1
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Heuer SE, Bloss EB, Howell GR. Strategies to dissect microglia-synaptic interactions during aging and in Alzheimer's disease. Neuropharmacology 2024; 254:109987. [PMID: 38705570 DOI: 10.1016/j.neuropharm.2024.109987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Age is the largest risk factor for developing Alzheimer's disease (AD), a neurodegenerative disorder that causes a progressive and severe dementia. The underlying cause of cognitive deficits seen in AD is thought to be the disconnection of neural circuits that control memory and executive functions. Insight into the mechanisms by which AD diverges from normal aging will require identifying precisely which cellular events are driven by aging and which are impacted by AD-related pathologies. Since microglia, the brain-resident macrophages, are known to have critical roles in the formation and maintenance of neural circuits through synaptic pruning, they are well-positioned to modulate synaptic connectivity in circuits sensitive to aging or AD. In this review, we provide an overview of the current state of the field and on emerging technologies being employed to elucidate microglia-synaptic interactions in aging and AD. We also discuss the importance of leveraging genetic diversity to study how these interactions are shaped across more realistic contexts. We propose that these approaches will be essential to define specific aging- and disease-relevant trajectories for more personalized therapeutics aimed at reducing the effects of age or AD pathologies on the brain. This article is part of the Special Issue on "Microglia".
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Affiliation(s)
- Sarah E Heuer
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Erik B Bloss
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, 04469, USA.
| | - Gareth R Howell
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, 04469, USA.
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2
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Poudel SB, Ruff RR, Yildirim G, Miller RA, Harrison DE, Strong R, Kirsch T, Yakar S. Development of primary osteoarthritis during aging in genetically diverse UM-HET3 mice. Arthritis Res Ther 2024; 26:118. [PMID: 38851726 PMCID: PMC11161968 DOI: 10.1186/s13075-024-03349-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Primary osteoarthritis (OA) occurs without identifiable underlying causes such as previous injuries or specific medical conditions. Age is a major contributing factor to OA, and as one ages, various joint tissues undergo gradual change, including degeneration of the articular cartilage, alterations in subchondral bone (SCB) morphology, and inflammation of the synovium. METHODS We investigated the prevalence of primary OA in aged, genetically diverse UM-HET3 mice. Articular cartilage (AC) integrity and SCB morphology were assessed in 182 knee joints of 22-25 months old mice using the Osteoarthritis Research Society International (OARSI) scoring system and micro-CT, respectively. Additionally, we explored the effects of methylene blue (MB) and mitoquinone (MitoQ), two agents that affect mitochondrial function, on the prevalence and progression of OA during aging. RESULTS Aged UM-HET3 mice showed a high prevalence of primary OA in both sexes. Significant positive correlations were found between cumulative AC (cAC) scores and synovitis in both sexes, and osteophyte formation in female mice. Ectopic chondrogenesis did not show significant correlations with cAC scores. Significant direct correlations were found between AC scores and inflammatory markers in chondrocytes, including matrix metalloproteinase-13, inducible nitric oxide synthase, and the NLR family pyrin domain containing-3 inflammasome in both sexes, indicating a link between OA severity and inflammation. Additionally, markers of cell cycle arrest, such as p16 and β-galactosidase, also correlated with AC scores. In male mice, no significant correlations were found between SCB morphology traits and cAC scores, while in female mice, significant correlations were found between cAC scores and tibial SCB plate bone mineral density. Notably, MB and MitoQ treatments influenced the disease's progression in a sex-specific manner. MB treatment significantly reduced cAC scores at the medial knee joint, while MitoQ treatment reduced cAC scores, but these did not reach significance. CONCLUSIONS Our study provides comprehensive insights into the prevalence and progression of primary OA in aged UM-HET3 mice, highlighting the sex-specific effects of MB and MitoQ treatments. The correlations between AC scores and various pathological factors underscore the multifaceted nature of OA and its association with inflammation and subchondral bone changes.
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Affiliation(s)
- Sher Bahadur Poudel
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24th Street, New York, NY, 10010-4086, USA
| | - Ryan R Ruff
- David B. Kriser Dental Center, Biostatistics Core, Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, NY, 10010-4086, USA
| | - Gozde Yildirim
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24th Street, New York, NY, 10010-4086, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI, 48105, USA
| | | | - Randy Strong
- Geriatric Research, Education and Clinical Center and Research Service, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Barshop Institute for Longevity and Aging Studies and Department of Pharmacology, The University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Thorsten Kirsch
- Department of Orthopaedic Surgery, NYU Grossman School of Medicine, New York, NY, 10100, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York, NY, 10010, USA
| | - Shoshana Yakar
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24th Street, New York, NY, 10010-4086, USA.
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3
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Tao M, Chen J, Cui C, Xu Y, Xu J, Shi Z, Yun J, Zhang J, Ou GZ, Liu C, Chen Y, Zhu ZR, Pan R, Xu S, Chen XX, Rokas A, Zhao Y, Wang S, Huang J, Shen XX. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. NATURE AGING 2024:10.1038/s43587-024-00641-z. [PMID: 38834883 DOI: 10.1038/s43587-024-00641-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Abstract
Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.
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Affiliation(s)
- Mei Tao
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Jiani Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunlai Cui
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yandong Xu
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Jingxiu Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zheyi Shi
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiaqi Yun
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junwei Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Zheng Ou
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeng-Rong Zhu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Suhong Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Xin Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yang Zhao
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Sibao Wang
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Jianhua Huang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China.
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China.
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4
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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. CELL GENOMICS 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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5
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Dumont BL, Gatti DM, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Lawal RA, Churchill GA, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. PLoS Genet 2024; 20:e1011228. [PMID: 38598567 PMCID: PMC11034653 DOI: 10.1371/journal.pgen.1011228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.
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Affiliation(s)
- Beth L. Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Mallory A. Ballinger
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Megan Phifer-Rixey
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Taichi A. Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, United States of America
| | - Lydia K. Wooldridge
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Raman Akinyanju Lawal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Gary A. Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology, Museum of Vertebrate Zoology, and Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America
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6
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Mansour H, Azrak R, Cook JJ, Hornburg KJ, Qi Y, Tian Y, Williams RW, Yeh FC, White LE, Johnson GA. An Open Resource: MR and light sheet microscopy stereotaxic atlas of the mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587246. [PMID: 38586051 PMCID: PMC10996689 DOI: 10.1101/2024.03.28.587246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
We have combined MR histology and light sheet microscopy (LSM) of five postmortem C57BL/6J mouse brains in a stereotaxic space based on micro-CT yielding a multimodal 3D atlas with the highest spatial and contrast resolution yet reported. Brains were imaged in situ with multi gradient echo (mGRE) and diffusion tensor imaging (DTI) at 15 μm resolution (∼ 2.4 million times that of clinical MRI). Scalar images derived from the average DTI and mGRE provide unprecedented contrast in 14 complementary 3D volumes, each highlighting distinct histologic features. The same tissues scanned with LSM and registered into the stereotaxic space provide 17 different molecular cell type stains. The common coordinate framework labels (CCFv3) complete the multimodal atlas. The atlas has been used to correct distortions in the Allen Brain Atlas and harmonize it with Franklin Paxinos. It provides a unique resource for stereotaxic labeling of mouse brain images from many sources.
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7
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Swanton C, Bernard E, Abbosh C, André F, Auwerx J, Balmain A, Bar-Sagi D, Bernards R, Bullman S, DeGregori J, Elliott C, Erez A, Evan G, Febbraio MA, Hidalgo A, Jamal-Hanjani M, Joyce JA, Kaiser M, Lamia K, Locasale JW, Loi S, Malanchi I, Merad M, Musgrave K, Patel KJ, Quezada S, Wargo JA, Weeraratna A, White E, Winkler F, Wood JN, Vousden KH, Hanahan D. Embracing cancer complexity: Hallmarks of systemic disease. Cell 2024; 187:1589-1616. [PMID: 38552609 DOI: 10.1016/j.cell.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Abstract
The last 50 years have witnessed extraordinary developments in understanding mechanisms of carcinogenesis, synthesized as the hallmarks of cancer. Despite this logical framework, our understanding of the molecular basis of systemic manifestations and the underlying causes of cancer-related death remains incomplete. Looking forward, elucidating how tumors interact with distant organs and how multifaceted environmental and physiological parameters impinge on tumors and their hosts will be crucial for advances in preventing and more effectively treating human cancers. In this perspective, we discuss complexities of cancer as a systemic disease, including tumor initiation and promotion, tumor micro- and immune macro-environments, aging, metabolism and obesity, cancer cachexia, circadian rhythms, nervous system interactions, tumor-related thrombosis, and the microbiome. Model systems incorporating human genetic variation will be essential to decipher the mechanistic basis of these phenomena and unravel gene-environment interactions, providing a modern synthesis of molecular oncology that is primed to prevent cancers and improve patient quality of life and cancer outcomes.
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Affiliation(s)
- Charles Swanton
- The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Elsa Bernard
- The Francis Crick Institute, London, UK; INSERM U981, Gustave Roussy, Villejuif, France
| | | | - Fabrice André
- INSERM U981, Gustave Roussy, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France; Paris Saclay University, Kremlin-Bicetre, France
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Allan Balmain
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | | | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gerard Evan
- The Francis Crick Institute, London, UK; Kings College London, London, UK
| | - Mark A Febbraio
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrés Hidalgo
- Department of Immunobiology, Yale University, New Haven, CT 06519, USA; Area of Cardiovascular Regeneration, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Johanna A Joyce
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | | | - Katja Lamia
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Department of Medical Oncology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Miriam Merad
- Department of immunology and immunotherapy, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn Musgrave
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK; Department of Haematology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sergio Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Jennifer A Wargo
- Department of Surgical Oncology, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashani Weeraratna
- Sidney Kimmel Cancer Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA; Ludwig Princeton Branch, Ludwig Institute for Cancer Research, Princeton, NJ, USA
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John N Wood
- Molecular Nociception Group, WIBR, University College London, London, UK
| | | | - Douglas Hanahan
- Lausanne Branch, Ludwig Institute for Cancer Research, Lausanne, Switzerland; Swiss institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland; Agora Translational Cancer Research Center, Lausanne, Switzerland.
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8
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Febo M, Mahar R, Rodriguez NA, Buraima J, Pompilus M, Pinto AM, Grudny MM, Bruijnzeel AW, Merritt ME. Age-related differences in affective behaviors in mice: possible role of prefrontal cortical-hippocampal functional connectivity and metabolomic profiles. Front Aging Neurosci 2024; 16:1356086. [PMID: 38524115 PMCID: PMC10957556 DOI: 10.3389/fnagi.2024.1356086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction The differential expression of emotional reactivity from early to late adulthood may involve maturation of prefrontal cortical responses to negative valence stimuli. In mice, age-related changes in affective behaviors have been reported, but the functional neural circuitry warrants further investigation. Methods We assessed age variations in affective behaviors and functional connectivity in male and female C57BL6/J mice. Mice aged 10, 30 and 60 weeks (wo) were tested over 8 weeks for open field activity, sucrose preference, social interactions, fear conditioning, and functional neuroimaging. Prefrontal cortical and hippocampal tissues were excised for metabolomics. Results Our results indicate that young and old mice differ significantly in affective behavioral, functional connectome and prefrontal cortical-hippocampal metabolome. Young mice show a greater responsivity to novel environmental and social stimuli compared to older mice. Conversely, late middle-aged mice (60wo group) display variable patterns of fear conditioning and during re-testing in a modified context. Functional connectivity between a temporal cortical/auditory cortex network and subregions of the anterior cingulate cortex and ventral hippocampus, and a greater network modularity and assortative mixing of nodes was stronger in young versus older adult mice. Metabolome analyses identified differences in several essential amino acids between 10wo mice and the other age groups. Discussion The results support differential expression of 'emotionality' across distinct stages of the mouse lifespan involving greater prefrontal-hippocampal connectivity and neurochemistry.
