DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases

Genome Biology

Volumn 17, Issue 1, 2016, Pages

  Ligthart, Symen ^a   Marzi, Carola ^b,c   Aslibekyan, Stella ^d   Mendelson, Michael M ^e,f,g   Conneely, Karen N ^h   Tanaka, Toshiko ⁱ   Colicino, Elena ^j   Waite, Lindsay L ^k   Joehanes, Roby ^l   Guan, Weihua ^m   Brody, Jennifer A ⁿ   Elks, Cathy ^o   Marioni, Riccardo ^p,q   Jhun, Min A ^r   Agha, Golareh ^j   Bressler, Jan ^s   Ward Caviness, Cavin K ^b   Chen, Brian H ⁱ   Huan, Tianxiao ^g   Bakulski, Kelly ^t   Salfati, Elias L ^u   Fiorito, Giovanni ^v,w   Wahl, Simone ^b,c   Schramm, Katharina ^b,x   Sha, Jin ^d   Hernandez, Dena G ⁱ   Just, Allan C ^j   Smith, Jennifer A ^r   Sotoodehnia, Nona ⁿ   Pilling, Luke C ^y   Pankow, James S ^m   Tsao, Phil S ^u,z   Liu, Chunyu ^g,aa   Zhao, Wei ^r   Guarrera, Simonetta ^v,w   Michopoulos, Vasiliki J ^h   Smith, Alicia K ^h   Peters, Marjolein J ^a   Melzer, David ^y   Vokonas, Pantel ^ab   Fornage, Myriam ^s   Prokisch, Holger ^b,x   Bis, Joshua C ⁿ   Chu, Audrey Y ^g   Herder, Christian ^c,ac   Grallert, Harald ^b,c   Yao, Chen ^g   Shah, Sonia ^q   McRae, Allan F ^q   Lin, Honghuang ^aa   Horvath, Steve ^ad   Fallin, Daniele ^t   Hofman, Albert ^a,j   Wareham, Nicholas J ^o   Wiggins, Kerri L ⁿ   Feinberg, Andrew P ^t   Starr, John M ^p   Visscher, Peter M ^p,q   Murabito, Joanne M ^e   Kardia, Sharon L R ^r   Absher, Devin M ^k   Binder, Elisabeth B ^h,ae   Singleton, Andrew B ⁱ   Bandinelli, Stefania ^af   Peters, Annette ^b   Waldenberger, Melanie ^b   Matullo, Giuseppe ^v,w   Schwartz, Joel D ^j   Demerath, Ellen W ^m   Uitterlinden, André G ^a   Meurs, Joyce B J ^a   Franco, Oscar H ^a   Chen, Yii Der Ida ^ag   Levy, Daniel ^e,g   Turner, Stephen T ^ah   Deary, Ian J ^p   Ressler, Kerry J ^h,l,ai   Dupuis, Josée ^aa   Ferrucci, Luigi ⁱ   Ong, Ken K ^o   Assimes, Themistocles L ^u   Boerwinkle, Eric ^s   Koenig, Wolfgang ^x,aj,ak   Arnett, Donna K ^al   Baccarelli, Andrea A ^j   Benjamin, Emelia J ^e,aa,am   Dehghan, Abbas ^a,an   more..

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

^c GERMAN CENTER FOR DIABETES RESEARCH DZD   (Germany)

^d UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^e BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f BOSTON CHILDREN S HOSPITAL   (United States)

^g NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^h EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ NATIONAL INSTITUTE ON AGING   (United States)

^j HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^k HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^l HARVARD MEDICAL SCHOOL   (United States)

^m UNIVERSITY OF MINNESOTA   (United States)

ⁿ UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^o UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^p UNIVERSITY OF EDINBURGH   (United Kingdom)

^q UNIVERSITY OF QUEENSLAND   (Australia)

^r UNIVERSITY OF MICHIGAN   (United States)

^s UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^t JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^u STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^v Human Genetics Foundation   (Italy)

^w UNIVERSITY OF TURIN   (Italy)

^x TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^y UNIVERSITY OF EXETER MEDICAL SCHOOL   (United Kingdom)

^z VA PALO ALTO HEALTH CARE SYSTEM   (United States)

^aa BOSTON UNIVERSITY SCHOOL OF PUBLIC HEALTH   (United States)

^ab VA BOSTON HEALTHCARE SYSTEM   (United States)

^ac LEIBNIZ CENTER FOR DIABETES RESEARCH AT HEINRICH HEINE UNIVERSITY DÜSSELDORF   (Germany)

^ad UNIVERSITY OF CALIFORNIA   (United States)

^ae MAX PLANCK INSTITUTE OF PSYCHIATRY   (Germany)

^af SANTA MARIA ANNUNZIATA HOSPITAL   (Italy)

^ag HARBOR UCLA MEDICAL CENTER   (United States)

^ah MAYO CLINIC   (United States)

^ai MCLEAN HOSPITAL   (United States)

^aj UNIVERSITY HOSPITAL ULM   (Germany)

^ak DZHK GERMAN CENTRE FOR CARDIOVASCULAR RESEARCH   (Germany)

^al UNIVERSITY OF KENTUCKY COLLEGE OF PUBLIC HEALTH   (United States)

^am FRAMINGHAM HEART STUDY   (United States)

^an Imperial College London   (United Kingdom)

more..

