Differentially methylated regions within lung cancer risk loci are enriched in deregulated enhancers

References

• Siegel RL, Miller KD, Jemal A. Cancer statistics, 2016. CA: A Cancer Journal for Clinicians. 2016;66(1):7–30.
   Google Scholar
• Wang Y, McKay JD, Rafnar T, et al. Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. Nat Genet. 2014;46(7):736–741.
   Google Scholar
• Landi MT, Chatterjee N, Yu K, et al. A Genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am J Hum Genet. 2009;85(5):679–691.
   Google Scholar
• Hung RJ, McKay JD, Gaborieau V, et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature. 2008;452(7187):633–637.
   Google Scholar
• McKay JD, Hung RJ, Han Y, et al. Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes. Nat Genet. 2017;49(7):1126–1132.
   Google Scholar
• Amos CI, Wu X, Broderick P, et al. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet. 2008;40(5):616–622.
   Google Scholar
• Hu Z, Wu C, Shi Y, et al. A genome-wide association study identifies two new lung cancer susceptibility loci at 13q12.12 and 22q12.2 in Han Chinese. Nat Genet. 2011;43(8):792–796.
   Google Scholar
• Lan Q, Hsiung CA, Matsuo K, et al. Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet. 2012;44(12):1330–1335.
   Google Scholar
• The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012;489(7417):519–525.
   Google Scholar
• The Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511(7511):543–550.
   Google Scholar
• Shi J, Marconett CN, Duan J, et al. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun. 2014;5:3365.
   Google Scholar
• Heyn H, Sayols S, Moutinho C, et al. Linkage of DNA methylation quantitative trait loci to human cancer risk. CellReports. 2014;7(2):331–338.
   Google Scholar
• Scherf DB, Sarkisyan N, Jacobsson H, et al. Epigenetic screen identifies genotype-specific promoter DNA methylation and oncogenic potential of CHRNB4. Oncogene. 2012;32(28):3329–3338.
   Google Scholar
• Jones GT, Marsman J, Bhat B, et al. DNA methylation profiling identifies a high effect genetic variant for lipoprotein(a) levels. Epigenetics. 2020;15(9):949–958.
   Google Scholar
• World Health Organization Classification of Tumours. Pathology and genetics of tumours of the lung, pleura, thymus and heart. International Agency for Research on Cancer IARC. 2004.
   Google Scholar
• Hovestadt V, Jones DTW, Picelli S, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature. 2014;510(7506):537–541.
   Google Scholar
• Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
   Google Scholar
• Database of Single Nucleotide Polymorphisms (dbSNP). 2015. Bethesda (MD): National center for biotechnology information, national library of medicine. (dbSNP Build ID: 135). Available from: http://www.ncbi.nlm.nih.gov/SNP/[Internet]
   Google Scholar
• Liu Y, Siegmund KD, Laird PW, et al. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012;13(7):R61.
   Google Scholar
• Akalin A, Kormaksson M, Li S, et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13(10):R87.
   Google Scholar
• Li S, Garrett-Bakelman FE, Akalin A, et al. An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics. 2013;14(Suppl 5):S10.
   Google Scholar
• Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, et al. Extensive variation in chromatin states across humans. Science. 2013;342(6159):750–752.
   Google Scholar
• Ehrlich M. DNA hypomethylation in cancer cells. Epigenomics. 2009;1(2):239–259.
   Google Scholar
• Yu H, Takeuchi M, LeBarron J, et al. Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Nat Chem Biol. 2015;11(11):847–854.
   Google Scholar
• Arab K, Park YJ, Lindroth AM, et al. Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Mol Cell. 2014;55(4):604–614.
   Google Scholar
• McHugh BJ, Murdoch A, Haslett C, et al. Loss of the integrin-activating transmembrane protein Fam38A (Piezo1) promotes a switch to a reduced integrin-dependent mode of cell migration. PLoS One. 2012;7(7):e40346.
   Google Scholar
• Cheng Y, Yan Z, Liu Y, et al. Analysis of DNA methylation patterns associated with the gastric cancer genome. Oncol Lett. 2014;7(4):1021–1026.
   Google Scholar
• Hogan PG, Chen L, Nardone J, et al. Transcriptional regulation by calcium, calcineurin, and NFAT. Genes Dev. 2003;17(18):2205–2232.
   Google Scholar
• Mancini M, Toker A. NFAT proteins: emerging roles in cancer progression. Nat Rev Cancer. 2009;9(11):810–820.
   Google Scholar
• Pan M-G, Xiong Y, Chen F. NFAT gene family in inflammation and cancer. Curr Mol Med. 2013;13(4):543–554.
   Google Scholar
• Shou J, Jing J, Xie J, et al. Nuclear factor of activated T cells in cancer development and treatment. Cancer Lett. 2015;361(2):174–184.
   Google Scholar
• Jauliac S, López-Rodriguez C, Shaw LM, et al. The role of NFAT transcription factors in integrin-mediated carcinoma invasion. Nat Cell Biol. 2002;4(7):540–544.
   Google Scholar
• Yoeli-Lerner M, Yiu GK, Rabinovitz I, et al. Akt blocks breast cancer cell motility and invasion through the transcription factor NFAT. Mol Cell. 2005;20(4):539–550.
   Google Scholar
• Liu M, Chen J, Hu L, et al. HORMAD2/CT46.2, a novel cancer/testis gene, is ectopically expressed in lung cancer tissues. Mol Hum Reprod. 2012;18(12):599–604.
   Google Scholar
• Wang H, Lou D, Wang Z. Crosstalk of genetic variants, allele-specific DNA methylation, and environmental factors for complex disease risk. Front Genet. 2019;9: 695.
   Google Scholar