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Green BB, Anderson ML, McClure JB, Ehrlich K, Hall YN, Hansell L, Hsu C, Margolis KL, Munson SA, Thompson MJ. Is Hypertension Diagnostic Testing and Diagnosis Associated With Psychological Distress? Am J Hypertens 2024; 37:69-76. [PMID: 37688515 DOI: 10.1093/ajh/hpad083] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/20/2023] [Accepted: 09/07/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Psychological impacts of hypertension diagnostic testing and new hypertension diagnoses are unclear. METHODS BP-CHECK was a randomized diagnostic study conducted in 2017-2019 in an integrated healthcare system. Participants with no hypertension diagnosis or medications and elevated blood pressure (BP) were randomized to one of three diagnostic regimens: (i) Clinic, (ii) Home, or (iii) Kiosk. Participants completed questionnaires at baseline, after completion of the diagnostic regimens, and at 6 months. Outcomes included changes from baseline in health-related quality of life (HRQOL), BP-related worry, and thoughts about having a stroke or heart attack. RESULTS Participants (n = 482) were mostly over age 50 (77.0%), and White race (80.3%). HRQOL did not significantly change from baseline to 3 weeks or 6 months. Among all participants, BP-related worry and concerns about having a heart attack or stroke increased significantly from baseline to 3 weeks, with heart attack and stroke concerns significantly higher in the Kiosk compared Clinic and Home groups. At 6 months, thoughts about having a heart attack or stroke returned to baseline overall and in the Kiosk group, however BP-related worry was significantly higher among those with, compared to those without, a new hypertension diagnosis. CONCLUSIONS The hypertension diagnostic process did not lead to short-term or intermediate-term changes in self-reported HRQOL. However, BP-related worry increased short-term and persisted at 6 months among individuals with a new hypertension diagnosis. Results warrant validation in more representative populations and additional exploration of the impacts of this worry on psychological well-being and hypertension control. CLINICALTRIALS.GOV IDENTIFIER NCT03130257.
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Affiliation(s)
- B B Green
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
- Washington Permanente Medical Group, Seattle, Washington, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, California, USA
| | - M L Anderson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - J B McClure
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J Tyson School of Medicine, Pasadena, California, USA
| | - K Ehrlich
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - Y N Hall
- VA Puget Sound Health Care System, Seattle, Washington, USA
| | - L Hansell
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - C Hsu
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - K L Margolis
- HealthPartners Institute, Minneapolis, Minnesota, USA
| | - S A Munson
- Department of Human Centered Design and Engineering, University of Washington, Seattle, Washington, USA
| | - M J Thompson
- Department of Family Medicine, University of Washington, Seattle, Washington, 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. 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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3
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Nieman DC, Sakaguchi CA, Pelleigrini M, Thompson MJ, Sumner S, Zhang Q. Healthy lifestyle linked to innate immunity and lipoprotein metabolism: a cross-sectional comparison using untargeted proteomics. Sci Rep 2023; 13:16728. [PMID: 37794065 PMCID: PMC10550951 DOI: 10.1038/s41598-023-44068-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
This study used untargeted proteomics to compare blood proteomic profiles in two groups of adults that differed widely in lifestyle habits. A total of 52 subjects in the lifestyle group (LIFE) (28 males, 24 females) and 52 in the control group (CON) (27 males, 25 females) participated in this cross-sectional study. Age, education level, marital status, and height did not differ significantly between LIFE and CON groups. The LIFE and CON groups differed markedly in body composition, physical activity patterns, dietary intake patterns, disease risk factor prevalence, blood measures of inflammation, triglycerides, HDL-cholesterol, glucose, and insulin, weight-adjusted leg/back and handgrip strength, and mood states. The proteomics analysis showed strong group differences for 39 of 725 proteins identified in dried blood spot samples. Of these, 18 were downregulated in the LIFE group and collectively indicated a lower innate immune activation signature. A total of 21 proteins were upregulated in the LIFE group and supported greater lipoprotein metabolism and HDL remodeling. Lifestyle-related habits and biomarkers were probed and the variance (> 50%) in proteomic profiles was best explained by group contrasts in indicators of adiposity. This cross-sectional study established that a relatively small number of proteins are associated with good lifestyle habits.
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Affiliation(s)
- David C Nieman
- Human Performance Laboratory, Biology Department, Appalachian State University, North Carolina Research Campus, Kannapolis, NC, USA.
| | - Camila A Sakaguchi
- Human Performance Laboratory, Biology Department, Appalachian State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Matteo Pelleigrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Thompson
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Susan Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, 28081, USA
| | - Qibin Zhang
- UNCG Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA
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4
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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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5
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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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Ahmed A, Buckley L, Maradana J, Nuvvula S, Tan Z, Thompson MJ, Zainal A. ODP452 A Case of Thymic Hyperplasia in Graves’ Disease. J Endocr Soc 2022. [PMCID: PMC9625800 DOI: 10.1210/jendso/bvac150.1555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Introduction We report a case of a patient with Graves’ Disease (GD) associated with thymic hyperplasia (TH) which regressed with treatment of GD. The association between these two conditions is under recognized. The causative mechanisms between TH associated with GD are still under investigation. Case Description A 39-year-old male patient presented with hemoptysis, dyspnea, palpitations, tremors and unintentional weight loss. His TSH was suppressed to < 0. 005 and free T4 was elevated to 5.51. As part of his work up a CT scan was performed which revealed a prominent anterior mediastinal mass. He was started on Methimazole and Atenolol. Lab work confirming positive TSI and TRAB antibodies consistent with Graves’ disease. At follow up, he opted for radioactive iodine ablation therapy with 20mCi. He had failure of therapy and was resumed on Methimazole. He ultimately underwent total thyroidectomy with subsequent thyroid hormone replacement with Levothyroxine 150mcg daily. His thyroid function tests normalized, and his symptoms resolved. A repeat CT thorax was performed which showed complete resolution of his mediastinal mass, consistent with GD associated TH. Conclusions GD associated TH was first described in 1914. Data supports TSH receptor antibody mediated thymic enlargement1. TH can be classified in two morphological types, lymphoid hyperplasia unassociated with thymic enlargement and true TH in which an increase in thymic volume is evident 2. Thymic cortical tissue expansion seems to be due to a hyperthyroid state involving increased levels of thymulin, a protein involved in lymphocyte differentiation whereas lymphoid hyperplasia correlates with the immune process in GD 2. Antithyroid drug therapy reduces circulating thyroid hormone levels causing a generalized immunosuppressive effect. This reduces hyperplasia of lymphatic organs including the thymus 3. There are no current guidelines for the management and surveillance of thymic hyperplasia in GD as the course and timeline of regression of TH can vary widely. Thymic biopsies are performed frequently to rule out malignancy, however, it is important to raise awareness that GD associated TH has a benign course and generally resolves with management of the underlying GD 3. It is imperative to avoid unnecessary invasive procedures and their subsequent complications in such GD patients. References: 1] Dalla Costa M (2014) Thymic hyperplasia in patients with Graves’ disease. J Endocrinol invest 37: 1175-1179. 2] Nakamura S (2012) Thymic enlargement in two cases of Graves’ disease. Internal Med 51: 673-674.3] Nakamura T et al (2004) A case of thymic enlargement in hyperthyroidism in a young woman. Thyroid 14: 307-310. Presentation: No date and time listed
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MacGregor KL, DeMartini KS, Barry-Menkhaus SA, Derr AG, Thompson MJ. The Impact of Integrated Behavioral Healthcare on Glycemic Control. J Clin Psychol Med Settings 2022; 29:636-644. [PMID: 34436717 DOI: 10.1007/s10880-021-09817-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
Integrated behavioral healthcare (IBH) is the "standard of care" to address psychosocial factors impacting diabetes outcomes; it is not standard in practice. This longitudinal, retrospective, chart-review examines IBH impact on glycemic control in an adult diabetes clinic. Adults (n = 374) with ≥ 1 behavioral health encounter, ≥ 2 hemoglobin A1c (HbA1c) values, and HbA1c value > 8% at initial IBH visit were included. Mixed effects linear piecewise models examined differences in slope trajectories for 365 days pre- and post-IBH intervention. Pre-intervention slope was not significant (z = - 1.09, p = 0.28). The post-intervention slope was significant (z = - 6.44, p < 0.001), indicating a significant linear decrease in HbA1c values. Results demonstrated that prior to engaging with behavioral health, there was no change in HbA1c. After initial IBH visit, there was a predicted reduction of > 1% in HbA1c over the following year. These results suggest that IBH significantly improves patients' metabolic status. Next steps for IBH research are offered.
