Systematic Analysis of Splice-Site-Creating Mutations in Cancer

Abstract

SUMMARYFor the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.

Pan-Cancer Repository of Validated Natural and Cryptic mRNA Splicing Mutations

“…Our results contrast with another TCGA study that investigated alternative mRNA splicing 21 and demonstrated a limited set of non-constitutive exon-exon junctions attributable to cis-acting splicing mutations (n = 32). The 2,736 novel or rare variants that we report which specifically activate cryptic splicing (significant 'junction-spanning cryptic site use' reads found by Veridical), exceed the number reported in another study that analyzed all available TCGA tumor transcriptomes (n=1,964) 22 .…”

RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer

“…Few tools are directed at linking aberrant splicing to variants in cis, and most are tailored to the authors' particular aims (Jayasinghe et al , 2018 ;Pertea et al , 2001 ;Jung et al , 2015) . RegTools is designed for broad applicability and computational efficiency ( Supplementary Figure 14) .…”

Molecular profiling of driver events and tumor-infiltrating lymphocytes in metastatic uveal melanoma

“…RNA sequencing data for 9,583 tumors from 32 cancer types were downloaded from the cgHub repository on December 18, 2015, and aligned to the hg19 human genome assembly, 14 excluding alternative haplotype regions, with hisat 62 0.1.6-beta (parameters: "--no-mixed -no-discordant --no-unal --known-splicesite-infile"), using splice junctions defined in the GENCODE (version 19) reference human genome annotation. Gene read counts were derived with htseq-count 54 (parameters: "-m intersection-strict -s no").…”