Whole Genome Expression Profiling of Epithelial-Myoepithelial Carcinoma of Salivary Glands

On 6 normal and 17 epithelial- myoepithelial carcinoma samples a whole transcriptome shotgun sequencing experiment was performed.

Statistical correlation analysis of the resulting data allowed continuing with a comparative analysis of 6 normal samples versus 13 neoplastic samples, 4 neoplastic samples were excluded. Using strict and conservative criteria 220 differentially expressed transcripts were found, with 36% up- and 64% downregulated. The transcripts were annotated using NCBI Entrez Gene, and computational analyzed with the Ingenuity Pathway Analysis program.

From these significantly changed expressions the analysis finds 26 cancer-related (ACAT1, ARPC1A, ATP5J, CANX, DDX39B, DDOST, EXT1, FGFR1, GOLPH3, MAGT1, MAPK8IP3, MAT2A, MMADHC, P4HB, PDK4, RHOA, SCARB2, SDHB, SDHD, SEC63, SSR1, SSR3, TM9SF2, TMED2, TRAM1, ZMPSTE24) and 16 transcripts which are related to mitochondrial dysfunction (ATP5A1, ATP5F1, ATP5J, COX7B, COX7C, MT-ND5, NCSTN, NDUFA4, NDUFA5, NDUFAB1, NDUFB11, NDUFV2, PDHA1, PRDX3, SDHB, SDHD), overlapping with 3 cancer-genes. These findings are well supported by existing literature about this cancer. From other strongly differentially expressed transcripts of microRNAs and certain genes the biological functions and their role in this cancer are still unknown.

These 220 differentially expressed genes and microRNAs provide here for the first time a sufficient large set to specifically define this sort of cancer.

In the next step these results need to be further experimentally confirmed and their biological function determined to find out whether they are suited as disease biomarkers, and whether they provide suitable targets for anti-cancer therapy.