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Research Paper

Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis

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Pages 67-80 | Received 24 Sep 2018, Accepted 04 Jan 2019, Published online: 29 Jan 2019

References

  • Paziewska A, Dabrowska M, Goryca K, et al. DNA methylation status is more reliable than gene expression at detecting cancer in prostate biopsy. Br J Cancer. 2014 Aug 12;111(4):781–789. PubMed PMID: 24937670; PubMed Central PMCID: PMCPMC4134497.
  • Wu D, Gong C, Su C. Genome-wide analysis of differential DNA methylation in Silver-Russell syndrome. Sci China Life Sci. 2017 Jul;60(7):692–699. PubMed PMID: 28624953.
  • Chen G, Shi T, Shi L. Characterizing and annotating the genome using RNA-seq data. Sci China Life Sci. 2017 Feb;60(2):116–125. PubMed PMID: 27294835.
  • Liu M, Shi T. Ten years of achievements in biological and medical sciences. Sci China Life Sci. 2017 Feb;60(2):111–115. PubMed PMID: 28215028.
  • Wang J, Han X, Sun Y. DNA methylation signatures in circulating cell-free DNA as biomarkers for the early detection of cancer. Sci China Life Sci. 2017 Apr;60(4):356–362. PubMed PMID: 28063009.
  • Lin RK, Wang YC. Dysregulated transcriptional and post-translational control of DNA methyltransferases in cancer. Cell Biosci. 2014;4:46. PubMed PMID: 25949795; PubMed Central PMCID: PMC4422219.
  • Rajaraman P, Anderson BO, Basu P, et al. Recommendations for screening and early detection of common cancers in India. Lancet Oncol. 2015;16(7):e352–e361.
  • Wei JH, Haddad A, Wu KJ, et al. A CpG-methylation-based assay to predict survival in clear cell renal cell carcinoma. Nat Commun. 2015 Oct 30;6:8699. PubMed PMID: 26515236; PubMed Central PMCID: PMCPMC4846314.
  • Hao X, Luo H, Krawczyk M, et al. DNA methylation markers for diagnosis and prognosis of common cancers. Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7414–7419. PubMed PMID: 28652331.
  • Tang W, Wan S, Yang Z, et al. Tumor origin detection with tissue-specific miRNA and DNA methylation markers. Bioinformatics. 2017 Sep 28. PubMed PMID: 29028927. DOI:10.1093/bioinformatics/btx622
  • Ji H, Ehrlich LI, Seita J, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010 Sep 16;467(7313):338–342. PubMed PMID: 20720541; PubMed Central PMCID: PMC2956609.
  • Rao X, Evans J, Chae H, et al. CpG island shore methylation regulates caveolin-1 expression in breast cancer. Oncogene. 2013 Sep 19;32(38):4519–4528. PubMed PMID: 23128390; PubMed Central PMCID: PMC3787796.
  • Irizarry RA, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009 Feb;41(2):178–186. PubMed PMID: 19151715; PubMed Central PMCID: PMC2729128.
  • Jjingo D, Conley AB, Yi SV, et al. On the presence and role of human gene-body DNA methylation. Oncotarget. 2012 Apr;3(4):462–474. PubMed PMID: 22577155; PubMed Central PMCID: PMC3380580.
  • Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biol. 2015 Jan 29;16:17. PubMed PMID: 25631659; PubMed Central PMCID: PMC4365533.
  • Yang X, Gao L, Zhang S. Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. Brief Bioinform. 2017 Sep 1;18(5):761–773. PubMed PMID: 27436122.
  • Chen T, Guestrin C, editors. Xgboost: A scalable tree boosting system. Proceedings of the 22nd acm sigkdd international conference on knowledge discovery and data mining. ACM. San Francisco, CA: University of Washington; 2016.
