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Cutler HB, Madsen S, Masson SWC, Cooke KC, Potter M, Burchfield JG, Stöckli J, Nelson ME, Cooney GJ, James DE. Dual Tracer Test to Measure Tissue-Specific Insulin Action in Individual Mice Identifies In Vivo Insulin Resistance Without Fasting Hyperinsulinemia. Diabetes 2024; 73:359-373. [PMID: 37699358 PMCID: PMC10882155 DOI: 10.2337/db23-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
The ability of metabolically active tissues to increase glucose uptake in response to insulin is critical to whole-body glucose homeostasis. This report describes the Dual Tracer Test, a robust method involving sequential retro-orbital injection of [14C]2-deoxyglucose ([14C]2DG) alone, followed 40 min later by injection of [3H]2DG with a maximal dose of insulin to quantify both basal and insulin-stimulated 2DG uptake in the same mouse. The collection of both basal and insulin-stimulated measures from a single animal is imperative for generating high-quality data since differences in insulin action may be misinterpreted mechanistically if basal glucose uptake is not accounted for. The approach was validated in a classic diet-induced model of insulin resistance and a novel transgenic mouse with reduced GLUT4 expression that, despite ubiquitous peripheral insulin resistance, did not exhibit fasting hyperinsulinemia. This suggests that reduced insulin-stimulated glucose disposal is not a primary contributor to chronic hyperinsulinemia. The Dual Tracer Test offers a technically simple assay that enables the study of insulin action in many tissues simultaneously. By administering two tracers and accounting for both basal and insulin-stimulated glucose transport, this assay halves the required sample size for studies in inbred mice and demonstrates increased statistical power to detect insulin resistance, relative to other established approaches, using a single tracer. The Dual Tracer Test is a valuable addition to the metabolic phenotyping toolbox. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Harry B Cutler
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Søren Madsen
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Stewart W C Masson
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Kristen C Cooke
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Meg Potter
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - James G Burchfield
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Jacqueline Stöckli
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Marin E Nelson
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales, Australia
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2
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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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Wulfridge P, Davidovich A, Salvador AC, Manno GC, Tryggvadottir R, Idrizi A, Huda MN, Bennett BJ, Adams LG, Hansen KD, Threadgill DW, Feinberg AP. Precision pharmacological reversal of strain-specific diet-induced metabolic syndrome in mice informed by epigenetic and transcriptional regulation. PLoS Genet 2023; 19:e1010997. [PMID: 37871105 PMCID: PMC10621921 DOI: 10.1371/journal.pgen.1010997] [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: 04/18/2023] [Revised: 11/02/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Diet-related metabolic syndrome is the largest contributor to adverse health in the United States. However, the study of gene-environment interactions and their epigenomic and transcriptomic integration is complicated by the lack of environmental and genetic control in humans that is possible in mouse models. Here we exposed three mouse strains, C57BL/6J (BL6), A/J, and NOD/ShiLtJ (NOD), to a high-fat, high-carbohydrate diet, leading to varying degrees of metabolic syndrome. We then performed transcriptomic and genome-wide DNA methylation analyses for each strain and found overlapping but also highly divergent changes in gene expression and methylation upstream of the discordant metabolic phenotypes. Strain-specific pathway analysis of dietary effects revealed a dysregulation of cholesterol biosynthesis common to all three strains but distinct regulatory networks driving this dysregulation. This suggests a strategy for strain-specific targeted pharmacologic intervention of these upstream regulators informed by epigenetic and transcriptional regulation. As a pilot study, we administered the drug GW4064 to target one of these genotype-dependent networks, the farnesoid X receptor pathway, and found that GW4064 exerts strain-specific protection against dietary effects in BL6, as predicted by our transcriptomic analysis. Furthermore, GW4064 treatment induced inflammatory-related gene expression changes in NOD, indicating a strain-specific effect in its associated toxicities as well as its therapeutic efficacy. This pilot study demonstrates the potential efficacy of precision therapeutics for genotype-informed dietary metabolic intervention and a mouse platform for guiding this approach.
