Epigenetic Signatures of Genes and Their Correlations with Various Signaling Pathways During Tumorigenesis

Abstract

During the past 15 years the epigenetic regulation of gene has been studied extensively. The genesis of cancer and epigenetic regulation of genes are deeply interconnected. DNA methylation, histone tail modification, nucleosome remodelling, and non-coding RNA regulate many biological processes that are elementary to the cancer development. This thesis evaluates the expression profile and epigenetic regulation (especially, DNA methylation and histone H3 modifications) of various genes, such as caveolin 1 (CAV1), clusterin (CLU), beta 1 integrin (β1 integrin), histone H3.3 and chromatin modifying enzymes like DNA methyltransferases (DNMTs), histone methyltransferases (HMTs) and histone acetyltransferases (HATs) in colon and breast cancers. Additionally, lipid raft, RAS/MEK/ERK and FAK signaling pathway mediated regulation of histone modifications in colon cancer is also examined. mRNA and protein level analysis of respective gene products in cancer tissue samples and cell lines demonstrated that CAV1 is expressed in a stage-specific manner whereas nuclear CLU (nCLU) is down-regulated; whereas, secretory CLU (sCLU), β1 integrin and H3.3 genes are up-regulated in both the cancers. Inhibition of cell growth in breast and colon cancer cell lines after treatment with epigenetic modulators is associated with up-regulation of CAV1 and nCLU; ultimately resulting in down-regulation of β1 integrin. On investigating the epigenetic regulatory mechanisms of CAV1 gene, it is observed that histone modifications (H3K4me3, H3K9me3, H3K9AcS10p) predominantly regulate CAV1 expression in both cancers whereas promoter DNA methylation is partially responsible in case of only breast cancer. Moreover, expression of CLU is associated with global histone marks in case of breast cancer. In colon cancer, promoter H3K4me, H3K9me3 and H3K9AcS10p enrichment is the predominant regulator of CLU gene expression. Along with expression pattern and epigenetic regulation this thesis also evaluated the involvement of different signaling responsible for histone modifications. The modulation of global and gene specific histone marks in colon cancer is demonstrated to be regulated by lipid raft, RAS/MEK/ERK and FAK signaling pathways. These pathways influence global H3K4me3, H3K9me3, H3K9AcS10p levels and in turn differentially regulate gene specific expression, such as that of CAV1.