1
|
Sun F, Desevin K, Fu Y, Parameswaran S, Mayall J, Rinaldi V, Krietenstein N, Manukyan A, Yin Q, Galan C, Yang CH, Shindyapina AV, Gladyshev VN, Garber M, Schjenken JE, Rando OJ. A single cell atlas of the mouse seminal vesicle. bioRxiv 2024:2024.04.08.588538. [PMID: 38645090 PMCID: PMC11030459 DOI: 10.1101/2024.04.08.588538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
During mammalian reproduction, sperm are delivered to the female reproductive tract bathed in a complex medium known as seminal fluid, which plays key roles in signaling to the female reproductive tract and in nourishing sperm for their onwards journey. Along with minor contributions from the prostate and the epididymis, the majority of seminal fluid is produced by a somewhat understudied organ known as the seminal vesicle. Here, we report the first single-cell RNA-seq atlas of the mouse seminal vesicle, generated using tissues obtained from 23 mice of varying ages, exposed to a range of dietary challenges. We define the transcriptome of the secretory cells in this tissue, identifying a relatively homogeneous population of the epithelial cells which are responsible for producing the majority of seminal fluid. We also define the immune cell populations - including large populations of macrophages, dendritic cells, T cells, and NKT cells - which have the potential to play roles in producing various immune mediators present in seminal plasma. Together, our data provide a resource for understanding the composition of an understudied reproductive tissue with potential implications for paternal control of offspring development and metabolism.
Collapse
|
2
|
Fernando R, Shindyapina AV, Ost M, Santesmasses D, Hu Y, Tyshkovskiy A, Yim SH, Weiss J, Gladyshev VN, Grune T, Castro JP. Downregulation of mitochondrial metabolism is a driver for fast skeletal muscle loss during mouse aging. Commun Biol 2023; 6:1240. [PMID: 38066057 PMCID: PMC10709625 DOI: 10.1038/s42003-023-05595-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Skeletal muscle aging is characterized by the loss of muscle mass, strength and function, mainly attributed to the atrophy of glycolytic fibers. Underlying mechanisms driving the skeletal muscle functional impairment are yet to be elucidated. To unbiasedly uncover its molecular mechanisms, we recurred to gene expression and metabolite profiling in a glycolytic muscle, Extensor digitorum longus (EDL), from young and aged C57BL/6JRj mice. Employing multi-omics approaches we found that the main age-related changes are connected to mitochondria, exhibiting a downregulation in mitochondrial processes. Consistent is the altered mitochondrial morphology. We further compared our mouse EDL aging signature with human data from the GTEx database, reinforcing the idea that our model may recapitulate muscle loss in humans. We are able to show that age-related mitochondrial downregulation is likely to be detrimental, as gene expression signatures from commonly used lifespan extending interventions displayed the opposite direction compared to our EDL aging signature.
Collapse
Affiliation(s)
- Raquel Fernando
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mario Ost
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany
- Paul-Flechsig-Institute of Neuropathology, University Clinic Leipzig, 04103, Leipzig, Germany
| | - Didac Santesmasses
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Yan Hu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119234, Russia
| | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, 79401, USA
| | - Jürgen Weiss
- German Center for Diabetes Research (DZD), Ingolstaedter Land Str. 1, 85764, Neuherberg, Germany
- German Diabetes Center (DDZ), Leibniz Center for Diabetes Research, Düsseldorf, Germany
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany.
- German Diabetes Center (DDZ), Leibniz Center for Diabetes Research, Düsseldorf, Germany.
- German Center for Cardiovascular Research (DZHK), 10117, Berlin, Germany.
- University of Potsdam, Institute of Nutritional Science, 14558, Nuthetal, Germany.
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - José Pedro Castro
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558, Nuthetal, Germany
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
- Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
| |
Collapse
|
3
|
Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Author Correction: Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1462. [PMID: 37674040 PMCID: PMC10645586 DOI: 10.1038/s43587-023-00499-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
4
|
Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1144-1166. [PMID: 37563227 PMCID: PMC10501909 DOI: 10.1038/s43587-023-00462-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.
Collapse
Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
5
|
Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NMS, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O'Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer ABA, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S. DNA methylation networks underlying mammalian traits. Science 2023; 381:eabq5693. [PMID: 37561875 DOI: 10.1126/science.abq5693] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.