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Affiliation(s)
- Marcelo Febo
- Department of Psychiatry, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL, United States
| | - Rohit Mahar
- Department of Chemistry, Hemvati Nandan Bahuguna Garhwal University (A Central University), Srinagar Garhwal, Uttarakhand, India
| | - Nicholas A. Rodriguez
- Department of Psychiatry, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL, United States
| | - Joy Buraima
- Department of Psychiatry, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL, United States
| | - Marjory Pompilus
- Department of Psychiatry, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL, United States
| | - Aeja M. Pinto
- Department of Psychiatry, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL, United States
| | - Matteo M. Grudny
- Department of Psychiatry, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL, United States
| | - Adriaan W. Bruijnzeel
- Department of Psychiatry, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, FL, United States
| | - Matthew E. Merritt
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL, United States
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9
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Li H, Kawatake-Kuno A, Inaba H, Miyake Y, Itoh Y, Ueki T, Oishi N, Murai T, Suzuki T, Uchida S. Discrete prefrontal neuronal circuits determine repeated stress-induced behavioral phenotypes in male mice. Neuron 2024; 112:786-804.e8. [PMID: 38228137 DOI: 10.1016/j.neuron.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/26/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Chronic stress is a major risk factor for psychiatric disorders, including depression. Although depression is a highly heterogeneous syndrome, it remains unclear how chronic stress drives individual differences in behavioral responses. In this study, we developed a subtyping-based approach wherein stressed male mice were divided into four subtypes based on their behavioral patterns of social interaction deficits and anhedonia, the core symptoms of psychiatric disorders. We identified three prefrontal cortical neuronal projections that regulate repeated stress-induced behavioral phenotypes. Among them, the medial prefrontal cortex (mPFC)→anterior paraventricular thalamus (aPVT) pathway determines the specific behavioral subtype that exhibits both social deficits and anhedonia. Additionally, we identified the circuit-level molecular mechanism underlying this subtype: KDM5C-mediated epigenetic repression of Shisa2 transcription in aPVT projectors in the mPFC led to social deficits and anhedonia. Thus, we provide a set of biological aspects at the cellular, molecular, and epigenetic levels that determine distinctive stress-induced behavioral phenotypes.
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Affiliation(s)
- Haiyan Li
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Ayako Kawatake-Kuno
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiromichi Inaba
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Department of Psychiatry, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuka Miyake
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Takatoshi Ueki
- Department of Integrative Anatomy, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Naoya Oishi
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Department of Psychiatry, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Toshiya Murai
- Department of Psychiatry, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki-shi, Osaka 567-0047, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Shusaku Uchida
- SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan; Kyoto University Medical Science and Business Liaison Organization, Medical Innovation Center, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan; Department of Integrative Anatomy, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
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10
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Cousineau CM, Loftus K, Churchill GA, Bridges D. Cross-sectional association between blood cholesterol and calcium levels in genetically diverse strains of mice. FEBS Open Bio 2024; 14:426-433. [PMID: 38129969 PMCID: PMC10909986 DOI: 10.1002/2211-5463.13757] [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: 08/30/2023] [Revised: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023] Open
Abstract
Genetically diverse outbred mice allow for the study of genetic variation in the context of high dietary and environmental control. Using a machine learning approach, we investigated clinical and morphometric factors that associate with serum cholesterol levels in 840 genetically unique Diversity Outbred mice of both sexes (n = 417 male and 423 female), and on both a control chow (% kcals in diet: protein 22%, carbohydrate 62%, fat 16%, no cholesterol) and high fat high sucrose (% kcals in diet: protein 15%, carbohydrate 41%, fat 45%, 0.05% cholesterol). We find expected elevations of cholesterol in male mice, as well as in mice with elevated serum triglycerides and/or fed a high fat high sucrose diet. The third strongest predictor was serum calcium which correlated with serum cholesterol across both diets and sexes (r = 0.39-0.48) in both Diversity Outbred (P = 3.0 × 10-43 ) and BXD (P = 0.005) mice. This is in-line with several human cohort studies which show associations between calcium and cholesterol, and calcium as an independent predictor of cardiovascular events.
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Affiliation(s)
- Cody M. Cousineau
- Department of Nutritional SciencesUniversity of Michigan School of Public HealthAnn ArborMIUSA
| | - Kaelin Loftus
- Department of Nutritional SciencesUniversity of Michigan School of Public HealthAnn ArborMIUSA
| | | | - Dave Bridges
- Department of Nutritional SciencesUniversity of Michigan School of Public HealthAnn ArborMIUSA
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11
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Morel C, Parise LF, Van der Zee Y, Issler O, Cai M, Browne C, Blando A, Leclair K, Haynes S, Williams RW, Mulligan MK, Russo SJ, Nestler EJ, Han MH. Male and female variability in response to chronic stress and morphine in C57BL/6J, DBA/2J, and their BXD progeny. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581795. [PMID: 38464110 PMCID: PMC10925176 DOI: 10.1101/2024.02.23.581795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Drug addiction is a multifactorial syndrome in which genetic predispositions and exposure to environmental stressors constitute major risk factors for the early onset, escalation, and relapse of addictive behaviors. While it is well known that stress plays a key role in drug addiction, the genetic factors that make certain individuals particularly sensitive to stress and thereby more vulnerable to becoming addicted are unknown. In an effort to test a complex set of gene x environment interactions-specifically gene x chronic stress -here we leveraged a systems genetics resource: BXD recombinant inbred mice (BXD5, BXD8, BXD14, BXD22, BXD29, and BXD32) and their parental mouse lines, C57BL/6J and DBA/2J. Utilizing the chronic social defeat stress (CSDS) and chronic variable stress (CVS) paradigms, we first showed sexual dimorphism in the behavioral stress response between the mouse strains. Further, we observed an interaction between genetic background and vulnerability to prolonged exposure to non-social stressors. Finally, we found that DBA/2J and C57BL/6J mice pre-exposed to stress displayed differences in morphine sensitivity. Our results support the hypothesis that genetic variation in predisposition to stress responses influences morphine sensitivity and is likely to modulate the development of drug addiction.
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12
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Febo M, Mahar R, Rodriguez NA, Buraima J, Pompilus M, Pinto AM, Grudny MM, Bruijnzeel AW, Merritt ME. Age-Related Differences in Affective Behaviors in Mice: Possible Role of Prefrontal Cortical-Hippocampal Functional Connectivity and Metabolomic Profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.13.566691. [PMID: 38014219 PMCID: PMC10680600 DOI: 10.1101/2023.11.13.566691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The differential expression of emotional reactivity from early to late adulthood may involve maturation of prefrontal cortical responses to negative valence stimuli. In mice, age-related changes in affective behaviors have been reported, but the functional neural circuitry warrants further investigation. We assessed age variations in affective behaviors and functional connectivity in male and female C57BL6/J mice. Mice aged 10, 30 and 60 weeks (wo) were tested over 8 weeks for open field activity, sucrose preference, social interactions, fear conditioning, and functional neuroimaging. Prefrontal cortical and hippocampal tissues were excised for metabolomics. Our results indicate that young and old mice differ significantly in affective behavioral, functional connectome and prefrontal cortical-hippocampal metabolome. Young mice show a greater responsivity to novel environmental and social stimuli compared to older mice. Conversely, late middle-aged mice (60wo group) display variable patterns of fear conditioning and with re-testing with a modified context. Functional connectivity between a temporal cortical/auditory cortex network and subregions of the anterior cingulate cortex and ventral hippocampus, and a greater network modularity and assortative mixing of nodes was stronger in young versus older adult mice. Metabolome analyses identified differences in several essential amino acids between 10wo mice and the other age groups. The results support differential expression of 'emotionality' across distinct stages of the mouse lifespan involving greater prefrontal-hippocampal connectivity and neurochemistry.
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13
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Sasani TA, Quinlan AR, Harris K. Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice. eLife 2024; 12:RP89096. [PMID: 38381482 PMCID: PMC10942616 DOI: 10.7554/elife.89096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.
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Affiliation(s)
- Thomas A Sasani
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
- Department of Biomedical Informatics, University of UtahSalt Lake CityUnited States
| | - Kelley Harris
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Herbold Computational Biology Program, Fred Hutch Cancer CenterSeattleUnited States
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14
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Yu T, Ji Y, Cui X, Liang N, Wu S, Xiang C, Li Y, Tao H, Xie Y, Zuo H, Wang W, Khan N, Ullah K, Xu F, Zhang Y, Lin C. Novel Pathogenic Mutation of P209L in TRPC6 Gene Causes Adult Focal Segmental Glomerulosclerosis. Biochem Genet 2024:10.1007/s10528-023-10651-y. [PMID: 38315264 DOI: 10.1007/s10528-023-10651-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a leading kidney disease, clinically associated with proteinuria and progressive renal failure. The occurrence of this disease is partly related to gene mutations. We describe a single affected family member who presented with FSGS. We used high-throughput sequencing, sanger sequencing to identify the pathogenic mutations, and a systems genetics analysis in the BXD mice was conducted to explore the genetic regulatory mechanisms of pathogenic genes in the development of FSGS. We identified high urinary protein (++++) and creatinine levels (149 μmol/L) in a 29-year-old male diagnosed with a 5-year history of grade 2 hypertension. Histopathology of the kidney biopsy showed stromal hyperplasia at the glomerular segmental sclerosis and endothelial cell vacuolation degeneration. Whole-exome sequencing followed by Sanger sequencing revealed a heterozygous missense mutation (c.643C > T) in exon 2 of TRPC6, leading to the substitution of arginine with tryptophan at position 215 (p.Arg215Trp). Systems genetics analysis of the 53 BXD mice kidney transcriptomes identified Pygm as the upstream regulator of Trpc6. Those two genes are jointly involved in the regulation of FSGS mainly via Wnt and Hippo signaling pathways. We present a novel variant in the TRPC6 gene that causes FSGS. Moreover, our data suggested TRPC6 works with PYGM, as well as Wnt and Hippo signaling pathways to regulate renal function, which could guide future clinical prevention and targeted treatment for FSGS outcomes.
