Laryngo-pharyngeal
squamous cell carcinomas are one of the most common head and
neck cancers. Despite the presence of a large body of information, molecular
biomarkers are not currently used in the diagnosis, treatment and management of patients for this group of
cancer. Here, we have profiled expression of genes and
microRNAs of larynx and hypopharynx
tumors using high-throughput sequencing experiments. We found that
matrix metalloproteinases along with SCEL, CRNN, KRT4, SPINK5, and TGM3 among others have significantly altered expression in these
tumors. Alongside gene expression, the
microRNAs hsa-miR-139,
hsa-miR-203 and the hsa-miR-424/503 cluster have aberrant expression in these
cancers. Using target genes for these
microRNAs, we found the involvement of pathways linked to cell cycle, p53 signaling, and viral
carcinogenesis significant (P-values 10(-13), 10(-9) and 10(-7) respectively). Finally, using an ensemble machine-learning tool, we discovered a unique 8-gene signature for this group of
cancers that differentiates the group from the other
tumor subsites of head and neck region. We investigated the role of promoter methylation in one of these genes, WIF1, and found no correlation between DNA methylation and down-regulation of WIF1. We validated our findings of gene expression, 8-gene signature and promoter methylation using q-PCR, data from TCGA and q-MSP respectively. Data presented in this manuscript has been submitted to the NCBI Geo database with the accession number GSE67994.