Tumor heterogeneity and prognostic impact of the aberrant splicing burden of colorectal cancers

Abstract

Abstract The colorectal cancer (CRC) transcriptome has important clinicopathological associations. Alternative splicing is a major determinant of transcriptomic complexity, but the impact of aberrant splicing on tumor heterogeneity and patient outcome from CRC is not well described. We investigated inter- and intra-tumor splicing heterogeneity among 504 primary tumor samples and 42 non-malignant colonic mucosa samples from 314 patients analyzed on splicing-sensitive microarrays. Most (62%) cancer-specific splicing events were rare across the tumors, and even heterogeneously expressed among multiregional samples, consistent with splicing noise. However, several novel events had high prevalence and a significant impact on the expression level of cancer-critical target genes, such as SFRP4 and RNF43. The tumor splicing burden (TSB) was identified as a main discriminatory feature of the splicing profiles of CRCs. The TSB was not driven by suspected noisy events, but correlated with gene set enrichment scores of splicing-related pathways and cell cycle progression. A high TSB was an independent predictor of a favorable 5-year relapse-free survival (multivariable hazard ratio 0.55, 95% confidence interval 0.32–0.92), and not confounded by immune cell infiltration or intra-tumor heterogeneity. This study highlights the contribution of splicing to tumor heterogeneity in CRC, and we propose the TSB as a prognostically relevant feature.