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Affiliation(s)
- Kristin L MacGregor
- Department of Psychiatry/Diabetes Center of Excellence, UMass Memorial Medical Center/UMass Medical School, Worcester, MA, 01655, USA.
| | - Kelly S DeMartini
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | - Alan G Derr
- Diabetes Center of Excellence, UMass Medical School, Worcester, MA, 01655, USA
| | - Michael J Thompson
- Diabetes Center of Excellence, UMass Medical School, Worcester, MA, 01655, USA
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8
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Miller KM, Kanapka LG, Rickels MR, Ahmann AJ, Aleppo G, Ang L, Bhargava A, Bode BW, Carlson A, Chaytor NS, Gannon G, Goland R, Hirsch IB, Kiblinger L, Kruger D, Kudva YC, Levy CJ, McGill JB, O'Malley G, Peters AL, Philipson LH, Philis-Tsimikas A, Pop-Busui R, Salam M, Shah VN, Thompson MJ, Vendrame F, Verdejo A, Weinstock RS, Young L, Pratley R. Benefit of Continuous Glucose Monitoring in Reducing Hypoglycemia Is Sustained Through 12 Months of Use Among Older Adults with Type 1 Diabetes. Diabetes Technol Ther 2022; 24:424-434. [PMID: 35294272 PMCID: PMC9208859 DOI: 10.1089/dia.2021.0503] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Objective: To evaluate glycemic outcomes in the Wireless Innovation for Seniors with Diabetes Mellitus (WISDM) randomized clinical trial (RCT) participants during an observational extension phase. Research Design and Methods: WISDM RCT was a 26-week RCT comparing continuous glucose monitoring (CGM) with blood glucose monitoring (BGM) in 203 adults aged ≥60 years with type 1 diabetes. Of the 198 participants who completed the RCT, 100 (98%) CGM group participants continued CGM (CGM-CGM cohort) and 94 (98%) BGM group participants initiated CGM (BGM-CGM cohort) for an additional 26 weeks. Results: CGM was used a median of >90% of the time at 52 weeks in both cohorts. In the CGM-CGM cohort, median time <70 mg/dL decreased from 5.0% at baseline to 2.6% at 26 weeks and remained stable with a median of 2.8% at 52 weeks (P < 0.001 baseline to 52 weeks). Participants spent more time in range 70-180 mg/dL (TIR) (mean 56% vs. 64%; P < 0.001) and had lower hemoglobin A1c (HbA1c) (mean 7.6% [59 mmol/mol] vs. 7.4% [57 mmol/mol]; P = 0.01) from baseline to 52 weeks. In BGM-CGM, from 26 to 52 weeks median time <70 mg/dL decreased from 3.9% to 1.9% (P < 0.001), TIR increased from 56% to 60% (P = 0.006) and HbA1c decreased from 7.5% (58 mmol/mol) to 7.3% (57 mmol/mol) (P = 0.025). In BGM-CGM, a severe hypoglycemic event was reported for nine participants while using BGM during the RCT and for two participants during the extension phase with CGM (P = 0.02). Conclusions: CGM use reduced hypoglycemia without increasing hyperglycemia in older adults with type 1 diabetes. These data provide further evidence for fully integrating CGM into clinical practice. Clinicaltrials.gov (NCT03240432).
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Affiliation(s)
| | - Lauren G. Kanapka
- Jaeb Center for Health Research, Tampa, Florida, USA
- Address correspondence to: Lauren G. Kanapka, MSc, Jaeb Center for Health Research, 15310 Amberly Drive, #350, Tampa, FL 33647, USA
| | - Michael R. Rickels
- Rodebaugh Diabetes Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrew J. Ahmann
- Division of Endocrinology, Diabetes, and Clinical Nutrition, Oregon Health and Science University, Portland, Oregon, USA
| | - Grazia Aleppo
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Lynn Ang
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Anuj Bhargava
- Iowa Diabetes and Endocrinology Research Center, Des Moines, Iowa, USA
| | - Bruce W. Bode
- Formally Atlanta Diabetes Associates, Atlanta, Georgia, USA
| | - Anders Carlson
- Park Nicollet International Diabetes Center, Minneapolis, Minnesota, USA
| | - Naomi S. Chaytor
- Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Gail Gannon
- Kovler Diabetes Center, University of Chicago, Chicago, Illinois, USA
| | - Robin Goland
- Naomi Berri Diabetes Center, Columbia University, New York, New York, USA
| | - Irl B. Hirsch
- Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, Washington, USA
| | - Lisa Kiblinger
- Formally Atlanta Diabetes Associates, Atlanta, Georgia, USA
| | | | | | - Carol J. Levy
- Division of Endocrinology, Diabetes and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Janet B. McGill
- Division of Endocrinology, Metabolism & Lipid Research, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Grenye O'Malley
- Division of Endocrinology, Diabetes and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anne L. Peters
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | | | | | - Rodica Pop-Busui
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Maamoun Salam
- Division of Endocrinology, Metabolism & Lipid Research, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Viral N. Shah
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Michael J. Thompson
- Department of Endocrinology-Diabetes, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Francesco Vendrame
- Division of Endocrinology, Diabetes, and Metabolism at the University of Miami School of Medicine, University of Miami, Miami, Florida, USA
| | | | - Ruth S. Weinstock
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Laura Young
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Richard Pratley
- AdventHealth Translation Research Institute, Orlando, Florida, USA
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9
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Arneson A, Haghani A, Thompson MJ, Pellegrini M, Kwon SB, Vu H, Maciejewski E, Yao M, Li CZ, Lu AT, Morselli M, Rubbi L, Barnes B, Hansen KD, Zhou W, Breeze CE, Ernst J, Horvath S. A mammalian methylation array for profiling methylation levels at conserved sequences. Nat Commun 2022; 13:783. [PMID: 35145108 PMCID: PMC8831611 DOI: 10.1038/s41467-022-28355-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [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: 11/15/2021] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures up to 36k CpGs per species that are well conserved across many mammalian species. We designed a set of probes that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development of epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others. Methods to probe DNA methylation in the majority of non-human mammals are lacking. Here the authors developed a Mammalian Methylation Array that includes 36k well-conserved CpGs in mammals which will facilitate cross-species comparisons. They annotate the conserved CpGs in > 200 species. The array allows one to measure methylation in all mammalian species including unsequenced ones.
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Affiliation(s)
- Adriana Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amin Haghani
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emily Maciejewski
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,Computer Science Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mingjia Yao
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Caesar Z Li
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Ake T Lu
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Marco Morselli
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Bret Barnes
- Illumina, Inc, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, USA
| | | | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA. .,Computer Science Department, University of California, Los Angeles, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Steve Horvath
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA. .,Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA. .,Altos Labs, San Diego, CA, USA.
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10
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Thompson MJ, Capilla-Lasheras P, Dominoni DM, Réale D, Charmantier A. Phenotypic variation in urban environments: mechanisms and implications. Trends Ecol Evol 2021; 37:171-182. [PMID: 34690006 DOI: 10.1016/j.tree.2021.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/22/2021] [Revised: 09/16/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022]
Abstract
In the past decade, numerous studies have explored how urbanisation affects the mean phenotypes of populations, but it remains unknown how urbanisation impacts phenotypic variation, a key target of selection that shapes, and is shaped by, eco-evolutionary processes. Our review suggests that urbanisation may often increase intraspecific phenotypic variation through several processes; a conclusion aligned with results from our illustrative analysis on tit morphology across 13 European city/forest population pairs. Urban-driven changes in phenotypic variation will have immense implications for urban populations and communities, particularly through urbanisation's effects on individual fitness, species interactions, and conservation. We call here for studies that incorporate phenotypic variation in urban eco-evolutionary research alongside advances in theory.
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Affiliation(s)
- M J Thompson
- Département des sciences biologiques, Université du Québec à Montréal, 141 Avenue du Président-Kennedy, Montréal, QC H2X 1Y4, Canada; CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
| | - P Capilla-Lasheras
- Institute of Biodiversity, Animal Health & Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - D M Dominoni
- Institute of Biodiversity, Animal Health & Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - D Réale
- Département des sciences biologiques, Université du Québec à Montréal, 141 Avenue du Président-Kennedy, Montréal, QC H2X 1Y4, Canada
| | - A Charmantier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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11
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Bors EK, Baker CS, Wade PR, O'Neill KB, Shelden KEW, Thompson MJ, Fei Z, Jarman S, Horvath S. An epigenetic clock to estimate the age of living beluga whales. Evol Appl 2021; 14:1263-1273. [PMID: 34025766 PMCID: PMC8127720 DOI: 10.1111/eva.13195] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
DNA methylation data facilitate the development of accurate molecular estimators of chronological age or "epigenetic clocks." We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. We used a custom methylation array to measure methylation levels at 37,491 cytosine-guanine sites (CpGs) from skin samples of dead whales (n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R 2 = 0.92 for the training data; and an R 2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross-validation. We applied the epigenetic clock to an independent dataset of 38 skin samples collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. The epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.