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Affiliation(s)
- Phillip Wulfridge
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Adam Davidovich
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Anna C. Salvador
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, Texas, United States of America
- Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
| | - Gabrielle C. Manno
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Rakel Tryggvadottir
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - M. Nazmul Huda
- Department of Nutrition, University of California, Davis, California, United States of America
- Obesity and Metabolism Research Unit, USDA, ARS, Western Human Nutrition Research Center, Davis, California, United States of America
| | - Brian J. Bennett
- Department of Nutrition, University of California, Davis, California, United States of America
- Obesity and Metabolism Research Unit, USDA, ARS, Western Human Nutrition Research Center, Davis, California, United States of America
| | - L. Garry Adams
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - David W. Threadgill
- Department of Cell Biology and Genetics, Texas A&M Health Science Center, College Station, Texas, United States of America
- Department of Nutrition, Texas A&M University, College Station, Texas, United States of America
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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4
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Mihaylova MM, Chaix A, Delibegovic M, Ramsey JJ, Bass J, Melkani G, Singh R, Chen Z, Ja WW, Shirasu-Hiza M, Latimer MN, Mattison JA, Thalacker-Mercer AE, Dixit VD, Panda S, Lamming DW. When a calorie is not just a calorie: Diet quality and timing as mediators of metabolism and healthy aging. Cell Metab 2023; 35:1114-1131. [PMID: 37392742 PMCID: PMC10528391 DOI: 10.1016/j.cmet.2023.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/07/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023]
Abstract
An epidemic of obesity has affected large portions of the world, increasing the risk of developing many different age-associated diseases, including cancer, cardiovascular disease, and diabetes. In contrast with the prevailing notion that "a calorie is just a calorie," there are clear differences, within and between individuals, in the metabolic response to different macronutrient sources. Recent findings challenge this oversimplification; calories from different macronutrient sources or consumed at different times of day have metabolic effects beyond their value as fuel. Here, we summarize discussions conducted at a recent NIH workshop that brought together experts in calorie restriction, macronutrient composition, and time-restricted feeding to discuss how dietary composition and feeding schedule impact whole-body metabolism, longevity, and healthspan. These discussions may provide insights into the long-sought molecular mechanisms engaged by calorie restriction to extend lifespan, lead to novel therapies, and potentially inform the development of a personalized food-as-medicine approach to healthy aging.
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Affiliation(s)
- Maria M Mihaylova
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA; The Ohio State University, Comprehensive Cancer Center, Wexner Medical Center, Arthur G. James Cancer Hospital, Columbus, OH, USA.
| | - Amandine Chaix
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mirela Delibegovic
- Aberdeen Cardiovascular and Diabetes Centre, Institute of Medical Sciences, University of Aberdeen, Foresterhill Health Campus, Aberdeen, UK
| | - Jon J Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Girish Melkani
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rajat Singh
- Department of Medicine, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - William W Ja
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michele Shirasu-Hiza
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Mary N Latimer
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Anna E Thalacker-Mercer
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishwa Deep Dixit
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA; Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Satchidananda Panda
- Regulatory Biology Lab, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Dudley W Lamming
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.
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5
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Zhang KK, Zhang P, Kodur A, Erturk I, Burns CM, Kenyon C, Miller RA, Endicott SJ. LAMP2A, and other chaperone-mediated autophagy related proteins, do not decline with age in genetically heterogeneous UM-HET3 mice. Aging (Albany NY) 2023; 15:204796. [PMID: 37315291 DOI: 10.18632/aging.204796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
Chaperone-mediated autophagy (CMA) selectively degrades proteins that are crucial for glycolysis, fatty acid metabolism, and the progression of several age-associated diseases. Several previous studies, each of which evaluated males of a single inbred mouse or rat strain, have reported that CMA declines with age in many tissues, attributed to an age-related loss of LAMP2A, the primary and indispensable component of the CMA translocation complex. This has led to a paradigm in the field of CMA research, stating that the age-associated decline in LAMP2A in turn decreases CMA, contributing to the pathogenesis of late-life disease. We assessed LAMP2A levels and CMA substrate uptake in both sexes of the genetically heterogeneous UM-HET3 mouse stock, which is the current global standard for the evaluation of anti-aging interventions. We found no evidence for age-related changes in LAMP2A levels, CMA substrate uptake, or whole liver levels of CMA degradation targets, despite identifying sex differences in CMA.
