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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.
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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.
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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.
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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.
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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
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Bing M, Shedd C, Lwin H, Kaza V, Bollineni S, Mahan L, Mohanka M, Lawrence A, Joerns J, Wait M, Peltz M, Huffman L, Hackmann A, Iacono A, Heid C, Torres F, Pham S, Timofte I. Clinical Implications of Microbiome on Acute Rejection in Lung Transplant Recipients. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Ravichandran R, Kaza V, Bremner R, Smith M, Mohanakumar T. Circulating Exosomes with Distinct Immune and Molecular Markers in Lung Transplanted Recipients for Cystic Fibrosis. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Seal B, Sharma A, Thronton M, Liu C, Hauptmann E, Ali M, Kaza V, Heid C, Peltz M, Wait M, Ring W, Murala J. Impact of Donor Vaping or Electronic Cigarette Use on Early Outcomes after Lung Transplantation- A Single Center's Experience. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Venishetty N, Mahan L, Schellinger J, Bollineni S, Mohanka M, Joerns J, Torres F, Lawrence A, Timofte I, Almandoz J, Kaza V. Impact of Collaborative Weight Management: Single Center Study. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Davis SW, Kiaris H, Kaza V, Felder MR. Genetic Analysis of the Stereotypic Phenotype in Peromyscus maniculatus (deer mice). Behav Genet 2023; 53:53-62. [PMID: 36422733 DOI: 10.1007/s10519-022-10124-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/20/2022] [Indexed: 11/26/2022]
Abstract
Peromyscus maniculatus, including the laboratory stock BW, have been used as a model organism for autism spectrum disorder and obsessive-compulsive disorder because of the high occurrence of stereotypy. Several studies have identified neurological and environmental components of the phenotype; however, the heritability of the phenotype has not been examined. This study characterizes the incidence and heritability of vertical jumping stereotypy (VS) and backflipping (BF) behavior in the BW stock of the Peromyscus Genetic Stock Center, which are indicative of autism spectrum disorders. In addition, interspecies crosses between P. maniculatus and P. polionotus were also performed to further dissect genetically stereotypic behavior. The inheritance pattern of VS suggests that multiple genes result in a quantitative trait with low VS being dominant over high VS. The inheritance pattern of BF suggests that fewer genes are involved, with one allele causing BF in a dominant fashion. An association analysis in BW could reveal the underlying genetic loci associated with stereotypy in P. maniculatus, especially for the BF behavior.
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Affiliation(s)
- Shannon W Davis
- Department of Biological Sciences, University of South Carolina, Columbia, USA.,University of South Carolina, Columbia, SC, 29208, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Science, University of South Carolina, Columbia, USA.,University of South Carolina, Columbia, SC, 29208, USA
| | - Vimala Kaza
- Department of Drug Discovery and Biomedical Science, University of South Carolina, Columbia, USA.,University of South Carolina, Columbia, SC, 29208, USA
| | - Michael R Felder
- Department of Biological Sciences, University of South Carolina, Columbia, USA. .,University of South Carolina, Columbia, SC, 29208, USA. .,Department of Biological Sciences, University of South Carolina, 715 Sumter St, CLS Room 401, Columbia, SC, 29208, USA.
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Naderi A, Farmaki E, Chavez B, Cai C, Kaza V, Zhang Y, Soltanmohammadi E, Daneshvar N, Chatzistamou I, Kiaris H. Beneficial effects of CCL8 inhibition at LPS-induced lung injury. iScience 2022; 25:105520. [PMCID: PMC9639378 DOI: 10.1016/j.isci.2022.105520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/10/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
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Connors C, Betts TT, Kaza V. Implementing Standard Physical Therapy Guidelines with Patients Acutely Post Single or Bilateral Lung Transplant: A Quality Initiative. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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11
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Varghese A, Ryan A, Wells C, Li G, Baer D, Parker E, Buko A, Kaza V, Banga A, Bollineni S, Mahan L, Mohanka M, Lawrence A, Joerns J, Torres F, Wait M, Iacono A, Verceles A, Terada L, Terrin M, Timofte I. Post-Transplant Metabolomics Profiles in Patients Undergoing Lung Transplantation. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Halverson Q, Batra K, Mahan L, Mohanka M, Lawrence A, Joerns J, Bollineni S, Kaza V, Timofte I, Kershaw C, Terada L, Torres F, Banga A. CARE Score on Chest Radiograph at Diagnosis Predicts Early and Late Outcomes Among Lung Transplant Patients with COVID-19. J Heart Lung Transplant 2022. [PMCID: PMC8988563 DOI: 10.1016/j.healun.2022.01.312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To assess the ability of an objective radiographic scoring system to predict outcomes among lung transplant (LT) patients with Coronavirus disease 2019 (COVID-19). Methods We included all LT patients diagnosed with COVID-19 during a one-year period (March 2020 to Feb 2021; n=54; median age: 60, 20-73 years; M:F 37:17) in our program. Patient characteristics and laboratory values during the acute illness were reviewed. Chest radiographs at time of COVID-19 diagnosis were scored by extent of ground-glass opacity and consolidation using the CARE score (0-18 for each lung). The CARE score was calculated using only the allograft in single LT and the average of both lungs in bilateral LT. Primary outcome was six-month survival after COVID-19. Hospital complications and one-month survival were secondary outcomes. Results A minority of patients had a clear allograft (CARE=0, n=12, 22.2%) at presentation. The median score was 2 (interquartile range 0.5-4.625), indicating mild abnormalities. Demographics, underlying diagnosis, comorbidities, symptoms, and spirometry changes were not associated with the baseline CARE score. Baseline CARE score >5 was strongly associated with development of respiratory failure (91.7% vs 35.7%; OR, 95% CI: 19.8, 2.3-168.7; p=0.001), ICU admission (p<0.001), need for ventilator support (p<0.001), and one-month mortality (41.7% vs 2.4%; OR, 95% CI: 29.4, 2.96-333.3; p=0.001). Overall six-month survival was 81.5%. The CARE score was significantly higher among non-survivors (7.7±4.1 vs 2.2±2.7; p=0.002). Patients with a CARE score>5 at diagnosis were significantly less likely to survive at six-month follow-up (41.7%.vs 92.3%; p<0.001). The CARE score had an excellent area under the curve (86.8%, 74.4%-99.2%; p<0.001) on the Receiver operating characteristic curve for predicting six-month survival after COVID-19. Conclusion The CARE score at time of COVID-19 diagnosis provides useful prognostic information among patients with LT.
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Horvath S, Haghani A, Zoller JA, Naderi A, Soltanmohammadi E, Farmaki E, Kaza V, Chatzistamou I, Kiaris H. Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy. GeroScience 2022; 44:447-461. [PMID: 34698996 PMCID: PMC8810952 DOI: 10.1007/s11357-021-00472-5] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
DNA methylation-based biomarkers of aging have been developed for humans and many other mammals and could be used to assess how stress factors impact aging. Deer mice (Peromyscus) are long-living rodents that have emerged as an informative model to study aging, adaptation to extreme environments, and monogamous behavior. In the present study, we have undertaken an exhaustive, genome-wide analysis of DNA methylation in Peromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We describe DNA methylation-based estimators of age for different species of deer mice based on novel DNA methylation data generated on highly conserved mammalian CpGs measured with a custom array. The multi-tissue epigenetic clock for deer mice was trained on 3 tissues (tail, liver, and brain). Two human-Peromyscus clocks accurately measure age and relative age, respectively. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Overall, this study provides a first step towards studying the epigenetic correlates of monogamous behavior and adaptation to high altitude in Peromyscus. The human-Peromyscus epigenetic clocks are expected to provide a significant boost to the attractiveness of Peromyscus as a biological model.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA
| | - Asieh Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC USA
| | - Elham Soltanmohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC USA
| | - Elena Farmaki
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC USA
| | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC USA
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, 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
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC USA
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Lucius MD, Ji H, Altomare D, Doran R, Torkian B, Havighorst A, Kaza V, Zhang Y, Gasparian AV, Magagnoli J, Shankar V, Shtutman M, Kiaris H. Genomic variation in captive deer mouse (Peromyscus maniculatus) populations. BMC Genomics 2021; 22:662. [PMID: 34521341 PMCID: PMC8438655 DOI: 10.1186/s12864-021-07956-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Deer mice (genus Peromyscus) are the most common rodents in North America. Despite the availability of reference genomes for some species, a comprehensive database of polymorphisms, especially in those maintained as living stocks and distributed to academic investigators, is missing. In the present study we surveyed two populations of P. maniculatus that are maintained at the Peromyscus Genetic Stock Center (PGSC) for polymorphisms across their 2.5 × 109 bp genome. RESULTS High density of variation was identified, corresponding to one SNP every 55 bp for the high altitude stock (SM2) or 207 bp for the low altitude stock (BW) using snpEff (v4.3). Indels were detected every 1157 bp for BW or 311 bp for SM2. The average Watterson estimator for the BW and SM2 populations is 248813.70388 and 869071.7671 respectively. Some differences in the distribution of missense, nonsense and silent mutations were identified between the stocks, as well as polymorphisms in genes associated with inflammation (NFATC2), hypoxia (HIF1a) and cholesterol metabolism (INSIG1) and may possess value in modeling pathology. CONCLUSIONS This genomic resource, in combination with the availability of P. maniculatus from the PGSC, is expected to promote genetic and genomic studies with this animal model.