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Affiliation(s)
- Tianxi Yu
- School of Clinical Medicine, Weifang Medical University, Weifang, 261042, China
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Yongqiang Ji
- Department of Nephrology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Xin Cui
- School of Clinical Medicine, Weifang Medical University, Weifang, 261042, China
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Ning Liang
- School of Clinical Medicine, Weifang Medical University, Weifang, 261042, China
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Shuang Wu
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Chongjun Xiang
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yue Li
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Huiying Tao
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yaqi Xie
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Hongwei Zuo
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Wenting Wang
- Central Laboratory, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Nauman Khan
- Department of Biology, Faculty of Biological and Biomedical Sciences, The University of Haripur, Haripur, KP, Pakistan
| | - Kamran Ullah
- Department of Biology, Faculty of Biological and Biomedical Sciences, The University of Haripur, Haripur, KP, Pakistan
| | - Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yan Zhang
- Department of Nephrology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China.
| | - Chunhua Lin
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China.
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15
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Poudel SB, Ruff RR, Yildirim G, Miller RA, Harrison DE, Strong R, Kirsch T, Yakar S. Development of primary osteoarthritis during aging in genetically diverse UM-HET3 mice. RESEARCH SQUARE 2024:rs.3.rs-3858256. [PMID: 38343826 PMCID: PMC10854287 DOI: 10.21203/rs.3.rs-3858256/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Background Primary osteoarthritis (OA) occurs without identifiable underlying causes such as previous injuries or specific medical conditions. Age is a major contributing factor to OA, and as one ages, various joint tissues undergo gradual change, including degeneration of the articular cartilage, alterations in subchondral bone (SCB) morphology, and inflammation of the synovium. Methods We investigated the prevalence of primary OA in aged, genetically diverse UM-HET3 mice. Articular cartilage (AC) integrity and SCB morphology were assessed in 182 knee joints of 22-25 months old mice using the Osteoarthritis Research Society International (OARSI) scoring system and micro-CT, respectively. Additionally, we explored the effects of methylene blue (MB) and mitoquinone (MitoQ), two agents that affect mitochondrial function, on the prevalence and progression of OA during aging. Results Aged UM-HET3 mice showed a high prevalence of primary OA in both sexes. Significant positive correlations were found between cumulative AC (cAC) scores and synovitis in both sexes, and osteophyte formation in female mice. Ectopic chondrogenesis did not show significant correlations with cAC scores. Significant direct correlations were found between AC scores and inflammatory markers in chondrocytes, including matrix metalloproteinase-13, inducible nitric oxide synthase, and the NLR family pyrin domain containing-3 inflammasome in both sexes, indicating a link between OA severity and inflammation. Additionally, markers of cell cycle arrest, such as p16 and β-galactosidase, also correlated with AC scores. In male mice, no significant correlations were found between SCB morphology traits and cAC scores, while in female mice, significant correlations were found between cAC scores and tibial SCB plate bone mineral density. Notably, MB and MitoQ treatments influenced the disease's progression in a sex-specific manner. MB treatment significantly reduced cAC scores at the medial knee joint, while MitoQ treatment reduced cAC scores, but these did not reach significance. Conclusions Our study provides comprehensive insights into the prevalence and progression of primary OA in aged UM-HET3 mice, highlighting the sex-specific effects of MB and MitoQ treatments. The correlations between AC scores and various pathological factors underscore the multifaceted nature of OA and its association with inflammation and subchondral bone changes.
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Affiliation(s)
- Sher Bahadur Poudel
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY
| | - Ryan R Ruff
- David B. Kriser Dental Center, Biostatistics Core, Department of Epidemiology and Health Promotion, New York University College of Dentistry New York, NY 10010-4086
| | - Gozde Yildirim
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Randy Strong
- Geriatric Research, Education and Clinical Center and Research Service, South Texas Veterans Health Care System, San Antonio, TX, USA; Barshop Institute for Longevity and Aging Studies and Department of Pharmacology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Thorsten Kirsch
- Department of Orthopaedic Surgery, NYU Grossman School of Medicine, and Department of Biomedical Engineering, NYU Tandon School of Engineering, New York, NY
| | - Shoshana Yakar
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY
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16
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Poudel SB, Ruff RR, Yildirim G, Miller RA, Harrison DE, Strong R, Kirsch T, Yakar S. Development of primary osteoarthritis during aging in genetically diverse UM-HET3 mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.16.571693. [PMID: 38168298 PMCID: PMC10760163 DOI: 10.1101/2023.12.16.571693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
This study investigated the prevalence and progression of primary osteoarthritis (OA) in aged UM-HET3 mice. Using the Osteoarthritis Research Society International (OARSI) scoring system, we assessed articular cartilage (AC) integrity in 182 knee joints of 22-25 months old mice. Aged UM-HET3 mice showed a high prevalence of primary OA in both sexes. Significant positive correlations were found between cumulative AC (cAC) scores and synovitis in both sexes, and osteophyte formation in female mice. Ectopic chondrogenesis did not show significant correlations with cAC scores. Significant direct correlations were found between AC scores and inflammatory markers in chondrocytes, including matrix metalloproteinase-13 (MMP-13), inducible nitric oxide synthase (iNOS), and the NLR family pyrin domain containing-3 (NLRP3) inflammasome in both sexes, indicating a link between OA severity and inflammation. Additionally, markers of cell cycle arrest, such as p16 and β-galactosidase, also correlated with AC scores. Using micro-CT, we examined the correlations between subchondral bone (SCB) morphology traits and AC scores. In male mice, no significant correlations were found between SCB morphology traits and cAC scores, while in female mice, significant correlations were found between cAC scores and tibial SCB plate bone mineral density. Finally, we explored the effects of methylene blue (MB) and mitoquinone (MitoQ), two agents that affect mitochondrial function, on the prevalence and progression of OA during aging. Notably, MB and MitoQ treatments influenced the disease's progression in a sex-specific manner. MB treatment significantly reduced cAC scores at the medial knee joint, while MitoQ treatment reduced cAC scores, but these did not reach significance. In conclusion, our study provides comprehensive insights into the prevalence and progression of primary OA in aged UM-HET3 mice, highlighting the sex-specific effects of MB and MitoQ treatments. The correlations between AC scores and various pathological factors underscore the multifaceted nature of OA and its association with inflammation and subchondral bone changes.
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17
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Saul MC, Litkowski EM, Hadad N, Dunn AR, Boas SM, Wilcox JAL, Robbins JE, Wu Y, Philip VM, Merrihew GE, Park J, De Jager PL, Bridges DE, Menon V, Bennett DA, Hohman TJ, MacCoss MJ, Kaczorowski CC. Hippocampus Glutathione S Reductase Potentially Confers Genetic Resilience to Cognitive Decline in the AD-BXD Mouse Population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574219. [PMID: 38260300 PMCID: PMC10802440 DOI: 10.1101/2024.01.09.574219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) is a prevalent and costly age-related dementia. Heritable factors account for 58-79% of variation in late-onset AD, but substantial variation remains in age-of- onset, disease severity, and whether those with high-risk genotypes acquire AD. To emulate the diversity of human populations, we utilized the AD-BXD mouse panel. This genetically diverse resource combines AD genotypes with multiple BXD strains to discover new genetic drivers of AD resilience. Comparing AD-BXD carriers to noncarrier littermates, we computed a novel quantitative metric for resilience to cognitive decline in the AD-BXDs. Our quantitative AD resilience trait was heritable and genetic mapping identified a locus on chr8 associated with resilience to AD mutations that resulted in amyloid brain pathology. Using a hippocampus proteomics dataset, we nominated the mitochondrial glutathione S reductase protein (GR or GSHR) as a resilience factor, finding that the DBA/2J genotype was associated with substantially higher GR abundance. By mapping protein QTLs (pQTLs), we identified synaptic organization and mitochondrial proteins coregulated in trans with a cis-pQTL for GR. We found four coexpression modules correlated with the quantitative resilience score in aged 5XFAD mice using paracliques, which were related to cell structure, protein folding, and postsynaptic densities. Finally, we found significant positive associations between human GSR transcript abundance in the brain and better outcomes on AD-related cognitive and pathology traits in the Religious Orders Study/Memory and Aging project (ROSMAP). Taken together, these data support a framework for resilience in which neuronal antioxidant pathway activity provides for stability of synapses within the hippocampus.
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18
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Bajpai AK, Gu Q, Jiao Y, Starlard-Davenport A, Gu W, Quarles LD, Xiao Z, Lu L. Systems genetics and bioinformatics analyses using ESR1-correlated genes identify potential candidates underlying female bone development. Genomics 2024; 116:110769. [PMID: 38141931 PMCID: PMC10811775 DOI: 10.1016/j.ygeno.2023.110769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/14/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Estrogen receptor α (ESR1) is involved in E2 signaling and plays a major role in postmenopausal bone loss. However, the molecular network underlying ESR1 has not been explored. We used systems genetics and bioinformatics to identify important genes associated with Esr1 in postmenopausal bone loss. We identified ~2300 Esr1-coexpressed genes in female BXD bone femur, functional analysis of which revealed 'osteoblast signaling' as the most enriched pathway. PPI network led to the identification of 25 'female bone candidates'. The gene-regulatory analysis revealed RUNX2 as a key TF. ANKRD1 and RUNX2 were significantly different between osteoporosis patients and healthy controls. Sp7, Col1a1 and Pth1r correlated with multiple femur bone phenotypes in BXD mice. miR-3121-3p targeted Csf1, Ankrd1, Sp7 and Runx2. β-estradiol treatment markedly increased the expression of these candidates in mouse osteoblast. Our study revealed that Esr1-correlated genes Ankrd1, Runx2, Csf1 and Sp7 may play important roles in female bone development.
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Affiliation(s)
- Akhilesh K Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Cardiology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Yan Jiao
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Weikuan Gu
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Leigh Darryl Quarles
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Zhousheng Xiao
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
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19
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Yu Z, Farage G, Williams RW, Broman KW, Sen Ś. BulkLMM: Real-time genome scans for multiple quantitative traits using linear mixed models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572698. [PMID: 38187625 PMCID: PMC10769382 DOI: 10.1101/2023.12.20.572698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Genetic studies often collect data using high-throughput phenotyping. That has led to the need for fast genomewide scans for large number of traits using linear mixed models (LMMs). Computing the scans one by one on each trait is time consuming. We have developed new algorithms for performing genome scans on a large number of quantitative traits using LMMs, BulkLMM, that speeds up the computation by orders of magnitude compared to one trait at a time scans. On a mouse BXD Liver Proteome data with more than 35,000 traits and 7,000 markers, BulkLMM completed in a few seconds. We use vectorized, multi-threaded operations and regularization to improve optimization, and numerical approximations to speed up the computations. Our software implementation in the Julia programming language also provides permutation testing for LMMs and is available at https://github.com/senresearch/BulkLMM.jl.
