Epigenetics is defined as molecular mechanisms of gene regulation (eg. histone methylation) that don't alter the underlying DNA sequence (6). The initiation and progression of cancer involves genetic and epigenetic aberrations, with global changes in the epigenetic landscape being a hallmark of cancer. Unlike genetic alterations, epigenetic aberrations are reversible, which has led to the possibility of epigenetic therapy for cancer. Tobacco and alcohol use are primary etiological factors for oral squamous cell carcinoma (OSCC) (22). Repeated exposure to carcinogens in these substances induces altered differentiation and morphology of epithelial cells, manifesting as leukoplakia. These lesions progress through benign hyperplasia and dysplasia to oral squamous cell carcinoma and finally, metastatic cancer (23). Di-methylated H3K4, a substrate of demethylase KDM1A, is elevated in several stages of OSCC development compared to normal tissue (24), suggesting the involvement of epigenetic aberrations in oral cavity carcinogenesis. My preliminary data show elevated KDM1A protein in human OSCC cell lines compared to immortal human oral epithelial cells and Oncomine (www.oncomine.org) data from Peng Head-Neck (2011) show KDM1A ranked in the top 1% of over- expressed genes in OSCC patients. These findings provide added support for aberrant regulation by KDM1A in OSCC. Additionally, KDM1A has been shown to interact with signaling by retinoids, a drug class extensively studied in OSCC (27). Therefore, I will delineate the epigenetic role of KDM1A in OSCC. I hypothesize that some KDM1A-target genes are aberrantly regulated within human OSCC. To test this hypothesis, in aim 1, I will identify the KDM1A-target genes in immortal oral epithelial cells and human OSCC cells by establishing which promoter sites KDM1A binds using ChIP-sequencing (ChIP-seq).
In aim 2, I will determine the KDM1A- target genes that are differentially expressed between immortal oral epithelial cells and human OSCC cells by integrating my acquired ChIP-seq data with RNA sequencing (RNA seq) data previously generated in our lab. Gene ontology analysis on these differentially expressed genes will be performed to identify the biological processes altered in OSCC and the top differentially expressed genes within each biological process will be selected for subsequent experiments. KDM1A regulation of these genes will be confirmed by measuring gene expression in response to KDM1A knockdown and inhibition.
In aim 3, I will evaluate the expression of selected KDM1A-target genes in other oral epithelial and human SCC cell lines to determine if KDM1A dysregulation of these genes is widespread in human OSCC. By completing these aims, I will elucidate the epigenetic roles of KDM1A in OSCC with the potential to advance epigenetic therapies and identify novel therapeutic targets.
This proposed research will advance our understanding of underlying epigenetic mechanisms in the carcinogenesis of oral squamous cell carcinoma. Exploration of how lysine-specific demethylase 1 (KDM1A) dysregulates gene expression will provide vital knowledge toward improving therapies and identifying novel therapeutic targets within oral squamous cell carcinoma, the sixth most common cancer worldwide (4).