Collapse
Affiliation(s)
- 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
| | - Caesar Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Janssen Research & Development, Spring House, PA, USA
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Joshua Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Victoria A Acosta-Rodríguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Danielle M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Abdulaziz N Alagaili
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Javier Almunia
- Loro Parque Fundacion, Avenida Loro Parque, Puerto de la Cruz, Tenerife, Spain
| | - Ajoy Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Nabil M S Amor
- Laboratory of Biodiversity, Parasitology, and Ecology, University of Tunis El Manar, Tunis, Tunisia
| | - Reza Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - Gareth Banks
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | - Daniel T Blumstein
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - Eleanor K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | | | - Robert T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - Janine L Brown
- Center for Species Survival, Smithsonian National Zoo and Conservation Biology, Front Royal, VA, USA
| | - Gerald Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Alex Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Julie M Cavin
- Gulf World Marine Park - Dolphin Company, Panama City Beach, FL, USA
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology & Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Andreas S Chavez
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kaiyang Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Priscila Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
| | - Joseph A Cook
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM, USA
| | - Lisa N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Marie-Laurence Cossette
- Department of Environmental & Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - Joanna Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Joseph DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Christopher Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Jonathan L Dunnum
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM, USA
| | | | - Candice K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Ebru Erbay
- Altos Labs, Bay Area Institute of Science, Redwood City, CA, USA
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Zhe Fei
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, CA, USA
| | - Steven H Ferguson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - Jean-Michel Gaillard
- University of Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Eva Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Livia Gerber
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rodolfo G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Matthew J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Bradley Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Daniel W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | | | - Andrew N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Taosheng Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | | | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Olga Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | | | | | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Michael S Kobor
- Edwin S. H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pawel Kordowitzki
- Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | | | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marianne Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Jean-François Lemaître
- University of Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Andrew J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xinmin Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cun Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - Andrea R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Thomas J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - June Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - Jennifer J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin Madison, Madison, WI, USA
| | - Gisele A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - Jason Munshi-South
- Louis Calder Center - Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Asieh Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Martina Nagy
- Museum fur Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Pritika Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Peter W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - Ngoc B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Justine K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | | | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Deutsches Krebsforschungszentrum, Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | | | | | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kim M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy B Pedersen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Matteo Pellegrini
- Department Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Katharina J Peters
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - Darren W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - Gabriela M Pinho
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jesse R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Natalia A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Pradeep Reddy
- Altos Labs, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Benjamin Rey
- University of Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Beate R Ritz
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | | | | | | | - Elena Rydkina
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Adam B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio, and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - Kyle M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dennis Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | | | | | - Lawrence B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Aaron B A Shafer
- Department of Forensic Science, Environmental & Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - Ishani Sinha
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jesse Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Russel G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Elham Soltanmohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | | | | | | | | | - Karen J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - Donald T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | | | - Balazs Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masaki Takasugi
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Michael J Thompson
- Department Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bill Van Bonn
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - Sonja C Vernes
- School of Biology, The University of St. Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Diego Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Harry V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - Qi Yan
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Mingjia Yao
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Brent G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Peng Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 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
- Altos Labs, Cambridge, UK
| |
Collapse
|
6
|
Zhang B, Lee DE, Trapp A, Tyshkovskiy A, Lu AT, Bareja A, Kerepesi C, McKay LK, Shindyapina AV, Dmitriev SE, Baht GS, Horvath S, Gladyshev VN, White JP. Multi-omic rejuvenation and life span extension on exposure to youthful circulation. Nat Aging 2023; 3:948-964. [PMID: 37500973 DOI: 10.1038/s43587-023-00451-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/06/2023] [Indexed: 07/29/2023]
Abstract
Heterochronic parabiosis (HPB) is known for its functional rejuvenation effects across several mouse tissues. However, its impact on biological age and long-term health is unknown. Here we performed extended (3-month) HPB, followed by a 2-month detachment period of anastomosed pairs. Old detached mice exhibited improved physiological parameters and lived longer than control isochronic mice. HPB drastically reduced the epigenetic age of blood and liver based on several clock models using two independent platforms. Remarkably, this rejuvenation effect persisted even after 2 months of detachment. Transcriptomic and epigenomic profiles of anastomosed mice showed an intermediate phenotype between old and young, suggesting a global multi-omic rejuvenation effect. In addition, old HPB mice showed gene expression changes opposite to aging but akin to several life span-extending interventions. Altogether, we reveal that long-term HPB results in lasting epigenetic and transcriptome remodeling, culminating in the extension of life span and health span.
Collapse
Affiliation(s)
- Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David E Lee
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Retro Biosciences, Redwood City, CA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Akshay Bareja
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Computer Science and Control (SZTAKI), Eötvös Loránd Research Network, Budapest, Hungary
| | - Lauren K McKay
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Retro Biosciences, Redwood City, CA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - James P White
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA.
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
7
|
Tyshkovskiy A, Ma S, Shindyapina AV, Tikhonov S, Lee SG, Bozaykut P, Castro JP, Seluanov A, Schork NJ, Gorbunova V, Dmitriev SE, Miller RA, Gladyshev VN. Distinct longevity mechanisms across and within species and their association with aging. Cell 2023; 186:2929-2949.e20. [PMID: 37269831 DOI: 10.1016/j.cell.2023.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2022] [Accepted: 05/02/2023] [Indexed: 06/05/2023]
Abstract
Lifespan varies within and across species, but the general principles of its control remain unclear. Here, we conducted multi-tissue RNA-seq analyses across 41 mammalian species, identifying longevity signatures and examining their relationship with transcriptomic biomarkers of aging and established lifespan-extending interventions. An integrative analysis uncovered shared longevity mechanisms within and across species, including downregulated Igf1 and upregulated mitochondrial translation genes, and unique features, such as distinct regulation of the innate immune response and cellular respiration. Signatures of long-lived species were positively correlated with age-related changes and enriched for evolutionarily ancient essential genes, involved in proteolysis and PI3K-Akt signaling. Conversely, lifespan-extending interventions counteracted aging patterns and affected younger, mutable genes enriched for energy metabolism. The identified biomarkers revealed longevity interventions, including KU0063794, which extended mouse lifespan and healthspan. Overall, this study uncovers universal and distinct strategies of lifespan regulation within and across species and provides tools for discovering longevity interventions.
