2,245
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Interethnic DNA Methylation Difference and Its Implications in Pharmacoepigenetics

&
Pages 1437-1454 | Received 24 Mar 2017, Accepted 04 Jul 2017, Published online: 08 Sep 2017

References

  • Portela A , EstellerM . Epigenetic modifications and human disease . Nat. Biotechnol.28 ( 10 ), 1057 – 1068 ( 2010 ).
  • Weber M , SchubelerD . Genomic patterns of DNA methylation: targets and function of an epigenetic mark . Curr. Opin. Cell Biol.19 ( 3 ), 273 – 280 ( 2007 ).
  • Lister R , PelizzolaM , DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences . Nature462 ( 7271 ), 315 – 322 ( 2009 ).
  • Jones PA . Functions of DNA methylation: islands, start sites, gene bodies and beyond . Nat. Rev. Genet.13 ( 7 ), 484 – 492 ( 2012 ).
  • Lechner M , BoshoffC , BeckS . Cancer epigenome . Adv. Genet.70 , 247 – 276 ( 2010 ).
  • Gomez A , Ingelman-SundbergM . Pharmacoepigenetics: its role in interindividual differences in drug response . Clin. Pharmacol. Ther.85 ( 4 ), 426 – 430 ( 2009 ).
  • Heyn H , EstellerM . DNA methylation profiling in the clinic: applications and challenges . Nat. Rev. Genet.13 ( 10 ), 679 – 692 ( 2012 ).
  • Winter S , FiselP , ButtnerFet al. Methylomes of renal cell lines and tumors or metastases differ significantly with impact on pharmacogenes . Sci. Rep.6 , 29930 ( 2016 ).
  • Esteller M , Garcia-FoncillasJ , AndionEet al. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents . N. Engl. J. Med.343 ( 19 ), 1350 – 1354 ( 2000 ).
  • Wiencke JK . Impact of race/ethnicity on molecular pathways in human cancer . Nat. Rev. Cancer4 ( 1 ), 79 – 84 ( 2004 ).
  • Kurian AK , CardarelliKM . Racial and ethnic differences in cardiovascular disease risk factors: a systematic review . Ethn. Dis.17 ( 1 ), 143 – 152 ( 2007 ).
  • Caprio S , DanielsSR , DrewnowskiAet al. Influence of race, ethnicity, and culture on childhood obesity: implications for prevention and treatment: a consensus statement of Shaping America’s Health and the Obesity Society . Diabetes Care31 ( 11 ), 2211 – 2221 ( 2008 ).
  • Chung WH , HungSI , HongHSet al. Medical genetics: a marker for Stevens–Johnson syndrome . Nature428 ( 6982 ), 486 ( 2004 ).
  • Maisano Delser P , FuselliS . Human loci involved in drug biotransformation: worldwide genetic variation, population structure, and pharmacogenetic implications . Hum. Genet.132 ( 5 ), 563 – 577 ( 2013 ).
  • Ramos E , DoumateyA , ElkahlounAGet al. Pharmacogenomics, ancestry and clinical decision-making for global populations . Pharmacogenomics J.14 ( 3 ), 217 – 222 ( 2014 ).
  • Fraser HB , LamLL , NeumannSM , KoborMS . Population-specificity of human DNA methylation . Genome Biol.13 ( 2 ), R8 ( 2012 ).
  • Moen EL , ZhangX , MuWet al. Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits . Genetics194 ( 4 ), 987 – 996 ( 2013 ).
  • Xia YY , DingYB , LiuXQet al. Racial/ethnic disparities in human DNA methylation . Biochim. Biophys. Acta1846 ( 1 ), 258 – 262 ( 2014 ).
  • Conway K , EdmistonSN , TseCKet al. Racial variation in breast tumor promoter methylation in the Carolina Breast Cancer Study . Cancer Epidemiol. Biomarkers Prev.24 ( 6 ), 921 – 930 ( 2015 ).