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Affiliation(s)
- Matthew D Lucius
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Hao Ji
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Diego Altomare
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Robert Doran
- Research Computing, Division of Information Technology, University of South Carolina, Columbia, SC, USA
| | - Ben Torkian
- Research Computing, Division of Information Technology, University of South Carolina, Columbia, SC, USA
| | - Amanda Havighorst
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - Youwen Zhang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Alexander V Gasparian
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Joseph Magagnoli
- Department of Clinical Pharmacy and Outcomes Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Vijay Shankar
- Center for Human Genetics, College of Science, Clemson University, Clemson, SC, USA
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, 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.
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA.
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15
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Naderi A, Soltanmaohammadi E, Kaza V, Barlow S, Chatzistamou I, Kiaris H. Persistent effects of pair bonding in lung cancer cell growth in monogamous Peromyscus californicus. eLife 2021; 10:e64711. [PMID: 33960931 PMCID: PMC8104960 DOI: 10.7554/elife.64711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/08/2020] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
Epidemiological evidence suggests that social interactions and especially bonding between couples influence tumorigenesis, yet whether this is due to lifestyle changes, homogamy (likelihood of individuals to marry people of similar health), or directly associated with host-induced effects in tumors remains debatable. In the present study, we explored if tumorigenesis is associated with the bonding experience in monogamous rodents at which disruption of pair bonds is linked to anxiety and stress. Comparison of lung cancer cell spheroids that formed in the presence of sera from bonded and bond-disrupted deer mice showed that in monogamous Peromyscus polionotus and Peromyscus californicus, but not in polygamous Peromyscus maniculatus, the disruption of pair bonds altered the size and morphology of spheroids in a manner that is consistent with the acquisition of increased oncogenic potential. In vivo, consecutive transplantation of human lung cancer cells between P. californicus, differing in bonding experiences (n = 9 for bonded and n = 7 for bond-disrupted), and nude mice showed that bonding suppressed tumorigenicity in nude mice (p<0.05), suggesting that the protective effects of pair bonds persisted even after bonding ceased. Unsupervised hierarchical clustering indicated that the transcriptomes of lung cancer cells clustered according to the serum donors' bonding history while differential gene expression analysis pointed to changes in cell adhesion and migration. The results highlight the pro-oncogenic effects of pair-bond disruption, point to the acquisition of expression signatures in cancer cells that are relevant to the bonding experiences of serum donors, and question the ability of conventional mouse models to capture the whole spectrum of the impact of the host in tumorigenesis.
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Affiliation(s)
- Asieh Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South CarolinaColumbiaUnited States
| | - Elham Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South CarolinaColumbiaUnited States
| | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South CarolinaColumbiaUnited States
| | - Shayne Barlow
- Department of Physiology, Pharmacology, and Neuroscience, School of Medicine and Department of Laboratory Animal Resources, University of South CarolinaColumbiaUnited States
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South CarolinaColumbiaUnited States
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South CarolinaColumbiaUnited States
- Peromyscus Genetic Stock Center, University of South CarolinaColumbiaUnited States
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16
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Fan R, Newton C, Kaza V. Antibody-Mediated Rejection of the Lung in Patients with Short Telomeres. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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17
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Soltanmohammadi E, Farmaki E, Zhang Y, Naderi A, Kaza V, Chatzistamou I, Kiaris H. Coordination in the unfolded protein response during aging in outbred deer mice. Exp Gerontol 2020; 144:111191. [PMID: 33290861 DOI: 10.1016/j.exger.2020.111191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/11/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
Endoplasmic reticulum (ER) stress has been linked to various metabolic pathologies, neurodegeneration and aging. Although various mechanistic aspects of the resulting unfolded protein response (UPR) have been elucidated, its regulation in genetically diverse populations remains elusive. In the present study we evaluated the expression of chaperones BiP/GRP78, GRP94 and calnexin (CANX) in the lungs, liver and brain of 7 months old and 2-3 years old outbred deer mice P. maniculatus and P. leucopus. Chaperones' expression was highly variable between species, tissues and ages suggesting that levels of expression of individual chaperones do not change consistently during aging. Despite this variation, a high degree of coordination was maintained between chaperones' expression indicating the tight regulation of the UPR which is consistent with its adaptive activity to maintain homeostasis. In the brain though of older P. maniculatus, at which neurodegenerative changes were detected, loss of coordination was revealed, especially between BiP and either of GRP94 or calnexin which indicates that de-coordination rather than aberrant expression is linked to deregulation of the UPR in aging. These findings underscore the involvement of UPR in the onset of aging-related pathologies and suggest that beyond levels of expression, concerted activation may be of significance to attain homeostasis. These findings emphasize the value of genetically diverse models and suggest that beyond levels of expression of individual targets the coordination of transcriptional networks should be considered when links to pathology are explored.
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Affiliation(s)
- E Soltanmohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC, USA
| | - E Farmaki
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC, USA
| | - Y Zhang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC, USA
| | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, SC, USA
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, SC, USA
| | - H Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC, USA; Peromyscus Genetic Stock Center, University of South Carolina, SC, USA.
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18
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Kanade R, Mohanka M, Bollineni S, Joerns J, Kaza V, Murala J, Peltz M, Wait M, Torres F, Banga A. Characteristics and Outcomes Among Patients With Early Venous Thromboembolic Events After Lung Transplant. Transplant Proc 2020; 53:303-310. [PMID: 32951862 DOI: 10.1016/j.transproceed.2020.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/08/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Despite several previous studies reporting a high frequency of venous thromboembolism (VTE) after lung transplant (LT), few actionable risk factors have been identified. There are limited data regarding the practice patterns of anticoagulation use among patients with LT. METHODS All adult patients with single or bilateral LT between 2012 and 2016 were included (n = 324; mean age, 56.3 ± 13.3 years; male, 61.1%). Demographic, clinical, and laboratory variables before and after LT were recorded. Follow-up data included survival up to 3 years post-transplant. Development of VTE during the first 30 days after LT was the primary outcome variable. RESULTS The overall incidence of VTE during the first 30 days after LT was 29.9% (n = 97), among which the majority were upper extremity thromboses. Female sex, personal history of VTE, hospitalization at the time of transplant, and use of 3 or more central venous catheters during index hospitalization were independently associated with VTE. The use of anticoagulants was independently associated with a reduced risk of VTE. Despite increased morbidity, the development of VTE was not associated with worse post-transplant survival. CONCLUSIONS A significant proportion of patients develop early VTE after LT. Limiting the number of central catheters to < 3 during the post-transplant period, along with the early institution of thromboprophylaxis, may lower the risk of VTE.
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Affiliation(s)
- R Kanade
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - M Mohanka
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - S Bollineni
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - J Joerns
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - V Kaza
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - J Murala
- Department of Cardiovascular and Thoracic Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - M Peltz
- Department of Cardiovascular and Thoracic Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - M Wait
- Department of Cardiovascular and Thoracic Surgery, University of Texas Southwestern Medical Center, Dallas, Texas
| | - F Torres
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - A Banga
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.