Collapse
Affiliation(s)
- Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stanislav Tikhonov
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Perinur Bozaykut
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - José P Castro
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Nicholas J Schork
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA, USA.
| |
Collapse
|
8
|
Ibragimova AG, Stanishevskiy YM, Plakkhin AM, Zubko AV, Darvish NA, Koassary AK, Shindyapina AV. Comparative analysis of calcified soft tissues revealed shared deregulated pathways. Front Aging Neurosci 2023; 15:1131548. [PMID: 37441678 PMCID: PMC10335799 DOI: 10.3389/fnagi.2023.1131548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 05/18/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Calcification of soft tissues is a common age-related pathology that primarily occurs within vascular tissue. The mechanisms underlying pathological calcification in humans and tissue specificity of the process is still poorly understood. Previous studies examined calcified tissues on one to one basis, thus preventing comparison of deregulated pathways across tissues. Purpose This study aimed to establish common and tissue-specific changes associated with calcification in aorta, artery tibial, coronary artery and pituitary gland in subjects from the Genotype-Tissue Expression (GTEx) dataset using its RNA sequencing and histological data. Methods We used publicly available data from the GTEx database https://gtexportal.org/home/aboutGTEx. All GTEx tissue samples were derived by the GTEx consorcium from deceased donors, with age from 20 to 79, both men and women. GTEx study authorization was obtained via next-of-kin consent for the collection and banking of de-identified tissue samples for scientific research. Hematoxylin and eosin (H&E) staining of arteries were manually graded based on the presence of calcification on a scale from zero to four, where zero designates absence of calcification and four designates severe calcification. Samples with fat contamination and mislabeled tissues were excluded, which left 430 aorta, 595 artery tibial, 124 coronary artery, and 283 pituitary samples for downstream gene expression analysis. Transcript levels of protein-coding genes were associated with calcification grade using sex, age bracket and cause of death as covariates, and tested for pathway enrichment using gene set enrichment analysis. Results We identified calcification deposits in 28 (6.5%) aortas, 121 (20%), artery tibials, 54 (43%), coronary arteries, and 24 (8%) pituitary glands of GTEx subjects. We observed an age-dependent increase in incidence of calcification in all vascular tissues, but not in pituitary. Subjects with calcification in the artery tibial were significantly more likely to have calcification in the coronary artery (OR = 2.56, p = 6.3e-07). Markers of calcification previously established in preclinical and in vitro studies, e.g., BMP2 and RUNX2, were deregulated in the calcified tibial and coronary arteries, confirming the relevance of these genes to human pathology. Differentially expressed genes associated with calcification poorly overlapped across tissues suggesting tissue-specific nuances in mechanisms of calcification. Nevertheless, calcified arteries unanimously down-regulated pathways of intracellular transport and up-regulated inflammatory pathways suggesting these as universal targets for pathological calcification. In particular, PD-1 and PD-L1 genes were up-regulated in calcified tissues but not in the blood of the same subjects, suggesting that localized inflammation contributes to pathological calcification. Conclusion Pathological calcification is a prevalent disease of aging that shares little changes in expression in individual genes across tissues. However, our analysis suggests that it potentially can be targeted by alleviating local inflammation of soft tissues.
Collapse
Affiliation(s)
| | | | | | | | - Nidal Akhmedovich Darvish
- Bakoulev National Medical Research Center for Cardiovascular Surgery, Russian Federation, Moscow, Russia
| | - Anton Karenovich Koassary
- Bakoulev National Medical Research Center for Cardiovascular Surgery, Russian Federation, Moscow, Russia
| | - Anastasia V. Shindyapina
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Retro Biosciences Inc., Redwood City, CA, United States
| |
Collapse
|
9
|
Shindyapina AV, Cho Y, Kaya A, Tyshkovskiy A, Castro JP, Deik A, Gordevicius J, Poganik JR, Clish CB, Horvath S, Peshkin L, Gladyshev VN. Rapamycin treatment during development extends life span and health span of male mice and Daphnia magna. Sci Adv 2022; 8:eabo5482. [PMID: 36112674 PMCID: PMC9481125 DOI: 10.1126/sciadv.abo5482] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/26/2022] [Indexed: 05/22/2023]
Abstract
Development is tightly connected to aging, but whether pharmacologically targeting development can extend life remains unknown. Here, we subjected genetically diverse UMHET3 mice to rapamycin for the first 45 days of life. The mice grew slower and remained smaller than controls for their entire lives. Their reproductive age was delayed without affecting offspring numbers. The treatment was sufficient to extend the median life span by 10%, with the strongest effect in males, and helped to preserve health as measured by frailty index scores, gait speed, and glucose and insulin tolerance tests. Mechanistically, the liver transcriptome and epigenome of treated mice were younger at the completion of treatment. Analogous to mice, rapamycin exposure during development robustly extended the life span of Daphnia magna and reduced its body size. Overall, the results demonstrate that short-term rapamycin treatment during development is a novel longevity intervention that acts by slowing down development and aging, suggesting that aging may be targeted already early in life.