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Affiliation(s)
- Zifan Yu
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Gregory Farage
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Śaunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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20
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Yang Y, Zhang M, Zhao Y, Deng T, Zhou X, Qian H, Wang M, Zhang C, Huo Z, Mao Z, Shao Z, Liu M, Yang C, Lin C, Xu F, Tian G, Zhang Y. HOXD8 suppresses renal cell carcinoma growth by upregulating SHMT1 expression. Cancer Sci 2023; 114:4583-4595. [PMID: 37752684 PMCID: PMC10728000 DOI: 10.1111/cas.15982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Amplification of amino acids synthesis is reported to promote tumorigenesis. The serine/glycine biosynthesis pathway is a reversible conversion of serine and glycine catalyzed by cytoplasmic serine hydroxymethyltransferase (SHMT)1 and mitochondrial SHMT2; however, the role of SHTM1 in renal cell carcinoma (RCC) is still unclear. We found that low SHMT1 expression is correlated with poor survival of RCC patients. The in vitro study showed that overexpression of SHMT1 suppressed RCC proliferation and migration. In the mouse tumor model, SHMT1 significantly retarded RCC tumor growth. Furthermore, by gene network analysis, we found several SHMT1-related genes, among which homeobox D8 (HOXD8) was identified as the SHMT1 regulator. Knockdown of HOXD8 decreased SHMT1 expression, resulting in faster RCC growth, and rescued the SHMT1 overexpression-induced cell migration defects. Additionally, ChIP assay found the binding site of HOXD8 to SHMT1 promoter was at the -456~-254 bp region. Taken together, SHMT1 functions as a tumor suppressor in RCC. The transcription factor HOXD8 can promote SHMT1 expression and suppress RCC cell proliferation and migration, which provides new mechanisms of SHMT1 in RCC tumor growth and might be used as a potential therapeutic target candidate for clinical treatment.
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Affiliation(s)
- Yang Yang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Minghui Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yaxuan Zhao
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Tingzhi Deng
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Xiang Zhou
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Hanxu Qian
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Mengxuan Wang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Chuanchuan Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Zhengjin Huo
- The First School of Clinical MedicineBinzhou Medical UniversityYantaiChina
| | - Zijun Mao
- The First School of Clinical MedicineBinzhou Medical UniversityYantaiChina
| | - Zhufeng Shao
- School of PharmacyBinzhou Medical UniversityYantaiChina
| | - Mengxue Liu
- School of PharmacyBinzhou Medical UniversityYantaiChina
| | - Chunhua Yang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Chunhua Lin
- Department of UrologyThe Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantaiChina
| | - Fuyi Xu
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Geng Tian
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yin Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
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21
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Mozhui K, Kim H, Villani F, Haghani A, Sen S, Horvath S. Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits. Epigenetics 2023; 18:2252631. [PMID: 37691384 PMCID: PMC10496549 DOI: 10.1080/15592294.2023.2252631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. Trans-modulated CpGs showed age-dependent changes and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and ageing resulted in a more 'aged methylome' for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analyses identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variations in body size and metabolic traits, and influence CpG methylation and epigenetic ageing that could have an impact on lifespan.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hyeonju Kim
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
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22
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Gómez-Pascual A, Glikman DM, Ng HX, Tomkins JE, Lu L, Xu Y, Ashbrook DG, Kaczorowski C, Kempermann G, Killmar J, Mozhui K, Aebersold R, Williams EG, Williams RW, Overall RW, Jucker M, de Bakker DEM. Polyglucosan body density in the aged mouse hippocampus is controlled by a novel modifier locus on chromosome 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.567373. [PMID: 38045339 PMCID: PMC10690248 DOI: 10.1101/2023.11.22.567373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Aging can be associated with the accumulation of hypobranched glycogen molecules (polyglucosan bodies, PGBs), particularly in astrocytes of the hippocampus. While PGBs have a detrimental effect on cognition in diseases such as adult polyglucosan body disease and Lafora disease, the underlying mechanism and clinical relevance of age-related PGB accumulation remains unknown. Here, we have investigated the genetic basis and functional impact of age-related PGB accumulation in 32 fully sequenced BXD-type strains of mice which exhibit a 400-fold variation in PGB burden in 16-18 month old females. We mapped a major locus controlling PGB density in the hippocampus to chromosome 1 at 72-75 Mb (linkage of 4.9 -logP), which we defined as the Pgb1 locus. To identify potentially causal gene variants within Pgb1, we generated extensive hippocampal transcriptome datasets and identified two strong candidate genes for which mRNA correlates with PGB density-Smarcal1 and Usp37. In addition, both Smarcal1 and Usp37 contain non-synonymous allele variations likely to impact protein function. A phenome-wide association analysis highlighted a trans-regulatory effect of the Pgb1 locus on expression of Hp1bp3, a gene known to play a role in age-related changes in learning and memory. To investigate the potential impact of PGBs on cognition, we performed conditioned fear memory testing on strains displaying varying degrees of PGB burden, and a phenome-wide association scan of ~12,000 traits. Importantly, we did not find any evidence suggesting a negative impact of PGB burden on cognitive capacity. Taken together, we have identified a major modifier locus controlling PGB burden in the hippocampus and shed light on the genetic architecture and clinical relevance of this strikingly heterogeneous hippocampal phenotype.
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Affiliation(s)
- A Gómez-Pascual
- Department of Information and Communications Engineering, University of Murcia, Murcia, Spain
| | - D M Glikman
- University of Vienna, Vienna, Austria
- Department of Neuronal Cell Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - H X Ng
- Department of Cognitive Science University of California, San Diego, USA
| | - J E Tomkins
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - L Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | - Y Xu
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - D G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | | | - G Kempermann
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
| | - J Killmar
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | - K Mozhui
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Center, Memphis, TN, USA
| | - R Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich. Zurich, Switzerland
| | - E G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | - R W Overall
- Humboldt University of Berlin, Berlin, Germany
| | - M Jucker
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - D E M de Bakker
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
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23
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Allayee H, Farber CR, Seldin MM, Williams EG, James DE, Lusis AJ. Systems genetics approaches for understanding complex traits with relevance for human disease. eLife 2023; 12:e91004. [PMID: 37962168 PMCID: PMC10645424 DOI: 10.7554/elife.91004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.
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Affiliation(s)
- Hooman Allayee
- Departments of Population & Public Health Sciences, University of Southern CaliforniaLos AngelesUnited States
- Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Departments of Biochemistry & Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Public Health Sciences, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
| | - Evan Graehl Williams
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgLuxembourgLuxembourg
| | - David E James
- School of Life and Environmental Sciences, University of SydneyCamperdownAustralia
- Faculty of Medicine and Health, University of SydneyCamperdownAustralia
- Charles Perkins Centre, University of SydneyCamperdownAustralia
| | - Aldons J Lusis
- Departments of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Medicine, University of California, Los AngelesLos AngelesUnited States
- Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLALos AngelesUnited States
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24
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Sasani TA, Quinlan AR, Harris K. Epistasis between mutator alleles contributes to germline mutation spectra variability in laboratory mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.537217. [PMID: 37162999 PMCID: PMC10168256 DOI: 10.1101/2023.04.25.537217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair [1], mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs [2,3]. In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh [4]. Its effect depended on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci had greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.
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Affiliation(s)
| | - Aaron R. Quinlan
- Department of Human Genetics, University of Utah; Department of Biomedical Informatics, University of Utah · Funded by NIH/NHGRI R01HG012252
| | - Kelley Harris
- Department of Genome Sciences, University of Washington · Funded by NIH/NIGMS R35GM133428; Burroughs Wellcome Career Award at the Scientific Interface; Searle Scholarship; Pew Scholarship; Sloan Fellowship; Allen Discovery Center for Cell Lineage Tracing
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25
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Chella Krishnan K. When diet meets genetics. eLife 2023; 12:e92714. [PMID: 37855820 PMCID: PMC10586802 DOI: 10.7554/elife.92714] [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] [Indexed: 10/20/2023] Open
Abstract
Gene expression profiling of a diverse mouse population helps to decipher how a fat-rich diet contributes to inflammatory bowel disease.
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Affiliation(s)
- Karthickeyan Chella Krishnan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of MedicineCincinnatiUnited States
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26
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Tian Y, Johnson GA, Williams RW, White LE. A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology. Front Neurosci 2023; 17:1223226. [PMID: 37841684 PMCID: PMC10569694 DOI: 10.3389/fnins.2023.1223226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Information on regional variation in cell numbers and densities in the CNS provides critical insight into structure, function, and the progression of CNS diseases. However, variability can be real or a consequence of methods that do not account for technical biases, including morphologic deformations, errors in the application of cell type labels and boundaries of regions, errors of counting rules and sampling sites. We address these issues in a mouse model by introducing a workflow that consists of the following steps: 1. Magnetic resonance histology (MRH) to establish the size, shape, and regional morphology of the mouse brain in situ. 2. Light-sheet microscopy (LSM) to selectively label neurons or other cells in the entire brain without sectioning artifacts. 3. Register LSM volumes to MRH volumes to correct for dissection errors and both global and regional deformations. 4. Implement stereological protocols for automated sampling and counting of cells in 3D LSM volumes. This workflow can analyze the cell densities of one brain region in less than 1 min and is highly replicable in cortical and subcortical gray matter regions and structures throughout the brain. This method demonstrates the advantage of not requiring an extensive amount of training data, achieving a F1 score of approximately 0.9 with just 20 training nuclei. We report deformation-corrected neuron (NeuN) counts and neuronal density in 13 representative regions in 5 C57BL/6J cases and 2 BXD strains. The data represent the variability among specimens for the same brain region and across regions within the specimen. Neuronal densities estimated with our workflow are within the range of values in previous classical stereological studies. We demonstrate the application of our workflow to a mouse model of aging. This workflow improves the accuracy of neuron counting and the assessment of neuronal density on a region-by-region basis, with broad applications for studies of how genetics, environment, and development across the lifespan impact cell numbers in the CNS.
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Affiliation(s)
- Yuqi Tian
- Duke Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, NC, United States
| | - G. Allan Johnson
- Duke Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, NC, United States
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Leonard E. White
- Department of Neurology, Duke University, Durham, NC, United States
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27
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Meade RK, Long JE, Jinich A, Rhee KY, Ashbrook DG, Williams RW, Sassetti CM, Smith CM. Genome-wide screen identifies host loci that modulate Mycobacterium tuberculosis fitness in immunodivergent mice. G3 (BETHESDA, MD.) 2023; 13:jkad147. [PMID: 37405387 PMCID: PMC10468300 DOI: 10.1093/g3journal/jkad147] [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: 03/07/2023] [Revised: 06/05/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023]
Abstract
Genetic differences among mammalian hosts and among strains of Mycobacterium tuberculosis (Mtb) are well-established determinants of tuberculosis (TB) patient outcomes. The advent of recombinant inbred mouse panels and next-generation transposon mutagenesis and sequencing approaches has enabled dissection of complex host-pathogen interactions. To identify host and pathogen genetic determinants of Mtb pathogenesis, we infected members of the highly diverse BXD family of strains with a comprehensive library of Mtb transposon mutants (TnSeq). Members of the BXD family segregate for Mtb-resistant C57BL/6J (B6 or B) and Mtb-susceptible DBA/2J (D2 or D) haplotypes. The survival of each bacterial mutant was quantified within each BXD host, and we identified those bacterial genes that were differentially required for Mtb fitness across BXD genotypes. Mutants that varied in survival among the host family of strains were leveraged as reporters of "endophenotypes," each bacterial fitness profile directly probing specific components of the infection microenvironment. We conducted quantitative trait loci (QTL) mapping of these bacterial fitness endophenotypes and identified 140 host-pathogen QTL (hpQTL). We located a QTL hotspot on chromosome 6 (75.97-88.58 Mb) associated with the genetic requirement of multiple Mtb genes: Rv0127 (mak), Rv0359 (rip2), Rv0955 (perM), and Rv3849 (espR). Together, this screen reinforces the utility of bacterial mutant libraries as precise reporters of the host immunological microenvironment during infection and highlights specific host-pathogen genetic interactions for further investigation. To enable downstream follow-up for both bacterial and mammalian genetic research communities, all bacterial fitness profiles have been deposited into GeneNetwork.org and added into the comprehensive collection of TnSeq libraries in MtbTnDB.