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Farmaki E, Kaza V, Chatzistamou I, Kiaris H. CCL8 Promotes Postpartum Breast Cancer by Recruiting M2 Macrophages. iScience 2020; 23:101217. [PMID: 32535027 PMCID: PMC7300153 DOI: 10.1016/j.isci.2020.101217] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 07/17/2019] [Revised: 04/27/2020] [Accepted: 05/26/2020] [Indexed: 12/23/2022] Open
Abstract
The microenvironment of postpartum mammary gland promotes tumor growth and metastasis in animal models and is linked to increased risk of breast cancer and poor disease outcome in patients. Our previous studies showed the involvement of the chemokine CCL8 in breast cancer metastasis through modulation of the tumor-promoting activity of the tumor microenvironment. Here we show that CCL8 is highly expressed during mammary gland involution and enhances the infiltration of M2 subtype macrophages at the second phase of involution. Cancer cell inoculation studies in Ccl8-deficient animals indicate that CCL8 accelerates tumor onset during involution but not in nulliparous animals. Depletion of macrophages abolished the tumor-promoting effect of CCL8 in involution suggesting the specific role of CCL8 in promoting tumor growth by recruiting macrophages. These results underscore the role of CCL8 in the development of postpartum breast cancer and suggest the potential value of targeting CCL8 in disease management. CCL8 exhibits increased expression during mammary gland involution CCL8 has tumor promoting activity and promotes postpartum breast cancer Targeting CCL8 could have beneficial value for the management of postpartum breast cancer
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Affiliation(s)
- Elena Farmaki
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC 29208, USA
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC 29209, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA; Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC 29208, USA.
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20
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Farmaki E, Kaza V, Chatzistamou I, Kiaris H. Abstract LB-133: Tumor-promoting activity of CCL8 in involution-associated breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Postpartum breast cancers that develop within 5 years after child birth have a poor prognosis because of increased risk of metastasis and remain a principal cause of mortality for young women. Therefore understanding the molecular physiology of postpartum breast cancers is imperative as it may provide novel therapeutic options. The increased risk for breast cancer immediately after pregnancy is linked to the extensive remodeling of the mammary gland that is designated as mammary involution. Immune cells such as macrophages and neutrophils, activated by a chemokine and cytokine cascade during involution, are actively involved in mammary gland remodeling and contribute to the disease development. Among the various chemokines activated in involution, the role of CCL8 in the development of postpartum breast cancer has not been addressed despite recent evidence demonstrating its role in metastatic disease. Our results show that CCL8 mRNA and protein levels increase in mammary gland during involution. Tumor growth studies involving CCL8-deficient animals that had been implanted with cancer cells prior to pregnancy or during involution indicated that CCL8 is tumor-promoting specifically following lactation, during involution. CCL8 is responsible for recruiting F4/80-positive macrophages to the mammary gland during the second phase of involution. Thus we asked if CCL8 promotes tumor development by recruiting macrophages in the involuting mammary gland. Our studies showed that CCL8 attracts primarily M2 type macrophages and that depletion of macrophages by liposomal clodronate abolished the tumor-promoting effect of CCL8 in the wt animals but did not affect CCL8KO animals, at which the M2 macrophages were already absent. These results illustrate the role of CCL8 in the development of postpartum breast cancer by recruiting M2 macrophages and suggest the potential value of targeting CCL8 for disease management.
Citation Format: Eleni Farmaki, Vimala Kaza, Ioulia Chatzistamou, Hippokratis Kiaris. Tumor-promoting activity of CCL8 in involution-associated breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-133.
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Havighorst A, Zhang Y, Farmaki E, Kaza V, Chatzistamou I, Kiaris H. Differential regulation of the unfolded protein response in outbred deer mice and susceptibility to metabolic disease. Dis Model Mech 2019; 12:dmm.037242. [PMID: 30733237 PMCID: PMC6398494 DOI: 10.1242/dmm.037242] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 09/20/2018] [Accepted: 01/28/2019] [Indexed: 01/10/2023] Open
Abstract
Endoplasmic reticulum (ER) stress has been causatively linked to the onset of various pathologies. However, whether and how inherent variations in the resulting unfolded protein response (UPR) affect predisposition to ER-stress-associated metabolic conditions remains to be established. By using genetically diverse deer mice (Peromyscus maniculatus) as a model, we show that the profile of tunicamycin-induced UPR in fibroblasts isolated at puberty varies between individuals and predicts deregulation of lipid metabolism and diet-induced hepatic steatosis later in life. Among the different UPR targets tested, CHOP (also known as Ddit3) more consistently predicted elevated plasma cholesterol and hepatic steatosis. Compared with baseline levels or inducibility, the maximal intensity of the UPR following stimulation best predicts the onset of pathology. Differences in the expression profile of the UPR recorded in cells from different populations of deer mice correlate with the varying response to ER stress in altitude adaptation. Our data suggest that the response to ER stress in cultured cells varies among individuals, and its profile early in life might predict the onset of ER-stress-associated disease in the elderly. This article has an associated First Person interview with the first author of the paper. Summary: By using genetically diverse deer mice, we show that the expression of different chaperones is highly coordinated in individual animals and its profile predicts the onset of metabolic pathology.
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Affiliation(s)
- Amanda Havighorst
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208-3402, USA
| | - Youwen Zhang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208-3402, USA
| | - Elena Farmaki
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208-3402, USA
| | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC 29208-3402, USA
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29208-3402, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208-3402, USA .,Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC 29208-3402, USA
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Liang J, Chen M, Hughes D, Chumanevich AA, Altilia S, Kaza V, Lim CU, Kiaris H, Mythreye K, Pena MM, Broude EV, Roninson IB. CDK8 Selectively Promotes the Growth of Colon Cancer Metastases in the Liver by Regulating Gene Expression of TIMP3 and Matrix Metalloproteinases. Cancer Res 2018; 78:6594-6606. [PMID: 30185549 DOI: 10.1158/0008-5472.can-18-1583] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/17/2018] [Accepted: 08/31/2018] [Indexed: 01/22/2023]
Abstract
: Unresectable hepatic metastases of colon cancer respond poorly to existing therapies and are a major cause of colon cancer lethality. In this study, we evaluated the therapeutic viability of targeting the mediator kinase CDK8, an early clinical stage drug target, as a means to suppress metastasis of colon cancer. CDK8 was amplified or overexpressed in many colon cancers and CDK8 expression correlated with shorter patient survival. Knockdown or inhibition of CDK8 had little effect on colon cancer cell growth but suppressed metastatic growth of mouse and human colon cancer cells in the liver. This effect was due in part to inhibition of already established hepatic metastases, indicating therapeutic potential of CDK8 inhibitors in the metastatic setting. In contrast, knockdown or inhibition of CDK8 had no significant effect on the growth of tumors implanted subcutaneously, intrasplenically, or orthotopically in the cecum. CDK8 mediated colon cancer growth in the liver through downregulation of matrix metalloproteinase (MMP) inhibitor TIMP3 via TGFβ/SMAD-driven expression of a TIMP3-targeting microRNA, miR-181b, along with induction of Mmp3 in murine or MMP9 in human colon cancer cells via Wnt/β-catenin-driven transcription. These findings reveal a new mechanism for negative regulation of gene expression by CDK8 and a site-specific role for CDK8 in colon cancer hepatic metastasis. Our results indicate the utility of CDK8 inhibitors for the treatment of colon cancer metastases in the liver and suggest that CDK8 inhibitors may be considered in other therapeutic settings involving TGFβ/SMAD or Wnt/β-catenin pathway activation. SIGNIFICANCE: These findings demonstrate that inhibition of the transcription-regulating kinase CDK8 exerts a site-specific tumor-suppressive effect on colon cancer growth in the liver, representing a unique therapeutic opportunity for the treatment of advanced colon cancer.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/23/6594/F1.large.jpg.
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Affiliation(s)
- Jiaxin Liang
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Mengqian Chen
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Daniel Hughes
- Department of Biology, University of South Carolina, Columbia, South Carolina
| | - Alexander A Chumanevich
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Serena Altilia
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Vimala Kaza
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Chang-Uk Lim
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Karthikeyan Mythreye
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina
| | | | - Eugenia V Broude
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Igor B Roninson
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina.