Collapse
Affiliation(s)
| | - Yongmin Cho
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Alexander Tyshkovskiy
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - José P. Castro
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jesse R. Poganik
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Vadim N. Gladyshev
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Corresponding author.
| |
Collapse
|
10
|
Ribeiro R, Macedo JC, Costa M, Ustiyan V, Shindyapina AV, Tyshkovskiy A, Gomes RN, Castro JP, Kalin TV, Vasques-Nóvoa F, Nascimento DS, Dmitriev SE, Gladyshev VN, Kalinichenko VV, Logarinho E. In vivo cyclic induction of the FOXM1 transcription factor delays natural and progeroid aging phenotypes and extends healthspan. Nat Aging 2022; 2:397-411. [PMID: 37118067 DOI: 10.1038/s43587-022-00209-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/15/2022] [Indexed: 04/30/2023]
Abstract
The FOXM1 transcription factor exhibits pleiotropic C-terminal transcriptional and N-terminal non-transcriptional functions in various biological processes critical for cellular homeostasis. We previously found that FOXM1 repression during cellular aging underlies the senescence phenotypes, which were vastly restored by overexpressing transcriptionally active FOXM1. Yet, it remains unknown whether increased expression of FOXM1 can delay organismal aging. Here, we show that in vivo cyclic induction of an N-terminal truncated FOXM1 transgene on progeroid and naturally aged mice offsets aging-associated repression of full-length endogenous Foxm1, reinstating both transcriptional and non-transcriptional functions. This translated into mitigation of several cellular aging hallmarks, as well as molecular and histopathological progeroid features of the short-lived Hutchison-Gilford progeria mouse model, significantly extending its lifespan. FOXM1 transgene induction also reinstated endogenous Foxm1 levels in naturally aged mice, delaying aging phenotypes while extending their lifespan. Thus, we disclose that FOXM1 genetic rewiring can delay senescence-associated progeroid and natural aging pathologies.
Collapse
Affiliation(s)
- Rui Ribeiro
- Aging and Aneuploidy Laboratory, i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology (GABBA), ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Joana C Macedo
- Aging and Aneuploidy Laboratory, i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Madalena Costa
- Anatomy Department, Unit for Multidisciplinary Biomedical Research, ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Vladimir Ustiyan
- Center for Lung Regenerative Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Rita N Gomes
- INEB - Instituto Nacional de Engenharia Biomédica, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - José Pedro Castro
- Aging and Aneuploidy Laboratory, i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Tanya V Kalin
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francisco Vasques-Nóvoa
- INEB - Instituto Nacional de Engenharia Biomédica, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Cardiovascular Research and Development Center, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Diana S Nascimento
- INEB - Instituto Nacional de Engenharia Biomédica, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vladimir V Kalinichenko
- Center for Lung Regenerative Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elsa Logarinho
- Aging and Aneuploidy Laboratory, i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
| |
Collapse
|
11
|
Walsh K, Raghavachari N, Kerr C, Bick AG, Cummings SR, Druley T, Dunbar CE, Genovese G, Goodell MA, Jaiswal S, Maciejewski J, Natarajan P, Shindyapina AV, Shuldiner AR, Van Den Akker EB, Vijg J. Clonal Hematopoiesis Analyses in Clinical, Epidemiologic, and Genetic Aging Studies to Unravel Underlying Mechanisms of Age-Related Dysfunction in Humans. Front Aging 2022; 3:841796. [PMID: 35821803 PMCID: PMC9261374 DOI: 10.3389/fragi.2022.841796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022]
Abstract
Aging is characterized by increased mortality, functional decline, and exponential increases in the incidence of diseases such as cancer, stroke, cardiovascular disease, neurological disease, respiratory disease, etc. Though the role of aging in these diseases is widely accepted and considered to be a common denominator, the underlying mechanisms are largely unknown. A significant age-related feature observed in many population cohorts is somatic mosaicism, the detectable accumulation of somatic mutations in multiple cell types and tissues, particularly those with high rates of cell turnover (e.g., skin, liver, and hematopoietic cells). Somatic mosaicism can lead to the development of cellular clones that expand with age in otherwise normal tissues. In the hematopoietic system, this phenomenon has generally been referred to as "clonal hematopoiesis of indeterminate potential" (CHIP) when it applies to a subset of clones in which mutations in driver genes of hematologic malignancies are found. Other mechanisms of clonal hematopoiesis, including large chromosomal alterations, can also give rise to clonal expansion in the absence of conventional CHIP driver gene mutations. Both types of clonal hematopoiesis (CH) have been observed in studies of animal models and humans in association with altered immune responses, increased mortality, and disease risk. Studies in murine models have found that some of these clonal events are involved in abnormal inflammatory and metabolic changes, altered DNA damage repair and epigenetic changes. Studies in long-lived individuals also show the accumulation of somatic mutations, yet at this advanced age, carriership of somatic mutations is no longer associated with an increased risk of mortality. While it remains to be elucidated what factors modify this genotype-phenotype association, i.e., compensatory germline genetics, cellular context of the mutations, protective effects to diseases at exceptional age, it points out that the exceptionally long-lived are key to understand the phenotypic consequences of CHIP mutations. Assessment of the clinical significance of somatic mutations occurring in blood cell types for age-related outcomes in human populations of varied life and health span, environmental exposures, and germline genetic risk factors will be valuable in the development of personalized strategies tailored to specific somatic mutations for healthy aging.
