Pathway based prognostic gene expression profile of buccal and gingivo-buccal oral squamous cell carcinoma in smokeless tobacco chewers.

BACKGROUND: The objective was to study comprehensive mRNA expression profiles of buccal mucosa oral squamous cell carcinoma (OSCC-BM) and gingivo-buccal OSCC (OSCC-GB) in smokeless tobacco chewers to understand the biological behavior of OSCC at these specific sites and identify diagnostic and prognostic markers. METHODS: High throughput RNA sequencing transcriptome of fresh buccal mucosa (4 samples) and gingivo-buccal (4 samples) OSCC with normal oral mucosa (3 samples) was performed on Illumina NextSeq500 paired end sequencing with 75x2bp. RESULTS: In the comparison between OSCC and normal, there were 402 differentially expressed genes (DEGs); between OSCC-BM and normal, there were 467 DEGs; and between OSCC-GB and normal oral tissue, there were 608 DEGs. Pathway-based analysis of gene expression was done. The inflammation mediated by chemokine and cytokine signaling pathway had the maximum gene hits. CONCLUSIONS: FZD2 and its interactions with the cadherins have a role in invasion and metastasis. immunosurveillance is evident in OSCC-GB with the downregulation of CADM1.