  • Lokk K , ModhukurV , RajashekarBet al. DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns . Genome Biol.15 ( 4 ), r54 ( 2014 ).
  • Cancer Genome Atlas N . Comprehensive molecular characterization of human colon and rectal cancer . Nature487 ( 7407 ), 330 – 337 ( 2012 ).
  • Cancer Genome Atlas N . Comprehensive molecular portraits of human breast tumours . Nature490 ( 7418 ), 61 – 70 ( 2012 ).
  • Cancer Genome Atlas Research Network , KandothC , SchultzNet al.Integrated genomic characterization of endometrial carcinoma . Nature497 ( 7447 ), 67 – 73 ( 2013 ).
  • Cancer Genome Atlas N . Comprehensive genomic characterization of head and neck squamous cell carcinomas . Nature517 ( 7536 ), 576 – 582 ( 2015 ).
  • Dedeurwaerder S , DefranceM , CalonneE , DenisH , SotiriouC , FuksF . Evaluation of the infinium methylation 450K technology . Epigenomics3 ( 6 ), 771 – 784 ( 2011 ).
  • Sandoval J , HeynH , MoranSet al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome . Epigenetics6 ( 6 ), 692 – 702 ( 2011 ).
  • Wang K , SinghD , ZengZet al. MapSplice: accurate mapping of RNA-seq reads for splice junction discovery . Nucleic Acids Res.38 ( 18 ), e178 ( 2010 ).
  • UNC Bioinformatics Utilities . https://github.com/mozack/ubu .
  • Li B , DeweyCN . RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome . BMC Bioinformatics12 , 323 ( 2011 ).
  • Lappalainen T , SammethM , FriedlanderMRet al. Transcriptome and genome sequencing uncovers functional variation in humans . Nature501 ( 7468 ), 506 – 511 ( 2013 ).
  • T Hoen PA , FriedlanderMR , AlmlofJet al. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories . Nat. Biotechnol.31 ( 11 ), 1015 – 1022 ( 2013 ).
  • Marco-Sola S , SammethM , GuigoR , RibecaP . The GEM mapper: fast, accurate and versatile alignment by filtration . Nat. Methods9 ( 12 ), 1185 – 1188 ( 2012 ).
  • Griebel T , ZacherB , RibecaPet al. Modelling and simulating generic RNA-Seq experiments with the flux simulator . Nucleic Acids Res.40 ( 20 ), 10073 – 10083 ( 2012 ).
  • Teschendorff AE , MarabitaF , LechnerMet al. A beta-mixture quantile normalization method for correcting probe design bias in illumina infinium 450 k DNA methylation data . Bioinformatics29 ( 2 ), 189 – 196 ( 2013 ).
  • Johnson WE , LiC , RabinovicA . Adjusting batch effects in microarray expression data using empirical Bayes’ methods . Biostatistics8 ( 1 ), 118 – 127 ( 2007 ).
  • Leek JT , StoreyJD . Capturing heterogeneity in gene expression studies by surrogate variable analysis . PLoS Genetics3 ( 9 ), 1724 – 1735 ( 2007 ).
  • Du P , ZhangX , HuangCCet al. Comparison of beta-value and M-value methods for quantifying methylation levels by microarray analysis . BMC Bioinformatics11 , 587 ( 2010 ).
  • Miller RG . Simultaneous Statistical Inference (2nd Edition) . Springer-Verlag , NY, USA ( 1981 ).
  • Hartmann O , SpyratosF , HarbeckNet al. DNA methylation markers predict outcome in node-positive, estrogen receptor-positive breast cancer with adjuvant anthracycline-based chemotherapy . Clin. Cancer Res.15 ( 1 ), 315 – 323 ( 2009 ).
  • Veeck J , RoperoS , SetienFet al. BRCA1 CpG island hypermethylation predicts sensitivity to poly(adenosine diphosphate)-ribose polymerase inhibitors . J. Clin. Oncol.28 ( 29 ), e563 – e564 ; author reply e565–e566 ( 2010 ).
