An epigenetic aging clock for dogs and wolves

Aging - Tập 9 Số 3 - Trang 1055-1068 - 2017
Michael J. Thompson1, Bridgett M. vonHoldt2, Steve Horvath3, Matteo Pellegrini4
1Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
2Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544 USA
3Department of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
4Joint first or last authors

Tóm tắt

Từ khóa


Tài liệu tham khảo

Spector, 2010, Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains., Genome Res, 2, 434, 10.1101/gr.103101.109

Marth, 2010, Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer., Genome Res, 2, 440, 10.1101/gr.103606.109

Ophoff, 2012, Aging effects on DNA methylation modules in human brain and blood tissue., Genome Biol, 1, R97, 10.1186/gb-2012-13-10-r97

Lipska, 2012, DNA methylation signatures in development and aging of the human prefrontal cortex., Am J Hum Genet, 9, 260, 10.1016/j.ajhg.2011.12.020

Warren, 2012, Age-associated DNA methylation in pediatric populations., Genome Res, 2, 623, 10.1101/gr.125187.111

Gyllensten, 2013, Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan., PLoS One, 8, e67378, 10.1371/journal.pone.0067378

Beck, 2013, Age-associated epigenetic drift: implications, and a case of epigenetic thrift?, Hum Mol Genet, 2, R7, 10.1093/hmg/ddt375

Pfeifer, 2015, Aging and DNA methylation., BMC Biol, 1, 7, 10.1186/s12915-015-0118-4

Teschendorff, 2016, Epigenetic drift, epigenetic clocks and cancer risk., Epigenomics, 8, 705, 10.2217/epi-2015-0017

Bergman, 2012, Programming of DNA methylation patterns., Annu Rev Biochem, 8, 97, 10.1146/annurev-biochem-052610-091920

Rohlf, 2012, Is adult stem cell aging driven by conflicting modes of chromatin remodeling?, BioEssays, 3, 841, 10.1002/bies.201100190

Galle, 2014, Understanding epigenetic changes in aging stem cells--a computational model approach., Aging Cell, 1, 320, 10.1111/acel.12177

Rossi, 2013, Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging., Cell Stem Cell, 1, 413, 10.1016/j.stem.2013.01.017

Rossi, 2014, Epigenetic regulation of hematopoietic stem cell aging., Exp Cell Res, 32, 192, 10.1016/j.yexcr.2014.09.013

Vilain, 2011, Epigenetic predictor of age., PLoS One, 6, e14821, 10.1371/journal.pone.0014821

Rajapakse, 2013, Genome-wide methylation profiles reveal quantitative views of human aging rates., Mol Cell, 4, 359, 10.1016/j.molcel.2012.10.016

Horvath, 2013, DNA methylation age of human tissues and cell types., Genome Biol, 1, R115, 10.1186/gb-2013-14-10-r115

Wagner, 2016, DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy., Aging (Albany NY), 8, 394, 10.18632/aging.100908

Gibbs, 2014, Biomarkers and ageing: the clock-watcher., Nature, 50, 168, 10.1038/508168a

Brunet, 2015, Epigenetic regulation of ageing: linking environmental inputs to genomic stability., Nat Rev Mol Cell Biol, 1, 593, 10.1038/nrm4048

Murphy, 2015, DNA methylation age of blood predicts all-cause mortality in later life., Genome Biol, 1, 25, 10.1186/s13059-015-0584-6

Christensen, 2015, DNA methylation age is associated with mortality in a longitudinal Danish twin study., Aging Cell

Brenner, 2016, Epigenetic age acceleration predicts cancer, cardiovascular, and all-cause mortality in a German case cohort., Clin Epigenetics, 8, 64, 10.1186/s13148-016-0228-z

Studenski, 2016, DNA methylation-based measures of biological age: meta-analysis predicting time to death., Aging (Albany NY), 8, 1844, 10.18632/aging.101020

Giuliani, 2015, Decreased epigenetic age of PBMCs from Italian semi-supercentenarians and their offspring., Aging (Albany NY), 7, 1159, 10.18632/aging.100861

Horvath, 2015, DNA methylation age of blood predicts future onset of lung cancer in the women’s health initiative., Aging (Albany NY), 7, 690, 10.18632/aging.100809

Murphy, 2015, The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936., Int J Epidemiol, 4, 1388, 10.1093/ije/dyu277

Horvath, 2015, Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer’s disease related cognitive functioning., Aging (Albany NY), 7, 1198, 10.18632/aging.100864

Coles, 2015, The cerebellum ages slowly according to the epigenetic clock., Aging (Albany NY), 7, 294, 10.18632/aging.100742

Franceschi, 2015, Accelerated epigenetic aging in Down syndrome., Aging Cell, 1, 491, 10.1111/acel.12325

Levine, 2015, HIV-1 infection accelerates age according to the epigenetic clock., J Infect Dis, 21, 1563, 10.1093/infdis/jiv277

Vinters, 2016, Huntington’s disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels., Aging (Albany NY), 8, 1485, 10.18632/aging.101005

Sipos, 2014, Obesity accelerates epigenetic aging of human liver., Proc Natl Acad Sci USA, 11, 15538, 10.1073/pnas.1412759111

Wong, 2016, Menopause accelerates biological aging., Proc Natl Acad Sci USA, 11, 9327, 10.1073/pnas.1604558113

Gonzalez, 2016, Specific increase of methylation age in osteoarthritis cartilage., Osteoarthritis Cartilage, 2, S63, 10.1016/j.joca.2016.01.140