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Affiliation(s)
- Katherine K Zhang
- University of Michigan, College of Literature, Science, and The Arts, Ann Arbor, MI 48109, USA
| | - Peichuan Zhang
- Calico Life Sciences, South San Francisco, CA 94080, USA
- Current Affiliation: WuXi AppTec, Shanghai, China
| | - Anagha Kodur
- University of Michigan, College of Literature, Science, and The Arts, Ann Arbor, MI 48109, USA
| | - Ilkim Erturk
- University of Michigan, Department of Pathology, Ann Arbor, MI 48109, USA
| | - Calvin M Burns
- University of Michigan, Department of Pathology, Ann Arbor, MI 48109, USA
| | - Cynthia Kenyon
- Calico Life Sciences, South San Francisco, CA 94080, USA
| | - Richard A Miller
- University of Michigan, Department of Pathology, Ann Arbor, MI 48109, USA
- University of Michigan Geriatrics Center, Ann Arbor, MI 48109, USA
| | - S Joseph Endicott
- University of Michigan, Department of Pathology, Ann Arbor, MI 48109, USA
- University of Michigan Geriatrics Center, Ann Arbor, MI 48109, USA
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6
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Flores V, Spicer AB, Sonsalla MM, Richardson NE, Yu D, Sheridan GE, Trautman ME, Babygirija R, Cheng EP, Rojas JM, Yang SE, Wakai MH, Hubbell R, Kasza I, Tomasiewicz JL, Green CL, Dantoin C, Alexander CM, Baur JA, Malecki KC, Lamming DW. Regulation of metabolic health by dietary histidine in mice. J Physiol 2023; 601:2139-2163. [PMID: 36086823 PMCID: PMC9995620 DOI: 10.1113/jp283261] [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: 04/26/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022] Open
Abstract
Low-protein (LP) diets are associated with a decreased risk of diabetes in humans, and promote leanness and glycaemic control in both rodents and humans. While the effects of an LP diet on glycaemic control are mediated by reduced levels of the branched-chain amino acids, we have observed that reducing dietary levels of the other six essential amino acids leads to changes in body composition. Here, we find that dietary histidine plays a key role in the response to an LP diet in male C57BL/6J mice. Specifically reducing dietary levels of histidine by 67% reduces the weight gain of young, lean male mice, reducing both adipose and lean mass without altering glucose metabolism, and rapidly reverses diet-induced obesity and hepatic steatosis in diet-induced obese male mice, increasing insulin sensitivity. This normalization of metabolic health was associated not with caloric restriction or increased activity, but with increased energy expenditure. Surprisingly, the effects of histidine restriction do not require the energy balance hormone Fgf21. Histidine restriction that was started in midlife promoted leanness and glucose tolerance in aged males but not females, but did not affect frailty or lifespan in either sex. Finally, we demonstrate that variation in dietary histidine levels helps to explain body mass index differences in humans. Overall, our findings demonstrate that dietary histidine is a key regulator of weight and body composition in male mice and in humans, and suggest that reducing dietary histidine may be a translatable option for the treatment of obesity. KEY POINTS: Protein restriction (PR) promotes metabolic health in rodents and humans and extends rodent lifespan. Restriction of specific individual essential amino acids can recapitulate the benefits of PR. Reduced histidine promotes leanness and increased energy expenditure in male mice. Reduced histidine does not extend the lifespan of mice when begun in midlife. Dietary levels of histidine are positively associated with body mass index in humans.