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Affiliation(s)
| | - C. Scott Baker
- Marine Mammal InstituteOregon State UniversityNewportORUSA
| | - Paul R. Wade
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | | | - Kim E. W. Shelden
- Marine Mammal LaboratoryAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanographic and Atmospheric AdministrationSeattleWAUSA
| | - Michael J. Thompson
- Molecular, Cell and Developmental BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | - Zhe Fei
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
| | - Simon Jarman
- School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Steve Horvath
- Department of BiostatisticsSchool of Public HealthUniversity of California‐Los AngelesLos AngelesCAUSA
- Department of Human GeneticsGonda Research CenterDavid Geffen School of MedicineLos AngelesCAUSA
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12
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Amante DJ, Harlan DM, Lemon SC, McManus DD, Olaitan OO, Pagoto SL, Gerber BS, Thompson MJ. Evaluation of a Diabetes Remote Monitoring Program Facilitated by Connected Glucose Meters for Patients With Poorly Controlled Type 2 Diabetes: Randomized Crossover Trial. JMIR Diabetes 2021; 6:e25574. [PMID: 33704077 PMCID: PMC7995078 DOI: 10.2196/25574] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 11/06/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Patients with poorly controlled type 2 diabetes (T2D) experience increased morbidity, increased mortality, and higher cost of care. Self-monitoring of blood glucose (SMBG) is a critical component of diabetes self-management with established diabetes outcome benefits. Technological advancements in blood glucose meters, including cellular-connected devices that automatically upload SMBG data to secure cloud-based databases, allow for improved sharing and monitoring of SMBG data. Real-time monitoring of SMBG data presents opportunities to provide timely support to patients that is responsive to abnormal SMBG recordings. Such diabetes remote monitoring programs can provide patients with poorly controlled T2D additional support needed to improve critical outcomes. OBJECTIVE To evaluate 6 months of a diabetes remote monitoring program facilitated by cellular-connected glucose meter, access to a diabetes coach, and support responsive to abnormal blood glucose recordings greater than 400 mg/dL or below 50 mg/dL in adults with poorly controlled T2D. METHODS Patients (N=119) receiving care at a diabetes center of excellence participated in a two-arm, 12-month randomized crossover study. The intervention included a cellular-connected glucose meter and phone-based diabetes coaching provided by Livongo Health. The coach answered questions, assisted in goal setting, and provided support in response to abnormal glucose levels. One group received the intervention for 6 months before returning to usual care (IV/UC). The other group received usual care before enrolling in the intervention (UC/IV) for 6 months. Change in hemoglobin A1c (HbA1c) was the primary outcome, and change in treatment satisfaction was the secondary outcome. RESULTS Improvements in mean HbA1c were seen in both groups during the first 6 months (IV/UC -1.1%, SD 1.5 vs UC/IV -0.8%, SD 1.5; P<.001). After crossover, there was no significant change in HbA1c in IV/UC (mean HbA1c change +0.2, SD 1.7, P=.41); however, those in UC/IV showed further improvement (mean HbA1c change -0.4%, SD 1.0, P=.008). A mixed-effects model showed no significant treatment effect (IV vs UC) over 12 months (P=.06). However, participants with higher baseline HbA1c and those in the first time period experienced greater improvements in HbA1c. Both groups reported similar improvements in treatment satisfaction throughout the study. CONCLUSIONS Patients enrolled in the diabetes remote monitoring program intervention experienced improvements in HbA1c and treatment satisfaction similar to usual care at a specialty diabetes center. Future studies on diabetes remote monitoring programs should incorporate scheduled coaching components and involve family members and caregivers. TRIAL REGISTRATION ClinicalTrials.gov NCT03124043; https://clinicaltrials.gov/ct2/show/NCT03124043.
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Affiliation(s)
- Daniel J Amante
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, United States
| | - David M Harlan
- Division of Diabetes, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| | - Stephenie C Lemon
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, United States
| | - David D McManus
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| | - Oladapo O Olaitan
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, United States
| | - Sherry L Pagoto
- Department of Allied Health Sciences, Institute for Collaborations on Health, Interventions, and Policy, University of Connecticut, Storrs, CT, United States
| | - Ben S Gerber
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Michael J Thompson
- Division of Diabetes, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, United States
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13
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Olcina MM, Balanis NG, Kim RK, Aksoy BA, Kodysh J, Thompson MJ, Hammerbacher J, Graeber TG, Giaccia AJ. Mutations in an Innate Immunity Pathway Are Associated with Poor Overall Survival Outcomes and Hypoxic Signaling in Cancer. Cell Rep 2019; 25:3721-3732.e6. [PMID: 30590044 PMCID: PMC6405289 DOI: 10.1016/j.celrep.2018.11.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 05/11/2018] [Revised: 10/01/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022] Open
Abstract
Complement-mediated cytotoxicity may act as a selective pressure for tumor overexpression of complement regulators. We hypothesize that the same selective pressure could lead to complement alterations at the genetic level. We find that, when analyzed as a pathway, mutations in complement genes occur at a relatively high frequency and are associated with changes in overall survival across a number of cancer types. Analysis of pathways expressed in patients with complement mutations that are associated with poor overall survival reveals crosstalk between complement and hypoxia in colorectal cancer. The importance of this crosstalk is highlighted by two key findings: hypoxic signaling is increased in tumors harboring complement mutations, and hypoxic tumor cells are resistant to complement-mediated cytotoxicity due, in part, to hypoxia-induced expression of complement regulator CD55. The range of strategies employed by tumors to dysregulate the complement system testifies to the importance of this pathway in tumor progression.
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Affiliation(s)
- Monica M Olcina
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA.
| | - Nikolas G Balanis
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Crump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ryan K Kim
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - B Arman Aksoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia Kodysh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael J Thompson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeff Hammerbacher
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Crump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA.
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14
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Thompson MJ, Chwiałkowska K, Rubbi L, Lusis AJ, Davis RC, Srivastava A, Korstanje R, Churchill GA, Horvath S, Pellegrini M. A multi-tissue full lifespan epigenetic clock for mice. Aging (Albany NY) 2019; 10:2832-2854. [PMID: 30348905 PMCID: PMC6224226 DOI: 10.18632/aging.101590] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/05/2018] [Indexed: 12/11/2022]
Abstract
Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs. However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions.
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Affiliation(s)
- Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Richard C Davis
- Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Ron Korstanje
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Steve Horvath
- Department of Human Genetics and Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
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15
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Olcina MM, Balanis NG, Kim RK, Thompson MJ, Graeber TG, Giaccia AJ. Abstract A097: Complement system mutations in cancer: Uncovering new relationships between tumor hypoxia and complement. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a097] [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 complement system has been proposed to facilitate cancer hallmarks such as increased metastatic potential, proliferation and apoptosis evasion. Despite the association between complement and tumor progression, a detailed characterization of cancer genetic alterations in the complement system has not been performed to date. Here, we report a number of previously unappreciated mutations in complement system genes. Taken together as a pathway, mutations in complement genes occur at a relatively high frequency and across a number of cancer types. Notably, when grouping complement mutations into functionally relevant subgroups according to gene function, mutations and copy number alterations in genes within these subgroups are associated with changes in overall survival outcomes in a range of cancers. We use specific complement component mutations in colorectal cancer to uncover and experimentally validate crosstalk between complement and hypoxia, providing new associations between this innate immunity pathway and a prevalent component of the tumor microenvironment. Our data highlight the complex mechanism employed by cancers to manipulate the innate immune system and point to the potential use of complement system mutations in successful patient stratification into clinically and biologically relevant groups.
Citation Format: Monica M. Olcina, Nikolas G. Balanis, Ryan K. Kim, Michael J. Thompson, Thomas G. Graeber, Amato J. Giaccia. Complement system mutations in cancer: Uncovering new relationships between tumor hypoxia and complement [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A097.
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Affiliation(s)
- Monica M. Olcina
- Stanford University, Stanford, CA; University of California, Los Angeles, Los Angeles, CA
| | - Nikolas G. Balanis
- Stanford University, Stanford, CA; University of California, Los Angeles, Los Angeles, CA
| | - Ryan K. Kim
- Stanford University, Stanford, CA; University of California, Los Angeles, Los Angeles, CA
| | - Michael J. Thompson
- Stanford University, Stanford, CA; University of California, Los Angeles, Los Angeles, CA
| | - Thomas G. Graeber
- Stanford University, Stanford, CA; University of California, Los Angeles, Los Angeles, CA
| | - Amato J. Giaccia
- Stanford University, Stanford, CA; University of California, Los Angeles, Los Angeles, CA
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16
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Olcina MM, Balanis NG, Kim RK, Thompson MJ, Graeber TG, Giaccia AJ. Abstract 4382: Complement system mutational landscape reveals C4BPA mutations enhance apoptosis in an immune-independent manner. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4382] [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 complement system is an important pathway in immunity. When dysregulated in the tumor microenvironment, complement is associated with suppression of antitumor immunity and tumorigenesis promotion. While complement has been reported to have important intracellular functions in immune cells, the role of intracellular complement in cancer has remained poorly understood to date. In this study we investigated the prevalence and significance of pathway-wide complement mutations as well as their role with respect to intracellular complement in cancer. We describe mutations in both individual genes as well as within functional groups that are significantly associated with altered survival outcomes. Analyzing mutations occurring across multiple TCGA cancer types highlighted the potential clinical significance of certain mutations that would otherwise not have surfaced at a single cancer level. As an example, we test the significance of mutations in complement regulator C4BPA in vitro and in vivo in a single cancer type. This approach allowed us to uncover a new immune-independent biologic function of the complement system with potential clinical implications for colorectal cancer patients. Specifically, we find that colorectal cancer cells with specific C4BPA mutations display increased oxaliplatin-induced intracellular C4BPA stabilization. By studying the mechanistic basis of this association we report novel crosstalk between intracellular complement and apoptosis signaling, occurring in an NFκB/RelA-dependent manner. Based on both experimental and patient outcome data, we therefore propose that assessing complement mutation status might facilitate patient stratification. In the case of C4BPA mutations, this would be particularly relevant to improve accuracy of prognosis assessment in stage II colorectal patients where TNM staging alone does not accurately predict outcome in patients who might benefit from adjuvant chemotherapy.
