Untargeted Metabolomics Reveals Multiple Metabolites influencing Smoking-Related DNA Methylation

References

• Peto R , LopezAD , BorehamJ , ThunM , HeathC , DollR . Mortality from smoking worldwide . Br. Med. Bull.52 ( 1 ), 12 – 21 ( 1996 ).
   PubMed Web of Science ®Google Scholar
• Ng M , FreemanMK , FlemingTDet al. Smoking prevalence and cigarette consumption in 187 countries, 1980–2012 . JAMA311 ( 2 ), 183 – 192 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Lim SS , VosT , FlaxmanADet al. A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010 . Lancet380 ( 9859 ), 2224 – 2260 ( 2013 ).
   Web of Science ®Google Scholar
• WHO . IARC monographs on the evaluation of carcinogenic risks to humans. Volume 88: formaldehyde, 2-butoxyethanol and 1-tert-butoxypropan-2-ol . WHO ( 2006 ). http://monographs.iarc.fr/ENG/Monographs/vol88/index.php .
   Google Scholar
• Hsu P-C , ZhouB , ZhaoYet al. Feasibility of identifying the tobacco-related global metabolome in blood by UPLC–QTOF-MS . J. Proteome Res.12 ( 2 ), 679 – 691 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Wang-Sattler R , YuY , MittelstrassKet al. Metabolic profiling reveals distinct variations linked to nicotine consumption in humans – first results from the KORA study . PLoS ONE3 ( 12 ), e3863 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Xu T , HolzapfelC , DongXet al. Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study . BMC Med.11 , 60 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Jones DP , WalkerDI , UppalK , RohrbeckP , MallonCOLTM , GoY-M . Metabolic pathways and networks associated with tobacco use in military personnel . J. Occup. Environ. Med.58 , S111 – S116 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Nikpay M , GoelA , WonH-Het al. A comprehensive 1000 genomes-based genome-wide association meta-analysis of coronary artery disease . Nat. Genet.47 ( 10 ), 1121 – 1130 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Phillips T . The role of methylation in gene expression . Nat. Educ.1 ( 1 ), 116 ( 2008 ).
   Google Scholar
• Bakulski KM , FallinMD . Epigenetic epidemiology: promises for public health research . Environ. Mol. Mutag.55 ( 3 ), 171 – 183 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Philibert RA , BeachSRH , BrodyGH . The DNA methylation signature of smoking: an archetype for the identification of biomarkers for behavioral illness . Nebr. Symp. Motiv.61 , 109 – 127 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Breitling LP , YangR , KornB , BurwinkelB , BrennerH . Tobacco-smoking-related differential DNA methylation: 27 K discovery and replication . Am. J. Hum. Genetics88 ( 4 ), 450 – 457 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Gao X , JiaM , ZhangY , BreitlingLP , BrennerH . DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies . Clin. Epigenetics7 , 113 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Ambatipudi S , CueninC , Hernandez-VargasHet al. Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study . Epigenomics8 ( 5 ), 599 – 618 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Joehanes R , JustAC , MarioniREet al. Epigenetic signatures of cigarette smoking . Circ. Cardiovasc. Genet.9 ( 5 ), 436 – 447 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Zeilinger S , KühnelB , KloppNet al. Tobacco smoking leads to extensive genome-wide changes in DNA methylation . PLoS ONE8 ( 5 ), e63812 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Suhre K , GiegerC . Genetic variation in metabolic phenotypes: study designs and applications . Nat. Rev. Genet.13 ( 11 ), 759 – 769 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Petersen AK , ZeilingerS , KastenmullerGet al. Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits . Hum. Mol. Genet.23 ( 2 ), 534 – 545 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Goldberg J , CurranB , VitekME , HendersonWG , BoykoEJ . The Vietnam Era Twin Registry . Twin Res.5 ( 5 ), 476 – 481 ( 2002 ).
   PubMedGoogle Scholar
• Vaccarino V , BrennanM-L , MillerAHet al. Association of major depressive disorder with serum myeloperoxidase and other markers of inflammation: a twin study . Biol. Psychiatry64 ( 6 ), 476 – 483 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Vaccarino V , LampertR , BremnerJDet al. Depressive symptoms and heart rate variability: evidence for a shared genetic substrate in a study of twins . Psychosom. Med.70 ( 6 ), 628 – 636 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Klebaner D , HuangY , HuiQet al. X chromosome-wide analysis identifies DNA methylation sites influenced by cigarette smoking . Clin. Epigenetics8 , 20 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Chen Y-A , LemireM , ChoufaniSet al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray . Epigenetics8 ( 2 ), 203 – 209 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Soltow QA , StrobelFH , MansfieldKG , WachtmanL , ParkY , JonesDP . High-performance metabolic profiling with dual chromatography-Fourier-transform mass spectrometry (DC-FTMS) for study of the exposome . Metabolomics9 ( 1 ), 132 – 143 ( 2013 ).