  • Teschendorff AE, Gao Y, Jones A, et al. DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer. Nat Commun. 2016 Jan 29;7:10478. PubMed PMID: 26823093; PubMed Central PMCID: PMCPMC4740178.
  • Luo Y, Wong CJ, Kaz AM, et al. Differences in DNA methylation signatures reveal multiple pathways of progression from adenoma to colorectal cancer. Gastroenterology. 2014 Aug;147(2):418–29 e8. PubMed PMID: 24793120; PubMed Central PMCID: PMCPMC4107146.
  • Kirby MK, Ramaker RC, Roberts BS, et al. Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns. BMC Cancer. 2017 Apr 17;17(1):273. PubMed PMID: 28412973; PubMed Central PMCID: PMC5392915.
  • Chen J, Wang Q, Zhang W, et al. [Biological effect of down-regulating of MTRR gene on cisplatin-resistant ovarian cancer SKOV3 cells in vitro and in vivo studies]. Zhonghua Fu Chan Ke Za Zhi. 2016 Feb;51(2):126–134. PubMed PMID: 26917482.
  • Chen D, Sun Q, Cheng X, et al. Genome-wide analysis of long noncoding RNA (lncRNA) expression in colorectal cancer tissues from patients with liver metastasis. Cancer Med. 2016 Jul;5(7):1629–1639. PubMed PMID: 27165481; PubMed Central PMCID: PMCPMC4867661.
  • Daugaard I, Dominguez D, Kjeldsen TE, et al. Identification and validation of candidate epigenetic biomarkers in lung adenocarcinoma. Sci Rep. 2016 Oct 26;6:35807. PubMed PMID: 27782156; PubMed Central PMCID: PMCPMC5080630 concerning MS-HRM technology.
  • Fleischer T, Tekpli X, Mathelier A, et al. DNA methylation at enhancers identifies distinct breast cancer lineages. Nat Commun. 2017 Nov 09;8(1):1379. PubMed PMID: 29123100.
  • Mundbjerg K, Chopra S, Alemozaffar M, et al. Identifying aggressive prostate cancer foci using a DNA methylation classifier. Genome Biol. 2017 Jan 12;18(1):3. PubMed PMID: 28081708; PubMed Central PMCID: PMCPMC5234101.
  • Patch AM, Christie EL, Etemadmoghadam D, et al. Whole-genome characterization of chemoresistant ovarian cancer. Nature. 2015 May 28;521(7553):489–494. PubMed PMID: 26017449.
  • Bjaanaes MM, Fleischer T, Halvorsen AR, et al. Genome-wide DNA methylation analyses in lung adenocarcinomas: association with EGFR, KRAS and TP53 mutation status, gene expression and prognosis. Mol Oncol. 2016 Feb;10(2):330–343. PubMed PMID: 26601720.
  • Kuramoto J, Arai E, Tian Y, et al. Genome-wide DNA methylation analysis during non-alcoholic steatohepatitis-related multistage hepatocarcinogenesis: comparison with hepatitis virus-related carcinogenesis. Carcinogenesis. 2017 Mar 01;38(3):261–270. PubMed PMID: 28426876.
  • Reyngold M, Turcan S, Giri D, et al. Remodeling of the methylation landscape in breast cancer metastasis. PloS one. 2014;9(8):e103896. PubMed PMID: 25083786; PubMed Central PMCID: PMC4118917.
  • Aryee MJ, Liu W, Engelmann JC, et al. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med. 2013 Jan 23;5(169):169ra10. PubMed PMID: 23345608; PubMed Central PMCID: PMC3577373.
  • Qin HD, Liao XY, Chen YB, et al. Genomic characterization of esophageal squamous cell carcinoma reveals critical genes underlying tumorigenesis and poor prognosis. Am J Hum Genet. 2016 Apr 07;98(4):709–727. PubMed PMID: 27058444; PubMed Central PMCID: PMCPMC4833434.
  • Holmila R, Sklias A, Muller DC, et al. Targeted deep sequencing of plasma circulating cell-free DNA reveals Vimentin and Fibulin 1 as potential epigenetic biomarkers for hepatocellular carcinoma. PloS one. 2017;12(3):e0174265. PubMed PMID: 28333958; PubMed Central PMCID: PMCPMC5363871.
