Cell-composition effects in the analysis of DNA methylation array data: A mathematical perspective

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Houseman, E Andres ^a   Kelsey, Karl T ^b   Wiencke, John K ^c   Marsit, Carmen J ^d  

^a OREGON STATE UNIVERSITY   (United States)

^b BROWN UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

Epigenetics; Epigenome wide association; Epigenomics; Immune; Infinium

Indexed keywords

ALKYLATION; BIOINFORMATICS; CELLS; CYTOLOGY; DNA; METHYLATION; MIXTURES;

EPIGENETICS; EPIGENOMES; EPIGENOMICS; IMMUNE; INFINIUM;

COMPOSITION EFFECTS;

ALGORITHM; DNA METHYLATION; DNA MICROARRAY; EPIGENETICS; GENETIC ASSOCIATION; GENETIC EPIGENESIS; HUMAN; LEUKOCYTE; METABOLISM; PHENOTYPE; PROCEDURES;

ALGORITHMS; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LEUKOCYTES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE;

EID: 84926624843     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0527-y     Document Type: Article

References (55)

1. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, et al. An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One. 2009;4(12):e8274.
2. Marsit CJ, Koestler DC, Christensen BC, Karagas MR, Houseman EA, Kelsey KT. DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. J Clin Oncol. 2011;29(9):1133-9.
3. Kim M, Long TI, Arakawa K, Wang R, Yu MC, Laird PW. DNA methylation as a biomarker for cardiovascular disease risk. PLoS One. 2010;5(3):e9692.
4. Dick KJ, Nelson CP, Tsaprouni L, Sandling JK, Aissi D, Wahl S, et al. DNA methylation and body-mass index: a genome-wide analysis. Lancet. 2014;383(9933):1990-8.
5. Kile ML, Houseman EA, Baccarelli AA, Quamruzzaman Q, Rahman M, Mostofa G, et al. Effect of prenatal arsenic exposure on DNA methylation and leukocyte subpopulations in cord blood. Epigenetics. 2014;9(5):774-82.
6. Koestler DC, Avissar-Whiting M, Houseman EA, Karagas MR, Marsit CJ. Differential DNA methylation in umbilical cord blood of infants exposed to low levels of arsenic in utero. Environ Health Perspect. 2013;121(8):971-7.
7. Joubert BR, Haberg SE, Nilsen RM, Wang X, Vollset SE, Murphy SK, et al. 450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy. Environ Health Perspect. 2012;120(10):1425-31.
8. Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010;467(7313):338. -342.
9. Khavari DA, Sen GL, Rinn JL. DNA methylation and epigenetic control of cellular differentiation. Cell Cycle. 2010;9(19):3880-3.
10. Natoli G. Maintaining cell identity through global control of genomic organization. Immunity. 2010;33(1):12-24.
11. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL, et al. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet. 2009;5(8):e1000602.
12. Monick MM, Beach SR, Plume J, Sears R, Gerrard M, Brody GH, et al. Coordinated changes in AHRR methylation in lymphoblasts and pulmonary macrophages from smokers. Am J Med Genet B Neuropsychiatr Genet. 2012;159(2):141-51.
13. Sung N, Choi K, Park E, Park K, Lee S, Lee A, et al. Smoking, alcohol and gastric cancer risk in Korean men: the National Health Insurance Corporation Study. British J Cancer. 2007;97(5):700-4.
14. Koestler DC, Marsit CJ, Christensen BC, Accomando W, Langevin SM, Houseman EA, et al. Peripheral blood immune cell methylation profiles are associated with nonhematopoietic cancers. Cancer Epidemiol Biomark Prev. 2012;21(8):1293-302.
15. Langevin SM, Houseman EA, Accomando WP, Koestler DC, Christensen BC, Nelson HH, et al. Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients. Epigenetics. 2014;9(6):884-95.
16. Langevin SM, Koestler DC, Christensen BC, Butler RA, Wiencke JK, Nelson HH, et al. Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma. Epigenetics. 2012;7(3):291-9.
17. Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol. 2013;31(2):142-7.
18. 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.
19. Houseman EA, Molitor J, Marsit CJ. Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics. 2014;30(10):1431-9.
20. Charlton J, Williams RD, Weeks M, Sebire NJ, Popov S, Vujanic G, et al. Methylome analysis identifies a wilms tumour epigenetic biomarker detectable in blood. Genome Biol. 2014;15(8):434.
21. Guintivano J, Aryee MJ, Kaminsky ZA. A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics. 2013;8(3):290-302.
22. Zou J, Lippert C, Heckerman D, Aryee M, Listgarten J. Epigenome-wide association studies without the need for cell-type composition. Nat Methods. 2014;11(3):309-11.
23. Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3(9):1724-35.
24. Teschendorff AE, Zhuang J, Widschwendter M. Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. Bioinformatics. 2011;27(11):1496-505.