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Affiliation(s)
- Victoria Flores
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alexandra B. Spicer
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Michelle M. Sonsalla
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nicole E. Richardson
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Endocrinology and Reproductive Physiology Graduate Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Deyang Yu
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grace E. Sheridan
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Michaela E. Trautman
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Reji Babygirija
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eunhae P. Cheng
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jennifer M. Rojas
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shany E. Yang
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Matthew H. Wakai
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ryan Hubbell
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ildiko Kasza
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Cara L. Green
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Claudia Dantoin
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Caroline M. Alexander
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Joseph A. Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen C. Malecki
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Dudley W. Lamming
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Interdepartmental Graduate Program in Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
- Endocrinology and Reproductive Physiology Graduate Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
- University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA
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7
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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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8
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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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9
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Investigating trajectories of aging using high-dimensional phenotyping in mice. Lab Anim (NY) 2023; 52:61-62. [PMID: 36693909 DOI: 10.1038/s41684-023-01122-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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10
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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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11
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Guo X, Su F, Gao Y, Tang L, Yu X, Zi J, Zhou Y, Wang H, Xue J, Wang X. Effects of dietary restriction on genome stability are sex and feeding regimen dependent. Food Funct 2023; 14:471-488. [PMID: 36519635 DOI: 10.1039/d2fo03138h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Preserving genome stability is essential to prevent aging and cancer. Dietary restriction (DR) is the most reproducible non-pharmacological way to improve health and extend lifespan in various species. Whether DR helps to preserve genome stability and whether this effect is altered by experimental variables remain unclear. Moreover, DR research relies heavily on experimental animals, making the development of reliable in vitro mimetics of great interest. Therefore, we tested the effects of sex and feeding regimen (time-restricted eating, alternate day fasting and calorie restriction) on genome stability in CF-1 mice and whether these effects can be recapitulated by cell culture paradigms. Here, we show that calorie restriction significantly decreases the spontaneous micronuclei (MN), a biomarker of genome instability, in bone marrow cells of females instead of males. Alternate day fasting significantly decreases cisplatin-induced MN in females instead of males. Unexpectedly, daily time-restricted eating significantly exacerbates cisplatin-induced MN in males but not in females. Additionally, we design several culture paradigms that are able to faithfully recapitulate the key effects of these DR regimens on genome stability. In particular, 30% reduction of serum, a mimetic of calorie restriction, exhibits a strong ability to decrease spontaneous and cisplatin-induced MN in immortalized human umbilical vein endothelial cells. We conclude that the effects of different DR regimens on genome stability are not universal and females from each diet regimen sustain a more stable genome than males. Our results provide novel insight into the understanding of how DR influences genome stability in a sex and regimen dependent way, and suggest that our in vitro DR mimetics could be adopted to study the underlying molecular mechanisms.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China. .,Yunnan Environmental Mutagen Society, Kunming 650500, Yunnan, China
| | - Fuping Su
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Yue Gao
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Liyan Tang
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Xixi Yu
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Jiangli Zi
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Yingshui Zhou
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China.