Citation Format: Monica M. Olcina, Nikolas G. Balanis, Ryan K. Kim, Michael J. Thompson, Thomas G. Graeber, Amato J. Giaccia. Complement system mutational landscape reveals C4BPA mutations enhance apoptosis in an immune-independent manner [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4382.
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17
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El-Khatib FH, Balliro C, Hillard MA, Magyar KL, Ekhlaspour L, Sinha M, Mondesir D, Esmaeili A, Hartigan C, Thompson MJ, Malkani S, Lock JP, Harlan DM, Clinton P, Frank E, Wilson DM, DeSalvo D, Norlander L, Ly T, Buckingham BA, Diner J, Dezube M, Young LA, Goley A, Kirkman MS, Buse JB, Zheng H, Selagamsetty RR, Damiano ER, Russell SJ. Home use of a bihormonal bionic pancreas versus insulin pump therapy in adults with type 1 diabetes: a multicentre randomised crossover trial. Lancet 2017; 389:369-380. [PMID: 28007348 PMCID: PMC5358809 DOI: 10.1016/s0140-6736(16)32567-3] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND The safety and effectiveness of a continuous, day-and-night automated glycaemic control system using insulin and glucagon has not been shown in a free-living, home-use setting. We aimed to assess whether bihormonal bionic pancreas initialised only with body mass can safely reduce mean glycaemia and hypoglycaemia in adults with type 1 diabetes who were living at home and participating in their normal daily routines without restrictions on diet or physical activity. METHODS We did a random-order crossover study in volunteers at least 18 years old who had type 1 diabetes and lived within a 30 min drive of four sites in the USA. Participants were randomly assigned (1:1) in blocks of two using sequentially numbered sealed envelopes to glycaemic regulation with a bihormonal bionic pancreas or usual care (conventional or sensor-augmented insulin pump therapy) first, followed by the opposite intervention. Both study periods were 11 days in length, during which time participants continued all normal activities, including athletics and driving. The bionic pancreas was initialised with only the participant's body mass. Autonomously adaptive dosing algorithms used data from a continuous glucose monitor to control subcutaneous delivery of insulin and glucagon. The coprimary outcomes were the mean glucose concentration and time with continuous glucose monitoring (CGM) glucose concentration less than 3·3 mmol/L, analysed over days 2-11 in participants who completed both periods of the study. This trial is registered with ClinicalTrials.gov, number NCT02092220. FINDINGS We randomly assigned 43 participants between May 6, 2014, and July 3, 2015, 39 of whom completed the study: 20 who were assigned to bionic pancreas first and 19 who were assigned to the comparator first. The mean CGM glucose concentration was 7·8 mmol/L (SD 0·6) in the bionic pancreas period versus 9·0 mmol/L (1·6) in the comparator period (difference 1·1 mmol/L, 95% CI 0·7-1·6; p<0·0001), and the mean time with CGM glucose concentration less than 3·3 mmol/L was 0·6% (0·6) in the bionic pancreas period versus 1·9% (1·7) in the comparator period (difference 1·3%, 95% CI 0·8-1·8; p<0·0001). The mean nausea score on the Visual Analogue Scale (score 0-10) was greater during the bionic pancreas period (0·52 [SD 0·83]) than in the comparator period (0·05 [0·17]; difference 0·47, 95% CI 0·21-0·73; p=0·0024). Body mass and laboratory parameters did not differ between periods. There were no serious or unexpected adverse events in the bionic pancreas period of the study. INTERPRETATION Relative to conventional and sensor-augmented insulin pump therapy, the bihormonal bionic pancreas, initialised only with participant weight, was able to achieve superior glycaemic regulation without the need for carbohydrate counting. Larger and longer studies are needed to establish the long-term benefits and risks of automated glycaemic management with a bihormonal bionic pancreas. FUNDING National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health, and National Center for Advancing Translational Sciences.
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Affiliation(s)
- Firas H El-Khatib
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Courtney Balliro
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mallory A Hillard
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kendra L Magyar
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laya Ekhlaspour
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Manasi Sinha
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Debbie Mondesir
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Aryan Esmaeili
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Celia Hartigan
- Center for Clinical and Translational Science and the Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michael J Thompson
- Center for Clinical and Translational Science and the Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Samir Malkani
- Center for Clinical and Translational Science and the Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - J Paul Lock
- Center for Clinical and Translational Science and the Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - David M Harlan
- Center for Clinical and Translational Science and the Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Paula Clinton
- Division of Pediatric Endocrinology and Diabetes, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Eliana Frank
- Division of Pediatric Endocrinology and Diabetes, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Darrell M Wilson
- Division of Pediatric Endocrinology and Diabetes, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Daniel DeSalvo
- Division of Pediatric Endocrinology and Diabetes, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lisa Norlander
- Division of Pediatric Endocrinology and Diabetes, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Trang Ly
- Division of Pediatric Endocrinology and Diabetes, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Bruce A Buckingham
- Division of Pediatric Endocrinology and Diabetes, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jamie Diner
- Diabetes Care Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Milana Dezube
- Diabetes Care Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Laura A Young
- Diabetes Care Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - April Goley
- Diabetes Care Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - M Sue Kirkman
- Diabetes Care Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - John B Buse
- Diabetes Care Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Hui Zheng
- Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Edward R Damiano
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Steven J Russell
- Diabetes Unit and Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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18
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Timmermans MJTN, Thompson MJ, Collins S, Vogler AP. Independent evolution of sexual dimorphism and female-limited mimicry in swallowtail butterflies (Papilio dardanus and Papilio phorcas). Mol Ecol 2017; 26:1273-1284. [PMID: 28100020 DOI: 10.1111/mec.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 03/04/2016] [Revised: 12/09/2016] [Accepted: 01/03/2017] [Indexed: 11/29/2022]
Abstract
Several species of swallowtail butterflies (genus Papilio) are Batesian mimics that express multiple mimetic female forms, while the males are monomorphic and nonmimetic. The evolution of such sex-limited mimicry may involve sexual dimorphism arising first and mimicry subsequently. Such a stepwise scenario through a nonmimetic, sexually dimorphic stage has been proposed for two closely related sexually dimorphic species: Papilio phorcas, a nonmimetic species with two female forms, and Papilio dardanus, a female-limited polymorphic mimetic species. Their close relationship indicates that female-limited polymorphism could be a shared derived character of the two species. Here, we present a phylogenomic analysis of the dardanus group using 3964 nuclear loci and whole mitochondrial genomes, showing that they are not sister species and thus that the sexually dimorphic state has arisen independently in the two species. Nonhomology of the female polymorphism in both species is supported by population genetic analysis of engrailed, the presumed mimicry switch locus in P. dardanus. McDonald-Kreitman tests performed on SNPs in engrailed showed the signature of balancing selection in a polymorphic population of P. dardanus, but not in monomorphic populations, nor in the nonmimetic P. phorcas. Hence, the wing polymorphism does not balance polymorphisms in engrailed in P. phorcas. Equally, unlike in P. dardanus, none of the SNPs in P. phorcas engrailed were associated with either female morph. We conclude that sexual dimorphism due to female polymorphism evolved independently in both species from monomorphic, nonmimetic states. While sexual selection may drive male-female dimorphism in nonmimetic species, in mimetic Papilios, natural selection for protection from predators in females is an alternative route to sexual dimorphism.
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Affiliation(s)
- M J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - M J Thompson
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK.,Department of Zoology, Cambridge University, Downing Street, Cambridge, CB2 3EJ, UK
| | - S Collins
- ABRI, PO Box 14308, Westlands, 0800, Nairobi, Kenya
| | - A P Vogler
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
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19
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Thompson RH, Patterson G, Thompson MJ, Slover HT. Separation of pairs of C-24 epimeric sterols by glass capillary gas liquid chromatography. Lipids 2016; 16:694-9. [PMID: 27519237 DOI: 10.1007/bf02535066] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/1981] [Indexed: 11/28/2022]
Abstract
Paris of C-24 epimeric sterols have been very difficult to separate by physical emthods. We report here the partial or complete separation of the trimethylsilyl ethers of nine pairs of C-24 epimeric sterols by gas liquid chromatography on a glass capillary column coated with SP-2340. The trimethylsilyl ethers of the epimeric pairs of sterols with saturated side chains and a pair with two double bonds in the side chain were completely separated from each other by GLC. The epimeric pairs with a double bond at C-22 showed partial separation. The 24β-epimer with a saturated side chain eluted before the corresponding 24α-epimer. This order was reversed for pairs of C-24 epimeric sterol trimethylsilyl ethers containing a double bond in the side chain at C-22.