25. Falvo JV, Jasenosky LD, Kruidenier L, Goldfeld AE. Epigenetic control of cytokine gene expression: regulation of the TNF/LT locus and T helper cell differentiation. Adv Immunol. 2013;118:37-128.
26. Walden TB, Hansen IR, Timmons JA, Cannon B, Nedergaard J. Recruited vs. nonrecruited molecular signatures of brown, "brite", and white adipose tissues. Am J Physiol Endocrinol Metabol. 2012;302(1):E19-31.
27. Houseman EA, Christensen BC, Yeh R-F, Marsit CJ, Karagas MR, Wrensch M, et al. Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics. 2008;9(1):365.
28. DeNardo DG, Coussens LM. Balancing immune response: crosstalk between adaptive and innate immune cells during breast cancer progression. Breast Cancer Res. 2007;9(4):212.
29. Lederer SL, Walters K-A, Proll S, Paeper B, Robinzon S, Boix L, et al. Distinct cellular responses differentiating alcohol-and hepatitis C virus-induced liver cirrhosis. Virol J. 2006;3(1):98.
30. Nakashima Y, Fujii H, Sumiyoshi S, Wight TN, Sueishi K. Early human atherosclerosis accumulation of lipid and proteoglycans in intimal thickenings followed by macrophage infiltration. Arterioscler Thromb Vasc Biol. 2007;27(5):1159-65.
31. Zhou X, Stemme S, Hansson GK. Evidence for a local immune response in atherosclerosis. CD4+ T cells infiltrate lesions of apolipoprotein-E-deficient mice. Am J Pathol. 1996;149(2):359.
32. Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature. 2011;469(7330):343-9.
33. Simon JA, Kingston RE. Occupying chromatin: polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol Cell. 2013;49(5):808-24.
34. Kolybaba A, Classen AK. Sensing cellular states-signaling to chromatin pathways targeting Polycomb and Trithorax group function. Cell Tissue Res. 2014;356(3):477-93.
35. Zhuang J, Jones A, Lee S-H, Ng E, Fiegl H, Zikan M, et al. The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer. PLoS Genet. 2012;8(2):e1002517.
36. Yao Y, Wang Y, Chen F, Huang Y, Zhu S, Leng Q, et al. NLRC5 regulates MHC class I antigen presentation in host defense against intracellular pathogens. Cell Res. 2012;22(5):836-47.
37. Davis BK, Roberts RA, Huang MT, Willingham SB, Conti BJ, Brickey WJ, et al. Cutting edge: NLRC5-dependent activation of the inflammasome. J Immunol. 2011;186(3):1333-7.
38. Liu Y, Ludes-Meyers J, Zhang Y, Munoz-Medellin D, Kim H-T, Lu C, et al. Inhibition of AP-1 transcription factor causes blockade of multiple signal transduction pathways and inhibits breast cancer growth. Oncogene. 2002;21(50):7680-9.
39. Zheng X, Zhao Q, Wu H-J, Li W, Wang H, Meyer CA, et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol. 2014;15(8):419.
40. Barker DJP, Robinson RJ. Fetal and infant origins of adult disease. London: British Medical Journal; 1992.
41. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nature Methods. 2013;10(10):949-55.
42. Hansen J-PFKD. Minfi tutorial BioC2014. 2014.
43. Teschendorff AE, Liu X, Caren H, Pollard SM, Beck S, Widschwendter M, et al. The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis. PLoS Comput Biol. 2014;10(7):e1003709.
44. Teschendorff AE, Widschwendter M. Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions. Bioinformatics. 2012;28(11):1487-94.
45. Y-a C, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013;8(2):203.
46. Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014;15(2):R31.
47. Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlén S-E, Greco D, et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PloS One. 2012;7(7):e41361.
48. Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 2006;20(9):1123-36.
49. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell. 2006;125(2):301-13.
50. Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nature Genet. 2006;39(2):232-6.
51. Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang S-w, et al. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res. 2006;16(7):890-900.
52. Accomando WP, Wiencke JK, Houseman EA, Butler RA, Zheng S, Nelson HH, et al. Decreased NK cells in patients with head and neck cancer determined in archival DNA. Clin Cancer Res. 2012;18(22):6147-54.
53. Zouridis H, Deng N, Ivanova T, Zhu Y, Wong B, Huang D, et al. Methylation subtypes and large-scale epigenetic alterations in gastric cancer. Sci Transl Med. 2012, 4(156).156ra140-156ra140.
54. Hlady RA, Tiedemann RL, Puszyk W, Zendejas I, Roberts LR, Choi J-H, et al. Epigenetic signatures of alcohol abuse and hepatitis infection during human hepatocarcinogenesis. Oncotarget. 2014;5(19):9425.
55. Zaina S, Heyn H, Carmona FJ, Varol N, Sayols S, Condom E, et al. A DNA methylation map of human atherosclerosis. Circ Cardiovasc Genet. 2014;7(5):692-700.