Author keywords

Body mass index; C reactive protein; Coronary heart disease; Diabetes; DNA methylation; Epigenome wide association study; Inflammation

Indexed keywords

C REACTIVE PROTEIN;

AFRICAN AMERICAN; ANCESTRY GROUP; ARTICLE; C REACTIVE PROTEIN BLOOD LEVEL; CHRONIC INFLAMMATION; CLINICAL OUTCOME; CPG ISLAND; DISEASE ASSOCIATION; DISEASE MARKER; DISEASE SEVERITY; DNA METHYLATION; EPIGENETICS; EUROPEAN; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; HEART DISEASE; HUMAN; META ANALYSIS (TOPIC); METABOLIC DISORDER; MOLECULAR GENETICS; PHENOTYPE; POPULATION GENETICS; POPULATION RESEARCH; PROTEIN BLOOD LEVEL; SCORING SYSTEM; BLOOD; CAUCASIAN; FEMALE; GENETIC EPIGENESIS; GENETIC VARIATION; GENETICS; INFLAMMATION; MALE; META ANALYSIS; NUCLEOTIDE MOTIF; QUANTITATIVE TRAIT LOCUS;

AFRICAN AMERICANS; C-REACTIVE PROTEIN; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENE EXPRESSION; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INFLAMMATION; MALE; NUCLEOTIDE MOTIFS; QUANTITATIVE TRAIT LOCI;

EID: 85003550816     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-1119-5     Document Type: Article

References (29)

1. Hansson GK, Hermansson A. The immune system in atherosclerosis. Nat Immunol. 2011;12:204-12.
2. Donath MY, Shoelson SE. Type 2 diabetes as an inflammatory disease. Nat Rev Immunol. 2011;11:98-107.
3. Pepys MB. The acute phase response and C-reactive protein. Oxford Textbook Med. 1995;2:1527-33.
4. Emerging Risk Factors Collaboration. C-reactive protein concentration and risk of coronary heart disease, stroke, and mortality: an individual participant meta-analysis. Lancet. 2010;375:132-40.
5. Xu H, Barnes GT, Yang Q, Tan G, Yang D, Chou CJ, et al. Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance. J Clin Investig. 2003;112:1821.
6. Dehghan A, Dupuis J, Barbalic M, Bis JC, Eiriksdottir G, Lu C, et al. Meta-analysis of genome-wide association studies in > 80 000 subjects identifies multiple loci for C-reactive protein levels. Circulation. 2011;123:731-8.
7. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484-92.
8. Barfield RT, Almli LM, Kilaru V, Smith AK, Mercer KB, Duncan R, et al. Accounting for population stratification in DNA methylation studies. Genet Epidemiol. 2014;38:231-41.
9. Hornung V, Ablasser A, Charrel-Dennis M, Bauernfeind F, Horvath G, Caffrey DR, et al. AIM2 recognizes cytosolic dsDNA and forms a caspase-1-activating inflammasome with ASC. Nature. 2009;458:514-8.
10. Martinon F, Tschopp J. Inflammatory caspases and inflammasomes: master switches of inflammation. Cell Death Differ. 2007;14:10-22.
11. Carow B, Rottenberg ME. SOCS3, a major regulator of infection and inflammation. Front Immunol. 2014;5:58.
12. Ortiz-Munoz G, Martin-Ventura JL, Hernandez-Vargas P, Mallavia B, Lopez-Parra V, Lopez-Franco O, et al. Suppressors of cytokine signaling modulate JAK/STAT-mediated cell responses during atherosclerosis. Arterioscler Thromb Vasc Biol. 2009;29:525-31.
13. Gao X, Jia M, Zhang Y, Breitling LP, Brenner H. DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies. Clin Epigenetics. 2015;7:1-10.
14. Chambers JC, Loh M, Lehne B, Drong A, Kriebel J, Motta V, et al. Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study. Lancet Diab Endocrinol. 2015;3:526-34.
15. Schnabel RB, Lunetta KL, Larson MG, Dupuis J, Lipinska I, Rong J, et al. The relation of genetic and environmental factors to systemic inflammatory biomarker concentrations. Circ Cardiovasc Genet. 2009;2:229-37.
16. Shah S, Bonder MJ, Marioni RE, Zhu Z, McRae AF, Zhernakova A, et al. Improving phenotypic prediction by combining genetic and epigenetic associations. Am J Hum Genet. 2015;97:75-85.
17. Jabs WJ, Busse M, Krüger S, Jocham D, Steinhoff J, Doehn C. Expression of C-reactive protein by renal cell carcinomas and unaffected surrounding renal tissue. Kidney Int. 2005;68:2103-10.
18. Kishimoto T, Akira S, Narazaki M, Taga T. Interleukin-6 family of cytokines and gp130. Blood. 1995;86:1243-54.
19. Dick KJ, Nelson CP, Tsaprouni L, Sandling JK, Aïssi D, Wahl S, et al. DNA methylation and body-mass index: a genome-wide analysis. Lancet. 2014;383:1990-8.
20. Psaty BM, O'Donnell CJ, Gudnason V, Lunetta KL, Folsom AR, Rotter JI, et al. Cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium design of prospective meta-analyses of genome-wide association studies from 5 cohorts. Circ Cardiovasc Genet. 2009;2:73-80.
21. Chen Y-A, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, et al. Discovery of cross-reactive probes and polymorphic CpG sites in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013;8:203-9.
22. Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012;13:86.
23. Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30:1363-9.
24. Willer CJ, Li Y, Abecasis GR. METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics. 2010;26:2190-1.
25. Faul F, Erdfelder E, Buchner A, Lang A-G. Statistical power analyses using G* Power 3.1: Tests for correlation and regression analyses. Behav Res Methods. 2009;41:1149-60.
26. Parker HS, Leek JT, Favorov AV, Considine M, Xia X, Chavan S, et al. Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. Bioinformatics. 2014;30:2757-63.
27. Westra H-J, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat Genet. 2013;45:1238-43.
28. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014;42:D1001-6.
29. Breeze CE, et al. "eFORGE: a tool for identifying cell type-specific signal in epigenomic data." Cell Reports 17.8. 2016:2137-2150.