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Affiliation(s)
- R H Thompson
- Nutrient Composition Laboratory, Beltsville Human Nutrition Research Center, Science and Education Administration, U.S. Department of Agriculture, 20705, Beltsville, MD
| | - G Patterson
- Department of Botany, University of Maryland, 20742, College Park, MD
| | - M J Thompson
- Insect Physiology Laboratory, Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, 20705, Beltsville, MD
| | - H T Slover
- Nutrient Composition Laboratory, Beltsville Human Nutrition Research Center, Science and Education Administration, U.S. Department of Agriculture, 20705, Beltsville, MD
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20
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Amante DJ, Thompson MJ. The promise of telecommunication tools to 'reach' the disengaged patient with diabetes. Curr Opin Endocrinol Diabetes Obes 2016; 23:111-20. [PMID: 26915036 DOI: 10.1097/med.0000000000000240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW To discuss recent research on the use of telecommunication technologies to improve care for disengaged patients with diabetes. RECENT FINDINGS It is established that patients who are disengaged with their healthcare have worse health outcomes. Reasons for disengagement vary but could be because of difficulties accessing or affording care or not possessing the skills or tools required to manage their disease. New patient-facing technologies are being used to improve communication and coordination of care for patients with diabetes. Early results show improvements in health outcomes. Utilizing these technologies to reach patient groups susceptible for disengagement has begun to demonstrate improvement. SUMMARY Research over the past year has continued to demonstrate the promise of using telecommunication tools to assist patients in the management of diabetes. Although a few studies looked specifically at disengaged patients, efforts to utilize appropriate technological interventions targeting specific groups of patients are needed.
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Affiliation(s)
- Daniel J Amante
- aDivision of Health Informatics and Implementation Science, Department of Quantitative Health SciencesbClinical and Population Health Research PhD Program, Graduate School of Biomedical SciencescDiabetes Center of Excellence, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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21
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Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol 2016; 25:1838-55. [PMID: 27112634 PMCID: PMC4849173 DOI: 10.1111/mec.13480] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022]
Abstract
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.
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Affiliation(s)
- Ilana Janowitz Koch
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Michelle M Clark
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48085, USA
| | - Lionel Duarte
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Eskender L McCoy
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert K Wayne
- Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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22
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Hay AD, Downing HE, Brookes ST, Young G, Harnden A, Hollinghurst SP, Kendrick D, Little P, May MT, Moore MV, Orton E, Wang K, Thompson MJ. S87 Are oral steroids effective in treating the symptoms of acute lower respiratory tract infection in non-asthmatic adults? The Oral Steroids for Acute Cough (OSAC) placebo-controlled randomised trial. Thorax 2015. [DOI: 10.1136/thoraxjnl-2015-207770.93] [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: 11/04/2022]
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23
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Merrill RM, Dasmahapatra KK, Davey JW, Dell'Aglio DD, Hanly JJ, Huber B, Jiggins CD, Joron M, Kozak KM, Llaurens V, Martin SH, Montgomery SH, Morris J, Nadeau NJ, Pinharanda AL, Rosser N, Thompson MJ, Vanjari S, Wallbank RWR, Yu Q. The diversification of Heliconius butterflies: what have we learned in 150 years? J Evol Biol 2015; 28:1417-38. [PMID: 26079599 DOI: 10.1111/jeb.12672] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [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: 01/26/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 11/27/2022]
Abstract
Research into Heliconius butterflies has made a significant contribution to evolutionary biology. Here, we review our understanding of the diversification of these butterflies, covering recent advances and a vast foundation of earlier work. Whereas no single group of organisms can be sufficient for understanding life's diversity, after years of intensive study, research into Heliconius has addressed a wide variety of evolutionary questions. We first discuss evidence for widespread gene flow between Heliconius species and what this reveals about the nature of species. We then address the evolution and diversity of warning patterns, both as the target of selection and with respect to their underlying genetic basis. The identification of major genes involved in mimetic shifts, and homology at these loci between distantly related taxa, has revealed a surprising predictability in the genetic basis of evolution. In the final sections, we consider the evolution of warning patterns, and Heliconius diversity more generally, within a broader context of ecological and sexual selection. We consider how different traits and modes of selection can interact and influence the evolution of reproductive isolation.
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Affiliation(s)
- R M Merrill
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - J W Davey
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - D D Dell'Aglio
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - J J Hanly
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - B Huber
- Department of Biology, University of York, York, UK.,Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - C D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - M Joron
- Smithsonian Tropical Research Institute, Panama City, Panama.,Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France.,Centre d'Ecologie Fonctionnelle et Evolutive, CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, Montpellier 5, France
| | - K M Kozak
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - V Llaurens
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - S H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - S H Montgomery
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - J Morris
- Department of Biology, University of York, York, UK
| | - N J Nadeau
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - A L Pinharanda
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - N Rosser
- Department of Biology, University of York, York, UK
| | - M J Thompson
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - S Vanjari
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - R W R Wallbank
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Q Yu
- Department of Zoology, University of Cambridge, Cambridge, UK.,School of Life Sciences, Chongqing University, Shapingba District, Chongqing, China
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Thompson MJ, Rubbi L, Dawson DW, Donahue TR, Pellegrini M. Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes. PLoS One 2015; 10:e0128814. [PMID: 26039411 PMCID: PMC4454596 DOI: 10.1371/journal.pone.0128814] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/30/2015] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is an epigenetic mark associated with regulation of transcription and genome structure. These markers have been investigated in a variety of cancer settings for their utility in differentiating normal tissue from tumor tissue. Here, we examine the direct correlation between DNA methylation and patient survival. We find that changes in the DNA methylation of key pancreatic developmental genes are strongly associated with patient survival.
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Affiliation(s)
- Michael J. Thompson
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Liudmilla Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - David W. Dawson
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Timothy R. Donahue
- Department of Surgery, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, 90095, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, United States of America
- * E-mail:
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25
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Abstract
Objectives The clinical utility of routine cross sectional imaging of the
abdomen and pelvis in the screening and surveillance of patients
with primary soft-tissue sarcoma of the extremities for metastatic
disease is controversial, based on its questionable yield paired
with concerns regarding the risks of radiation exposure, cost, and
morbidity resulting from false positive findings. Methods Through retrospective review of 140 patients of all ages (mean
53 years; 2 to 88) diagnosed with soft-tissue sarcoma of the extremity
with a mean follow-up of 33 months (0 to 291), we sought to determine
the overall incidence of isolated abdominopelvic metastases, their
temporal relationship to chest involvement, the rate of false positives, and
to identify disparate rates of metastases based on sarcoma subtype. Results A total of four patients (2.9%) exhibited isolated abdominopelvic
metastatic disease during the surveillance period. In all cases
of concomitant chest and abdominopelvic disease, chest involvement
preceded abominopelvic involvement. There was a significant false
positive rate requiring invasive workup. Conclusions In the setting of a relative paucity of evidence concerning a
rare disease process and in difference to recently published investigations,
we add a clinical cohort not supportive of routine cross sectional
imaging of the abdomen and pelvis. Cite this article: Bone Joint Res 2015;4:45–9.