   Web of Science ®Google Scholar
• Go Y-M , WalkerDI , LiangYet al. Reference standardization for mass spectrometry and high-resolution metabolomics applications to exposome research . Toxicol. Sci.148 ( 2 ), 531 – 543 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Walker DI , PennellKD , UppalKet al. Pilot metabolome-wide association study of benzo(a)pyrene in serum from military personnel . J. Occup. Environ. Med.58 , S44 – S52 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Yu T , ParkY , JohnsonJM , JonesDP . apLCMS--adaptive processing of high-resolution LC/MS data . Bioinformatics25 ( 15 ), 1930 – 1936 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Uppal K , SoltowQA , StrobelFHet al. xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data . BMC Bioinformatics14 ( 1 ), 15 ( 2013 ).
   PubMedGoogle Scholar
• Smith CA , MailleGO , WantEJet al. METLIN: a metabolite mass spectral database . Ther. Drug Monit.27 ( 6 ), 747 – 751 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Wishart DS , JewisonT , GuoACet al. HMDB 3.0 – the Human Metabolome Database in 2013 . Nucleic Acids Res.41 ( D1 ), D801 – D807 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Carlin JB . Regression models for twin studies: a critical review . Int. J. Epidemiol.34 ( 5 ), 1089 – 1099 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Schymanski EL , JeonJ , GuldeRet al. Identifying small molecules via high resolution mass spectrometry: communicating confidence . Environ. Sci. Technol.48 ( 4 ), 2097 – 2098 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Houseman EA , AccomandoWP , KoestlerDCet al. DNA methylation arrays as surrogate measures of cell mixture distribution . BMC Bioinformatics13 ( 1 ), 86 ( 2012 ).
   PubMedGoogle Scholar
• Barfield RT , AlmliLM , KilaruVet al. Accounting for population stratification in DNA methylation studies . Genet. Epidemiol.38 ( 3 ), 231 – 241 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Boker S , NealeM , MaesHet al. OpenMx: an open source extended structural equation modeling framework . Psychometrika76 ( 2 ), 306 – 317 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• The R Project for Statistical Computing . www.r-project.org/ .
   Google Scholar
• Stahl JM , SharmaA , CheungMet al. Deregulated Akt3 activity promotes development of malignant melanoma . Cancer Res.64 ( 19 ), 7002 – 7010 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Cristiano BE , ChanJC , HannanKMet al. A specific role for AKT3 in the genesis of ovarian cancer through modulation of G(2)-M phase transition . Cancer Res.66 ( 24 ), 11718 – 11725 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Tai YL , ChenLC , ShenTL . Emerging roles of focal adhesion kinase in cancer . BioMed Res. Int. 2015 , 690690 ( 2015 ).
   Web of Science ®Google Scholar
• Kaufmann R , RahnS , PollrichKet al. Thrombin-mediated hepatocellular carcinoma cell migration: cooperative action via proteinase-activated receptors 1 and 4 . J. Cell. Physiol.211 ( 3 ), 699 – 707 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Farias EF , ArapshianA , BleiweissIJ , WaxmanS , ZelentA , MiraYLR . Retinoic acid receptor alpha2 is a growth suppressor epigenetically silenced in MCF-7 human breast cancer cells . Cell Growth Differ.13 ( 8 ), 335 – 341 ( 2002 ).
   PubMedGoogle Scholar
• Zhang Y , SchöttkerB , Ordóñez-MenaJet al. F2RL3 methylation, lung cancer incidence and mortality . Int. J. Cancer137 ( 7 ), 1739 – 1748 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• DAVID Bioinformatics Resources 6.8 . https://david.ncifcrf.gov/ .
   Google Scholar
• Sun YV , SmithAK , ConneelyKNet al. Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans . Hum. Genet.132 ( 9 ), 1027 – 1037 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Walker DI , GoY-M , LiuK , PennellKD , JonesDP . Population screening for biological and environmental properties of the human metabolic phenotype . In : Metabolic Phenotyping in Personalized and Public Healthcare . Academic Press , CA, USA , 167 – 211 ( 2016 ).
   Google Scholar
• Treur JL , TaylorAE , WareJJet al. Associations between smoking and caffeine consumption in two European cohorts . Addiction (Abingdon, England)111 ( 6 ), 1059 – 1068 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Aberg KA , McClayJL , NerellaSet al. Methylome-wide association study of schizophrenia . JAMA Psychiatry71 ( 3 ), 255 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Uppal K , WalkerDI , LiuK , LiS , GoY-M , JonesDP . Computational metabolomics: a framework for the million metabolome . Chem. Res. Toxicol.29 ( 12 ), 1956 – 1975 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Sun YV , HuY-J . Integrative analysis of multi-omics data for discovery and functional studies of complex human diseases . Adv. Genet.93 , 147 – 190 ( 2016 ).
   PubMed Web of Science ®Google Scholar