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Chatzistamou I, Farmaki E, Kaza V, Kiaris H. The Value of Outbred Rodent Models in Cancer Research. Trends Cancer 2018; 4:468-471. [PMID: 29937045 DOI: 10.1016/j.trecan.2018.05.004] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 02/03/2023]
Abstract
Mouse models of breast cancer are valuable research tools, but their usefulness is restricted by a series of features inherent to their physiology, such as low endogenous estrogens and genetics (inbred status). Depending on the specific questions asked, outbred rodents like Peromyscus may provide answers that laboratory mice cannot.
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Affiliation(s)
- Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, SC, USA
| | - Elena Farmaki
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC, USA
| | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, SC, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC, USA; Peromyscus Genetic Stock Center, University of South Carolina, SC, USA.
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Kaza V, Rao U, Sharma M, Mohanka M, Banga A, Bollineni S, Mullins J, Torres F, Mohanakumar T. Antibodies to Lung Self-antigens in Lung Transplant Recipients and Implications for Outcomes. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Mohanka M, Kanade R, Garcia H, Mullins J, Bollineni S, Kaza V, Torres F, Banga A. “My Best Spirometry Numbers- What Do They Mean?”. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.1163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Abstract
Modeling breast cancer in general and hormone-sensitive breast cancer, in particular in mice, has several limitations. These are related to the inbred nature of laboratory mice, and do not allow adequate appreciation of the contribution of the host's genetic heterogeneity in tumor growth. In addition, the naturally low estrogen levels of mice makes estradiol supplementation obligatory for tumor growth. Here, we show that Peromyscus californicus, following cyclosporine-mediated immunosuppression, supports the growth of both MDA-MB-231 estrogen-independent and MCF7 estrogen receptor-positive breast cancers without exogenous estradiol supplementation. Tumor growth was inhibited by fulvestrant or letrozole, confirming that MCF7 xenografts remain hormone dependent in vivo and suggesting that P. californicus can be used as an alternative to conventional mice for the study of hormone-sensitive breast cancer. The fact that Peromyscus stocks are outbred also facilitates the study of breast cancer in genetically heterogenous populations. Summary: Outbred stocks of Peromyscus californicus (California mice), upon pharmacological immunosuppression, provide an alternative to conventional inbred mice models, and can support the growth of hormone-insensitive and hormone-sensitive human breast cancers.
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Affiliation(s)
- Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, SC 29208, USA
| | - Elena Farmaki
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC 29208, USA
| | - Amanda Havighorst
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC 29208, USA
| | - Janet Crossland
- Peromyscus Genetic Stock Center, University of South Carolina, SC 29208, USA
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, SC 29208, USA
| | - Hippokratis Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, SC 29208, USA .,Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, SC 29208, USA
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Liang J, Chen M, Karthikeyan M, Pena MM, Hughes D, Kaza V, Lim CU, Broude E, Roninson IB. Abstract 4896: Role of CDK8 in colon cancer hepatic metastasis. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
About half of all colon cancer patients will develop liver metastases and the 5-year survival for these patients is less than 13%, making colon cancer the second most lethal cancer worldwide. Cyclin dependent kinase 8 (CDK8), which regulates transcription but not cell cycle progression, has been identified as an oncogene amplified in many colon cancers. CDK8 acts as a positive mediator of oncogenic transcription pathways regulated by Wnt/beta-catenin and TGF-beta, both of which are strongly associated with tumor metastasis. In a colon cancer liver metastasis model based on splenic injection of CT26 murine colon carcinoma cells, treatment with Senexin B, a highly selective small-molecule inhibitor of CDK8 and its paralog CDK19, strongly inhibited metastatic growth in the liver and prolonged the survival of mice with hepatic metastases. In contrast to the effect on liver metastasis, CDK8 inhibition had little or no effect on cell growth in culture or at primary tumor sites. Hepatic metastasis was inhibited to the same extent when Senexin B was administered starting from the time of tumor injection or only during a later part of the study, suggesting that the drug affected metastatic growth in the liver rather than just initial colonization. Liver metastasis was similarly decreased by CDK8 knockdown in CT26 cells, suggesting that the anti-metastatic activity of Senexin B was due at least in part to its effect on tumor cells. Transcription profiling indicated that CDK8 inhibition by shRNA or Senexin B strongly decreased the expression of metastasis-associated metalloproteinases MMP 13, MMP10, and MMP3 and at the same time drastically increased the expression of TIMP3, a metalloproteinase inhibitor. TIMP3 overexpression in CT26 cells, like CDK8 inhibition, decreased hepatic metastasis. CDK8 inhibition also blocked TGF-beta or Wnt3a-stimulated transwell Matrigel invasion of CT26 cells in vitro. Knockdown of beta-catenin in CT26 cells decreased the expression of MMP3 and MMP13, while knockdown of SMAD4 (transcriptional mediator of TGF-beta pathway) induced TIMP3 expression. Beta-catenin knockdown decreased both the primary tumor growth in the spleen and metastatic growth in the liver, whereas SMAD4 knockdown, like that of CDK8, selectively inhibited liver metastasis. Senexin B also suppressed hepatic metastasis after splenic injection of human HCT116 colon carcinoma cells. In summary, our data identified CDK8 as a key transcriptional regulator of colon cancer metastatic growth in the liver, interacting with TGF-beta and Wnt/beta-catenin pathways and regulating the expression of MMPs and Timp3. CDK8/19 inhibitors, which are now entering clinical trials, may be effective for the treatment of hepatic metastasis of colon cancer.
Citation Format: Jiaxin Liang, Mengqian Chen, Mythreye Karthikeyan, M. Marjorette Pena, Daniel Hughes, Vimala Kaza, Chang-Uk Lim, Eugenia Broude, Igor B. Roninson. Role of CDK8 in colon cancer hepatic metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4896. doi:10.1158/1538-7445.AM2017-4896
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Banga A, Mohanka M, Mullins J, Bollineni S, Kaza V, Torres F. Predictors of Early Mortality After Lung Transplantation in the Lung Allocation Score Era. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.1177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Sullivan D, Torres F, Banga A, Mohanka M, Bollineni S, Mullins J, Rao U, Lacelle C, Duddupudi P, Surapaneni D, Ring W, Wait M, Kaza V. Outcomes of Treatment of Donor Specific Antibodies: A Single Center Experience. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.1173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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30
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Banga A, Mohanka M, Bollineni S, Mullins J, Kaza V, Torres F. Characteristics and Outcome of Patients with Stroke After Lung Transplant Surgery in the Lung Allocation Score Era. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.1151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Farmaki E, Kaza V, Papavassiliou AG, Chatzistamou I, Kiaris H. Induction of the MCP chemokine cluster cascade in the periphery by cancer cell-derived Ccl3. Cancer Lett 2016; 389:49-58. [PMID: 28041977 DOI: 10.1016/j.canlet.2016.12.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 01/31/2023]
Abstract
The induction of localized pro-inflammatory niches in the periphery is instrumental in metastasis. In order to better understand how tumors engage distal sites and activate a pro-inflammatory response we utilized syngeneic breast cancers as a model and showed that soluble factors from the neoplastic epithelium activate the expression of the monocyte chemoattractive protein (MCP) chemokines of the mouse 11C cluster that include Ccl1, Ccl2, Ccl7, Ccl8, Ccl11 and Ccl12. Tissues such as the lungs and the brain, that are more prone to colonization by breast cancer cells, were more sensitive to MCP cluster chemokine induction than others such as the liver. Subsequent analyses involving chemokine arrays in breast cancer cells and media followed by functional validation assays in in vitro and in vivo identified the cytokine Ccl3 as the principle mediator of the communication between the neoplastic epithelium and the peripheral tissues in terms of MCP cluster chemokine induction. Our results show that MCP chemokines are activated in peripheral tissues of breast cancer-bearing mice, by a mechanism that involves breast cancer cell-derived Ccl3. Interference with the expression of cancer cell-derived Ccl3 may find application in the management of breast cancer metastases.