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Affiliation(s)
- M J Thompson
- Virginia Commonwealth University Medical Center, P.O. Box 980153, Richmond, Virginia 23298-0153, USA
| | - J Ross
- Virginia Commonwealth University Medical Center, P.O. Box 980153, Richmond, Virginia 23298-0153, USA
| | - G Domson
- Virginia Commonwealth University Medical Center, P.O. Box 980153, Richmond, Virginia 23298-0153, USA
| | - W Foster
- Virginia Commonwealth University Medical Center, P.O. Box 980153, Richmond, Virginia 23298-0153, USA
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McIntosh SW, Wang X, Leamon RJ, Davey AR, Howe R, Krista LD, Malanushenko AV, Markel RS, Cirtain JW, Gurman JB, Pesnell WD, Thompson MJ. DECIPHERING SOLAR MAGNETIC ACTIVITY. I. ON THE RELATIONSHIP BETWEEN THE SUNSPOT CYCLE AND THE EVOLUTION OF SMALL MAGNETIC FEATURES. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/0004-637x/792/1/12] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Robinson HS, Desimone R, Hartway C, Gude JA, Thompson MJ, Mitchell MS, Hebblewhite M. A test of the compensatory mortality hypothesis in mountain lions: A management experiment in West-Central Montana. J Wildl Manage 2014. [DOI: 10.1002/jwmg.726] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hugh S. Robinson
- Panthera; 8 West 40th St. New York NY 10018 USA
- Montana Cooperative Wildlife Research Unit; University of Montana; Missoula MT 59812 USA
| | | | - Cynthia Hartway
- Wildlife Biology Program; College of Forestry and Conservation; University of Montana; Missoula MT 59812 USA
| | | | | | - Michael S. Mitchell
- U.S. Geological Survey; Montana Cooperative Wildlife Research Unit; University of Montana; Missoula MT 59812 USA
| | - Mark Hebblewhite
- Wildlife Biology Program; College of Forestry and Conservation; University of Montana; Missoula MT 59812 USA
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28
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Affiliation(s)
- Michael J. Thompson
- Dept. Political Science; William Paterson University; Raubinger Hall 300 Pompton Road Wayne NJ 07470
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29
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Mitchell MS, Gude JA, Anderson NJ, Ramsey JM, Thompson MJ, Sullivan MG, Edwards VL, Gower CN, Cochrane JF, Irwin ER, Walshe T. Using structured decision making to manage disease risk for Montana wildlife. WILDLIFE SOC B 2012. [DOI: 10.1002/wsb.237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Rabiee A, Galiatsatos P, Salas-Carrillo R, Thompson MJ, Andersen DK, Elahi D. Pancreatic polypeptide administration enhances insulin sensitivity and reduces the insulin requirement of patients on insulin pump therapy. J Diabetes Sci Technol 2011; 5:1521-8. [PMID: 22226275 PMCID: PMC3262724 DOI: 10.1177/193229681100500629] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The effects of pancreatic polypeptide (PP) infusion were examined in patients on insulin pump therapy to determine whether PP administration can reduce insulin requirements in patients with type 1 diabetes mellitus (T1DM) or type 3c diabetes mellitus (T3cDM; pancreatogenic). METHODS Ten subjects with long-standing T1DM (n = 7) or T3cDM (n = 3) on insulin pump treatment received a 72 h subcutaneous infusion of 2 pmol/kg/min bovine PP or saline by portable infusion pump in a single-blinded, randomized, crossover design. RESULTS Pancreatic polypeptide infusion raised plasma PP levels to 450-700 pmol/liter. Daily insulin infusion requirements (I) fell from 48 ± 6.9 to 40 ± 7.5 U on day 2 (p < .05) and from 46 ± 7.7 to 37 ± 6.6 U on day 3 (p < .05) of PP infusion compared with saline. Corrected for average blood glucose concentration (G), I/G fell in 10/10 subjects during the second 24 h period and in 7/10 subjects during the third 24 h period; sensitivity to insulin, calculated as 1/(I/G), increased 45% ± 12% on day 2 (p < .01) and 34% ± 14% on day 3 (p < .05) of PP infusion. Pancreatic polypeptide responses to a test meal were compared with the change in insulin infusion requirements in 5 subjects; the reduction in insulin requirements seen during PP infusion correlated with the degree of baseline PP deficiency (p < .002). CONCLUSIONS A concurrent subcutaneous infusion of PP enhances insulin sensitivity and reduces insulin requirements in patients with long-standing T1DM and T3cDM on insulin pump therapy. The benefit of PP infusion correlated with the degree of PP deficiency.
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Affiliation(s)
- Atoosa Rabiee
- Department of Surgery, Johns Hopkins Bayview Medical Center, Baltimore, Maryland 21224 , USA
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31
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Thompson MJ. Safety through education. Prevention is better than the law. BMJ 2011; 342:d3028. [PMID: 21586464 DOI: 10.1136/bmj.d3028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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32
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Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, Chee M, Roth FP, Giaever G, Nislow C. Quantitative phenotyping via deep barcode sequencing. Genome Res 2009; 19:1836-42. [PMID: 19622793 DOI: 10.1101/gr.093955.109] [Citation(s) in RCA: 219] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.
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Affiliation(s)
- Andrew M Smith
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
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33
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King M, Pearson T, Shultz LD, Leif J, Bottino R, Trucco M, Atkinson MA, Wasserfall C, Herold KC, Woodland RT, Schmidt MR, Woda BA, Thompson MJ, Rossini AA, Greiner DL. A new Hu-PBL model for the study of human islet alloreactivity based on NOD-scid mice bearing a targeted mutation in the IL-2 receptor gamma chain gene. Clin Immunol 2007; 126:303-14. [PMID: 18096436 DOI: 10.1016/j.clim.2007.11.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 11/07/2007] [Accepted: 11/12/2007] [Indexed: 11/25/2022]
Abstract
Immunodeficient NOD-scid mice bearing a targeted mutation in the IL2 receptor common gamma chain (Il2rgamma(null)) readily engraft with human stem cells. Here we analyzed human peripheral blood mononuclear cells (PBMC) for their ability to engraft NOD-scid Il2rgamma(null) mice and established engraftment kinetics, optimal cell dose, and the influence of injection route. Even at low PBMC input, NOD-scid Il2rgamma(null) mice reproducibly support high human PBMC engraftment that plateaus within 3-4 weeks. In contrast to previous stocks of immunodeficient mice, we observed low intra- and inter-donor variability of engraftment. NOD-scid Il2rgamma(null) mice rendered hyperglycemic by streptozotocin treatment return to normoglycemia following transplantation with human islets. Interestingly, these human islet grafts are rejected following injection of HLA-mismatched human PBMC as evidenced by return to hyperglycemia and loss of human C-peptide. These data suggest that humanized NOD-scid Il2rgamma(null) mice may represent an important surrogate for investigating in vivo mechanisms of human islet allograft rejection.
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Affiliation(s)
- Marie King
- Department of Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01655, USA
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34
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Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJW, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 2007; 447:453-7. [PMID: 17468747 DOI: 10.1038/nature05695] [Citation(s) in RCA: 1730] [Impact Index Per Article: 101.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Accepted: 02/19/2007] [Indexed: 12/14/2022]
Abstract
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-beta spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of beta-sheets, with the facing side chains of the two sheets interdigitated in a dry 'steric zipper'. Here we report some 30 other segments from fibril-forming proteins that form amyloid-like fibrils, microcrystals, or usually both. These include segments from the Alzheimer's amyloid-beta and tau proteins, the PrP prion protein, insulin, islet amyloid polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein and beta(2)-microglobulin, suggesting that common structural features are shared by amyloid diseases at the molecular level. Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
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Affiliation(s)
- Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, California 90095-1570, USA
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35
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Abstract
The objectives of this study are (a) to review the current technologies, (b) to examine comparative costing data for six selected representative devices, and (c) to discuss the clinical factors related to selection of devices for intermittent temperature measurement. Financial estimates indicate that mercury-in-glass thermometers are the cheapest devices. Compact electronic and chemical (phase change) thermometers are cheaper alternatives than multi-patient contact thermometers requiring probe covers and infrared sensing models, which are commonly adopted in hospitals and clinical practice. However, time required to obtain readings will influence overall costs. Rigorous independent clinical research studies are now needed to establish which of these alternative technologies are 'fit for purpose'. As a minimum they should offer comparable clinical accuracy and reliability to mercury-in-glass and be suitable for most clinical measurement situations. Furthermore any additional costs should bring demonstrable benefits to the patient, user and healthcare system.
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Affiliation(s)
- D C Crawford
- Medical Physics and Clinical Engineering Directorate, University Hospital of Wales, Cardiff, CF14 4XW, UK.
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36
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Contois JH, Hartigan C, Rao LV, Snyder LM, Thompson MJ. Analytical validation of an HPLC assay for urinary albumin. Clin Chim Acta 2006; 367:150-5. [PMID: 16423336 DOI: 10.1016/j.cca.2005.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Revised: 12/05/2005] [Accepted: 12/05/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND Microalbuminuria is the earliest clinical finding for renal disease. Diabetic individuals often produce modified forms of albumin, perhaps due to impaired lysosomal processing, that are undetectable by common immunoassays but accurately measured by HPLC. METHODS We evaluated the performance of a commercially available, FDA-approved HPLC assay (AusAm Biotechnologies, NY) and compare results to our immunoturbidimetric assay (ITA, Beckman-Coulter, CA) using random urine specimens from 32 nondiabetic and 60 type 1 and 2 diabetic subjects. RESULTS The HPLC assay was linear to 963 mg/l with a limit of detection of 6.1 mg/l. Within-run and between-run precision was <2% and 7-10%, respectively. Unpreserved urine was stable for at least 3 days at room temperature and 10 days at 4 degrees C. In both diabetic and nondiabetic subjects urinary albumin concentrations were higher by HPLC than by ITA, and many more diabetic and nondiabetic individuals were classified as microalbuminuric by HPLC than by ITA. The HPLC assay showed acceptable performance; however, because urinary albumin concentrations are higher in apparently healthy nondiabetic as well as diabetic subjects, different cutpoints will be necessary to accurately differentiate microalbuminuria. CONCLUSIONS Prospective studies are necessary to determine whether the HPLC assay can effectively detect microalbuminuria earlier than current assays without a concomitant increase in the false positive rate.
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Affiliation(s)
- John H Contois
- Department of Hospital Laboratories, UMass Memorial Medical Center, Worcester, MA, USA.
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37
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Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci U S A 2006; 103:4074-8. [PMID: 16537487 PMCID: PMC1449648 DOI: 10.1073/pnas.0511295103] [Citation(s) in RCA: 318] [Impact Index Per Article: 17.7] [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: 01/14/2023] Open
Abstract
Based on the crystal structure of the cross-beta spine formed by the peptide NNQQNY, we have developed a computational approach for identifying those segments of amyloidogenic proteins that themselves can form amyloid-like fibrils. The approach builds on experiments showing that hexapeptides are sufficient for forming amyloid-like fibrils. Each six-residue peptide of a protein of interest is mapped onto an ensemble of templates, or 3D profile, generated from the crystal structure of the peptide NNQQNY by small displacements of one of the two intermeshed beta-sheets relative to the other. The energy of each mapping of a sequence to the profile is evaluated by using ROSETTADESIGN, and the lowest energy match for a given peptide to the template library is taken as the putative prediction. If the energy of the putative prediction is lower than a threshold value, a prediction of fibril formation is made. This method can reach an accuracy of approximately 80% with a P value of approximately 10(-12) when a conservative energy threshold is used to separate peptides that form fibrils from those that do not. We see enrichment for positive predictions in a set of fibril-forming segments of amyloid proteins, and we illustrate the method with applications to proteins of interest in amyloid research.