Collapse
Affiliation(s)
- Kenneth Walsh
- University of Virginia, Charlottesville, VA, United States
| | - Nalini Raghavachari
- National Institute on Aging, NIH, Bethesda, MD, United States,*Correspondence: Nalini Raghavachari,
| | - Candace Kerr
- National Institute on Aging, NIH, Bethesda, MD, United States
| | | | - Steven R. Cummings
- University of California, San Francisco, San Francisco, CA, United States
| | - Todd Druley
- Angle Biosciences, St. Louis, MO, United States
| | - Cynthia E. Dunbar
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD, United States
| | | | | | | | | | | | | | | | | | - Jan Vijg
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
12
|
Santesmasses D, Castro JP, Zenin AA, Shindyapina AV, Gerashchenko MV, Zhang B, Kerepesi C, Yim SH, Fedichev PO, Gladyshev VN. COVID-19 is an emergent disease of aging. Aging Cell 2020; 19:e13230. [PMID: 33006233 PMCID: PMC7576244 DOI: 10.1111/acel.13230] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/25/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
COVID-19 is an ongoing pandemic caused by the SARS-CoV-2 coronavirus that poses one of the greatest challenges to public health in recent years. SARS-CoV-2 is known to preferentially target older subjects and those with pre-existing conditions, but the reason for this age dependence is unclear. Here, we found that the case fatality rate for COVID-19 grows exponentially with age in all countries tested, with the doubling time approaching that of all-cause human mortality. In addition, men and those with multiple age-related diseases are characterized by increased mortality. Moreover, similar mortality patterns were found for all-cause pneumonia. We further report that the gene expression of ACE2, the SARS-CoV-2 receptor, grows in the lung with age, except for subjects on a ventilator. Together, our findings establish COVID-19 as an emergent disease of aging, and age and age-related diseases as its major risk factors. In turn, this suggests that COVID-19, and deadly respiratory diseases in general, may be targeted, in addition to antiviral approaches, by approaches that target the aging process.
Collapse
Affiliation(s)
- Didac Santesmasses
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - José Pedro Castro
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Aleksandr A. Zenin
- GERO PTE. LTDSingapore CitySingapore
- Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Anastasia V. Shindyapina
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Bohan Zhang
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Csaba Kerepesi
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Sun Hee Yim
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Peter O. Fedichev
- GERO PTE. LTDSingapore CitySingapore
- Research Center for Molecular Mechanisms of Aging and Age Related DiseasesMoscow Institute of Physics and Technology (National Research University)DolgoprudnyRussia
| | - Vadim N. Gladyshev
- Division of Genetics, Department of MedicineBrigham and Women’s Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| |
Collapse
|
13
|
Shindyapina AV, Zenin AA, Tarkhov AE, Santesmasses D, Fedichev PO, Gladyshev VN. Germline burden of rare damaging variants negatively affects human healthspan and lifespan. eLife 2020; 9:e53449. [PMID: 32254024 PMCID: PMC7314550 DOI: 10.7554/elife.53449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Heritability of human lifespan is 23-33% as evident from twin studies. Genome-wide association studies explored this question by linking particular alleles to lifespan traits. However, genetic variants identified so far can explain only a small fraction of lifespan heritability in humans. Here, we report that the burden of rarest protein-truncating variants (PTVs) in two large cohorts is negatively associated with human healthspan and lifespan, accounting for 0.4 and 1.3 years of their variability, respectively. In addition, longer-living individuals possess both fewer rarest PTVs and less damaging PTVs. We further estimated that somatic accumulation of PTVs accounts for only a small fraction of mortality and morbidity acceleration and hence is unlikely to be causal in aging. We conclude that rare damaging mutations, both inherited and accumulated throughout life, contribute to the aging process, and that burden of ultra-rare variants in combination with common alleles better explain apparent heritability of human lifespan.
