Genome Sequencing and RNA-Motif Analysis Reveal Novel Damaging Noncoding Mutations in Human Tumors

Abstract

A major challenge in cancer research is to determine the biological and clinical significance of somatic mutations in noncoding regions. This has been studied in terms of recurrence, functional impact, and association to individual regulatory sites, but the combinatorial contribution of mutations to common RNA regulatory motifs has not been explored. Therefore, we developed a new method, MIRA (mutation identification for RNA alterations), to perform an unbiased and comprehensive study of significantly mutated regions (SMR) affecting binding sites for RNA-binding proteins (RBP) in cancer. Extracting signals related to RNA-related selection processes and using RNA sequencing (RNA-seq) data from the same specimens, we identified alterations in RNA expression and splicing linked to mutations on RBP binding sites. We found SRSF10 and MBNL1 motifs in introns, HNRPLL motifs at 5' UTRs, as well as 5' and 3' splice-site motifs, among others, with specific mutational patterns that disrupt the motif and impact RNA processing. MIRA facilitates the integrative analysis of multiple genome sites that operate collectively through common RBPs and aids in the interpretation of noncoding variants in cancer. MIRA is available at https://github.com/comprna/mira The study of recurrent cancer mutations on potential RBP binding sites reveals new alterations in introns, untranslated regions, and long noncoding RNAs that impact RNA processing and provide a new layer of insight that can aid in the interpretation of noncoding variants in cancer genomes. .

Alternative splicing links histone modifications to stem cell fate decision

“…A higher cutoff is always helpful in reducing the false positive while compromising the sensitivity. The cutoff, |ΔΨ| ≥ 0.1 or |ΔΨ| ≥ 10%, is widely accepted and used in AS identification [ 25 , 106 – 108 ]. Many other studies even used 0.05 as the cutoff [ 109 – 113 ].…”

SNPs and Somatic Mutation on Long Non-Coding RNA: New Frontier in the Cancer Studies?

“…In parallel, Singh et al developed the mutation identification for RNA alterations (MIRA) method to study significantly mutated regions (SMR) affecting binding sites for RNA-binding proteins (RBP) in cancer. They found one exon SMR and 11 intron SMRs in TCL6, suggesting that lncRNA introns could be as relevant as exonic sequences in tumorigenesis [66]. Moreover, a study on papillary thyroid carcinoma (PTC) has shown that the lncRNA GAS8 Antisense RNA 1 (GAS8) is the second most frequently altered gene in this tumor type, confirming its oncosuppressor role [67].…”

MBNL1 alternative splicing isoforms play opposing roles in cancer

“…MBNL1 is a well-studied RNA-binding protein (RBP) involved in splicing, RNA export, and stability ( Goers et al, 2010 ; Tran et al, 2011 ; Masuda et al, 2012 ; Konieczny et al, 2014 ; Sznajder et al, 2016 ). Whereas its role in cellular differentiation and in the mechanism underlying myotonic dystrophy has been deeply investigated in the past decades ( Lee & Cooper, 2009 ; Timchenko, 2013 ), its function in cancer has been explored only recently ( Fish et al, 2016 ; Singh et al, 2018 ). To systematically assess isoforms' function in an endogenous setting, we took advantage of the splice-switching antisense oligonucleotide (AON) technology.…”