Literature DB >> 32619550

Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome.

Tina Wang1, Jianzhu Ma1, Andrew N Hogan2, Samson Fong3, Katherine Licon1, Brian Tsui1, Jason F Kreisberg1, Peter D Adams4, Anne-Ruxandra Carvunis5, Danika L Bannasch6, Elaine A Ostrander2, Trey Ideker7.   

Abstract

All mammals progress through similar physiological stages throughout life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects underlying genomic events is unclear. Here, we map the common methylation changes experienced by mammalian genomes as they age, focusing on comparison of humans with dogs, an emerging model of aging. Using oligo-capture sequencing, we characterize methylomes of 104 Labrador retrievers spanning a 16-year age range, achieving >150× coverage within mammalian syntenic blocks. Comparison with human methylomes reveals a nonlinear relationship that translates dog-to-human years and aligns the timing of major physiological milestones between the two species, with extension to mice. Conserved changes center on developmental gene networks, which are sufficient to translate age and the effects of anti-aging interventions across multiple mammals. These results establish methylation not only as a diagnostic age readout but also as a cross-species translator of physiological aging milestones.
Copyright © 2020 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  aging; canine; dog; epigenetic aging; epigenetic clock; epigenetics; epigenome; evolution; methylation; methylome

Year:  2020        PMID: 32619550      PMCID: PMC7484147          DOI: 10.1016/j.cels.2020.06.006

Source DB:  PubMed          Journal:  Cell Syst        ISSN: 2405-4712            Impact factor:   10.304


  51 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

Authors:  Albert J Vilella; Jessica Severin; Abel Ureta-Vidal; Li Heng; Richard Durbin; Ewan Birney
Journal:  Genome Res       Date:  2008-11-24       Impact factor: 9.043

3.  Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map.

Authors:  Daniele Merico; Ruth Isserlin; Gary D Bader
Journal:  Methods Mol Biol       Date:  2011

Review 4.  Tools and Strategies for Analysis of Genome-Wide and Gene-Specific DNA Methylation Patterns.

Authors:  Aniruddha Chatterjee; Euan J Rodger; Ian M Morison; Michael R Eccles; Peter A Stockwell
Journal:  Methods Mol Biol       Date:  2017

5.  Mortality in north american dogs from 1984 to 2004: an investigation into age-, size-, and breed-related causes of death.

Authors:  J M Fleming; K E Creevy; D E L Promislow
Journal:  J Vet Intern Med       Date:  2011-02-25       Impact factor: 3.333

Review 6.  The dog aging project: translational geroscience in companion animals.

Authors:  Matt Kaeberlein; Kate E Creevy; Daniel E L Promislow
Journal:  Mamm Genome       Date:  2016-05-03       Impact factor: 2.957

7.  Genome-wide methylation profiles reveal quantitative views of human aging rates.

Authors:  Gregory Hannum; Justin Guinney; Ling Zhao; Li Zhang; Guy Hughes; SriniVas Sadda; Brandy Klotzle; Marina Bibikova; Jian-Bing Fan; Yuan Gao; Rob Deconde; Menzies Chen; Indika Rajapakse; Stephen Friend; Trey Ideker; Kang Zhang
Journal:  Mol Cell       Date:  2012-11-21       Impact factor: 17.970

8.  The UCSC Genome Browser database: 2015 update.

Authors:  Kate R Rosenbloom; Joel Armstrong; Galt P Barber; Jonathan Casper; Hiram Clawson; Mark Diekhans; Timothy R Dreszer; Pauline A Fujita; Luvina Guruvadoo; Maximilian Haeussler; Rachel A Harte; Steve Heitner; Glenn Hickey; Angie S Hinrichs; Robert Hubley; Donna Karolchik; Katrina Learned; Brian T Lee; Chin H Li; Karen H Miga; Ngan Nguyen; Benedict Paten; Brian J Raney; Arian F A Smit; Matthew L Speir; Ann S Zweig; David Haussler; Robert M Kuhn; W James Kent
Journal:  Nucleic Acids Res       Date:  2014-11-26       Impact factor: 19.160

9.  DNA methylation age of human tissues and cell types.

Authors:  Steve Horvath
Journal:  Genome Biol       Date:  2013       Impact factor: 13.583