Ritz, 2015, Increased epigenetic age and granulocyte counts in the blood of Parkinson’s disease patients., Aging (Albany NY), 7, 1130, 10.18632/aging.100859

Boyko, 2011, The domestic dog: man’s best friend in the genomic era., Genome Biol, 1, 216, 10.1186/gb-2011-12-2-216

Promislow, 2016, The dog aging project: translational geroscience in companion animals., Mamm Genome, 2, 279, 10.1007/s00335-016-9638-7

Ostrander, 2013, A copy number variant at the KITLG locus likely confers risk for canine squamous cell carcinoma of the digit., PLoS Genet, 9, e1003409, 10.1371/journal.pgen.1003409

Ostrander, 2015, Homologous Mutation to Human BRAF V600E Is Common in Naturally Occurring Canine Bladder Cancer--Evidence for a Relevant Model System and Urine-Based Diagnostic Test., Mol Cancer Res, 1, 993, 10.1158/1541-7786.MCR-14-0689

Bronson, 1982, Variation in age at death of dogs of different sexes and breeds., Am J Vet Res, 4, 2057

Brodbelt, 2013, Longevity and mortality of owned dogs in England., Vet J, 19, 638, 10.1016/j.tvjl.2013.09.020

Speakman, 2005, Body size, energy metabolism and lifespan., J Exp Biol, 20, 1717, 10.1242/jeb.01556

Wolf, 1996, Cellular proliferative capacity and life span in small and large dogs., J Gerontol A Biol Sci Med Sci, 5, B403, 10.1093/gerona/51A.6.B403

Mech, 1998, Evaluation of age determination techniques for gray wolves., J Wildl Manage, 6, 674, 10.2307/3802343

Mech, 2002, Accuracy and precision of estimating age of gray wolves by tooth wear., J Wildl Manage, 6, 752, 10.2307/3802745

LD M. (2006). Estimated age structure of wolves in northeastern Minnesota. (USGS Northern Prairie Wildlife Research Center.

Mech, 1976, Reproductive activity in nine- and ten-month-old wolves., J Mammal, 5, 406, 10.2307/1379708

Mech, 1991, Dispersal of wolves () in northeastern Minnesota., Can J Zool, 6, 2946, 10.1139/z91-415

Stahler, 2016, pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grew wolves., Mol Ecol, 2, 1838, 10.1111/mec.13480

Wayne, 2005, The canine genome., Genome Res, 1, 1706, 10.1101/gr.3736605

Ostrander, 2010, Man’s best friend becomes biology’s best in show: genome analyses in the domestic dog., Annu Rev Genet, 4, 309, 10.1146/annurev-genet-102808-115200

Ostrander, 2014, Insights into morphology and disease from the dog genome project., Annu Rev Cell Dev Biol, 3, 535, 10.1146/annurev-cellbio-100913-012927

Palmiter, 1988, Expression of insulin-like growth factor I in transgenic mice with elevated levels of growth hormone is correlated with growth., Endocrinology, 12, 433, 10.1210/endo-123-1-433

Bartke, 2005, Minireview: role of the growth hormone/insulin-like growth factor system in mammalian aging., Endocrinology, 14, 3718, 10.1210/en.2005-0411

Stewart, 1993, IGF-I is required for normal embryonic growth in mice., Genes Dev, 7, 2609, 10.1101/gad.7.12b.2609

Reynolds, 2010, A simple genetic architecture underlies morphological variation in dogs., PLoS Biol, 8, e1000451, 10.1371/journal.pbio.1000451

Parker, 2007, A single IGF1 allele is a major determinant of small size in dogs., Science, 31, 112, 10.1126/science.1137045

Pellegrini, 2015, Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes., PLoS One, 1, e0128814, 10.1371/journal.pone.0128814

Benjamini Y, and Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing.J R Stat Soc Ser B Methodological. 1995; 57:289-300.

Li, 2016, An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease., Genome Biol, 1, 171, 10.1186/s13059-016-1030-0

Horvath, 2016, Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum., Nat Commun, 7, 10561, 10.1038/ncomms10561

Quach A, Levine ME, Tanaka T, Lu AT, Chen BH, Ferrucci L, Ritz B, Bandinelli S, Neuhouser ML, Beasley JM, Snetselaar L, Wallace RB, Tsao PS, et al. Epigenetic clock analysis of diet, exercise, education, and lifestyle factors. Aging (Albany NY). 2017. 14;9(2):419-446.

Pearson, 1934, E.S. The use of confidence or fiducial limits illustrated in the case of the binomial., Biometrika, 2, 404, 10.1093/biomet/26.4.404

Tibshirani, 2010, Spectral Regularization Algorithms for Learning Large Incomplete Matrices., J Mach Learn Res, 1, 2287

Tibshirani, 2010, Regularization Paths for Generalized Linear Models via Coordinate Descent., J Stat Softw, 3, 1, 10.18637/jss.v033.i01

Haussler, 2002, The human genome browser at UCSC., Genome Res, 1, 996, 10.1101/gr.229102

Bejerano, 2010, GREAT improves functional interpretation of cis-regulatory regions., Nat Biotechnol, 2, 495, 10.1038/nbt.1630

Mesirov, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles., Proc Natl Acad Sci USA, 10, 15545, 10.1073/pnas.0506580102

Weinberg, 2008, An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors., Nat Genet, 4, 499, 10.1038/ng.127