Transcriptome-Based Epigenetic Screening identifies DNA Hypermethylation Signatures as Prognostic Biomarkers in Oral Squamous Cell Carcinoma

We analyzed five human oral squamous cell carcinoma (OSCC) cell lines: Ca9-22, HSC-3, OSC-20, SAS, and YD-10B. Cells were treated with 5-azacytidine (5-Aza), trichostatin A (TSA), or vehicle alone (Mock). Total RNA was extracted from each sample, and RNA-seq libraries were prepared and sequenced on an Illumina platform.Sequencing reads were aligned to the human reference genome (GRCh38/hg38) using TopHat. Transcripts were assembled with Cufflinks, and gene expression levels were estimated as fragments per kilobase of transcript per million mapped reads (FPKM). Differential expression was analyzed separately for each cell line using Cuffdiff by comparing Mock-treated cells with 5-Aza-treated cells (M vs. A) and Mock-treated cells with TSA-treated cells (M vs. T).