| | - Han Wang
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China. .,Yunnan Environmental Mutagen Society, Kunming 650500, Yunnan, China
| | - Jinglun Xue
- Yeda Institute of Gene and Cell Therapy, Taizhou 318000, Zhejiang, China
| | - Xu Wang
- School of Life Sciences and The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming 650500, Yunnan, China. .,Yunnan Environmental Mutagen Society, Kunming 650500, Yunnan, China.,Yeda Institute of Gene and Cell Therapy, Taizhou 318000, Zhejiang, China
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12
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Cootes TA, Bhattacharyya ND, Huang SS, Daniel L, Bell-Anderson KS, Stifter SA, Chew T, Solon-Biet SM, Saraiva LR, Cai Y, Chen X, Simpson SJ, Feng CG. The quality of energy- and macronutrient-balanced diets regulates host susceptibility to influenza in mice. Cell Rep 2022; 41:111638. [DOI: 10.1016/j.celrep.2022.111638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 08/28/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
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13
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Sleiman MB, Roy S, Gao AW, Sadler MC, von Alvensleben GVG, Li H, Sen S, Harrison DE, Nelson JF, Strong R, Miller RA, Kutalik Z, Williams RW, Auwerx J. Sex- and age-dependent genetics of longevity in a heterogeneous mouse population. Science 2022; 377:eabo3191. [PMID: 36173858 PMCID: PMC9905652 DOI: 10.1126/science.abo3191] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DNA variants that modulate life span provide insight into determinants of health, disease, and aging. Through analyses in the UM-HET3 mice of the Interventions Testing Program (ITP), we detected a sex-independent quantitative trait locus (QTL) on chromosome 12 and identified sex-specific QTLs, some of which we detected only in older mice. Similar relations between life history and longevity were uncovered in mice and humans, underscoring the importance of early access to nutrients and early growth. We identified common age- and sex-specific genetic effects on gene expression that we integrated with model organism and human data to create a hypothesis-building interactive resource of prioritized longevity and body weight genes. Finally, we validated Hipk1, Ddost, Hspg2, Fgd6, and Pdk1 as conserved longevity genes using Caenorhabditis elegans life-span experiments.
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Affiliation(s)
- Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center (UTHSC), Memphis, TN 38163, USA
| | - Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Marie C. Sadler
- Institute of Primary Care and Public Health (Unisante), University of Lausanne, Lausanne 1011, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Giacomo V. G. von Alvensleben
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Hao Li
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | | | - James F. Nelson
- Barshop Center for Longevity Studies at the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Randy Strong
- Barshop Center for Longevity Studies at the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- South Texas Veterans Healthcare System, San Antonio, TX 78229, USA
| | - Richard A. Miller
- Department of Pathology, University of Michigan Geriatrics Center, Ann Arbor, MI 48109-2200, USA
| | - Zoltán Kutalik
- Institute of Primary Care and Public Health (Unisante), University of Lausanne, Lausanne 1011, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center (UTHSC), Memphis, TN 38163, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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14
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Mozhui K, Lu AT, Li CZ, Haghani A, Sandoval-Sierra JV, Wu Y, Williams RW, Horvath S. Genetic loci and metabolic states associated with murine epigenetic aging. eLife 2022; 11:e75244. [PMID: 35389339 PMCID: PMC9049972 DOI: 10.7554/elife.75244] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
Changes in DNA methylation (DNAm) are linked to aging. Here, we profile highly conserved CpGs in 339 predominantly female mice belonging to the BXD family for which we have deep longevity and genomic data. We use a 'pan-mammalian' microarray that provides a common platform for assaying the methylome across mammalian clades. We computed epigenetic clocks and tested associations with DNAm entropy, diet, weight, metabolic traits, and genetic variation. We describe the multifactorial variance of methylation at these CpGs and show that high-fat diet augments the age-related changes. Entropy increases with age. The progression to disorder, particularly at CpGs that gain methylation over time, was predictive of genotype-dependent life expectancy. The longer-lived BXD strains had comparatively lower entropy at a given age. We identified two genetic loci that modulate epigenetic age acceleration (EAA): one on chromosome (Chr) 11 that encompasses the Erbb2/Her2 oncogenic region, and the other on Chr19 that contains a cytochrome P450 cluster. Both loci harbor genes associated with EAA in humans, including STXBP4, NKX2-3, and CUTC. Transcriptome and proteome analyses revealed correlations with oxidation-reduction, metabolic, and immune response pathways. Our results highlight concordant loci for EAA in humans and mice, and demonstrate a tight coupling between the metabolic state and epigenetic aging.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los AngelesLos AngelesUnited States