  • Wright JL , ReisIM , ZhaoWet al. Racial disparity in estrogen receptor positive breast cancer patients receiving trimodality therapy . Breast21 ( 3 ), 276 – 283 ( 2012 ).
  • Tichy JR , DealAM , AndersCK , Reeder-HayesK , CareyLA . Race, response to chemotherapy and outcome within clinical breast cancer subtypes . Breast Cancer Res. Treat150 ( 3 ), 667 – 674 ( 2015 ).
  • Mihaly Z , KormosM , LanczkyAet al. A meta-analysis of gene expression-based biomarkers predicting outcome after tamoxifen treatment in breast cancer . Breast Cancer Res. Tr.140 ( 2 ), 219 – 232 ( 2013 ).
  • Eltayeb AE , DemasDM , ClarkeR , Shajahan-HaqAN . The unfolded protein response may contribute to racial disparity in endocrine responsiveness in breast cancer . Cancer Res.1 ( 3 ), 640 – 644 ( 2015 ).
  • Dombroski BA , NayakRR , EwensKG , AnkenerW , CheungVG , SpielmanRS . Gene expression and genetic variation in response to endoplasmic reticulum stress in human cells . Am. J. Hum. Genet.86 ( 5 ), 719 – 729 ( 2010 ).
  • Li Q , SuZ , XuXet al. AS1DHRS4, a head-to-head natural antisense transcript, silences the DHRS4 gene cluster in cis and trans . Proc. Natl Acad. Sci. USA109 ( 35 ), 14110 – 14115 ( 2012 ).
  • Korkola JE , BlaveriE , DevriesSet al. Identification of a robust gene signature that predicts breast cancer outcome in independent data sets . BMC Cancer7 , 61 ( 2007 ).
  • Subramanian A , TamayoP , MoothaVKet al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles . Proc. Natl Acad. Sci. USA102 ( 43 ), 15545 – 15550 ( 2005 ).
  • Schlattner U , Tokarska-SchlattnerM , WallimannT . Mitochondrial creatine kinase in human health and disease . BBA Mol. Basis Dis.1762 ( 2 ), 164 – 180 ( 2006 ).
  • Brewster LM , CoronelCMD , SluiterW , ClarkJF , Van MontfransGA . Ethnic differences in tissue creatine kinase activity: an observational study . PLoS ONE7 ( 3 ), e32471 ( 2012 ).
  • Danforth DN . Disparities in breast cancer outcomes between Caucasian and African American women: a model for describing the relationship of biological and nonbiological factors . Breast Cancer Res.15 ( 3 ), 208 ( 2013 ).
  • Grafodatskaya D , ChoufaniS , FerreiraJCet al. EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines . Genomics95 ( 2 ), 73 – 83 ( 2010 ).
  • Caliskan M , CusanovichDA , OberC , GiladY . The effects of EBV transformation on gene expression levels and methylation profiles . Hum. Mol. Genet.20 ( 8 ), 1643 – 1652 ( 2011 ).
  • Heyn H , MoranS , Hernando-HerraezIet al. DNA methylation contributes to natural human variation . Genome Res.23 ( 9 ), 1363 – 1372 ( 2013 ).
  • Yi X , HongM , GuiBet al. RNA Processing and modification protein, carbon catabolite Repression 4 (Ccr4), arrests the cell cycle through p21-dependent and p53-independent pathway . J. Biol. Chem.287 ( 25 ), 21045 – 21057 ( 2012 ).
  • Wilkinson S , PatersonHF , MarshallCJ . Cdc42-MRCK and Rho-ROCK signalling cooperate in myosin phosphorylation and cell invasion . Nat. Cell Biol.7 ( 3 ), U255 – U245 ( 2005 ).
  • Liu YJ , WangF , LiuYSet al. RNF135, RING finger protein, promotes the proliferation of human glioblastoma cells in vivo and in vitro via the ERK pathway . Sci. Rep.6 , 20642 ( 2016 ).