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Affiliation(s)
- Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01655, USA
- Research Animal Diagnostic Services, Charles River Laboratories, Wilmington, MA 01887, USA
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10021, USA
| | - David G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
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28
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Pan L, Cho KS, Wei X, Xu F, Lennikov A, Hu G, Tang J, Guo S, Chen J, Kriukov E, Kyle R, Elzaridi F, Jiang S, Dromel PA, Young M, Baranov P, Do CW, Williams RW, Chen J, Lu L, Chen DF. IGFBPL1 is a master driver of microglia homeostasis and resolution of neuroinflammation in glaucoma and brain tauopathy. Cell Rep 2023; 42:112889. [PMID: 37527036 PMCID: PMC10528709 DOI: 10.1016/j.celrep.2023.112889] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/08/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023] Open
Abstract
Microglia shift toward an inflammatory phenotype during aging that is thought to exacerbate age-related neurodegeneration. The molecular and cellular signals that resolve neuroinflammation post-injury are largely undefined. Here, we exploit systems genetics methods based on the extended BXD murine reference family and identify IGFBPL1 as an upstream cis-regulator of microglia-specific genes to switch off inflammation. IGFBPL1 is expressed by mouse and human microglia, and higher levels of its expression resolve lipopolysaccharide-induced neuroinflammation by resetting the transcriptome signature back to a homeostatic state via IGF1R signaling. Conversely, IGFBPL1 deficiency or selective deletion of IGF1R in microglia shifts these cells to an inflammatory landscape and induces early manifestation of brain tauopathy and retinal neurodegeneration. Therapeutic administration of IGFBPL1 drives pro-homeostatic microglia and prevents glaucomatous neurodegeneration and vision loss in mice. These results identify IGFBPL1 as a master driver of the counter-inflammatory microglial modulator that presents an endogenous resolution of neuroinflammation to prevent neurodegeneration in eye and brain.
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Affiliation(s)
- Li Pan
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; School of Optometry, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Kin-Sang Cho
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Xin Wei
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Anton Lennikov
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Guangan Hu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jing Tang
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuai Guo
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Julie Chen
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Emil Kriukov
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Robert Kyle
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Farris Elzaridi
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Shuhong Jiang
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Pierre A Dromel
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Michael Young
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Petr Baranov
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Chi-Wai Do
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jianzhu Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Dong Feng Chen
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
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29
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Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice. Cell Rep 2023; 42:112856. [PMID: 37481717 PMCID: PMC10530068 DOI: 10.1016/j.celrep.2023.112856] [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: 11/16/2022] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
To identify addiction genes, we evaluate intravenous self-administration of cocaine or saline in 84 inbred and recombinant inbred mouse strains over 10 days. We integrate the behavior data with brain RNA-seq data from 41 strains. The self-administration of cocaine and that of saline are genetically distinct. We maximize power to map loci for cocaine intake by using a linear mixed model to account for this longitudinal phenotype while correcting for population structure. A total of 15 unique significant loci are identified in the genome-wide association study. A transcriptome-wide association study highlights the Trpv2 ion channel as a key locus for cocaine self-administration as well as identifying 17 additional genes, including Arhgef26, Slc18b1, and Slco5a1. We find numerous instances where alternate splice site selection or RNA editing altered transcript abundance. Our work emphasizes the importance of Trpv2, an ionotropic cannabinoid receptor, for the response to cocaine.
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Affiliation(s)
- Arshad H Khan
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jared R Bagley
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Nathan LaPierre
- Department of Computer Science, UCLA, Los Angeles, CA 90095, USA
| | | | - Tadeo C Spencer
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Eleazar Eskin
- Department of Computational Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James D Jentsch
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Desmond J Smith
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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30
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Takasugi M, Yoshida Y, Nonaka Y, Ohtani N. Gene expressions associated with longer lifespan and aging exhibit similarity in mammals. Nucleic Acids Res 2023; 51:7205-7219. [PMID: 37351606 PMCID: PMC10415134 DOI: 10.1093/nar/gkad544] [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: 03/09/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Although molecular features underlying aging and species maximum lifespan (MLS) have been comprehensively studied by transcriptome analyses, the actual impact of transcriptome on aging and MLS remains elusive. Here, we found that transcriptional signatures that are associated with mammalian MLS exhibited significant similarity to those of aging. Moreover, transcriptional signatures of longer MLS and aging both exhibited significant similarity to that of longer-lived mouse strains, suggesting that gene expression patterns associated with species MLS contribute to extended lifespan even within a species and that aging-related gene expression changes overall represent adaptations that extend lifespan rather than deterioration. Finally, we found evidence of co-evolution of MLS and promoter sequences of MLS-associated genes, highlighting the evolutionary contribution of specific transcription factor binding motifs such as that of E2F1 in shaping MLS-associated gene expression signature. Our results highlight the importance of focusing on adaptive aspects of aging transcriptome and demonstrate that cross-species genomics can be a powerful approach for understanding adaptive aging transcriptome.
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Affiliation(s)
- Masaki Takasugi
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Yuya Yoshida
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Yoshiki Nonaka
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Naoko Ohtani
- Department of Pathophysiology, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
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31
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Masson SWC, Madsen S, Cooke KC, Potter M, Vegas AD, Carroll L, Thillainadesan S, Cutler HB, Walder KR, Cooney GJ, Morahan G, Stöckli J, James DE. Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance. eLife 2023; 12:RP86961. [PMID: 37494090 PMCID: PMC10371229 DOI: 10.7554/elife.86961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Systems genetics has begun to tackle the complexity of insulin resistance by capitalising on computational advances to study high-diversity populations. 'Diversity Outbred in Australia (DOz)' is a population of genetically unique mice with profound metabolic heterogeneity. We leveraged this variance to explore skeletal muscle's contribution to whole-body insulin action through metabolic phenotyping and skeletal muscle proteomics of 215 DOz mice. Linear modelling identified 553 proteins that associated with whole-body insulin sensitivity (Matsuda Index) including regulators of endocytosis and muscle proteostasis. To enrich for causality, we refined this network by focusing on negatively associated, genetically regulated proteins, resulting in a 76-protein fingerprint of insulin resistance. We sought to perturb this network and restore insulin action with small molecules by integrating the Broad Institute Connectivity Map platform and in vitro assays of insulin action using the Prestwick chemical library. These complementary approaches identified the antibiotic thiostrepton as an insulin resistance reversal agent. Subsequent validation in ex vivo insulin-resistant mouse muscle and palmitate-induced insulin-resistant myotubes demonstrated potent insulin action restoration, potentially via upregulation of glycolysis. This work demonstrates the value of a drug-centric framework to validate systems-level analysis by identifying potential therapeutics for insulin resistance.
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Affiliation(s)
- Stewart W C Masson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Søren Madsen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Meg Potter
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Alexis Diaz Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Luke Carroll
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, Australia
| | - Senthil Thillainadesan
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Harry B Cutler
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Ken R Walder
- School of Medicine, Deakin University, Geelong, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Murdoch, Australia
| | - Jacqueline Stöckli
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
- School of Medical Sciences University of Sydney, Sydney, Australia
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32
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Robertson SJ, Bedard O, McNally KL, Shaia C, Clancy CS, Lewis M, Broeckel RM, Chiramel AI, Shannon JG, Sturdevant GL, Rosenke R, Anzick SL, Forte E, Preuss C, Baker CN, Harder JM, Brunton C, Munger S, Bruno DP, Lack JB, Leung JM, Shamsaddini A, Gardina P, Sturdevant DE, Sun J, Martens C, Holland SM, Rosenthal NA, Best SM. Genetically diverse mouse models of SARS-CoV-2 infection reproduce clinical variation in type I interferon and cytokine responses in COVID-19. Nat Commun 2023; 14:4481. [PMID: 37491352 PMCID: PMC10368652 DOI: 10.1038/s41467-023-40076-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/05/2023] [Indexed: 07/27/2023] Open
Abstract
Inflammation in response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection drives severity of coronavirus disease 2019 (COVID-19) and is influenced by host genetics. To understand mechanisms of inflammation, animal models that reflect genetic diversity and clinical outcomes observed in humans are needed. We report a mouse panel comprising the genetically diverse Collaborative Cross (CC) founder strains crossed to human ACE2 transgenic mice (K18-hACE2) that confers susceptibility to SARS-CoV-2. Infection of CC x K18-hACE2 resulted in a spectrum of survival, viral replication kinetics, and immune profiles. Importantly, in contrast to the K18-hACE2 model, early type I interferon (IFN-I) and regulated proinflammatory responses were required for control of SARS-CoV-2 replication in PWK x K18-hACE2 mice that were highly resistant to disease. Thus, virus dynamics and inflammation observed in COVID-19 can be modeled in diverse mouse strains that provide a genetically tractable platform for understanding anti-coronavirus immunity.
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Affiliation(s)
- Shelly J Robertson
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | | | - Kristin L McNally
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Chad S Clancy
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Matthew Lewis
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Rebecca M Broeckel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Abhilash I Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Jeffrey G Shannon
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Gail L Sturdevant
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA
| | - Sarah L Anzick
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Elvira Forte
- The Jackson Laboratory, Bar Harbor, ME, USA
- Springer Nature, New York, NY, USA
| | | | | | | | | | | | - Daniel P Bruno
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Justin B Lack
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jacqueline M Leung
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Amirhossein Shamsaddini
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Paul Gardina
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Daniel E Sturdevant
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jian Sun
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Craig Martens
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Steven M Holland
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Nadia A Rosenthal
- The Jackson Laboratory, Bar Harbor, ME, USA.
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA.
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT, USA.
