Identification of New Differentially Methylated Genes That Have Potential Functional Consequences in Prostate Cancer

Jin W. Kim, Seong Tae Kim, Aubrey R. Turner, Tracey Young, Shelly Smith, Wennuan Liu, Johan Lindberg, Lars Egevad, Henrik Gronberg, William B Isaacs, Jianfeng Xu

Research output: Contribution to journalArticle

Abstract

Many differentially methylated genes have been identified in prostate cancer (PCa), primarily using candidate gene-based assays. Recently, several global DNA methylation profiles have been reported in PCa, however, each of these has weaknesses in terms of ability to observe global DNA methylation alterations in PCa. We hypothesize that there remains unidentified aberrant DNA methylation in PCa, which may be identified using higher resolution assay methods. We used the newly developed Illumina HumanMethylation450 BeadChip in PCa (n = 19) and adjacent normal tissues (n = 4) and combined these with gene expression data for identifying new DNA methylation that may have functional consequences in PCa development and progression. We also confirmed our methylation results in an independent data set. Two aberrant DNA methylation genes were validated among an additional 56 PCa samples and 55 adjacent normal tissues. A total 28,735 CpG sites showed significant differences in DNA methylation (FDR adjusted P

Original languageEnglish (US)
Article numbere48455
JournalPLoS One
Volume7
Issue number10
DOIs
StatePublished - Oct 31 2012

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prostatic neoplasms
DNA methylation
DNA Methylation
Prostatic Neoplasms
Genes
genes
Assays
Tissue
Methylation
Gene expression
assays
methylation
Gene Expression
gene expression

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Identification of New Differentially Methylated Genes That Have Potential Functional Consequences in Prostate Cancer. / Kim, Jin W.; Kim, Seong Tae; Turner, Aubrey R.; Young, Tracey; Smith, Shelly; Liu, Wennuan; Lindberg, Johan; Egevad, Lars; Gronberg, Henrik; Isaacs, William B; Xu, Jianfeng.

In: PLoS One, Vol. 7, No. 10, e48455, 31.10.2012.

Research output: Contribution to journalArticle

Kim, JW, Kim, ST, Turner, AR, Young, T, Smith, S, Liu, W, Lindberg, J, Egevad, L, Gronberg, H, Isaacs, WB & Xu, J 2012, 'Identification of New Differentially Methylated Genes That Have Potential Functional Consequences in Prostate Cancer', PLoS One, vol. 7, no. 10, e48455. https://doi.org/10.1371/journal.pone.0048455
Kim, Jin W. ; Kim, Seong Tae ; Turner, Aubrey R. ; Young, Tracey ; Smith, Shelly ; Liu, Wennuan ; Lindberg, Johan ; Egevad, Lars ; Gronberg, Henrik ; Isaacs, William B ; Xu, Jianfeng. / Identification of New Differentially Methylated Genes That Have Potential Functional Consequences in Prostate Cancer. In: PLoS One. 2012 ; Vol. 7, No. 10.
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