  • Kostareli E, Holzinger D, Bogatyrova O, et al. HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas. J Clin Invest. 2013 Jun;123(6):2488–2501. PubMed PMID: 23635773; PubMed Central PMCID: PMC3668826.
  • Hoshino I, Akutsu Y, Murakami K, et al. Histone demethylase LSD1 inhibitors prevent cell growth by regulating gene expression in esophageal squamous cell carcinoma cells. Ann Surg Oncol. 2016 Jan;23(1):312–320. PubMed PMID: 25791791.
  • Yi F, Du J, Ni W, et al. Tbx2 confers poor prognosis in glioblastoma and promotes temozolomide resistance with change of mitochondrial dynamics. Onco Targets Ther. 2017;10:1059–1069. PubMed PMID: 28260920; PubMed Central PMCID: PMCPMC5325101.
  • Kandimalla R, van Tilborg AA, Kompier LC, et al. Genome-wide analysis of CpG island methylation in bladder cancer identified TBX2, TBX3, GATA2, and ZIC4 as pTa-specific prognostic markers. Eur Urol. 2012 Jun;61(6):1245–1256. PubMed PMID: 22284968.
  • Hu B, Mu HP, Zhang YQ, et al. Prognostic significance of TBX2 expression in non-small cell lung cancer. J Mol Histol. 2014 Aug;45(4):421–426. PubMed PMID: 24531749.
  • Liu F, Zhu C, Huang X, et al. A low level of GPR37 is associated with human hepatocellular carcinoma progression and poor patient survival. Pathol Res Pract. 2014 Dec;210(12):885–892. PubMed PMID: 25169131.
  • Bo TH, Dysvik B, Jonassen I. LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Res. 2004 Feb 20;32(3):e34. PubMed PMID: 14978222; PubMed Central PMCID: PMC374359.
  • Teschendorff AE, Marabita F, Lechner M, et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics. 2013 Jan 15;29(2):189–196. PubMed PMID: 23175756; PubMed Central PMCID: PMC3546795.
  • Cancer Genome Atlas N. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 Jan 29;517(7536):576–582. PubMed PMID: 25631445; PubMed Central PMCID: PMC4311405.
  • Cancer Genome Atlas Research N. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20;507(7492):315–322. PubMed PMID: 24476821; PubMed Central PMCID: PMC3962515.
  • Cancer Genome Atlas Research N, Kandoth C, Schultz N, et al. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 2;497(7447):67–73. PubMed PMID: 23636398; PubMed Central PMCID: PMC3704730.
  • Hoadley KA, Yau C, Wolf DM, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14;158(4):929–944. PubMed PMID: 25109877; PubMed Central PMCID: PMC4152462.
  • Zhang H, Deng Y, Zhang Y, et al. Cooperative genomic alteration network reveals molecular classification across 12 major cancer types. Nucleic Acids Res. 2017 Jan 25;45(2):567–582. PubMed PMID: 27899621; PubMed Central PMCID: PMC5314758.
  • Jones E, Oliphant T, Peterson P. {SciPy}: open source scientific tools for {Python}. 2014. https://www.scipy.org
  • Naumov VA, Generozov EV, Zaharjevskaya NB, et al. Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips. Epigenetics. 2013 Sep;8(9):921–934. PubMed PMID: 23867710; PubMed Central PMCID: PMCPMC3883769.
  • da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57. PubMed PMID: 19131956.
  • da Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009 Jan;37(1):1–13. PubMed PMID: 19033363; PubMed Central PMCID: PMCPMC2615629.
  • Friedman JH. Greedy function approximation: A gradient boosting machine. Ann Stat. 2001 Oct;29(5):1189–1232. PubMed PMID: WOS:000173361700001; English.
  • Pedregosa F, Varoquaux G, Gramfort A, et al. Scikit-learn: machine learning in Python. J Mach Learn Res. 2011;12(Oct):2825–2830.

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