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33
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Mozhui K, O’Callaghan JP, Ashbrook DG, Prins P, Zhao W, Lu L, Jones BC. Epigenetic analysis in a murine genetic model of Gulf War illness. FRONTIERS IN TOXICOLOGY 2023; 5:1162749. [PMID: 37389175 PMCID: PMC10300436 DOI: 10.3389/ftox.2023.1162749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023] Open
Abstract
Of the nearly 1 million military personnel who participated in the 1990-1991 Gulf War, between 25% and 35% became ill with what now is referred to as Gulf War Illness (GWI) by the Department of Defense. Symptoms varied from gastrointestinal distress to lethargy, memory loss, inability to concentrate, depression, respiratory, and reproductive problems. The symptoms have persisted for 30 years in those afflicted but the basis of the illness remains largely unknown. Nerve agents and other chemical exposures in the war zone have been implicated but the long-term effects of these acute exposures have left few if any identifiable signatures. The major aim of this study is to elucidate the possible genomic basis for the persistence of symptoms, especially of the neurological and behavioral effects. To address this, we performed a whole genome epigenetic analysis of the proposed cause of GWI, viz., exposure to organophosphate neurotoxicants combined with high circulating glucocorticoids in two inbred mouse strains, C57BL/6J and DBA/2J. The animals received corticosterone in their drinking water for 7 days followed by injection of diisopropylfluorophosphate, a nerve agent surrogate. Six weeks after DFP injection, the animals were euthanized and medial prefrontal cortex harvested for genome-wide DNA methylation analysis using high-throughput sequencing. We observed 67 differentially methylated genes, notably among them, Ttll7, Akr1c14, Slc44a4, and Rusc2, all related to different symptoms of GWI. Our results support proof of principle of genetic differences in the chronic effects of GWI-related exposures and may reveal why the disease has persisted in many of the now aging Gulf War veterans.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - James P. O’Callaghan
- Molecular Neurotoxicology Laboratory, Toxicology, and Molecular Biology Branch, Health Effects Laboratory Division, U. S. Centers for Disease Control and Prevention, NIOSH, Morgantown, WV, United States
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wenyuan Zhao
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Byron C. Jones
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Pharmacology, Addiction Science, and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
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34
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Tyler AL, Spruce C, Kursawe R, Haber A, Ball RL, Pitman WA, Fine AD, Raghupathy N, Walker M, Philip VM, Baker CL, Mahoney JM, Churchill GA, Trowbridge JJ, Stitzel ML, Paigen K, Petkov PM, Carter GW. Variation in histone configurations correlates with gene expression across nine inbred strains of mice. Genome Res 2023; 33:857-871. [PMID: 37217254 PMCID: PMC10519406 DOI: 10.1101/gr.277467.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
The Diversity Outbred (DO) mice and their inbred founders are widely used models of human disease. However, although the genetic diversity of these mice has been well documented, their epigenetic diversity has not. Epigenetic modifications, such as histone modifications and DNA methylation, are important regulators of gene expression and, as such, are a critical mechanistic link between genotype and phenotype. Therefore, creating a map of epigenetic modifications in the DO mice and their founders is an important step toward understanding mechanisms of gene regulation and the link to disease in this widely used resource. To this end, we performed a strain survey of epigenetic modifications in hepatocytes of the DO founders. We surveyed four histone modifications (H3K4me1, H3K4me3, H3K27me3, and H3K27ac), as well as DNA methylation. We used ChromHMM to identify 14 chromatin states, each of which represents a distinct combination of the four histone modifications. We found that the epigenetic landscape is highly variable across the DO founders and is associated with variation in gene expression across strains. We found that epigenetic state imputed into a population of DO mice recapitulated the association with gene expression seen in the founders, suggesting that both histone modifications and DNA methylation are highly heritable mechanisms of gene expression regulation. We illustrate how DO gene expression can be aligned with inbred epigenetic states to identify putative cis-regulatory regions. Finally, we provide a data resource that documents strain-specific variation in the chromatin state and DNA methylation in hepatocytes across nine widely used strains of laboratory mice.
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Affiliation(s)
- Anna L Tyler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Catrina Spruce
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Annat Haber
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Robyn L Ball
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Wendy A Pitman
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Alexander D Fine
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael Walker
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - J Matthew Mahoney
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Gary A Churchill
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Kenneth Paigen
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Petko M Petkov
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA;
| | - Gregory W Carter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
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35
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Reid K, Daniels EG, Vasam G, Kamble R, Janssens GE, Hu IM, Green AE, Houtkooper RH, Menzies KJ. Reducing mitochondrial ribosomal gene expression does not alter metabolic health or lifespan in mice. Sci Rep 2023; 13:8391. [PMID: 37225705 PMCID: PMC10209074 DOI: 10.1038/s41598-023-35196-3] [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: 11/14/2022] [Accepted: 05/14/2023] [Indexed: 05/26/2023] Open
Abstract
Maintaining mitochondrial function is critical to an improved healthspan and lifespan. Introducing mild stress by inhibiting mitochondrial translation invokes the mitochondrial unfolded protein response (UPRmt) and increases lifespan in several animal models. Notably, lower mitochondrial ribosomal protein (MRP) expression also correlates with increased lifespan in a reference population of mice. In this study, we tested whether partially reducing the gene expression of a critical MRP, Mrpl54, reduced mitochondrial DNA-encoded protein content, induced the UPRmt, and affected lifespan or metabolic health using germline heterozygous Mrpl54 mice. Despite reduced Mrpl54 expression in multiple organs and a reduction in mitochondrial-encoded protein expression in myoblasts, we identified few significant differences between male or female Mrpl54+/- and wild type mice in initial body composition, respiratory parameters, energy intake and expenditure, or ambulatory motion. We also observed no differences in glucose or insulin tolerance, treadmill endurance, cold tolerance, heart rate, or blood pressure. There were no differences in median life expectancy or maximum lifespan. Overall, we demonstrate that genetic manipulation of Mrpl54 expression reduces mitochondrial-encoded protein content but is not sufficient to improve healthspan in otherwise healthy and unstressed mice.
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Affiliation(s)
- Kim Reid
- Department of Biology and Ottawa Institute of Systems Biology, University of Ottawa, 30 Marie Curie Private, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada
| | - Eileen G Daniels
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands
| | - Goutham Vasam
- Interdisciplinary School of Health Sciences, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Rashmi Kamble
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands
| | - Iman M Hu
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands
| | - Alexander E Green
- Interdisciplinary School of Health Sciences, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Amsterdam Gastroenterology Endocrinology and Metabolism Institute, Amsterdam, The Netherlands.
- Amsterdam Cardiovascular Sciences Institute, Amsterdam, The Netherlands.
| | - Keir J Menzies
- Interdisciplinary School of Health Sciences, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON, Canada.
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Maksimov MO, Wu C, Ashbrook DG, Villani F, Colonna V, Mousavi N, Ma N, Lu L, Pritchard JK, Goren A, Williams RW, Palmer AA, Gymrek M. A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice. Genome Res 2023; 33:689-702. [PMID: 37127331 PMCID: PMC10317118 DOI: 10.1101/gr.277576.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
Short tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1-6 bp. We leveraged whole-genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map loci that modulate genome-wide patterns of new mutations arising during parent-to-offspring transmission at STRs. We defined quantitative phenotypes describing the numbers and types of germline STR mutations in each strain and performed quantitative trait locus (QTL) analyses for each of these phenotypes. We identified a locus on Chromosome 13 at which strains inheriting the C57BL/6J (B) haplotype have a higher rate of STR expansions than those inheriting the DBA/2J (D) haplotype. The strongest candidate gene in this locus is Msh3, a known modifier of STR stability in cancer and at pathogenic repeat expansions in mice and humans, as well as a current drug target against Huntington's disease. The D haplotype at this locus harbors a cluster of variants near the 5' end of Msh3, including multiple missense variants near the DNA mismatch recognition domain. In contrast, the B haplotype contains a unique retrotransposon insertion. The rate of expansion covaries positively with Msh3 expression-with higher expression from the B haplotype. Finally, detailed analysis of mutation patterns showed that strains carrying the B allele have higher expansion rates, but slightly lower overall total mutation rates, compared with those with the D allele, particularly at tetranucleotide repeats. Our results suggest an important role for inherited variants in Msh3 in modulating genome-wide patterns of germline mutations at STRs.
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Affiliation(s)
- Mikhail O Maksimov
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Cynthia Wu
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California 92093, USA
| | - David G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Vincenza Colonna
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
- Institute of Genetics and Biophysics, National Research Council, Naples 80111, Italy
| | - Nima Mousavi
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Nichole Ma
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Alon Goren
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Abraham A Palmer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
- Department of Psychiatry, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Melissa Gymrek
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA
- Department of Biomedical Informatics
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37
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Johnson GA, Tian Y, Ashbrook DG, Cofer GP, Cook JJ, Gee JC, Hall A, Hornburg K, Qi Y, Yeh FC, Wang N, White LE, Williams RW. Merged magnetic resonance and light sheet microscopy of the whole mouse brain. Proc Natl Acad Sci U S A 2023; 120:e2218617120. [PMID: 37068254 PMCID: PMC10151475 DOI: 10.1073/pnas.2218617120] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/10/2023] [Indexed: 04/19/2023] Open
Abstract
We have developed workflows to align 3D magnetic resonance histology (MRH) of the mouse brain with light sheet microscopy (LSM) and 3D delineations of the same specimen. We start with MRH of the brain in the skull with gradient echo and diffusion tensor imaging (DTI) at 15 μm isotropic resolution which is ~ 1,000 times higher than that of most preclinical MRI. Connectomes are generated with superresolution tract density images of ~5 μm. Brains are cleared, stained for selected proteins, and imaged by LSM at 1.8 μm/pixel. LSM data are registered into the reference MRH space with labels derived from the ABA common coordinate framework. The result is a high-dimensional integrated volume with registration (HiDiver) with alignment precision better than 50 µm. Throughput is sufficiently high that HiDiver is being used in quantitative studies of the impact of gene variants and aging on mouse brain cytoarchitecture and connectomics.
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Affiliation(s)
| | - Yuqi Tian
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN38162
| | - Gary P. Cofer
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - James J. Cook
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - James C. Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Adam Hall
- LifeCanvas Technology, Cambridge, MA02141
| | | | - Yi Qi
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - Fang-Cheng Yeh
- Department of Neurologic Surgery, University of Pittsburgh, Pittsburgh, PA15260
| | - Nian Wang
- Department of Radiology, Indiana University, Bloomington, IN47401
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN38162
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Jurrjens AW, Seldin MM, Giles C, Meikle PJ, Drew BG, Calkin AC. The potential of integrating human and mouse discovery platforms to advance our understanding of cardiometabolic diseases. eLife 2023; 12:e86139. [PMID: 37000167 PMCID: PMC10065800 DOI: 10.7554/elife.86139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Cardiometabolic diseases encompass a range of interrelated conditions that arise from underlying metabolic perturbations precipitated by genetic, environmental, and lifestyle factors. While obesity, dyslipidaemia, smoking, and insulin resistance are major risk factors for cardiometabolic diseases, individuals still present in the absence of such traditional risk factors, making it difficult to determine those at greatest risk of disease. Thus, it is crucial to elucidate the genetic, environmental, and molecular underpinnings to better understand, diagnose, and treat cardiometabolic diseases. Much of this information can be garnered using systems genetics, which takes population-based approaches to investigate how genetic variance contributes to complex traits. Despite the important advances made by human genome-wide association studies (GWAS) in this space, corroboration of these findings has been hampered by limitations including the inability to control environmental influence, limited access to pertinent metabolic tissues, and often, poor classification of diseases or phenotypes. A complementary approach to human GWAS is the utilisation of model systems such as genetically diverse mouse panels to study natural genetic and phenotypic variation in a controlled environment. Here, we review mouse genetic reference panels and the opportunities they provide for the study of cardiometabolic diseases and related traits. We discuss how the post-GWAS era has prompted a shift in focus from discovery of novel genetic variants to understanding gene function. Finally, we highlight key advantages and challenges of integrating complementary genetic and multi-omics data from human and mouse populations to advance biological discovery.