Collapse
Affiliation(s)
| | - Aleksandr A Zenin
- Gero LLCMoscowRussian Federation
- The Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State UniversityMoscowRussian Federation
| | - Andrei E Tarkhov
- Gero LLCMoscowRussian Federation
- Skolkovo Institute of Science and Technology, Skolkovo Innovation CenterMoscowRussian Federation
| | | | - Peter O Fedichev
- Gero LLCMoscowRussian Federation
- Moscow Institute of Physics and TechnologyMoscowRussian Federation
| | - Vadim N Gladyshev
- Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| |
Collapse
|
14
|
Sheshukova EV, Komarova TV, Ershova NM, Shindyapina AV, Dorokhov YL. An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene. Front Plant Sci 2017; 8:2137. [PMID: 29312392 PMCID: PMC5742262 DOI: 10.3389/fpls.2017.02137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP, a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is "matryoshka," containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5'-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves.
Collapse
Affiliation(s)
- Ekaterina V. Sheshukova
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V. Komarova
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia M. Ershova
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasia V. Shindyapina
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri L. Dorokhov
- Department of Genetics and Biotechnology, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
15
|
Shindyapina AV, Komarova TV, Sheshukova EV, Ershova NM, Tashlitsky VN, Kurkin AV, Yusupov IR, Mkrtchyan GV, Shagidulin MY, Dorokhov YL. The Antioxidant Cofactor Alpha-Lipoic Acid May Control Endogenous Formaldehyde Metabolism in Mammals. Front Neurosci 2017; 11:651. [PMID: 29249928 PMCID: PMC5717020 DOI: 10.3389/fnins.2017.00651] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/09/2017] [Indexed: 12/15/2022] Open
Abstract
The healthy human body contains small amounts of metabolic formaldehyde (FA) that mainly results from methanol oxidation by pectin methylesterase, which is active in a vegetable diet and in the gastrointestinal microbiome. With age, the ability to maintain a low level of FA decreases, which increases the risk of Alzheimer's disease and dementia. It has been shown that 1,2-dithiolane-3-pentanoic acid or alpha lipoic acid (ALA), a naturally occurring dithiol and antioxidant cofactor of mitochondrial α-ketoacid dehydrogenases, increases glutathione (GSH) content and FA metabolism by mitochondrial aldehyde dehydrogenase 2 (ALDH2) thus manifests a therapeutic potential beyond its antioxidant property. We suggested that ALA can contribute to a decrease in the FA content of mammals by acting on ALDH2 expression. To test this assumption, we administered ALA in mice in order to examine the effect on FA metabolism and collected blood samples for the measurement of FA. Our data revealed that ALA efficiently eliminated FA in mice. Without affecting the specific activity of FA-metabolizing enzymes (ADH1, ALDH2, and ADH5), ALA increased the GSH content in the brain and up-regulated the expression of the FA-metabolizing ALDH2 gene in the brain, particularly in the hippocampus, but did not impact its expression in the liver in vivo or in rat liver isolated from the rest of the body. After ALA administration in mice and in accordance with the increased content of brain ALDH2 mRNA, we detected increased ALDH2 activity in brain homogenates. We hypothesized that the beneficial effects of ALA on patients with Alzheimer's disease may be associated with accelerated ALDH2-mediated FA detoxification and clearance.
Collapse
Affiliation(s)
- Anastasia V Shindyapina
- Department of Genetics and Biotechnology, N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia.,Department of Chemistry and Biochemistry of Nucleoproteins, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Komarova
- Department of Genetics and Biotechnology, N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia.,Department of Chemistry and Biochemistry of Nucleoproteins, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina V Sheshukova
- Department of Genetics and Biotechnology, N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia.,Department of Chemistry and Biochemistry of Nucleoproteins, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia M Ershova
- Department of Genetics and Biotechnology, N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia.,Department of Chemistry and Biochemistry of Nucleoproteins, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Ildar R Yusupov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Garik V Mkrtchyan
- Department of Chemistry and Biochemistry of Nucleoproteins, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Murat Y Shagidulin
- Academician V. I. Schumakov Federal Research Center of Transplantology and Artificial Organs, Moscow, Russia
| | - Yuri L Dorokhov
- Department of Genetics and Biotechnology, N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia.,Department of Chemistry and Biochemistry of Nucleoproteins, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
16
|
Sheshukova EV, Komarova TV, Pozdyshev DV, Ershova NM, Shindyapina AV, Tashlitsky VN, Sheval EV, Dorokhov YL. The Intergenic Interplay between Aldose 1-Epimerase-Like Protein and Pectin Methylesterase in Abiotic and Biotic Stress Control. Front Plant Sci 2017; 8:1646. [PMID: 28993784 PMCID: PMC5622589 DOI: 10.3389/fpls.2017.01646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/07/2017] [Indexed: 05/22/2023]
Abstract
The mechanical damage that often precedes the penetration of a leaf by a pathogen promotes the activation of pectin methylesterase (PME); the activation of PME leads to the emission of methanol, resulting in a "priming" effect on intact leaves, which is accompanied by an increased sensitivity to Tobacco mosaic virus (TMV) and resistance to bacteria. In this study, we revealed that mRNA levels of the methanol-inducible gene encoding Nicotiana benthamiana aldose 1-epimerase-like protein (NbAELP) in the leaves of intact plants are very low compared with roots. However, stress and pathogen attack increased the accumulation of the NbAELP mRNA in the leaves. Using transiently transformed plants, we obtained data to support the mechanism underlying AELP/PME-related negative feedback The insertion of the NbAELP promoter sequence (proNbAELP) into the N. benthamiana genome resulted in the co-suppression of the natural NbAELP gene expression, accompanied by a reduction in the NbAELP mRNA content and increased PME synthesis. Knockdown