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Affiliation(s)
- Elena Farmaki
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, SC, USA
| | - Vimala Kaza
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, SC, USA
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, SC, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, SC, USA; Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Peromyscus Genetic Stock Center, University of South Carolina, SC, USA.
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Farmaki E, Chatzistamou I, Kaza V, Kiaris H. Abstract A26: A self-sustained gradient of CCL8 drives breast cancer metastasis. Cancer Res 2016. [DOI: 10.1158/1538-7445.tummet15-a26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The establishment of chemoattractive gradients between the neoplastic epithelium, the stroma and the peripheral tissues represents an attractive, yet elusive, mechanism that may contribute to metastasis. Here we provide evidence for the maintenance of a gradient of increasing CCL8 concentration between the epithelium, the stroma and the periphery that is instrumental for breast cancer cells dissemination promoting the directional movement of cancer cells from the site of primary tumor towards the periphery. Experiments in breast cancer cells cultured in vitro and in vivo studies in tumor-bearing mice showed that CCL8 production is enhanced in stromal fibroblasts at the tumor margins and in tissues at which breast cancer cells tend to metastasize such as the lungs and the brain. This stimulation of CCL8 expression in the stroma was driven by signals elicited by the neoplastic epithelium and could be recapitulated by administration of breast cancer cells conditioned media in tumor free mice. Experiments involving transwell-based migration assays established that CCL8-mediated chemoattraction was produced in breast cancer cells while genetic and antibody-based manipulation of CCL8 activity in mice influenced the histology of the tumors and promoted all major steps of the metastatic process such as invasion to adjacent stroma, intravasation and ultimately extravasation and seeding. Specifically, tumors growing in CCL8 deficient animals had well defined borders and high cellularity as opposed to the ill-defined margins of the tumors of wild type animals. In tumor-bearing mice acute i.v. administration of CCL8 increased the number of circulating tumor cells while antibody-mediated inhibition of CCL8 activity reduced the number of cancer cells invading towards adjacent fibroblasts that had been enclosed in matrigel and implanted proximally to the tumors. Only fibroblasts inoculated in the vicinity of breast tumors exhibited elevated CCL8 expression but not the fibroblasts growing in tumor-free mice, which is consistent with the active role of the epithelium in triggering CCL8 expression in the stroma. The stromal origin of CCL8 is also consistent with the strong correlation observed between circulating levels of CCL8 and tumor size, in EO771 mouse breast cancers at which CCL8 expression is minimal and in human MDA-MB-231 breast cancers at which species specific immunoassays permit the distinction between CCL8 originating from the neoplastic epithelium or the host. Analysis of publicly available data suggested that CCL8 is overexpressed in breast tumors as compared to normal breast tissue while high CCL8 expression in clinical breast cancers is associated with poor prognosis. These findings exemplify how self-sustained CCL8-like gradients of chemoattractive factors, between the epithelium, the stroma and the periphery can be induced by breast cancer cells to drive the metastatic process and suggest that interference with their operation may provide means for breast cancer management.
Citation Format: Elena Farmaki, Ioulia Chatzistamou, Vimala Kaza, Hippokratis Kiaris. A self-sustained gradient of CCL8 drives breast cancer metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Metastasis; 2015 Nov 30-Dec 3; Austin, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(7 Suppl):Abstract nr A26.
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McDermott MSJ, Györffy B, Chumanevich AA, Kaza V, Porter DC, Catroppo JF, Chen M, Oliver D, Shtutman M, Roninson IB, Broude EV. Abstract P5-04-07: CDK8 protein complex as a potential biomarker and therapeutic target in breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p5-04-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cyclin-dependent kinase 8 (CDK8) and its paralog CDK19 are transcriptional regulators that, in complex with CCNC, MED12 and MED13, mediate several carcinogenic signalling pathways such as NFκβ, TGFβ/BMP, WNT/β-catenin, HIF1A and serum growth factor network. Using immunohistochemical analysis, we found that CDK8/19 protein is overexpressed in invasive ductal carcinomas of the breast relative to non-malignant mammary tissues. TCGA database analysis showed that gene amplification is the most frequent type of genetic alterations of CDK8, CDK19, CCNC and MED13 in breast cancers, with MED13 appearing as one of the most frequently amplified genes in breast cancer (amplified in 9.7% of samples), whereas point mutations are more common in MED12. CDK8, CDK19 and CCNC expression was strongly increased but MED12 expression was decreased in tumors with mutant p53. Meta-analysis of transcriptome databases revealed that higher expression of CDK8, CDK19, CCNC and MED13 (but not MED12) is associated with shorter relapse-free survival (RFS) in the four molecular subtypes of breast cancer. The RFS correlations were much stronger in patients who underwent systemic adjuvant therapy than in untreated patients, suggesting that CDK8 and its interactive genes impact the failure of systemic therapy. This result is in agreement with the role of CDK8 as a mediator of the chemotherapy-induced paracrine network that promotes drug resistance and metastasis (Porter et al., PNAS, 109, 13799, 2012) and with our finding that a small-molecule CDK8/19 inhibitor augmented the efficacy of doxorubicin in a triple-negative breast cancer xenograft model. The expression levels of CDK8, CDK19, CCNC and MED13 in breast cancer samples were directly correlated with each other and with the expression of MYC but inversely correlated with estrogen receptor (ER)α expression. Since MYC is known to be a positive downstream mediator of the ER activity, we hypothesized that CDK8 may play a similar role, with an increase in CDK8 augmenting estrogen mitogenic signalling in tumors with decreased ER. Confirming this hypothesis, we have found that CDK8 inhibition by selective small-molecule CDK8/19 inhibitors or by shRNA knockdown suppresses estrogen-induced transcription in ER-positive breast cancer cell lines. CDK8/19 inhibition abrogates the mitogenic effect of estrogen on ER-positive cells and synergizes with the ER antagonist fulvestrant. Treatment of estrogen-deprived ER-positive cells with a CDK8/19 inhibitor significantly impeded the outgrowth of estrogen-independent cells, to a greater extent than did mTOR or HER2 targeted drugs. These results indicate that the expression of CDK8 and its interactive genes has a profound impact on the response to treatment in breast cancer and may provide novel biomarkers for relapse-free survival after adjuvant therapy. CDK8/19 inhibition may be useful to augment chemotherapy and hormone therapy of breast cancer and to prevent the development of tumors resistant to estrogen deprivation.
Citation Format: McDermott MSJ, Györffy B, Chumanevich AA, Kaza V, Porter DC, Catroppo JF, Chen M, Oliver D, Shtutman M, Roninson IB, Broude EV. CDK8 protein complex as a potential biomarker and therapeutic target in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-04-07.
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Affiliation(s)
- MSJ McDermott
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - B Györffy
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - AA Chumanevich
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - V Kaza
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - DC Porter
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - JF Catroppo
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - M Chen
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - D Oliver
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - M Shtutman
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - IB Roninson
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
| | - EV Broude
- University of South Carolina, Columbia, SC; MTA TTK Lendület Cancer Biomarker Research Group; MTA-SE Pediatrics and Nephrology Research Group; Semmelweis University, Budapest, Hungary; Senex Biotechnology, Inc., Columbia, SC
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Goswami MT, Reka AK, Kurapati H, Kaza V, Chen J, Standiford TJ, Keshamouni VG. Regulation of complement-dependent cytotoxicity by TGF-β-induced epithelial-mesenchymal transition. Oncogene 2015; 35:1888-98. [PMID: 26148233 PMCID: PMC4703565 DOI: 10.1038/onc.2015.258] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 04/08/2015] [Accepted: 04/24/2015] [Indexed: 12/23/2022]
Abstract
The process of Epithelial-mesenchymal transition (EMT), in addition to being an initiating event for tumor metastasis, is implicated in conferring several clinically relevant properties to disseminating cancer cells. These include stem cell like properties, resistance to targeted therapies and ability to evade immune surveillance. Enrichment analysis of gene expression changes during TGF-β induced EMT in lung cancer cells identified complement cascade as one of the significantly enriched pathway. Further analysis of the genes in the complement pathway revealed an increase in the expression of complement inhibitors and a decrease in the expression of proteins essential for complement activity. In this study, we tested whether EMT confers resistance to complement-dependent cytotoxicity (CDC) in lung cancer cells and promotes tumor progression. CD59 is a potent inhibitor of membrane attack complex that mediates complement-dependent cell lysis. We observed a significant increase in the CD59 expression on the surface of cells after TGF-β-induced EMT. Furthermore, CD59 knock down restored susceptibility of cells undergoing EMT to Cetuximab-mediated CDC. TGF-β-induced CD59 expression during EMT is dependent on Smad3 but not Smad2. ChIP analysis confirmed that Smad3 directly binds to the CD59 promoter. Stable knock-down of CD59 in A549 cells inhibited experimental metastasis. These results demonstrate that TGF-β-induced EMT and CD59 expression confers an immune evasive mechanism to disseminating tumor cells facilitating tumor progression. Together, our data demonstrates that CD59 inhibition may serve as an adjuvant to enhance the efficacy of antibody-mediated therapies, as well as to inhibit metastasis in lung cancer.
