prevention and Treatment of Visual Lo
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Gralinski LE, Ferris MT, Aylor DL, Whitmore AC, Green R, Frieman MB, Deming D, Menachery VD, Miller DR, Buus RJ, Bell TA, Churchill GA, Threadgill DW, Katze MG, McMillan L, Valdar W, Heise MT, Pardo-Manuel de Villena F, Baric RS. Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross. PLoS Genet 2015; 11:e1005504. [PMID: 26452100 PMCID: PMC4599853 DOI: 10.1371/journal.pgen.1005504] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/15/2015] [Indexed: 01/21/2023] Open
Abstract
New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes. Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel, we demonstrate a greatly expanded range of phenotypes relative to classical mouse models of SARS-CoV infection including lung pathology, weight loss and viral titer. Genetic mapping revealed several loci contributing to differential disease responses, including an 8.5Mb locus associated with vascular cuffing on chromosome 3 that contained 23 genes and 13 noncoding RNAs. Integrating phenotypic and genetic data narrowed this region to a single gene, Trim55, an E3 ubiquitin ligase with a role in muscle fiber maintenance. Lung pathology and transcriptomic data from mice genetically deficient in Trim55 were used to validate its role in SARS-CoV-induced vascular cuffing and inflammation. These data establish the Collaborative Cross platform as a powerful genetic resource for uncovering genetic contributions of complex traits in microbial disease severity, inflammation and virus replication in models of outbred populations.
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Affiliation(s)
- Lisa E. Gralinski
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David L. Aylor
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alan C. Whitmore
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Richard Green
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Matthew B. Frieman
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Damon Deming
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Vineet D. Menachery
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Darla R. Miller
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ryan J. Buus
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Timothy A. Bell
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - David W. Threadgill
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America
| | - Michael G. Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - William Valdar
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Mark T. Heise
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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48
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The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis. Cell 2015; 162:23-32. [PMID: 26140590 DOI: 10.1016/j.cell.2015.06.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 01/16/2023]
Abstract
Research into the genetic and environmental factors behind complex trait variation has traditionally been segregated into distinct scientific camps. The reductionist approach aims to decrypt phenotypic variability bit by bit, founded on the underlying hypothesis that genome-to-phenome relations are largely constructed from the additive effects of their molecular players. In contrast, the systems approach aims to examine large-scale interactions of many components simultaneously, on the premise that interactions in gene networks can be both linear and non-linear. Both approaches are complementary, and they are becoming increasingly intertwined due to developments in gene editing tools, omics technologies, and population resources. Together, these strategies are beginning to drive the next era in complex trait research, paving the way to improve agriculture and toward more personalized medicine.
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Dawes M, Kochan KJ, Riggs PK, Timothy Lightfoot J. Differential miRNA expression in inherently high- and low-active inbred mice. Physiol Rep 2015; 3:3/7/e12469. [PMID: 26229004 PMCID: PMC4552544 DOI: 10.14814/phy2.12469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/26/2015] [Indexed: 01/12/2023] Open
Abstract
Despite established health benefits of regular exercise, the majority of Americans do not meet the recommended levels of physical activity. While it is known that voluntary activity levels are largely heritable, the genetic mechanisms that regulate activity are not well understood. MicroRNAs (miRNAs) are small non-coding RNAs that inhibit transcription by binding to a target gene, inhibiting protein production. The purpose of this study was to investigate differential miRNA expression between inherently high- (C57L/J) and low- (C3H/HeJ) active inbred mice in soleus, extensor digitorum longus (EDL), and nucleus accumbens tissues. Expression was initially determined by miRNA microarray analysis, and selected miRNAs were validated by qRT-PCR. Expression of 13 miRNAs varied between strains in the nucleus accumbens, 20 in soleus, and eight in EDL, by microarray analysis. Two miRNAs were validated by qRT-PCR in the nucleus accumbens; miR-466 was downregulated (∼4 fold; P < 0.0004), and miR-342-5p was upregulated (∼115 fold; P < 0.0001) in high-active mice. MiR-466 was downregulated (∼5 fold; P < 0.0001) in the soleus of high-active mice as well. Interestingly, miR-466 is one of several miRNA families with sequence located in intron 10 of Sfmbt2; miRNAs at this locus are thought to drive imprinting of this gene. “Pathways in cancer” and “TGFβ signaling” were the most significant pathways of putative target genes in both the soleus and nucleus accumbens. Our results are the first to consider differential miRNA expression between high- and low-active mice, and suggest that miRNAs may play a role in regulation of physical activity.
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Affiliation(s)
- Michelle Dawes
- Department of Health and Kinesiology, Texas A&M University, College Station, Texas, USA
| | - Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - Penny K Riggs
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - J Timothy Lightfoot
- Department of Health and Kinesiology, Texas A&M University, College Station, Texas, USA
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Genetic regulation of bone strength: a review of animal model studies. BONEKEY REPORTS 2015; 4:714. [PMID: 26157577 DOI: 10.1038/bonekey.2015.83] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/16/2015] [Indexed: 12/24/2022]
Abstract
Population- and family-based studies have established that fragility fracture risk is heritable; yet, the genome-wide association studies published to date have only accounted for a small fraction of the known variation for fracture risk of either the femur or the lumbar spine. Much work has been carried out using animal models toward finding genetic loci that are associated with bone strength. Studies using animal models overcome some of the issues associated with using patient data, but caution is needed when interpreting the results. In this review, we examine the types of tests that have been used for forward genetics mapping in animal models to identify loci and/or genes that regulate bone strength and discuss the limitations of these test methods. In addition, we present a summary of the quantitative trait loci that have been mapped for bone strength in mice, rats and chickens. The majority of these loci co-map with loci for bone size and/or geometry and thus likely dictate strength via modulating bone size. Differences in bone matrix composition have been demonstrated when comparing inbred strains of mice, and these matrix differences may be associated with differences in bone strength. However, additional work is needed to identify loci that act on bone strength at the materials level.
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