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Affiliation(s)
- Michael J. Thompson
- *Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and University of California–Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095; and
| | - Stuart A. Sievers
- *Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and University of California–Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095; and
| | - John Karanicolas
- Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Magdalena I. Ivanova
- *Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and University of California–Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095; and
| | - David Baker
- Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - David Eisenberg
- *Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, and University of California–Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095; and
- To whom correspondence should be addressed. E-mail:
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38
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Abstract
Identifying sequence determinants of fibril-forming proteins is crucial for understanding the processes causing >20 proteins to form pathological amyloid depositions. Our approach to identifying which sequences form amyloid-like fibrils is to screen the amyloid-forming proteins human insulin and beta(2)-microglobulin for segments that form fibrils. Our screen is of 60 sequentially overlapping peptides, 59 being six residues in length and 1 being five residues, covering every noncysteine-containing segment in these two proteins. Each peptide was characterized as amyloid-like or nonfibril-forming. Amyloid-like peptides formed fibrils visible in electron micrographs or needle-like microcrystals showing a cross-beta diffraction pattern. Eight of the 60 peptides (three from insulin and five from beta(2)-microglobulin) were identified as amyloid-like. The results of the screen were used to assess the computational method, and good agreement between prediction and experiments was found. This agreement suggests that the pair-of-sheets, zipper spine model on which the computational method is based is at least approximately correct for the structure of the fibrils and suggests the nature of the sequence signal for formation of amyloid-like fibrils.
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Affiliation(s)
- Magdalena I. Ivanova
- Howard Hughes Medical Institute and University of California–Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Michael J. Thompson
- Howard Hughes Medical Institute and University of California–Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - David Eisenberg
- Howard Hughes Medical Institute and University of California–Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
- *To whom correspondence should be addressed. E-mail:
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39
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Abstract
The helioseismic investigation of the solar interior to elucidate the behaviour of the Sun's magnetic field and the interior's role in the solar interior is considered. Such study may be called magnetohelioseismology (from the Greek roots magnetis, helios and seismos).
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Affiliation(s)
- Michael J Thompson
- Department of Applied Mathematics, University of Sheffield, Sheffield S3 7RH, UK.
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40
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di Bernardo D, Thompson MJ, Gardner TS, Chobot SE, Eastwood EL, Wojtovich AP, Elliott SJ, Schaus SE, Collins JJ. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol 2005; 23:377-83. [PMID: 15765094 DOI: 10.1038/nbt1075] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.3] [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: 12/14/2022]
Abstract
A major challenge in drug discovery is to distinguish the molecular targets of a bioactive compound from the hundreds to thousands of additional gene products that respond indirectly to changes in the activity of the targets. Here, we present an integrated computational-experimental approach for computing the likelihood that gene products and associated pathways are targets of a compound. This is achieved by filtering the mRNA expression profile of compound-exposed cells using a reverse-engineered model of the cell's gene regulatory network. We apply the method to a set of 515 whole-genome yeast expression profiles resulting from a variety of treatments (compounds, knockouts and induced expression), and correctly enrich for the known targets and associated pathways in the majority of compounds examined. We demonstrate our approach with PTSB, a growth inhibitory compound with a previously unknown mode of action, by predicting and validating thioredoxin and thioredoxin reductase as its target.
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41
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Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res 2004; 31:7099-109. [PMID: 14654685 PMCID: PMC291866 DOI: 10.1093/nar/gkg924] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [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: 11/12/2022] Open
Abstract
Genome-wide functional linkages among proteins in cellular complexes and metabolic pathways can be inferred from high throughput experimentation, such as DNA microarrays, or from bioinformatic analyses. Here we describe a method for the visualization and interpretation of genome-wide functional linkages inferred by the Rosetta Stone, Phylogenetic Profile, Operon and Conserved Gene Neighbor computational methods. This method involves the construction of a genome-wide functional linkage map, where each significant functional linkage between a pair of proteins is displayed on a two-dimensional scatter-plot, organized according to the order of genes along the chromosome. Subsequent hierarchical clustering of the map reveals clusters of genes with similar functional linkage profiles and facilitates the inference of protein function and the discovery of functionally linked gene clusters throughout the genome. We illustrate this method by applying it to the genome of the pathogenic bacterium Mycobacterium tuberculosis, assigning cellular functions to previously uncharacterized proteins involved in cell wall biosynthesis, signal transduction, chaperone activity, energy metabolism and polysaccharide biosynthesis.
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Affiliation(s)
- Michael Strong
- Howard Hughes Medical Institute, University of California at Los Angeles, Box 951570, Los Angeles, CA 90095-1570, USA
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42
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Abstract
The photoactive yellow protein (PYP) is a bacterial photosensor containing a para-coumaryl thioester chromophore that absorbs blue light, initiating a photocycle involving a series of conformational changes. Here, we present computational studies to resolve uncertainties and controversies concerning the correspondence between atomic structures and spectroscopic measurements on early photocycle intermediates. The initial nanoseconds of the PYP photocycle are examined using time-dependent density functional theory (TDDFT) to calculate the energy profiles for chromophore photoisomerization and proton transfer, and to calculate excitation energies to identify photocycle intermediates. The calculated potential energy surface for photoisomerization matches key, experimentally determined, spectral parameters. The calculated excitation energy of the photocycle intermediate cryogenically trapped in a crystal structure by Genick et al. [Genick, U. K.; Soltis, S. M.; Kuhn, P.; Canestrelli, I. L.; Getzoff, E. D. Nature 1998, 392, 206-209] supports its assignment to the PYP(B) (I(0)) intermediate. Differences between the time-resolved room temperature (298 K) spectrum of the PYP(B) intermediate and its low temperature (77 K) absorbance are attributed to a predominantly deprotonated chromophore in the former and protonated chromophore in the latter. This contrasts with the widely held belief that chromophore protonation does not occur until after the PYP(L) (I(1) or pR) intermediate. The structure of the chromophore in the PYP(L) intermediate is determined computationally and shown to be deprotonated, in agreement with experiment. Calculations based on our PYP(B) and PYP(L) models lead to insights concerning the PYP(BL) intermediate, observed only at low temperature. The results suggest that the proton is more mobile between Glu46 and the chromophore than previously realized. The findings presented here provide an example of the insights that theoretical studies can contribute to a unified analysis of experimental structures and spectra.
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Affiliation(s)
- Michael J Thompson
- Department of Molecular Biology, MB4, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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43
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Thompson MJ, Behranwala A, Campanella C, Walker WS, Cameron EWJ. Immediate and long-term results of mitral prosthetic replacement using a right thoracotomy beating heart technique. Eur J Cardiothorac Surg 2003; 24:47-51; discussion 51. [PMID: 12853044 DOI: 10.1016/s1010-7940(03)00188-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE Repeat median sternotomy is a potentially dangerous technique providing variable but mainly poor access to the mitral valve. Right thoracotomy is an alternative route previously used to access the mitral valve in the early years of cardiac surgery that offers the advantage of a fresh surgical field in the context of redo surgery. We have reviewed our experience with mitral prosthetic replacement undertaken via a right thoracotomy in order to determine the immediate and long-term results obtained with this approach. METHODS The operation was carried out on a beating heart using normothermic bypass without cross-clamping the aorta. Arterial inflow was achieved via the femoral artery or ascending aorta and venous drainage with bi-caval cannulae. Pre-, intra- and postoperative data were documented from case note review. Long-term follow-up was established from the UK Heart Valve Registry, referring Cardiologist, direct patient contact and the Scottish Registry for births and deaths. Statistical analysis was undertaken using a desktop computer package. RESULTS One hundred and twenty-five patients (mean age 63 years) underwent mitral prosthetic replacement by this technique. One hundred and eleven patients (86%) were in NYHA grades III or IV preoperatively. Twenty-two patients (16.6%) had also undergone previous CABG. Thirty-five patients (28%) had undergone two or more sternotomies. Mean bypass time was 83.6 min (SD 43.1). Postoperatively, mean duration of ventilation was 44 h; mean ITU stay was 4 days (SD 5.3) and mean inpatient total stay was 12 days. Thirty-six patients (28.8%) required inotropic support postoperatively. Complication rates were low: pleuro-pulmonary, 30 patients (24%), re-operation for bleeding, four patients (3.2%) and CVA, two patients (1.6%). Eight patients (6.4%) died within 30 days. Ten-year survival figures (Kaplan-Meier) were: 47% for all causes of mortality and 82.9% when only valve related causes of death were considered. Most of the patients (97.5%) had not required re-operation at 10 years. CONCLUSION Mitral prosthetic replacement via a right thoracotomy on beating heart under normothermic bypass offers a safe alternative to redo median sternotomy in this high-risk group. Operative access is facilitated and procedural time reduced. Complication rates are low and perioperative mortality is lower than that generally reported with conventional surgery.
