In silico DNA methylation analysis identifies potential prognostic biomarkers in type 2 papillary renal cell carcinoma

Cancer Medicine
Man YangKeith D Robertson

Abstract

There are currently no effective treatments for advanced-stage papillary renal cell carcinoma (PRCC). The goal of this study is to define potential DNA methylation-based markers and treatment targets for advanced-stage type 2 PRCC. Progressive DNA methylation changes and copy number variation (CNV) from localized to advanced-stage type 2 PRCC are analyzed by using methylation data generated by TCGA's kidney renal papillary cell carcinoma (TCGA-KIRP, 450k array) project. Survival analyses are performed for the identified biomarkers and genes with CNV. In addition, expression of the corresponding genes is investigated by RNA-seq analysis. Progressive methylation changes in several CpGs from localized to advanced-stage type 2 PRCC are observed. Four CpGs (cg00489401, cg27649239, cg20555674, and cg07196505) in particular are identified as markers for differentiating between localized and advanced-stage type 2 PRCC. Copy number analysis reveals that copy gain of PTK7 mostly occurs in advanced-stage type 2 PRCC. Both the four CpG methylation changes and PTK7 copy number gain are associated with patient survival. RNA-seq analysis demonstrates that PTK7 copy gain leads to higher PTK7 expression relative to tumors without copy number ga...Continue Reading

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Datasets Mentioned

BETA
GSM1536837
GSM1697009

Methods Mentioned

BETA
biopsy

Software Mentioned

IDAT
R package “
R package “ ChAMP
R
rms
RnBeads ”
R package “ EdgeR
R package “ pROC ”
R package “ pamr
R package “ CNTools ”

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