Abstract 2425: Delving into molecular phenomena of methylation, polyadenylation and mutation suggests their importance in regulating gene expression in GBSCC
Authors: Richa Singh, Esita Chattopadhyay, Roshni Roy, Bidyut Roy
Journal: Cancer Research (2017)

Abstract Background: Gingivo-buccal squamous cell carcinoma (GBSCC) is one of the most prevalent types of oral cancers in India. Although whole exome studies in oral cancer have reported somatic mutational driver genes, studies on methylation, mutations and alternative polyadenylation (APA) to identify differentially expressed transcripts and exons, respectively, are rare. The aim of our study is to investigate possible causes of expression deregulation due to methylation, APA or mutations. Methods: Whole transcriptome data was generated from 12 tumor-normal paired GBSCC tissues and analyzed for differential gene expression, differential exon usage and predicting APA site. Whole exome sequencing was performed with same sample set and the data was analyzed to identify somatic mutations. Reduced representation of bisulphate sequencing (RRBS) was also done for some of these samples to inquire about the methylation status of deregulated genes. Results: A total of 465 genes were found to have differential exon usage in tumor leading to expression of different isoforms and change in overall gene expression. About 194 genes were predicted to utilize alternate polyadenylation site in tumors. Amongst these, 11 genes including ERBB3, CDC25B and LTBP4 were shown to have differential exon usage in tumor with altered gene expression hinting upon the influence of polyadenylation in expression change. From the exome sequencing study, 180 SNVs and 11 indel somatic mutations per sample were observed. Apart from other non-silent exonic mutations at TP53, CASP8, DIS3 and DLG1, splice site mutations were also found in 37 and 4 genes due to point and indel mutations respectively. Genes such as TPM3, NBN, CXCL12 along with others showed differential exon usage and were found to harbor somatic mutations and APA site. This suggests for coupled regulation by APA and mutation in altering expression of those genes. Apart from this, a subset of deregulated genes (n=54) were observed to have differential methylation in tumors. Expression change of TAP1, SLN, ELN etc. corroborated with their methylation status suggesting the influence of methylation in regulating expression of these genes. Conclusion: Differential exon usage suggested different transcript formation leading to overall change in gene expression in tumor. Upon excavating into the regulatory causes, a subset of genes showed change in methylation pattern while few others showed change in APA site with/without somatic mutation effect. These molecular phenomena explain how different mechanisms are involved in expression deregulation of genes observed in GBSCC which would help in further functional research for cure of the disease. Citation Format: Richa Singh, Esita Chattopadhyay, Roshni Roy, Bidyut Roy. Delving into molecular phenomena of methylation, polyadenylation and mutation suggests their importance in regulating gene expression in GBSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2425. doi:10.1158/1538-7445.AM2017-2425