10.  LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.

Authors:  Nathan C Sheffield; Christoph Bock
Journal:  Bioinformatics       Date:  2015-10-27       Impact factor: 6.937

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  21 in total

1.  Plasma Neurofilament Light Chain as a Translational Biomarker of Aging and Neurodegeneration in Dogs.

Authors:  Wojciech K Panek; Margaret E Gruen; David M Murdoch; Robert D Marek; Alexandra F Stachel; Freya M Mowat; Korinn E Saker; Natasha J Olby
Journal:  Mol Neurobiol       Date:  2020-05-30       Impact factor: 5.590

2.  The effects of age, sex, weight, and breed on canid methylomes.

Authors:  Liudmilla Rubbi; Haoxuan Zhang; Junxi Feng; Christopher He; Patrick Kurnia; Prashansa Ratan; Aakash Tammana; Sabina House; Michael Thompson; Colin Farrell; Sagi Snir; Daniel Stahler; Elaine A Ostrander; Bridgett M vonHoldt; Matteo Pellegrini
Journal:  Epigenetics       Date:  2022-05-03       Impact factor: 4.861

3.  Modified formulas for calculation of encephalization: quotient in dogs.

Authors:  Saganuwan Alhaji Saganuwan
Journal:  BMC Res Notes       Date:  2021-06-03

4.  How Old Is My Dog? Identification of Rational Age Groupings in Pet Dogs Based Upon Normative Age-Linked Processes.

Authors:  Naomi D Harvey
Journal:  Front Vet Sci       Date:  2021-04-27

Review 5.  Dog Models of Aging.

Authors:  Audrey Ruple; Evan MacLean; Noah Snyder-Mackler; Kate E Creevy; Daniel Promislow
Journal:  Annu Rev Anim Biosci       Date:  2021-10-26       Impact factor: 8.923

6.  DNA methylation as a tool to explore ageing in wild roe deer populations.

Authors:  Jean-François Lemaître; Benjamin Rey; Jean-Michel Gaillard; Corinne Régis; Emmanuelle Gilot-Fromont; François Débias; Jeanne Duhayer; Sylvia Pardonnet; Maryline Pellerin; Amin Haghani; Joseph A Zoller; Caesar Z Li; Steve Horvath
Journal:  Mol Ecol Resour       Date:  2021-10-30       Impact factor: 8.678

7.  DNA methylation predicts age and provides insight into exceptional longevity of bats.

Authors:  Gerald S Wilkinson; Steve Horvath; Danielle M Adams; Amin Haghani; Ake T Lu; Joseph Zoller; Charles E Breeze; Bryan D Arnold; Hope C Ball; Gerald G Carter; Lisa Noelle Cooper; Dina K N Dechmann; Paolo Devanna; Nicolas J Fasel; Alexander V Galazyuk; Linus Günther; Edward Hurme; Gareth Jones; Mirjam Knörnschild; Ella Z Lattenkamp; Caesar Z Li; Frieder Mayer; Josephine A Reinhardt; Rodrigo A Medellin; Martina Nagy; Brian Pope; Megan L Power; Roger D Ransome; Emma C Teeling; Sonja C Vernes; Daniel Zamora-Mejías; Joshua Zhang; Paul A Faure; Lucas J Greville; L Gerardo Herrera M; José J Flores-Martínez
Journal:  Nat Commun       Date:  2021-03-12       Impact factor: 17.694

Review 8.  Epigenetic age prediction.

Authors:  Daniel J Simpson; Tamir Chandra
Journal:  Aging Cell       Date:  2021-08-20       Impact factor: 9.304

9.  Histone acetylation at the sulfotransferase 1a1 gene is associated with its hepatic expression in normal aging.

Authors:  Mohamad M Kronfol; Sara Abudahab; Mikhail G Dozmorov; Fay M Jahr; Matthew S Halquist; MaryPeace McRae; Dayanjan S Wijesinghe; Elvin T Price; Patricia W Slattum; Joseph L McClay
Journal:  Pharmacogenet Genomics       Date:  2021-12-01       Impact factor: 2.089

Review 10.  Cross-species comparisons and in vitro models to study tempo in development and homeostasis.

Authors:  Teresa Rayon; James Briscoe
Journal:  Interface Focus       Date:  2021-04-16       Impact factor: 3.906

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