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Affiliation(s)
- M T Goswami
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - A K Reka
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - H Kurapati
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - V Kaza
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - J Chen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - T J Standiford
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - V G Keshamouni
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
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Murthy R, Williams D, Kinnebrew S, Waters J, Torres F, Kaza V, Ring W, Wait M, Peltz M. Oropharyngeal Dysphagia and Aspiration After Lung Transplantation in the Current Era. J Heart Lung Transplant 2015. [DOI: 10.1016/j.healun.2015.01.700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Porter DC, Chen M, Liang J, Kaza V, Chumanevich A, Altilia S, Farmaki E, Pena M, Schools GP, Chatzistamou I, Friedhoff LT, Wentland MP, Broude EV, Kiaris H, Roninson IB. Abstract PR08: Targeting tumor microenvironment with selective small-molecule inhibitors of CDK8/19. Cancer Res 2015. [DOI: 10.1158/1538-7445.chtme14-pr08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cyclin-dependent kinase 8 (CDK8), along with its closely related paralog CDK19, are transcription-regulating kinases that, unlike some other members of the CDK family, do not regulate cell cycle progression and are not required for the growth of normal cells or most of the tumor cell types. CDK8 has been identified as an oncogene that enhances the activity of several tumor-promoting transcriptional pathways (such as TGFβ, β-catenin, HIF1A and serum factors), mediating the elongation of transcription of newly activated genes. We have previously reported the discovery of the first selective small-molecule inhibitors of CDK8/19 and their ability to block chemotherapy-induced tumor-promoting paracrine activities of both tumor and normal cells (Porter et al., PNAS 109, 13799, 2012). We now conducted chemical optimization of the original inhibitors, yielding an optimized preclinical lead compound, Senexin B. Senexin B inhibits CDK8/19 in low nanomolar range in vitro and in vivo as an ATP pocket binder, with very high target selectivity as indicated by kinome profiling. It is highly water-soluble, bioavailable, and produces no limiting toxicity upon prolonged administration in mice, at doses that yield plasma concentrations exceeding cellular IC50 by 2-3 orders of magnitude. Senexin B has been tested for efficacy in several animal models addressing different aspects of tumor growth and progression. (i) Pretreatment of tumor-free mice with Senexin B significantly inhibited the growth of triple-negative breast cancer (TNBC) cells inoculated into mice subsequently to Senexin B administration, indicating a general chemopreventive effect on the normal tissue “soil”. (ii) Senexin B potentiated the tumor-suppressive effect of doxorubicin on established TNBC xenografts; this effect was associated with the suppression of NFκB-mediated transcriptional induction of tumor-promoting cytokines. (iii) Senexin B inhibited invasive growth into the muscle layer in an orthotopic xenograft model of MDA-MB-468 TNBC cells. (iv) In a spleen-to-liver colon cancer metastasis model of syngeneic mouse CT26 tumors, Senexin B treatment of mice had the same effect as CDK8 knockdown in tumor cells: suppression of metastatic growth in the liver without a significant effect on primary tumor growth in the spleen. Taken together, these results indicate that CDK8/19 inhibition produces chemopotentiating, chemopreventive and anti-metastatic effects in different types of cancer, inhibiting tumor progression by acting both at the tumor cells (the “seed”) and the tumor microenvironment (the “soil”) of cancers.
Citation Format: Donald C. Porter, Mengqian Chen, Jiaxin Liang, Vimala Kaza, Alexander Chumanevich, Serena Altilia, Elena Farmaki, Marj Pena, Gary P. Schools, Ioulia Chatzistamou, Lawrence T. Friedhoff, Mark P. Wentland, Eugenia V. Broude, Hippokratis Kiaris, Igor B. Roninson. Targeting tumor microenvironment with selective small-molecule inhibitors of CDK8/19. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr PR08. doi:10.1158/1538-7445.CHTME14-PR08
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Affiliation(s)
| | | | | | | | | | | | | | - Marj Pena
- 2University of South Carolina, Columbia, SC,
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Porter DC, Liang J, Kaza V, Chumanevich AA, Altilia S, Farmaki E, Chen M, Schools GP, Chatzistamou I, Pena MM, Friedhoff LT, Wentland MP, Broude E, Kiaris H, Roninson IB. Abstract 4879: Targeting the seed and the soil of cancers with selective small-molecule inhibitors of CDK8/19: Chemopotentiating, chemopreventive, anti-invasive and anti-metastatic activities. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-4879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cyclin-dependent kinase 8 (CDK8), along with its closely related paralog CDK19, are transcription-regulating kinases that, unlike some other members of the CDK family, do not regulate cell cycle progression and are not required for the growth of normal cells or most of the tumor cell types. CDK8 has been identified as an oncogene that enhances the activity of several tumor-promoting transcription factors, mediating the elongation of transcription of newly activated genes. We have previously reported the discovery of the first selective small-molecule inhibitors of CDK8/19 and their ability to block chemotherapy-induced tumor-promoting paracrine activities of both tumor and normal cells (Porter et al., PNAS 109, 13799, 2012). We now conducted chemical optimization of the original inhibitors, yielding an optimized preclinical lead compound, Senexin B. Senexin B inhibits CDK8/19 in low nanomolar range in vitro and in vivo as an ATP pocket binder, with very high target selectivity as indicated by kinome profiling. It is highly water-soluble, bioavailable, and produces no limiting toxicity upon prolonged administration in mice, at doses that yield plasma concentrations exceeding cellular IC50 by 2-3 orders of magnitude. Senexin B has been tested for efficacy in several animal models addressing different aspects of tumor growth and progression. (i) Pretreatment of tumor-free mice with Senexin B significantly inhibited the growth of triple-negative breast cancer (TNBC) cells inoculated into mice subsequently to Senexin B administration, indicating a general chemopreventive effect on the normal tissue “soil”. (ii) Senexin B potentiated the tumor-suppressive effect of doxorubicin on established TNBC xenografts. (iii) Senexin B inhibited invasive growth into the muscle layer in an orthotopic xenograft model of MDA-MB-468 TNBC cells. (iv) In a spleen-to-liver metastasis model of syngeneic mouse CT26 tumors, Senexin B treatment of mice had the same effect as CDK8 knockdown in tumor cells: suppression of metastatic growth in the liver without a significant effect on primary tumor growth in the spleen. Taken together, these results indicate that CDK8/19 inhibition produces chemopotentiating, chemopreventive and anti-metastatic effects in different types of cancer, inhibiting tumor progression at the organismal level.
