Estimation of isoform expression of PI3K and FGFR signaling pathway components by transcriptome analysis in bladder cancer

Aberrant pre-mRNA alternative splicing is a common event in cancer cells. Many abnormally spliced RNA variants have been observed in tumor cells and they can be used as biomarkers or therapeutic targets in new drug design. Increasing our knowledge in understanding the mechanisms of alternative pre-mRNA splicing for cancer-related genes and determination of cancer specific isoforms are important for the development of new strategies in cancer therapy. The aim of this study was isoforms identification and expression of PIK3CA, FGFR3 and FGFR1 genes in bladder cancer by RNA Sequencing and Real-Time PCR.
This cross-sectional study was conducted at Urology Research Center of Sina Hospital, Tehran University of Medical Sciences, Tehran, from September 2014 to October 2016. Paired tumor and adjacent normal tissues samples were obtained from 30 bladder cancer subjects. Total RNAs were extracted from bladder tumor and normal tissues. Quantitative and qualitative examinations have been done. After quality control, fragmentation of RNAs and cDNA library construction, next-generation RNA sequencing was performed. Resulting raw data were analyzed with different bioinformatics software. Differential expression was confirmed by Real-Time PCR.
RNA sequencing results showed the number of PIK3CA (1 vs 3), FGFR3 (7 vs 6) and FGFR1 (9 vs 12) isoforms and their expression were different in bladder normal tissues in comparison to tumor tissues. Overexpression of PIK3CA gene have been observed in 42% of tumor samples but statistically was not significant. Increased FGFR3 gene (P=0.01) and decreased FGFR1 (P=0.01) expression were significant. There was an association with overexpression of FGFR3 and cigarette smoking ((P=0.037) and family history (P=0.004).
RNA sequencing make possible to do the accurate assessment of transcript abundance and identification of different isoforms resulted from aberrant pre-mRNA alternative splicing, which is a crucial process for the maturation of transcripts of multi-exon genes. Regarding the differences in isoforms expression in tumor and normal tissues of bladder cancer, they have potential to be used as biomarkers and sensitive targets for cancer therapy.