Splicing factor gene mutations in hematologic malignancies

Abstract

Alternative splicing generates a diversity of messenger RNA (mRNA) transcripts from a single mRNA precursor and contributes to the complexity of our proteome. Splicing is perturbed by a variety of mechanisms in cancer. Recurrent mutations in splicing factors have emerged as a hallmark of several hematologic malignancies. Splicing factor mutations tend to occur in the founding clone of myeloid cancers, and these mutations have recently been identified in blood cells from normal, healthy elderly individuals with clonal hematopoiesis who are at increased risk of subsequently developing a hematopoietic malignancy, suggesting that these mutations contribute to disease initiation. Splicing factor mutations change the pattern of splicing in primary patient and mouse hematopoietic cells and alter hematopoietic differentiation and maturation in animal models. Recent developments in this field are reviewed here, with an emphasis on the clinical consequences of splicing factor mutations, mechanistic insights from animal models, and implications for development of novel therapies targeting the precursor mRNA splicing pathway.

Figure 1.

Consequences of somatic mutations affecting cis-acting pre-mRNA sequences. (A) A representative 3-exon pre-mRNA model is depicted with annotation of the location of common cis-acting sequences affected by somatic mutations. (B) Common splicing outcomes that are caused by somatic mutations in cis-acting sequences or splicing factors include exon inclusion, exon skipping, and intron retention. Other splicing outcomes include alternative 5′ or 3′ splice sites (mutually exclusive exons, coordinate cassette exons, and alternative first and last exons are not shown). The yellow color in exons 1 and 2 represents exonic sequence that is excluded when splicing into an alternative cryptic splice site occurs, as indicated by the dashed lines at the bottom of each cartoon. (C) The predominant type of pre-mRNA splicing alteration induced by mutations in various cis-acting sequences.

Figure 2.

Splicing factor (trans-acting) mutations and their impact on splicing in hematologic malignancies. (A) SF3B1 mutations lead to alternative 3′ splicing site (SS) usage because of the increased recognition of cryptic splice sites between the branch point and the canonical 3′ splice site. (B) U2AF1 mutations affect 3′ splice site recognition, leading to an increase in exon skipping because of use of an alternative splice sites. S34F-mutant-U2AF1 losses affinity for the 3′ SS motif when a T(U) is present in position −3. Conversely, mutations at the Q157 residue promote the recognition of 3′ SS when a G is present in position +1 and repress those bearing an A. (C) SRSF2 mutations affect its normal RNA-binding activity to the consensus ESE motif (SSNG). Mutant SRSF2 recognizes with higher affinity the CCNG motif vs the GGNG, promoting or repressing the inclusion of exons containing C- or G-rich motifs. (D) ZRSR2 loss-of-function mutations specifically affect splicing of U12-type introns leading to intron retention. BP, branch point; Py-tract, polypyrimidine-tract; snRNP, small nuclear ribonucleoproteins; Y, pyrimidine.

Figure 3.

Potential therapeutic strategies targeting splicing factor mutations and splicing changes. A schematic of the major spliceosome components illustrates potential strategies to modulate splicing. (A) Small molecules (eg, PB and FR derivatives and analogs) alter the function of the U2 snRNP, leading to the accumulation of unspliced products. (B) Inhibition of SR protein phosphorylation alters intracellular trafficking and binding of SR proteins to exonic splice enhancers, leading to altered utilization of cassette exons. (C) Oligonucleotides and transplicing modulators can change splicing preference at specific targets. (D) Depletion or replacement of spliced products. BPS, branch point sequence; CLK, CDC-like kinase; PPT, polypyrimidine tract; SRPK, SR protein kinase.