Citation Format: Donald C. Porter, Jiaxin Liang, Vimala Kaza, Alexander A. Chumanevich, Serena Altilia, Elena Farmaki, Mengqian Chen, Gary P. Schools, Ioulia Chatzistamou, Marj M. Pena, Lawrence T. Friedhoff, Mark P. Wentland, Eugenia Broude, Hippokratis Kiaris, Igor B. Roninson. Targeting the seed and the soil of cancers with selective small-molecule inhibitors of CDK8/19: Chemopotentiating, chemopreventive, anti-invasive and anti-metastatic activities. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4879. doi:10.1158/1538-7445.AM2014-4879
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Chen M, Kaza V, Liang J, McDermott M, Roninson I. Abstract 616: Transcription-regulating kinases CDK8 and CDK19 as novel therapeutic targets for advanced prostate cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Most of castration-refractory prostate cancers (CRPC) continue to express androgen receptor (AR) that maintains its activity at low levels or even in the absence of androgen, driving tumor cell proliferation. Androgen-depleting drugs and androgen antagonists have little or no effect against AR+ cancers that are fully androgen-independent (AI). On the other hand, experimental compounds that cause AR degradation prevent AR-mediated repression of tumor-promoting genes, a tumor-suppressive effect of AR. We report a novel druggable target for CRPC, which mediates the induction but not the repression of gene expression by AR and inhibits the growth of AI prostate cancer (PCa) cells. This target is two closely related transcription-regulating kinases CDK8/CDK19 that unlike some other members of the CDK family are not required for cell cycle progression but play critical roles in several transcriptional signaling pathways. CDK8 and CDK19 are highly expressed in AR+ PCa cells and elevated under the conditions of androgen deprivation; CDK19 is overexpressed in AR+ PCa cell lines and in metastatic clinical PCa. A novel selective CDK8/19 kinase inhibitor (Senexin B) blocks ligand-induced AR-mediated transcriptional activation in androgen-dependent (AD) PCa cells but does not affect the AR-mediated gene repression. The CDK8/19 inhibitor also inhibits ligand-independent AR activation and AI cell growth in AI-PCa cells resistant to the anti-androgenic drug enzalutamide, both in vitro and in a mouse xenograft model. We have also discovered that CDK8/19 inhibition decreases NFκB mediated transcriptional activation of a group of tumor-promoting chemokines, such as CXCL1, CXCL2 and IL8, suggesting that CDK8/19 may promote prostate cancer chemoresistance and metastasis through the NFκB pathway. The above results suggest that CDK8/19 is an especially attractive therapeutic target for advanced PCa, which controls both AR-driven cell proliferation and other oncogenic pathways.
Citation Format: Mengqian Chen, Vimala Kaza, Jiaxin Liang, Martina McDermott, Igor Roninson. Transcription-regulating kinases CDK8 and CDK19 as novel therapeutic targets for advanced prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 616. doi:10.1158/1538-7445.AM2014-616
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Upadhyay R, Sanduja S, Kaza V, Dixon DA. Genetic polymorphisms in RNA binding proteins contribute to breast cancer survival. Int J Cancer 2012; 132:E128-38. [PMID: 22907529 DOI: 10.1002/ijc.27789] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 08/07/2012] [Indexed: 12/26/2022]
Abstract
The RNA-binding proteins TTP and HuR control expression of numerous genes associated with breast cancer pathogenesis by regulating mRNA stability. However, the role of genetic variation in TTP (ZFP36) and HuR (ELAVL1) genes is unknown in breast cancer prognosis. A total of 251 breast cancer patients (170 Caucasians and 81 African-Americans) were enrolled and followed up from 2001 to 2011 (or until death). Genotyping was performed for 10 SNPs in ZFP36 and 7 in ELAVL1 genes. On comparing both races with one another, significant differences were found for clinical and genetic variables. The influence of genetic polymorphisms on survival was analyzed by using Cox-regression, Kaplan-Meier analysis and the log-rank test. Univariate (Kaplan-Meier/Cox-regression) and multivariate (Cox-regression) analysis showed that the TTP gene polymorphism ZFP36*2 A > G was significantly associated with poor prognosis of Caucasian patients (HR = 2.03; 95% CI = 1.09-3.76; p = 0.025; log-rank p = 0.022). None of the haplotypes, but presence of more than six risk genotypes in Caucasian patients, was significantly associated with poor prognosis (HR=2.42; 95% CI = 1.17-4.99; p = 0.017; log-rank p = 0.007). The effect of ZFP36*2 A > G on gene expression was evaluated from patients' tissue samples. Both TTP mRNA and protein expression was significantly decreased in ZFP36*2 G allele carriers compared to A allele homozygotes. Conversely, upregulation of the TTP-target gene COX-2 was observed ZFP36*2 G allele carriers. Through its ability to attenuate TTP gene expression, the ZFP36*2 A > G gene polymorphism has appeared as a novel prognostic breast cancer marker in Caucasian patients.
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Affiliation(s)
- Rohit Upadhyay
- Department of Biological Sciences and Cancer Research Center, University of South Carolina, Columbia, SC, USA
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Abstract
Messenger RNA decay is a critical mechanism to control the expression of many inflammation- and cancer-associated genes. These transcripts are targeted for rapid degradation through AU-rich element (ARE) motifs present in the mRNA 3' untranslated region (3'UTR). Tristetraprolin (TTP) is an RNA-binding protein that plays a significant role in regulating the expression of ARE-containing mRNAs. Through its ability to bind AREs and target the bound mRNA for rapid degradation, TTP can limit the expression of a number of critical genes frequently overexpressed in inflammation and cancer. Regulation of TTP occurs on multiple levels through cellular signaling events to control transcription, mRNA turnover, phosphorylation status, cellular localization, association with other proteins, and proteosomal degradation, all of which impact TTP's ability to promote ARE-mediated mRNA decay along with decay-independent functions of TTP. This review summarizes the current understanding of post-transcriptional regulation of ARE-containing gene expression by TTP and discusses its role in maintaining homeostasis and the pathological consequences of losing TTP expression.
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Affiliation(s)
- Sandhya Sanduja
- Department of Biological Sciences and Cancer Research Center, University of South Carolina, Columbia, SC 29203, USA
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Sanduja S, Kaza V, Dixon DA. Abstract 3204: The mRNA decay factor tristetraprolin (TTP) induces senescence in human papillomavirus-transformed cervical cancer cells by targeting E6-AP ubiquitin ligase. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-3204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cervical cancer is the second most common cancer among women worldwide. A necessary factor in the development of nearly all cases of cervical cancer is the human papillomavirus (HPV) infection. High-risk HPV (HPV16 and 18) mediates cellular transformation and carcinogenesis through the concerted actions of viral oncoproteins E6 and E7 that disrupt the normal cell cycle regulation by targeting the p53 and Rb tumor suppressor pathways respectively. In the present study, we found that expression of the mRNA decay factor TTP is lost in HPV18-positive HeLa cells and introduction of TTP in cells lead to inhibition of cell proliferation and tumorigenesis by inducing cellular senescence. Consistent with this, TTP-expressing cells showed enhanced p53 protein stability and p53-dependent transcriptional activity. In cells expressing TTP, no changes were observed in the RNA levels of E6 and E7 indicating that these viral factors are not targets of TTP-mediated RNA decay. Whereas the E6-associated protein (E6-AP), the cellular ubiquitin ligase required for E6-mediated p53 degradation, was found to be down regulated both at mRNA and protein levels in presence of TTP. Furthermore, the association of E6 and E6-AP promotes transcriptional activation of hTERT, and TTP-dependent down regulation of E6-AP resulted in inhibition of hTERT expression and decreased cellular telomerase activity. Analysis of E6-AP mRNA revealed potential AU-rich element (ARE) binding sites of TTP present in the 3’ untranslated region (3′UTR) and RNA-binding studies demonstrate a physical interaction between TTP and E6-AP mRNA leading to rapid decay of E6-AP mRNA in a 3’UTR-dependent manner. Similar results were obtained with other high-risk HPV-positive cell lines that employ E6-AP pathway to control p53 and hTERT levels. Consistent with this, we found TTP expression to be lost or significantly reduced in squamous cell carcinomas as compared to normal cervical tissue. Finally, our studies indicate that loss of TTP expression in cervical cancer occurs through epigenetic mechanisms involving promoter methylation and histone deacetylation. These findings demonstrate the ability of TTP to act as a tumor suppressor through inhibition of the E6-AP pathway and indicate TTP loss to be a critical event during HPV-mediated carcinogenesis.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3204.