of NbAELP resulted in high activity of PME in the cell wall and a decrease in the leaf glucose level, creating unfavorable conditions for Agrobacterium tumefaciens reproduction in injected leaves. Our results showed that NbAELP is capable of binding the TMV movement protein (MPTMV) in vitro and is likely to affect the cellular nucleocytoplasmic transport, which may explain the sensitivity of NbAELP knockdown plants to TMV. Although NbAELP was primarily detected in the cell wall, the influence of this protein on cellular PME mRNA levels might be associated with reduced transcriptional activity of the PME gene in the nucleus. To confirm this hypothesis, we isolated the N. tabacum PME gene promoter (proNtPME) and showed the inhibition of proNtPME-directed GFP and GUS expression in leaves when co-agroinjected with the NbAELP-encoding plasmid. We hypothesized that plant wounding and/or pathogen attack lead to PME activation and increased methanol emission, followed by increased NbAELP expression, which results in reversion of PME mRNA level and methanol emission to levels found in the intact plant.
Collapse
Affiliation(s)
| | - Tatiana V. Komarova
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | | | - Natalia M. Ershova
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | - Anastasia V. Shindyapina
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | | | - Eugene V. Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | - Yuri L. Dorokhov
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
- *Correspondence: Yuri L. Dorokhov
| |
Collapse
|
17
|
Sheshukova EV, Shindyapina AV, Komarova TV, Dorokhov YL. ["Matreshka" Genes with Alternative Reading Frames]. Genetika 2016; 52:146-163. [PMID: 27215029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although a relatively small part of the human genome contains protein encoding genes, the latest data on the discovery of alternative open reading frames (ORFs) in conventional mRNAs has highlighted the expanded coding potential of these genes. Until recently, it was believed that each mRNA transcript encodes a single protein. Recent proteogenomics data indicate the existence of exceptions to this rule, which greatly changes the usual meaning of the term "gene". The topology of a gene with overlapping ORFs resembles a Russian "matreshka" toy. There are two levels of "matreshka" genetic systems. First, the chromosomal level, when the "nested" gene is located within introns and exons of the main chromosomal gene, both in the sense and antisense orientation relative to the external gene. The second level is a mature mRNA molecule containing overlapping ORFs or an ORF with an alternative-start codon. In this review we will focus on the properties of "matreshka" genes of the second type and methods for their detection and verification. Particular attention is paid to the biological properties of the polypeptides encoded by these genes.
Collapse
|
18
|
Abstract
Methanol has been historically considered an exogenous product that leads only to pathological changes in the human body when consumed. However, in normal, healthy individuals, methanol and its short-lived oxidized product, formaldehyde, are naturally occurring compounds whose functions and origins have received limited attention. There are several sources of human physiological methanol. Fruits, vegetables, and alcoholic beverages are likely the main sources of exogenous methanol in the healthy human body. Metabolic methanol may occur as a result of fermentation by gut bacteria and metabolic processes involving S-adenosyl methionine. Regardless of its source, low levels of methanol in the body are maintained by physiological and metabolic clearance mechanisms. Although human blood contains small amounts of methanol and formaldehyde, the content of these molecules increases sharply after receiving even methanol-free ethanol, indicating an endogenous source of the metabolic methanol present at low levels in the blood regulated by a cluster of genes. Recent studies of the pathogenesis of neurological disorders indicate metabolic formaldehyde as a putative causative agent. The detection of increased formaldehyde content in the blood of both neurological patients and the elderly indicates the important role of genetic and biochemical mechanisms of maintaining low levels of methanol and formaldehyde.
Collapse
Affiliation(s)
- Yuri L Dorokhov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia; and N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Anastasia V Shindyapina
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia; and N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Ekaterina V Sheshukova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia; and N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Tatiana V Komarova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia; and N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| |
Collapse
|
19
|
Shindyapina AV, Petrunia IV, Komarova TV, Sheshukova EV, Kosorukov VS, Kiryanov GI, Dorokhov YL. Dietary methanol regulates human gene activity. PLoS One 2014; 9:e102837. [PMID: 25033451 PMCID: PMC4102594 DOI: 10.1371/journal.pone.0102837] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/23/2014] [Indexed: 12/02/2022] Open
Abstract
Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH to formaldehyde (FA), which is toxic. Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and a modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. Here, we demonstrate directly that study volunteers displayed increasing concentrations of MeOH and FA in their blood plasma when consuming citrus pectin, ethanol and red wine. A microarray analysis of white blood cells (WBC) from volunteers after pectin intake showed various responses for 30 significantly differentially regulated mRNAs, most of which were somehow involved in the pathogenesis of Alzheimer's disease (AD). There was also a decreased synthesis of hemoglobin mRNA, HBA and HBB, the presence of which in WBC RNA was not a result of red blood cells contamination because erythrocyte-specific marker genes were not significantly expressed. A qRT-PCR analysis of volunteer WBCs after pectin and red wine intake confirmed the complicated relationship between the plasma MeOH content and the mRNA accumulation of both genes that were previously identified, namely, GAPDH and SNX27, and genes revealed in this study, including MME, SORL1, DDIT4, HBA and HBB. We hypothesized that human plasma MeOH has an impact on the WBC mRNA levels of genes involved in cell signaling.
