Comprehensive RNA-seq analysis of alternative splicing events that distinguishes between metastatic oral cancer of gingiva and tongue

Introduction: Oral cancer (OC) is a multifactorial disease caused due to various genomic changes. Alternative splicing (AS) is a regulatory genetic process through which messenger RNA forms diverse protein variants. This study a ims to study the variation in the AS events at tongue and gingiva locations of OC. Materials and Methods: FortyForty-five paired end OC RNA RNA-seq data were downloaded from Sequence Read Archive (SRA) data repository. Twenty four paired end OC (tongue ۱۳, gingival ۱۱) RNA sequences passed the stringent inclusion/ exclusion criteria which were analyzed foll owing Tuxedo pipeline. The ClueGO (v۲.۵.۸) tool in Cytoscape app manager (v۳.۷.۱) was used for gene set enrichment analysis keeping false discovery rate (FDR <=۰.۰۵). Results: EightyEighty-three genes were identified to be signific antly alternatively spliced when comparison was made between RNA sequences from normal tissues and tumor tissues from the gingiva region (p<۰.۰۵). Similarly, ۳۹ genes were found to be significantly alternatively spliced when comparison was made between nor mal tissues and tumor tissues from tongue region of OC. Of these, only ۴ genes i.e. AHRAHR, AL۳۵۶۴۸۸AL۳۵۶۴۸۸.۲ , KREMEN۱KREMEN۱, SH۳TC۱ were similar in gingiva and tongue whereas others were unique to their location location. Conclusion: GenomeGenome-wide AS events vary considerably in gingival and to ngue locations of OC. Hence, these events need to be thoroughly investigated for defining the treatment strategy. Further functional studies are needed to decipher the role of AS in OC OC.

کلیدواژه ها:

Gingiva cancer ، Oral cancer ، RNA RNA-seq ، Alternative splicing ، Tongue cancer