  • Li M , ZhangYQ , LiuZJet al. Aberrant expression of zinc transporter ZIP4 (SLC39A4) significantly contributes to human pancreatic cancer pathogenesis and progression . Proc. Natl Acad. Sci. USA104 ( 47 ), 18636 – 18641 ( 2007 ).
  • Lapenna S , GiordanoA . Cell cycle kinases as therapeutic targets for cancer . Nat. Rev. Drug Discov.8 ( 7 ), 547 – 566 ( 2009 ).
  • Malumbres M , BarbacidM . Cell cycle, CDKs and cancer: a changing paradigm . Nat. Rev. Cancer9 ( 3 ), 153 – 166 ( 2009 ).
  • Wilkinson S , CroftDR , O’preyJet al. The cyclin-dependent kinase PITSLRE/CDK11 is required for successful autophagy . Autophagy7 ( 11 ), 1295 – 1301 ( 2011 ).
  • Murase D , HachiyaA , TakanoKet al. Autophagy has a significant role in determining skin color by regulating melanosome degradation in keratinocytes . J. Invest. Dermatol.133 ( 10 ), 2416 – 2424 ( 2013 ).
  • Zhang X , MoenEL , LiuCet al. Linking the genetic architecture of cytosine modifications with human complex traits . Hum. Mol. Genet.23 ( 22 ), 5893 – 5905 ( 2014 ).
  • Barrow TM , MichelsKB . Epigenetic epidemiology of cancer . Biochem. Biophys. Res. Commun.455 ( 1–2 ), 70 – 83 ( 2014 ).
  • Suzuki H , YamamotoE , MaruyamaR , NiinumaT , KaiM . Biological significance of the CpG island methylator phenotype . Biochem. Biophys. Res. Commun.455 ( 1–2 ), 35 – 42 ( 2014 ).
  • Weisenberger DJ , LevineAJ , LongTIet al. Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family history . Cancer Epidemiol. Biomarkers Prev.24 ( 3 ), 512 – 519 ( 2015 ).
  • Fang F , TurcanS , RimnerAet al. Breast cancer methylomes establish an epigenomic foundation for metastasis . Sci. Transl. Med.3 ( 75 ), 75ra25 ( 2011 ).
  • Hinoue T , WeisenbergerDJ , LangeCPet al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer . Genome Res.22 ( 2 ), 271 – 282 ( 2012 ).
  • Ogino S , ChanAT , FuchsCS , GiovannucciE . Molecular pathological epidemiology of colorectal neoplasia: an emerging transdisciplinary and interdisciplinary field . Gut60 ( 3 ), 397 – 411 ( 2011 ).
  • Ogino S , LochheadP , ChanATet al. Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease . Mod. Pathol.26 ( 4 ), 465 – 484 ( 2013 ).
  • Ogino S , NishiharaR , VanderweeleTJet al. The role of molecular pathological epidemiology in the study of neoplastic and non-neoplastic diseases in the era of precision medicine . Epidemiology27 ( 4 ), 602 – 611 ( 2016 ).
  • Anisimov VN , SikoraE , PawelecG . Relationships between cancer and aging: a multilevel approach . Biogerontology10 ( 4 ), 323 – 338 ( 2009 ).
  • De Magalhaes JP . How ageing processes influence cancer . Nat. Rev. Cancer13 ( 5 ), 357 – 365 ( 2013 ).
  • Mangoni AA , JacksonSH . Age-related changes in pharmacokinetics and pharmacodynamics: basic principles and practical applications . Br. J. Clin. Pharmacol.57 ( 1 ), 6 – 14 ( 2004 ).
  • Horvath S . DNA methylation age of human tissues and cell types . Genome Biol.14 ( 10 ), R115 ( 2013 ).
  • Horvath S , GurvenM , LevineMEet al. An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease . Genome Biol.17 ( 1 ), 171 ( 2016 ).