Identification of Epigenetic Regulation on The Expression of The Aberrant Gene of Kidney Renal Clear Cell Carcinoma Patients Observed in a Specific Race

Abstract

Aberrant expression of genes in cancer is mainly caused by a mutation where there is a change in DNA sequences. However, the aberrant expression was also found without a change in the DNA sequences where epigenetic modification such as DNA methylation, histone modifications and microRNA become the main regulator in another layer of the cancer mechanism. The nature of epigenetic is heritable and reversible. It is important to search for the epigenetic mechanism in disease development in order to design epigenetic therapy and drugs. Methylation inhibitors and HDAC inhibitors drug already yielded seven FDA approved epigenetic drugs for myelodysplastic syndrome, cutaneous T-cell lymphoma, Multiple myelomas, peripheral T-cell lymphoma. This study search for the epigenetic mechanism in a kidney renal cell carcinoma patients in a white race. The dataset of transcriptome profiling and epigenetic was downloaded from The Cancer Genome Atlas (TCGA) database. Some programming languages such as R, Python, Matlab and MySQL database were used to pre-processing the datasets and correlation computation part. This study found 14 aberrant genes which significantly correlated with 19 aberrant methylation probes with the correlation score less than equal to -0.7 and p-value < 0.01. Some of those down-regulated genes such as ZNF542, ZFP28, TMEM25, STK33 are correlated with hypermethylation in more than one sites. It is suggested that those methylation sites can affect the down-regulation of their expression in cancer formation. Further study is needed to validate the results through wet lab analysis.