The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer

Abstract

Alternative splicing allows for the expression of multiple RNA and protein isoforms from one gene, making it a major contributor to transcriptome and proteome diversification in eukaryotes. Advances in next generation sequencing technologies and genome-wide analyses have recently underscored the fact that the vast majority of multi-exon genes under normal physiology engage in alternative splicing in tissue-specific and developmental-specific manner. On the other hand, cancer cells exhibit remarkable transcriptome alterations partly by adopting cancer-specific splicing isoforms. These isoforms and their encoded proteins are not insignificant byproducts of the abnormal physiology of cancer cells, but either drivers of cancer progression or small but significant contributors to specific cancer hallmarks. Thus, it is paramount that the pathways that regulate alternative splicing in cancer, including the splicing factors that bind to pre-mRNAs and modulate spliceosome recruitment. In this review, we present a few distinct cases of alternative splicing in cancer, with an emphasis on their regulation as well as their contribution to cancer cell phenotype. Several categories of splicing aberrations are highlighted, including alterations in cancer-related genes that directly affect their pre-mRNA splicing, mutations in genes encoding splicing factors or core spliceosomal subunits, and the seemingly mutation-free disruptions in the balance of the expression of RNA-binding proteins, including components of both the major (U2-dependent) and minor (U12-dependent) spliceosomes. Given that the latter two classes cause global alterations in splicing that affect a wide range of genes, it remains a challenge to identify the ones that contribute to cancer progression. These challenges necessitate a systematic approach to decipher these aberrations and their impact on cancer. Ultimately, a sufficient understanding of splicing deregulation in cancer is predicted to pave the way for novel and innovative RNA-based therapies.

Keywords: alternative splicing; cancer spliceome; exons; introns; splicing.

Figure 1

Alternative splicing as a source of diversification. A schematic diagram that depicts the various types of alternative splicing events that potentially exist in cells.

Figure 2

TP53 pre-mRNA splicing has significant consequences on the gene product, p53 protein. A schematic diagram of p53 pre-mRNA shows 11 exons (red boxes for canonical exons and blue boxes for cryptic intronic exon 9, i9) and 10 introns (gray lines). The size and shade of the exon indicate whether it is untranslated region (narrow, light red) or coding (wide, dark red). The various domains and the exons encoding them are also indicated (adopted from Surget et al., 2013). These are: Transactivation domains I and II (TAD I and TAD II), proline-rich region (PXXP), DNA-binding domain (DBD), nuclear localization signal (NLS), oligomerization domain (OD), and negative regulation domain (NRD). A fully spliced mRNA containing the 11 canonical exons encodes for full length and functional p53 protein. Several isoforms with various alternative first exons can be generated for p53 pre-mRNA. In this case, the first exon is what is usually exon 5 in the canonical transcript, leading to the production of p53 protein lacking TADs, PXXP, and part of DBD. This truncated p53 is expected to be dominant negative. A similar protein can be encoded by transcripts in which intron 2 is retained, leading to the usage of start codon in exon 4 rather than the canonical start codon in exon 2. On the other hand, retention of intron 9 and/or inclusion of the cryptic intronic exon 9, i9, change the reading frame causing the loss of the encoded amino acids from exons 10 and 11. The resulting p53 proteins lack OD and NRD. These truncated p53 proteins could compete with wild type p53 for DNA binding but are not functional as they cannot oligomerize.