Collapse
Affiliation(s)
- Anastasia V. Shindyapina
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Igor V. Petrunia
- N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Tatiana V. Komarova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | | | | | - Gleb I. Kiryanov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Yuri L. Dorokhov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| |
Collapse
|
20
|
Shindyapina AV, Mkrtchyan GV, Gneteeva T, Buiucli S, Tancowny B, Kulka M, Aliper A, Zhavoronkov A. Mineralization of the Connective Tissue: A Complex Molecular Process Leading to Age-Related Loss of Function. Rejuvenation Res 2014; 17:116-33. [DOI: 10.1089/rej.2013.1475] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Anastasia V. Shindyapina
- Lomonosov Moscow State University, Moscow, Russian Federation
- Bioinformatics and Medical Information Technology Laboratory. Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
- First Open Institute for Regenerative Medicine for Young Scientists, Moscow, Russia
| | - Garik V. Mkrtchyan
- Lomonosov Moscow State University, Moscow, Russian Federation
- Bioinformatics and Medical Information Technology Laboratory. Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
- First Open Institute for Regenerative Medicine for Young Scientists, Moscow, Russia
| | - Tatiana Gneteeva
- First Open Institute for Regenerative Medicine for Young Scientists, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sveatoslav Buiucli
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
- First Open Institute for Regenerative Medicine for Young Scientists, Moscow, Russia
| | - B. Tancowny
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- National Institute for Nanotechnology, National Research Council, Edmonton, Alberta, Canada
| | - M. Kulka
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- National Institute for Nanotechnology, National Research Council, Edmonton, Alberta, Canada
| | - Alexander Aliper
- Bioinformatics and Medical Information Technology Laboratory. Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
- First Open Institute for Regenerative Medicine for Young Scientists, Moscow, Russia
| | - Alexander Zhavoronkov
- Bioinformatics and Medical Information Technology Laboratory. Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
- First Open Institute for Regenerative Medicine for Young Scientists, Moscow, Russia
- The Biogerontology Research Foundation, Reading, United Kingdom
| |
Collapse
|
21
|
Komarova TV, Petrunia IV, Shindyapina AV, Silachev DN, Sheshukova EV, Kiryanov GI, Dorokhov YL. Endogenous methanol regulates mammalian gene activity. PLoS One 2014; 9:e90239. [PMID: 24587296 PMCID: PMC3937363 DOI: 10.1371/journal.pone.0090239] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/28/2014] [Indexed: 11/18/2022] Open
Abstract
We recently showed that methanol emitted by wounded plants might function as a signaling molecule for plant-to-plant and plant-to-animal communications. In mammals, methanol is considered a poison because the enzyme alcohol dehydrogenase (ADH) converts methanol into toxic formaldehyde. However, the detection of methanol in the blood and exhaled air of healthy volunteers suggests that methanol may be a chemical with specific functions rather than a metabolic waste product. Using a genome-wide analysis of the mouse brain, we demonstrated that an increase in blood methanol concentration led to a change in the accumulation of mRNAs from genes primarily involved in detoxification processes and regulation of the alcohol/aldehyde dehydrogenases gene cluster. To test the role of ADH in the maintenance of low methanol concentration in the plasma, we used the specific ADH inhibitor 4-methylpyrazole (4-MP) and showed that intraperitoneal administration of 4-MP resulted in a significant increase in the plasma methanol, ethanol and formaldehyde concentrations. Removal of the intestine significantly decreased the rate of methanol addition to the plasma and suggested that the gut flora may be involved in the endogenous production of methanol. ADH in the liver was identified as the main enzyme for metabolizing methanol because an increase in the methanol and ethanol contents in the liver homogenate was observed after 4-MP administration into the portal vein. Liver mRNA quantification showed changes in the accumulation of mRNAs from genes involved in cell signalling and detoxification processes. We hypothesized that endogenous methanol acts as a regulator of homeostasis by controlling the mRNA synthesis.
Collapse
Affiliation(s)
- Tatiana V. Komarova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | - Igor V. Petrunia
- N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
| | | | - Denis N. Silachev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | | | - Gleb I. Kiryanov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Yuri L. Dorokhov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- N. I. Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
- * E-mail:
| |
Collapse
|