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Affiliation(s)
- Aaron W Jurrjens
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, United States
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Brian G Drew
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - Anna C Calkin
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
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Welikovitch LA, Dujardin S, Dunn AR, Fernandes AR, Khasnavis A, Chibnik LB, Kaczorowski CC, Hyman BT. Rate of tau propagation is a heritable disease trait in genetically diverse mouse strains. iScience 2023; 26:105983. [PMID: 36756365 PMCID: PMC9900390 DOI: 10.1016/j.isci.2023.105983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/04/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
The speed and scope of cognitive deterioration in Alzheimer's disease is highly associated with the advancement of tau neurofibrillary lesions across brain networks. We tested whether the rate of tau propagation is a heritable disease trait in a large, well-characterized cohort of genetically divergent mouse strains. Using an AAV-based model system, P301L-mutant human tau (hTau) was introduced into the entorhinal cortex of mice derived from 18 distinct lines. The extent of tau propagation was measured by distinguishing hTau-producing cells from neurons that were recipients of tau transfer. Heritability calculation revealed that 43% of the variability in tau spread was due to genetic variants segregating across background strains. Strain differences in glial markers were also observed, but did not correlate with tau propagation. Identifying unique genetic variants that influence the progression of pathological tau may uncover novel molecular targets to prevent or slow the pace of tau spread and cognitive decline.
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Affiliation(s)
- Lindsay A. Welikovitch
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Simon Dujardin
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Amy R. Dunn
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Anita Khasnavis
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Lori B. Chibnik
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Bradley T. Hyman
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Harvard Medical School, Boston, MA 02115, USA
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40
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Leonardo M, Brunty S, Huffman J, Lester DB, Dickson PE. Effects of isolation housing stress and mouse strain on intravenous cocaine self-administration, sensory stimulus self-administration, and reward preference. Sci Rep 2023; 13:2810. [PMID: 36797314 PMCID: PMC9935522 DOI: 10.1038/s41598-023-29579-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Sensory stimuli are natural rewards in mice and humans. Consequently, preference for a drug reward relative to a sensory reward may be an endophenotype of addiction vulnerability. In this study, we developed a novel behavioral assay to quantify the preference for intravenous drug self-administration relative to sensory stimulus self-administration. We used founder strains of the BXD recombinant inbred mouse panel (C57BL/6J, DBA/2J) and a model of stress (isolation vs enriched housing) to assess genetic and epigenetic effects. Following 10 weeks of differential housing, all mice were tested under three reward conditions: sensory rewards available, cocaine rewards available, both rewards available. When a single reward was available (sensory stimuli or cocaine; delivered using distinct levers), DBA/2J mice self-administered significantly more rewards than C57BL/6J mice. When both rewards were available, DBA/2J mice exhibited a significant preference for cocaine relative to sensory stimuli; in contrast, C57BL/6J mice exhibited no preference. Housing condition influenced sensory stimulus self-administration and strain-dependently influenced inactive lever pressing when both rewards were available. Collectively, these data reveal strain effects, housing effects, or both on reward self-administration and preference. Most importantly, this study reveals that genetic mechanisms underlying preference for a drug reward relative to a nondrug reward can be dissected using the full BXD panel.
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Affiliation(s)
- Michael Leonardo
- grid.259676.90000 0001 2214 9920Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV 25703 USA
| | - Sarah Brunty
- grid.259676.90000 0001 2214 9920Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV 25703 USA
| | - Jessica Huffman
- grid.259676.90000 0001 2214 9920Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV 25703 USA
| | - Deranda B. Lester
- grid.56061.340000 0000 9560 654XDepartment of Psychology, University of Memphis, 202 Psychology Building, Memphis, TN 38152 USA
| | - Price E. Dickson
- grid.259676.90000 0001 2214 9920Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV 25703 USA
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41
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Tabbaa M, Knoll A, Levitt P. Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency. Neuron 2023; 111:539-556.e5. [PMID: 36738737 PMCID: PMC9960295 DOI: 10.1016/j.neuron.2023.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Preclinical models of neurodevelopmental disorders typically use single inbred mouse strains, which fail to capture the genetic diversity and symptom heterogeneity that is common clinically. We tested whether modeling genetic background diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. We measured clinically relevant phenotypes in >1,000 mice from 33 strains, including brain and body weights and cognition, activity, anxiety, and social behaviors, using 5 behavioral assays: cued fear conditioning, open field tests in dark and bright light, direct social interaction, and social dominance. Trait disruptions mimicked those seen clinically, with robust strain and sex differences. Some strains exhibited large effect-size trait disruptions, sometimes in opposite directions, and-remarkably-others expressed resilience. Therefore, systematically introducing genetic diversity into models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies.
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Affiliation(s)
- Manal Tabbaa
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Allison Knoll
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Pat Levitt
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
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42
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Cousineau CM, Loftus K, Churchill GA, Bridges D. Cross-sectional association between blood cholesterol and calcium levels in genetically diverse strains of mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527123. [PMID: 36798159 PMCID: PMC9934644 DOI: 10.1101/2023.02.08.527123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Genetically diverse outbred mice allow for the study of genetic variation in the context of high dietary and environmental control. Using a machine learning approach we investigated clinical and morphometric factors that associate with serum cholesterol levels in 840 genetically unique mice of both sexes, and on both a control chow and high fat high sucrose diet. We find expected elevations of cholesterol in male mice, those with elevated serum triglycerides and/or fed a high fat high sucrose diet. The third strongest predictor was serum calcium which correlated with serum cholesterol across both diets and sexes (r=0.39-0.48). This is in-line with several human cohort studies which show associations between calcium and cholesterol, and calcium as an independent predictor of cardiovascular events.
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Affiliation(s)
- Cody M. Cousineau
- Department of Nutritional Sciences, University of Michigan School of Public Health
| | - Kaelin Loftus
- Department of Nutritional Sciences, University of Michigan School of Public Health
| | | | - Dave Bridges
- Department of Nutritional Sciences, University of Michigan School of Public Health
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43
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Bajpai AK, Gu Q, Orgil BO, Xu F, Torres-Rojas C, Zhao W, Chen C, Starlard-Davenport A, Jones B, Lebeche D, Towbin JA, Purevjav E, Lu L, Zhang W. Cardiac copper content and its relationship with heart physiology: Insights based on quantitative genetic and functional analyses using BXD family mice. Front Cardiovasc Med 2023; 10:1089963. [PMID: 36818345 PMCID: PMC9931904 DOI: 10.3389/fcvm.2023.1089963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background Copper (Cu) is essential for the functioning of various enzymes involved in important cellular and physiological processes. Although critical for normal cardiac function, excessive accumulation, or deficiency of Cu in the myocardium is detrimental to the heart. Fluctuations in cardiac Cu content have been shown to cause cardiac pathologies and imbalance in systemic Cu metabolism. However, the genetic basis underlying cardiac Cu levels and their effects on heart traits remain to be understood. Representing the largest murine genetic reference population, BXD strains have been widely used to explore genotype-phenotype associations and identify quantitative trait loci (QTL) and candidate genes. Methods Cardiac Cu concentration and heart function in BXD strains were measured, followed by QTL mapping. The candidate genes modulating Cu homeostasis in mice hearts were identified using a multi-criteria scoring/filtering approach. Results Significant correlations were identified between cardiac Cu concentration and left ventricular (LV) internal diameter and volumes at end-diastole and end-systole, demonstrating that the BXDs with higher cardiac Cu levels have larger LV chamber. Conversely, cardiac Cu levels negatively correlated with LV posterior wall thickness, suggesting that lower Cu concentration in the heart is associated with LV hypertrophy. Genetic mapping identified six QTLs containing a total of 217 genes, which were further narrowed down to 21 genes that showed a significant association with cardiac Cu content in mice. Among those, Prex1 and Irx3 are the strongest candidates involved in cardiac Cu modulation. Conclusion Cardiac Cu level is significantly correlated with heart chamber size and hypertrophy phenotypes in BXD mice, while being regulated by multiple genes in several QTLs. Prex1 and Irx3 may be involved in modulating Cu metabolism and its downstream effects and warrant further experimental and functional validations.
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Affiliation(s)
- Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,Department of Cardiology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Buyan-Ochir Orgil
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN, United States,Le Bonheur Children’s Hospital, Children’s Foundation Research Institute, Memphis, TN, United States
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong, China
| | - Carolina Torres-Rojas
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wenyuan Zhao
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Chen Chen
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Byron Jones
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Djamel Lebeche
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jeffrey A. Towbin
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN, United States,Le Bonheur Children’s Hospital, Children’s Foundation Research Institute, Memphis, TN, United States,Pediatric Cardiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Enkhsaikhan Purevjav
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN, United States,Le Bonheur Children’s Hospital, Children’s Foundation Research Institute, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,*Correspondence: Lu Lu,
| | - Wenjing Zhang
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,Wenjing Zhang,
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44
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Leonardo M, Brunty S, Huffman J, Kastigar A, Dickson PE. Intravenous fentanyl self-administration in male and female C57BL/6J and DBA/2J mice. Sci Rep 2023; 13:799. [PMID: 36646781 PMCID: PMC9842734 DOI: 10.1038/s41598-023-27992-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The genetic mechanisms underlying fentanyl addiction, a highly heritable disease, are unknown. Identifying these mechanisms will lead to better risk assessment, early diagnosis, and improved intervention. To this end, we used intravenous fentanyl self-administration to quantify classical self-administration phenotypes and addiction-like fentanyl seeking in male and female mice from the two founder strains of the BXD recombinant inbred mouse panel (C57BL/6J and DBA/2J). We reached three primary conclusions from these experiments. First, mice from all groups rapidly acquired intravenous fentanyl self-administration and exhibited a dose-response curve, extinction burst, and extinction of the learned self-administration response. Second, fentanyl intake (during acquisition and dose response) and fentanyl seeking (during extinction) were equivalent among groups. Third, strain effects, sex effects, or both were identified for several addiction-like behaviors (cue-induced reinstatement, stress-induced reinstatement, escalation of intravenous fentanyl self-administration). Collectively, these data indicate that C57BL/6J and DBA/2J mice of both sexes were able to acquire, regulate, and extinguish intravenous fentanyl self-administration. Moreover, these data reveal novel strain and sex effects on addiction-like behaviors in the context of intravenous fentanyl self-administration in mice and indicate that the full BXD panel can be used to identify and dissect the genetic mechanisms underlying these effects.
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Affiliation(s)
- Michael Leonardo
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV, 25703, USA
| | - Sarah Brunty
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV, 25703, USA
| | - Jessica Huffman
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV, 25703, USA
| | - Alexis Kastigar
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV, 25703, USA
| | - Price E Dickson
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, 1700 3rd Ave., Huntington, WV, 25703, USA.
