The interplay between non-coding RNAs and alternative splicing: from regulatory mechanism to therapeutic implications in cancer

Abstract

Alternative splicing (AS) is a common and conserved process in eukaryotic gene regulation. It occurs in approximately 95% of multi-exon genes, greatly enriching the complexity and diversity of mRNAs and proteins. Recent studies have found that in addition to coding RNAs, non-coding RNAs (ncRNAs) are also inextricably linked with AS. Multiple different types of ncRNAs are generated by AS of precursor long non-coding (pre-lncRNAs) or precursor messenger RNAs (pre-mRNAs). Furthermore, ncRNAs, as a novel class of regulators, can participate in AS regulation by interacting with the cis-acting elements or trans-acting factors. Several studies have implicated abnormal expression of ncRNAs and ncRNA-related AS events in the initiation, progression, and therapy resistance in various types of cancers. Therefore, owing to their roles in mediating drug resistance, ncRNAs, AS-related factors and AS-related novel antigens may serve as promising therapeutic targets in cancer treatment. In this review, we summarize the interaction between ncRNAs and AS processes, emphasizing their great influences on cancer, especially on chemoresistance, and highlighting their potential values in clinical treatment.

Keywords: Alternative splicing; Cancer; Chemotherapy; Drug resistance; Immunotherapy; Non-coding RNA; Targeted therapy.

Figure 1

The regulation mechanism and mode of RNA splicing. (A) The cis-acting elements on the primary transcription product include a 5' splice site (5'SS), 3' splice site (3'SS), branch point site (BPS), polypyrimidine tract (PPT), and splicing regulatory elements (SREs) in the proximity of splice site. The SREs are subdivided into intronic and exonic splice enhancers and silencers (ISEs, ISSs, ESEs, and ESSs, respectively). SR proteins as splicing activators enhance the utilization of splice sites by preferentially combining with ESEs and ISEs; and conversely, hnRNPs as splicing repressors inhibit the binding to the splice sites by interacting with ESSs and ISSs. (B) U1 snRNP recognizes 5'SS and binds it via base pairing, while SF1, U2AF2 and U2AF1 combines separately the BPS, PPT and 3'SS, forming early complex E. Then U2 snRNP replaces SF1 and binds to the BPS to form complex A. The U4/U6-U5 tri- snRNP complex is subsequently recruited to form a pre-catalytic spliceosome. The complex B is rearranged to form catalytically activated complex B*, which catalyzes the first transesterification reaction to produce Complex C, followed by the second transesterification reaction. Lastly, exons are interlinked to form mature mRNA, and the introns are degraded rapidly as the lariat and snRNPs are recovered. (C) RNA splicing consists of constitutive splicing (CS) and alternative splicing (AS), and various AS modes are generated based on the multiple splice sites and ways of exon linking, including exon skipping (ES), alternative 5' or 3' splice site selection (A5SS or A3SS), mutually exclusive exons (MXE) and intron retention (IR).

Figure 2

Non-coding RNAs produced by RNA splicing. (A) Precursor long non-coding RNAs (pre-lncRNAs) undergo splicing factor-mediated alternative splicing, which triggers the L/S switch. The long splicing isoforms, such as PXN-AS1-L, PXN-AS1-IR3, PCAT19-Long and NEAT1_2, have been reported to promote tumorigenesis. (B) LncRNAs PNUTS and PD-L1-lnc generated by bifunctional pre-mRNA splicing can promote carcinogenesis. (C) CircRNAs produced by backing splicing of host genes are involved in the regulation of several biological processes. For instance, CDR1as, circSMARCA5 and circPPP1R12A affect cancer progression through sponging miR-7, forming an R-loop with parental DNA, and producing peptides, respectively. (D) SnoRNAs (SNORA23 and SNORA42) are produced by splicing of the intronic region of the host genes, while sno-derived RNAs (sdRNAs) sdRNA68 and sdRNA104 are produced by FUS-mediated self-splicing of some snoRNAs. Both snoRNAs and sdRNAs are reported to alter the process of tumorigenesis in some cancers.

Figure 3

Regulation of alternative splicing by ncRNAs. Noncoding RNAs including lncRNAs, circRNAs, miRNAs, and snoRNAs regulate the occurrence of carcinogenesis-related AS events through two main splicing regulatory mechanisms. One way is to interact with the trans-acting factors, comprising acting as "Interactors" or "Hijackers" of SFs, participating in ceRNA regulatory network, encoding functional peptides and modulating chromatin signatures, all of which influence the expression and function of SFs. The second way is ncRNAs form dsRNA duplexes with the cis-acting elements, thus affecting tumorigenesis. The symbols (+) and (-) denote that ncRNAs act as oncogenes and tumor suppressor genes, respectively.

Figure 4

NcRNA-regulated AS events mediate drug resistance in oncology. Some lncRNAs, miRNAs and circRNAs impact drug resistance of cancer cells by triggering AS of cell death-related genes and metabolism-related genes. AS of cell death-related genes decreases the ratio of pro-/anti-apoptotic splicing isoforms to promote apoptotic tolerance in tumor cells, while AS of metabolism-related genes causes the upregulation of PKM2 expression to promote glycolysis in cancer cells.

Figure 5

Strategies targeting AS of ncRNAs or AS-related ncRNAs for cancer therapy. Several antitumor strategies have been developed to alter AS events at distinct levels and consequently reverse the course of drug-resistant cells or carcinogenesis. These strategies include small molecule inhibitors of targeting SFs (such as RBM39) and splicesomal components (such as SF3B1), splice-switching antisense oligonucleotides (SSOs) targeting splicing "switch", antisense oligonucleotides (ASOs) targeting specific RNA isoforms, specific antibodies and protein degraders targeting oncogenic protein variants, and RNA therapies targeting AS-related ncRNAs.