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Sanduja S, Kaza V, Dixon DA. The mRNA decay factor tristetraprolin (TTP) induces senescence in human papillomavirus-transformed cervical cancer cells by targeting E6-AP ubiquitin ligase. Aging (Albany NY) 2009; 1:803-17. [PMID: 20157568 PMCID: PMC2815738 DOI: 10.18632/aging.100086] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [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: 08/02/2009] [Accepted: 09/08/2009] [Indexed: 12/31/2022]
Abstract
The RNA-binding
protein tristetraprolin (TTP) regulates expression of many
cancer-associated and proinflammatory factors through binding AU-rich
elements (ARE) in the 3'-untranslated region (3'UTR) and facilitating rapid
mRNA decay. Here we report on the ability of TTP to act in an
anti-proliferative capacity in HPV18-positive HeLa cells by inducing
senescence. HeLa cells maintain a dormant p53 pathway and elevated
telomerase activity resulting from HPV-mediated transformation, whereas TTP
expression counteracted this effect by stabilizing p53 protein and
inhibiting hTERT expression. Presence of TTP did not alter E6 and E7 viral
mRNA levels indicating that these are not TTP targets. It was found that
TTP promoted rapid mRNA decay of the cellular
ubiquitin ligase E6-associated protein (E6-AP). RNA-binding studies
demonstrated TTP and E6-AP mRNA interaction and deletion of the E6-AP mRNA
ARE-containing 3'UTR imparts resistance to TTP-mediated downregulation.
Similar results were obtained with high-risk HPV16-positive cells that
employ the E6-AP pathway to control p53 and hTERT levels. Furthermore, loss
of TTP expression was consistently observed in cervical cancer tissue
compared to normal tissue. These findings demonstrate the ability of TTP to
act as a tumor suppressor by inhibiting the E6-AP pathway
and indicate TTP loss to be a critical event during HPV-mediated
carcinogenesis.
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Affiliation(s)
- Sandhya Sanduja
- Department of Biological Sciences and Cancer Research Center, University of South Carolina, Columbia, SC 29203, USA
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Sussman N, Kaza V, Barshes N, Stribling R, Goss J, O'Mahony C, Zhang E, Vierling J, Frost A. Successful liver transplantation following medical management of portopulmonary hypertension: a single-center series. Am J Transplant 2006; 6:2177-82. [PMID: 16796721 DOI: 10.1111/j.1600-6143.2006.01432.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Severe portopulmonary hypertension (POPH) is an absolute contraindication to orthotopic liver transplantation (OLT). Vasodilators have been used, but the safety of subsequent transplantation and the reversibility of pulmonary hypertension after transplantation are uncertain. This study examined the feasibility and post-transplant effects of liver transplantation following medical control of POPH. Eight consecutive patients (three females and five males, ages 39-51) with POPH as their only contraindication to transplantation were treated with continuous intravenous epoprostenol. Liver transplantation was considered if the mean pulmonary artery pressure (PAM) was lowered to <35 mmHg. Epoprostenol 2-8 ng/kg/min successfully improved hemodynamics in seven of eight patients, usually within 6.5 months of initiating therapy. PAM declined from an average of 43-33 mmHg (p=0.03); mean pulmonary vascular resistance declined from 410 to 192 dyn s cm-5 (p=0.01) and cardiac output increased from 6.6 to 10 L/min (p=0.02). Six of the seven responders were actively listed for liver transplantation. Two died on the waiting list; the remaining four were transplanted and remain alive and well 9-18 months post-OLT-two without vasodilators, and two on oral medication. We conclude that pulmonary vasodilators permit safe liver transplantation in some cases, and that POPH may be reversible after transplantation.
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Affiliation(s)
- N Sussman
- Department of Medicine, Surgery, Baylor College of Medicine, Houston, Texas, USA.
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Yang D, Goldsmith EB, Lin Y, Waldman BC, Kaza V, Waldman AS. Genetic exchange between homeologous sequences in mammalian chromosomes is averted by local homology requirements for initiation and resolution of recombination. Genetics 2006; 174:135-44. [PMID: 16816418 PMCID: PMC1569803 DOI: 10.1534/genetics.106.060590] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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] [Indexed: 11/18/2022] Open
Abstract
We examined the mechanism by which recombination between imperfectly matched sequences (homeologous recombination) is suppressed in mammalian chromosomes. DNA substrates were constructed, each containing a thymidine kinase (tk) gene disrupted by insertion of an XhoI linker and referred to as a "recipient" gene. Each substrate also contained one of several "donor" tk sequences that could potentially correct the recipient gene via recombination. Each donor sequence either was perfectly homologous to the recipient gene or contained homeologous sequence sharing only 80% identity with the recipient gene. Mouse Ltk(-) fibroblasts were stably transfected with the various substrates and tk(+) segregants produced via intrachromosomal recombination were recovered. We observed exclusion of homeologous sequence from gene conversion tracts when homeologous sequence was positioned adjacent to homologous sequence in the donor but not when homeologous sequence was surrounded by homology in the donor. Our results support a model in which homeologous recombination in mammalian chromosomes is suppressed by a nondestructive dismantling of mismatched heteroduplex DNA (hDNA) intermediates. We suggest that mammalian cells do not dismantle mismatched hDNA by responding to mismatches in hDNA per se but rather rejection of mismatched hDNA appears to be driven by a requirement for localized homology for resolution of recombination.
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Affiliation(s)
- Derek Yang
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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Kaza V, Sussman N, O’Mahoney C, Goss J, Stribling R, Frost A. 385. J Heart Lung Transplant 2006. [DOI: 10.1016/j.healun.2005.11.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Chen PP, Ariyasu RG, Kaza V, LaBree LD, McDonnell PJ. A randomized trial comparing mitomycin C and conjunctival autograft after excision of primary pterygium. Am J Ophthalmol 1995; 120:151-60. [PMID: 7639298 DOI: 10.1016/s0002-9394(14)72602-9] [Citation(s) in RCA: 221] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
PURPOSE To determine the rate of recurrence and complications after bare sclera excision of primary pterygia followed by low-dose mitomycin C (0.2 mg/ml twice daily for five days), placebo (balanced saline solution), or conjunctival autograft. METHODS We performed a prospective, double-masked clinical trial of 64 patients (60 Hispanic) randomly assigned to a treatment group. Twenty-four patients received mitomycin C, 23 conjunctival autograft, and 17 placebo. Recurrence was defined as fibrovascular tissue over the corneoscleral limbus onto clear cornea in the area of previous pterygium excision. RESULTS The recurrence rate after mitomycin C and conjunctival autograft was 38% and 39% of eyes, respectively, after mean follow-up (in recurrence-free patients) of 12.3 and 13.5 months, respectively. The recurrence rate after placebo treatment was significantly higher (P = .002), 88%, after mean follow-up (in recurrence-free patients) of 9.3 months. Increasing age was associated with significantly fewer recurrences (P = .006) after controlling for pterygium type (atrophic, noninflamed, or inflamed) and treatment group. The mean time to recurrence varied from 3.7 to 4.8 months; only 6% of recurrences were noted after the sixth postoperative month. Major complications included symblepharon (two), loose autograft (one), and pyogenic granuloma (two). No group had significantly more complications. CONCLUSIONS Conjunctival autograft and low-dose topical mitomycin C are equally effective as adjunctive treatment after excision of primary pterygia in this young, southern California, predominantly Hispanic population. Both methods have significantly lower rates of recurrence than bare sclera excision alone, and neither is associated with severe complications after one year of follow-up. Increasing patient age is associated with significantly less risk of recurrence.
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Affiliation(s)
- P P Chen
- Doheny Eye Institute, University of Southern California School of Medicine, Los Angeles, USA
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Abstract
Rose bengal and fluorescein are photosensitive dyes in widespread use in the evaluation of ocular surface diseases, including herpes simplex virus (HSV) keratitis. These dyes have recently been shown to penetrate living cells, and rose bengal was previously reported to possess antiviral activity. Several experiments reported herein suggest that these dyes do possess the potential for potent antiviral activity against extracellular virus, but only in the presence of light. Rose bengal is substantially more effective in vitro than fluorescein, and the effect is greater with increasing concentration of dye and duration of light exposure. Electron microscopic evaluation of treated virus showed no structural difference from untreated virus, in spite of 4- to 5-log decreases in virus titer. Intracellular virus was found to be markedly resistant to photoinactivation. In a rabbit model of acute primary HSV keratitis, daily application of topical rose bengal followed by light exposure had no therapeutic effect, although an adverse effect on culture sensitivity testing was seen.
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Affiliation(s)
- S E Brooks
- Department of Ophthalmology, Los Angeles County-University of Southern California Medical Center
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