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45
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Murdy TJ, Dunn AR, Singh S, Telpoukhovskaia MA, Zhang S, White JK, Kahn I, Febo M, Kaczorowski CC. Leveraging genetic diversity in mice to inform individual differences in brain microstructure and memory. Front Behav Neurosci 2023; 16:1033975. [PMID: 36703722 PMCID: PMC9871587 DOI: 10.3389/fnbeh.2022.1033975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023] Open
Abstract
In human Alzheimer's disease (AD) patients and AD mouse models, both differential pre-disease brain features and differential disease-associated memory decline are observed, suggesting that certain neurological features may protect against AD-related cognitive decline. The combination of these features is known as brain reserve, and understanding the genetic underpinnings of brain reserve may advance AD treatment in genetically diverse human populations. One potential source of brain reserve is brain microstructure, which is genetically influenced and can be measured with diffusion MRI (dMRI). To investigate variation of dMRI metrics in pre-disease-onset, genetically diverse AD mouse models, we utilized a population of genetically distinct AD mice produced by crossing the 5XFAD transgenic mouse model of AD to 3 inbred strains (C57BL/6J, DBA/2J, FVB/NJ) and two wild-derived strains (CAST/EiJ, WSB/EiJ). At 3 months of age, these mice underwent diffusion magnetic resonance imaging (dMRI) to probe neural microanatomy in 83 regions of interest (ROIs). At 5 months of age, these mice underwent contextual fear conditioning (CFC). Strain had a significant effect on dMRI measures in most ROIs tested, while far fewer effects of sex, sex*strain interactions, or strain*sex*5XFAD genotype interactions were observed. A main effect of 5XFAD genotype was observed in only 1 ROI, suggesting that the 5XFAD transgene does not strongly disrupt neural development or microstructure of mice in early adulthood. Strain also explained the most variance in mouse baseline motor activity and long-term fear memory. Additionally, significant effects of sex and strain*sex interaction were observed on baseline motor activity, and significant strain*sex and sex*5XFAD genotype interactions were observed on long-term memory. We are the first to study the genetic influences of brain microanatomy in genetically diverse AD mice. Thus, we demonstrated that strain is the primary factor influencing brain microstructure in young adult AD mice and that neural development and early adult microstructure are not strongly altered by the 5XFAD transgene. We also demonstrated that strain, sex, and 5XFAD genotype interact to influence memory in genetically diverse adult mice. Our results support the usefulness of the 5XFAD mouse model and convey strong relationships between natural genetic variation, brain microstructure, and memory.
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Affiliation(s)
| | - Amy R. Dunn
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Surjeet Singh
- The Jackson Laboratory, Bar Harbor, ME, United States
| | | | | | | | - Itamar Kahn
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Marcelo Febo
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, FL, United States
| | - Catherine C. Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME, United States,*Correspondence: Catherine C. Kaczorowski,
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46
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Tian Y, Cook JJ, Johnson GA. Restoring morphology of light sheet microscopy data based on magnetic resonance histology. Front Neurosci 2023; 16:1011895. [PMID: 36685227 PMCID: PMC9846533 DOI: 10.3389/fnins.2022.1011895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
The combination of cellular-resolution whole brain light sheet microscopy (LSM) images with an annotated atlas enables quantitation of cellular features in specific brain regions. However, most existing methods register LSM data with existing canonical atlases, e.g., The Allen Brain Atlas (ABA), which have been generated from tissue that has been distorted by removal from the skull, fixation and physical handling. This limits the accuracy of the regional morphologic measurement. Here, we present a method to combine LSM data with magnetic resonance histology (MRH) of the same specimen to restore the morphology of the LSM images to the in-skull geometry. Our registration pipeline which maps 3D LSM big data (terabyte per dataset) to MRH of the same mouse brain provides registration with low displacement error in ∼10 h with limited manual input. The registration pipeline is optimized using multiple stages of transformation at multiple resolution scales. A three-step procedure including pointset initialization, automated ANTs registration with multiple optimized transformation stages, and finalized application of the transforms on high-resolution LSM data has been integrated into a simple, structured, and robust workflow. Excellent agreement has been seen between registered LSM data and reference MRH data both locally and globally. This workflow has been applied to a collection of datasets with varied combinations of MRH contrasts from diffusion tensor images and LSM with varied immunohistochemistry, providing a routine method for streamlined registration of LSM images to MRH. Lastly, the method maps a reduced set of the common coordinate framework (CCFv3) labels from the Allen Brain Atlas onto the geometrically corrected full resolution LSM data. The pipeline maintains the individual brain morphology and allows more accurate regional annotations and measurements of volumes and cell density.
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Dietrich P, Dragatsis I. Striatum-specific mechanisms regulate neuronal cell cycle re-entry: the choice between life and death. Neural Regen Res 2023; 18:523-524. [DOI: 10.4103/1673-5374.346482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Hollingsworth TJ, Wang X, Simpson RN, White WA, Williams RW, Jablonski MM. Current Advancements in Mouse Models of Retinal Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:371-376. [PMID: 37440059 DOI: 10.1007/978-3-031-27681-1_54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The field of retinal degenerative (RDs) disease study has been in a state of exponential growth from discovering the underlying genetic components of such diseases as age-related macular degeneration (AMD) and retinitis pigmentosa (RP) to the first gene therapy developed and approved for human Leber congenital amaurosis. However, a source for high-fidelity animal models of these complex, multifactorial, and/or polygenic diseases is a need that has yet to be fulfilled. While models for AMD and RP do exist, they often require aging the animals for a year or more, feeding special diets, or introduction of external modulators such as exposure to cigarette smoke. Currently, work is being done to uncover high-fidelity naturally occurring models of these retinal diseases with the hope and intent of providing the vision community the tools it needs to better understand, treat, and, one day, cure the patients suffering from these devastating afflictions.
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Affiliation(s)
- T J Hollingsworth
- Department of Ophthalmology, University of Tennessee Health Sciences Center, Memphis, TN, USA.
- Department of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA.
- Hamilton Eye Institute, University of Tennessee Health Sciences Center, Memphis, TN, USA.
| | - Xiangdi Wang
- Department of Ophthalmology, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Hamilton Eye Institute, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Raven N Simpson
- Department of Ophthalmology, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Hamilton Eye Institute, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - William A White
- Department of Ophthalmology, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Hamilton Eye Institute, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Robert W Williams
- Department of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Hamilton Eye Institute, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Monica M Jablonski
- Department of Ophthalmology, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Department of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
- Hamilton Eye Institute, University of Tennessee Health Sciences Center, Memphis, TN, USA
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49
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Wang X, Bajpai AK, Gu Q, Ashbrook DG, Starlard-Davenport A, Lu L. Weighted gene co-expression network analysis identifies key hub genes and pathways in acute myeloid leukemia. Front Genet 2023; 14:1009462. [PMID: 36923792 PMCID: PMC10008864 DOI: 10.3389/fgene.2023.1009462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Introduction: Acute myeloid leukemia (AML) is the most common type of leukemia in adults. However, there is a gap in understanding the molecular basis of the disease, partly because key genes associated with AML have not been extensively explored. In the current study, we aimed to identify genes that have strong association with AML based on a cross-species integrative approach. Methods: We used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify co-expressed gene modules significantly correlated with human AML, and further selected the genes exhibiting a significant difference in expression between AML and healthy mouse. Protein-protein interactions, transcription factors, gene function, genetic regulation, and coding sequence variants were integrated to identify key hub genes in AML. Results: The cross-species approach identified a total of 412 genes associated with both human and mouse AML. Enrichment analysis confirmed an association of these genes with hematopoietic and immune-related functions, phenotypes, processes, and pathways. Further, the integrated analysis approach identified a set of important module genes including Nfe2, Trim27, Mef2c, Ets1, Tal1, Foxo1, and Gata1 in AML. Six of these genes (except ETS1) showed significant differential expression between human AML and healthy samples in an independent microarray dataset. All of these genes are known to be involved in immune/hematopoietic functions, and in transcriptional regulation. In addition, Nfe2, Trim27, Mef2c, and Ets1 harbor coding sequence variants, whereas Nfe2 and Trim27 are cis-regulated, making them attractive candidates for validation. Furthermore, subtype-specific analysis of the hub genes in human AML indicated high expression of NFE2 across all the subtypes (M0 through M7) and enriched expression of ETS1, LEF1, GATA1, and TAL1 in M6 and M7 subtypes. A significant correlation between methylation status and expression level was observed for most of these genes in AML patients. Conclusion: Findings from the current study highlight the importance of our cross-species approach in the identification of multiple key candidate genes in AML, which can be further studied to explore their detailed role in leukemia/AML.
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Affiliation(s)
- Xinfeng Wang
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Akhilesh K Bajpai
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Qingqing Gu
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - David G Ashbrook
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
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50
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Hu W, Liu J, Hu Y, Xu Q, Deng T, Wei M, Lu L, Mi J, Bergquist J, Xu F, Tian G. Transcriptome-wide association study reveals cholesterol metabolism gene Lpl is a key regulator of cognitive dysfunction. Front Mol Neurosci 2022; 15:1044022. [PMID: 36590920 PMCID: PMC9798092 DOI: 10.3389/fnmol.2022.1044022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Cholesterol metabolism in the brain plays a crucial role in normal physiological function, and its aberrations are associated with cognitive dysfunction. The present study aimed to determine which cholesterol-related genes play a vital role in cognitive dysfunction and to dissect its underlying molecular mechanisms using a systems genetics approach in the BXD mice family. We first systematically analyzed the association of expression of 280 hippocampal genes related to cholesterol metabolism with cognition-related traits and identified lipoprotein lipase (Lpl) as a critical regulator. This was further confirmed by phenome-wide association studies that indicate Lpl associated with hippocampus volume residuals and anxiety-related traits. By performing expression quantitative trait locus mapping, we demonstrate that Lpl is strongly cis-regulated in the BXD hippocampus. We also identified ∼3,300 genes significantly (p < 0.05) correlated with the Lpl expression. Those genes are mainly involved in the regulation of neuron-related traits through the MAPK signaling pathway, axon guidance, synaptic vesicle cycle, and NF-kappa B signaling pathway. Furthermore, a protein-protein interaction network analysis identified several direct interactors of Lpl, including Rab3a, Akt1, Igf1, Crp, and Lrp1, which indicates that Lpl involves in the regulation of cognitive dysfunction through Rab3a-mediated synaptic vesicle cycle and Akt1/Igf1/Crp/Lrp1-mediated MAPK signaling pathway. Our findings demonstrate the importance of the Lpl, among the cholesterol-related genes, in regulating cognitive dysfunction and highlighting the potential signaling pathways, which may serve as novel therapeutic targets for the treatment of cognitive dysfunction.
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Affiliation(s)
- Wei Hu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Jian Liu
- Department of Plastic Surgery, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China,Jinan Clinical Research Center for Tissue Engineering Skin Regeneration and Wound Repair, Jinan, Shandong, China
| | - Yaorui Hu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Qingling Xu
- Department of Ultrasound, Yantai Affiliated Hospital, Binzhou Medical University, Yantai, Shandong, China
| | - Tingzhi Deng
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Mengna Wei
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jia Mi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Jonas Bergquist
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China,Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden,*Correspondence: Jonas Bergquist,
| | - Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China,Fuyi Xu,
| | - Geng Tian
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China,Geng Tian,
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