Colorectal cancer (CRC) is a severe risk to public health, and there is growing evidence that alternative splicing (AS) plays a crucial role in cancer. However, the AS biomarkers in CRC are seldom reported. In this study, we perform transcriptome analysis of colorectal samples for cancer-specific AS and transcriptomic alterations. We identify 1577 splice events in 885 genes, enriched in CRC-associated pathways and functions. In parallel, we find 10 splicing factors (SFs) with transcriptome variation or significant differential expression. Based on co-expression and binding motif, we construct an SF-AS regulatory network, revealing the association between cancer-specific AS and aberrant SF. Integrating The Cancer Genome Atlas and published sources, we observed that some recurrent AS is an indicator of poor prognosis. Through further experimental verification, we found that the AS of six genes showed significant differences between the tumor sample and the normal sample, and AS of TCF7, COL12A1, GK, and UBA1 can be used as new potential biomarkers in CRC. Our study provides an important analysis of CRC-associated AS, which could act as a starting point for future functional explorations, the development of biomarkers and AS-based target therapy.
Keywords: RNA-seq; alternative splicing; colorectal cancer; splicing factor.