RNA-Seq reveals differentially expressed isoforms and novel splice variants in buccal mucosal cancer

Buccal mucosal cancer (BMC) is a multifactorial disease with poorly defined genetic profile and prognosis due to late detection stage and unavailability of reliable prognostic markers. To identify aberrant transcriptional events, we employed high throughput RNA-Seq analysis of BMC and normal tissue. Comparative transcriptome analysis with Cufflinks revealed 260 up and 328 down regulated genes whereas, 350 up and 397 down regulated isoforms by at least two folds over buccal normal in BMC. Study revealed 46 splice variants in normal and 106 in cancer, out of which 10 variants were validated with end point RT-PCR. Expression of two isoforms of CD74 was validated using RT-qPCR and found in accordance with RNA-Seq. Further extensive follow up analysis of modulator genes, isoforms and splice variants found in this study, might be useful in deep understanding of pathological changes in BMC and development of prospective intervention strategies. ⺠RNA-Seq analysis of BMC and normal sample through 454 sequencing ⺠Transcript assembly and expression analysis by Cufflinks and Cuffdiff respectively ⺠Identification of novel splice variants by Cuffcompare ⺠Validation of selected 10 novel splice variants by RT-PCR ⺠qRT-PCR validation of differentially expressed CD74 isoforms