| | - Caesar Z Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los AngelesLos AngelesUnited States
| | - Amin Haghani
- Department of Biostatistics, Fielding School of Public Health, University of California Los AngelesLos AngelesUnited States
| | - Jose Vladimir Sandoval-Sierra
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
| | - Yibo Wu
- YCI Laboratory for Next-Generation Proteomics, RIKEN Center for Integrative Medical SciencesYokohamaJapan
- University of GenevaGenevaSwitzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los AngelesLos AngelesUnited States
- Department of Biostatistics, Fielding School of Public Health, University of California Los AngelesLos AngelesUnited States
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15
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New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork. Genes (Basel) 2022; 13:genes13040614. [PMID: 35456420 PMCID: PMC9024903 DOI: 10.3390/genes13040614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/18/2022] Open
Abstract
Gene-by-environment interactions are important for all facets of biology, especially behaviour. Families of isogenic strains of mice, such as the BXD strains, are excellently placed to study these interactions, as the same genome can be tested in multiple environments. BXD strains are recombinant inbred mouse strains derived from crossing two inbred strains—C57BL/6J and DBA/2J mice. Many reproducible genometypes can be leveraged, and old data can be reanalysed with new tools to produce novel insights. We obtained drug and behavioural phenotypes from Philip et al. Genes, Brain and Behaviour 2010, and reanalysed their data with new genotypes from sequencing, as well as new models (Genome-wide Efficient Mixed Model Association (GEMMA) and R/qtl2). We discovered QTLs on chromosomes 3, 5, 9, 11, and 14, not found in the original study. We reduced the candidate genes based on their ability to alter gene expression or protein function. Candidate genes included Slitrk6 and Cdk14. Slitrk6, in a Chromosome14 QTL for locomotion, was found to be part of a co-expression network involved in voluntary movement and associated with neuropsychiatric phenotypes. Cdk14, one of only three genes in a Chromosome5 QTL, is associated with handling induced convulsions after ethanol treatment, that is regulated by the anticonvulsant drug valproic acid. By using families of isogenic strains, we can reanalyse data to discover novel candidate genes involved in response to drugs of abuse.
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16
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Williams EG, Pfister N, Roy S, Statzer C, Haverty J, Ingels J, Bohl C, Hasan M, Čuklina J, Bühlmann P, Zamboni N, Lu L, Ewald CY, Williams RW, Aebersold R. Multiomic profiling of the liver across diets and age in a diverse mouse population. Cell Syst 2022; 13:43-57.e6. [PMID: 34666007 PMCID: PMC8776606 DOI: 10.1016/j.cels.2021.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 01/21/2023]
Abstract
We profiled the liver transcriptome, proteome, and metabolome in 347 individuals from 58 isogenic strains of the BXD mouse population across age (7 to 24 months) and diet (low or high fat) to link molecular variations to metabolic traits. Several hundred genes are affected by diet and/or age at the transcript and protein levels. Orthologs of two aging-associated genes, St7 and Ctsd, were knocked down in C. elegans, reducing longevity in wild-type and mutant long-lived strains. The multiomics data were analyzed as segregating gene networks according to each independent variable, providing causal insight into dietary and aging effects. Candidates were cross-examined in an independent diversity outbred mouse liver dataset segregating for similar diets, with ∼80%-90% of diet-related candidate genes found in common across datasets. Together, we have developed a large multiomics resource for multivariate analysis of complex traits and demonstrate a methodology for moving from observational associations to causal connections.
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Affiliation(s)
- Evan G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Niklas Pfister
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Cyril Statzer
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Jack Haverty
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jesse Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Casey Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Moaraj Hasan
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Jelena Čuklina
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Peter Bühlmann
- Department of Mathematics, Seminar for Statistics, ETH Zürich, Zurich, Switzerland
| | - Nicola Zamboni
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Collin Y Ewald
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland; Faculty of Science, University of Zürich, Zurich, Switzerland
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17
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Affiliation(s)
- Cara L Green
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Dudley W Lamming
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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