Splicing and cancer: Challenges and opportunities

Abstract

Constitutive splicing is favored in strong splice sites, which have the conserved consensus sequences at 5 0 (CAG|GUAAGU) and 3 0 (NYAG|G) splice sites. Exons are usually shorter sequences, ranging from 50 to 250 bp, whereas introns can have broader length variation, from <100 bp to more than 1,000 bp, and around 20% of human introns are larger than 5 kb (Lander et al., 2001). In addition to constitutive exon splicing, the presence of alternative splice sites leads to variable ways to mature an mRNA ( Figure 2). Exons and introns might host alternative splice sites, which are similar to, but usually not as strong as, consensus splice sites (Fu & Ares, 2014;Kornblihtt et al., 2013). If a 5 0 or 3 0 alternative site lies within an exon, part of this exon might be read as an intron. Also, alternative splicing can lead to exon skipping, in which a constitutive 3 0 splice site fails to be recognized and assembly of spliceosome proceeds to the next available 3 0 splice site, which can result in exclusion of an exon. Alternatively, 5 0 splice sites might not be read as well, resulting in intron retention. In some transcripts, a mutual exclusion of exons might take place generating different messages . Cryptic splice sites are similar to consensus sites, but they are usually recognized only after a mutation in the gene, or of a spliceosome component, leading to alterations in the final message. In breast cancer, mutations in splicing factor 3B subunit 1 (SF3B1), for example, induce the use of cryptic 3 0 splice sites (DeBoever et al., 2015). Single nucleotide variants (SNVs) of 1,812 tumor samples were analyzed by whole-exome sequencing and revealed exon skipping and intron retention were among the most frequently observed alternative splicing events (Jung et al., 2015; Box 1).Alternative splicing mechanisms are dependent on recognition of splice site sequences in the pre-mRNA, which in turn depends on both the strength of sequences as well as the presence of proteins and signals that guide the spliceosome to these regions. Alternative exons in humans and mice are surrounded by more conserved regulatory sequences than constitutive exons, indicating the former ones are under strict regulation. Consistently, 30-50% of ISEs are located nearby alternative exons (Yeo, Van Nostrand, & Liang, 2007). Interestingly, ISEs and ESSs show a positional overlap in different pre-mRNA substrates, indicating the regulation depends on their positioning with respect to the 5 0 upstream exon and the bound proteins (Y. Wang et al., 2012). The ISSs can interfere with exon inclusion in different pre-mRNAs, and regulate 5 0 splice site choice, therefore, exerting alternative splicing regulation (Y. Wang et al., 2013). In this sense, mutations in exonic and intronic sequences are critical and might affect the balance of regulatory sequences and also their activity, since most effects in splicing are location-dependent. Intronic mutations are commonly associated with nonsense-mediated decay responses, caused by an increased rate of premature stop ...

Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development

“…Statistical significance is determined by paired t-test (*P < 0.05; **P < 0.01). c Sequence chromatograms illustrate the editing level of the indicated sites (1)(2)(3)(4) in HEK293T cells that were co-transfected with the indicated minigene and overexpression construct. Black arrowhead indicates editing position.…”

“…A lternative splicing and RNA editing are the two major pre-messenger RNA (pre-mRNA) processing steps diversifying transcriptome in eukaryotes. Regulation of alternative splicing involves cis-acting elements, such as exonic/ intronic splicing enhancers/silencers (ESE/S, ISE/S), and transacting factors, such as serine arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs), transcription, chromatin modification, and RNA secondary structure [1][2][3][4][5][6][7][8][9][10][11] . Aberrant splicing is associated with numerous cancers and it is generally caused by mutations in cis-and trans-splicing regulatory elements and altered expression of splicing factors 4 .…”

Splicing Dysregulation as Oncogenic Driver and Passenger Factor in Brain Tumors

“…The aberrant expression of oncogenic and tumor-suppressor transcription factors often underlies the alteration of transcriptional and post-transcriptional mechanisms in cancer cells. Furthermore, the dysregulation of splicing regulatory mechanisms has clearly emerged as a typical feature of cancer cells, which can either drive or contribute to tumor onset and progression [16,17].…”

“…In this way, cells modulate their proteome to withstand changes in the surrounding environment, or in response to the activation of a specific differentiation program [20]. Nevertheless, its remarkable flexibility represents a risk factor, and splicing dysregulation concurs with many human diseases [20] including cancer [16,17]. The aberrant splicing events occurring in cancer cells often lead to generation of protein variants displaying altered function, which can contribute to tumorigenesis [16].…”

Insights into the involvement of spliceosomal mutations in myelodysplastic disorders from an analysis of SACY-1/DDX41 inCaenorhabditis elegans

“…Mutations affecting components of the spliceosome are frequently found in hematological malignancies, including myelodysplastic syndromes (MDS; Yoshida et al 2011;reviewed by Yoshida and Ogawa 2014;Coltri et al 2019), which comprise a heterogeneous set of myeloid neoplasms characterized by anemia and cytopenia that progress to acute myeloid leukemia (AML) to varying degrees (Tefferi and Vardiman 2009). The genetic properties and genomic impacts of disease-causing missense mutations in DDX41 and other spliceosomal proteins have been uncertain.…”