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Affiliation(s)
- M J Thompson
- Department of Cardiothoracic Surgery, Royal Infirmary NHS Trust, 1 Lauriston Place, Edinburgh EH3 9YW, UK
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44
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Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol 2003; 4:R59. [PMID: 12952538 PMCID: PMC193659 DOI: 10.1186/gb-2003-4-9-r59] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2003] [Revised: 07/11/2003] [Accepted: 07/28/2003] [Indexed: 11/23/2022] Open
Abstract
The genome of Mycobacterium tuberculosis was analyzed using recently developed computational approaches to infer protein function and protein linkages. We evaluated and employed a method to infer genes likely to belong to the same operon, as judged by the nucleotide distance between genes in the same genomic orientation, and combined this method with those of the Rosetta Stone, Phylogenetic Profile and conserved Gene Neighbor computational methods for the inference of protein function.
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Affiliation(s)
- Michael Strong
- Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095-1570, USA.
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45
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Holwell SE, Cooper PA, Thompson MJ, Pettit GR, Lippert LW, Martin SW, Bibby MC. Anti-tumor and anti-vascular effects of the novel tubulin-binding agent combretastatin A-1 phosphate. Anticancer Res 2002; 22:3933-40. [PMID: 12553015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The combretastatins are derived from an African medicinal plant Combretum caffrum (Combretaceae). They have previously been shown to be potent inhibitors of microtubule assembly that cause marked haemorrhagic necrosis in murine subcutaneous tumors. Promising clinical trial results with combretastatin A-4 phosphate led to this investigation of the anti-tumor and anti-vascular effects of a close structural analog, combretastatin A-1 phosphate. This compound caused identical disruption of the tubulin cytoskeleton in HUVECs in vitro at similar concentrations and duration of exposure as combretastatin A-4 phosphate. Treatment of a well-vascularised murine colon adenocarcinoma (MAC 29) with an effective dose (150 mg/kg) of combretastatin A-1 phosphate resulted in a dramatic decrease in functional vascular volume 2 hours after administration. Vascular shutdown was complete within 4 hours after treatment apart from in small areas of the tumor periphery. Morphological examination of hepatic deposits of HT29 and DLD-1 human colon tumors in nude mice demonstrated that combretastatin A-1 phosphate displays greater anti-tumor effects than the A-4 analog at the same dose and this order of activity (A-1 > A-4) is mirrored in the subcutaneous site with the same tumor type. In summary, combretastatin A-1 phosphate can exert its anti-tumor action via an anti-vascular mechanism. The results indicate that, despite having similar in vitro anti-tubulin properties, combretastatin A-1 phosphate seems to have greater in vivo anti-tumor activity than combretastatin A-4 phosphate at the same doses and may therefore be more successful in the clinic.
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Affiliation(s)
- S E Holwell
- Cancer Research Unit, University of Bradford, West Yorkshire, BD7 1DP, U.K
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46
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Smith PA, Thompson MJ, Edwards JW. Estimating occupational exposure to the pyrethroid termiticide bifenthrin by measuring metabolites in urine. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 778:113-20. [PMID: 12376119 DOI: 10.1016/s0378-4347(01)00440-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [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: 11/25/2022]
Abstract
The control of subterranean termites in Australia is predominantly through the application of chemical barriers in the soil beneath and surrounding buildings. The chemicals used to repel or kill termites are the organophosphorus insecticide, chlorpyrifos, and the synthetic pyrethroid, bifenthrin. These are applied through surface sprays and subfloor injection by licensed pest control operators. To determine the exposure of these personnel to these pesticides it is most usual to measure airborne concentrations or dermal deposition rates. However, to support information obtained from these methods it is often appropriate to determine the amount of the chemicals absorbed, using biological monitoring techniques including measurement of the chemicals or their metabolites in urine. While there are effective techniques for the monitoring of chlorpyrifos exposure by measuring either the alkyl phosphate or trichloropyridinol metabolites, there have been no published reports of suitable methods to measure bifenthrin metabolites in urine. This paper describes an extraction and HPLC-UV method used to simultaneously measure the urinary excretion of 2-methyl-3-phenylbenzoic acid (MPA), a metabolite of bifenthrin, and 3-phenoxybenzoic acid (PBA), a metabolite of several other common pyrethroid insecticides, with a detection limit for each of 2.5 ng/ml. The paper also describes the pilot application of this method to a study of South Australian pest control operators handling bifenthrin. MPA ranged from 1.8 to 31.9 microg/g creatinine and PBA from 1.3 to 30.0 microg/g in the urine of pest control workers. MPA was detected in urine of control workers without bifenthrin exposure only at low levels (1.0-1.4 microg/g creatinine), but PBA was found in both at higher levels (1.2-61.1 microg/g creatinine).
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Affiliation(s)
- P A Smith
- Department of Environmental Health, School of Medicine, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
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47
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Byers BH, Curran TP, Thompson MJ, Sauer LJ. Reaction of hydrogen chloride with photoproduced base-substituted manganese carbonyl radicals. Organometallics 2002. [DOI: 10.1021/om00075a020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Bands of slower and faster rotation, the so-called torsional oscillations, are observed at the Sun's surface to migrate in latitude over the 11-year solar cycle. Here, we report on the temporal variations of the Sun's internal rotation from solar p-mode frequencies obtained over nearly 6 years by the Michelson Doppler Imager (MDI) instrument on board the Solar and Heliospheric Observatory (SOHO) satellite. The entire solar convective envelope appears to be involved in the torsional oscillations, with phase propagating poleward and equatorward from midlatitudes at all depths throughout the convective envelope.
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Affiliation(s)
- S V Vorontsov
- Astronomy Unit, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
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Salazar GE, Schmitz TL, Cama R, Sheen P, Franchi LM, Centeno G, Valera C, Leyva M, Montenegro-James S, Oberhelman R, Gilman RH, Thompson MJ. Pulmonary tuberculosis in children in a developing country. Pediatrics 2001; 108:448-53. [PMID: 11483814 DOI: 10.1542/peds.108.2.448] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE We evaluated the clinical and epidemiologic characteristics of Peruvian children presenting with pulmonary tuberculosis (PTB) to determine whether features predictive of confirmed PTB could be identified. STUDY DESIGN This was a cross-sectional study of 135 children (mean age: 6.8 years) presenting to the Hospital del Niño in Lima, Peru, with presumptive diagnosis of PTB. Clinical, epidemiologic, and laboratory findings were compared between 3 groups of pediatric patients with a presumptive diagnosis of PTB: those with positive Mycobacterium tuberculosis (MTB) cultures, those likely to have PTB based on clinical criteria but with negative cultures, and those who did not meet clinical diagnostic criteria or have positive cultures. RESULTS A total of 50 (37%) patients were diagnosed with definitive PTB based on positive sputum culture. Another 55 (47%) patients were classified as having probable PTB based on meeting at least 2 of the following criteria: cough lasting for at least 2 weeks, typical chest radiograph changes, purified protein derivative (PPD) >/=10 mm, or history of tuberculosis family contact. Patients with definitive or probable PTB were significantly older than patients without clinical PTB, and those with symptomatic disease were significantly older than those with asymptomatic disease. Patients with PTB diagnosed by culture were significantly more likely than those diagnosed using clinical criteria to have cough lasting >/=2 weeks, fever, and a PPD >/=10 mm. CONCLUSIONS The typical presentation of PTB in Peruvian children includes symptoms of active pulmonary disease similar to those seen in adults. This presentation differs significantly from that reported in developed countries, where many children have minimal or no symptoms at the time of presentation. The diagnostic criteria for pediatric PTB must be modified in hyperendemic developing country environments where features may differ from those described in the United States. The triad of cough lasting >/=2 weeks, fever, and a PPD >/=10 mm was highly predictive for culture-positive PTB among children in this low-income Peruvian population.
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Affiliation(s)
- G E Salazar
- University of Illinois at Chicago, Department of Pediatrics, Chicago, Illinois, USA
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Thompson MJ, Rivara FP. Bicycle-related injuries. Am Fam Physician 2001; 63:2007-14. [PMID: 11388717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Bicycle riding is a popular form of recreation among persons of all ages, and related injuries cause significant morbidity and mortality. Most injuries occur in males and are associated with riding at high speed; most serious injuries and fatalities result from collisions with motor vehicles. Although superficial soft tissue injuries and musculoskeletal trauma are the most common injuries, head injuries are responsible for most fatalities and long-term disabilities. Overuse injuries may contribute to a variety of musculoskeletal complaints, compression neuropathies, perineal and genital complaints. Physicians treating such patients should consider medical factors, as well as suggest adjusting various components of the bicycle, such as the seat height and handlebars. Encouraging bicycle riders to wear helmets is key to preventing injuries; protective clothing and equipment, and general safety advice also may offer some protection.
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Affiliation(s)
- M J Thompson
- Department of Family Medicine, University of Washington School of Medicine, Seattle 98195-4696, USA.
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