The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations

Abstract

SUMMARY Mutations in several general pre-mRNA splicing factors have been linked to myelodysplastic syndromes (MDSs) and solid tumors. These mutations have generally been assumed to cause disease by the resultant splicing defects, but different mutations appear to induce distinct splicing defects, raising the possibility that an alternative common mechanism is involved. Here we report a chain of events triggered by multiple splicing factor mutations, especially high-risk alleles in SRSF2 and U2AF1, including elevated R-loops, replication stress, and activation of the ataxia telangiectasia and Rad3-related protein (ATR)-Chk1 pathway. We further demonstrate that enhanced R-loops, opposite to the expectation from gained RNA binding with mutant SRSF2, result from impaired transcription pause release because the mutant protein loses its ability to extract the RNA polymerase II (Pol II) C-terminal domain (CTD) kinase—the positive transcription elongation factor complex (P-TEFb)—from the 7SK complex. Enhanced R-loops are linked to compromised proliferation of bone-marrow-derived blood progenitors, which can be partially rescued by RNase H overexpression, suggesting a direct contribution of augmented R-loops to the MDS phenotype.

U2‐related proteins CHERP and SR140 contribute to colorectal tumorigenesis via alternative splicing regulation

“…The maintenance of genomic stability is of paramount importance to living organisms including cancer cells; thus, many proteins including splicing factors and RNA surveillance factors have been known to participate in DNA damage response. 17,[30][31][32][33] Our studies have identified that CHERP/SR140 and UPF3A are novel players involved in DNA damage response, as loss of them leads to DSB and triggers spontaneous DNA damage response and cell death. It is amazing that splicing factors and RNA surveillance factors are not only connected by alternative splicing but also by functional similarity involved in genomic maintenance, although the mechanism behind them are quite different.…”

“…The maintenance of genomic stability is of paramount importance to living organisms including cancer cells; thus, many proteins including splicing factors and RNA surveillance factors have been known to participate in DNA damage response . Our studies have identified that CHERP/SR140 and UPF3A are novel players involved in DNA damage response, as loss of them leads to DSB and triggers spontaneous DNA damage response and cell death.…”

FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R‐loops during mild replication stress

“…It has been well established that deregulated or impaired RNA processing results in elevated formation of R‐loops . Since hnRNP U is an important regulator of splicing, we hypothesized that the hnRNP U bound by FANCD2 at the genomic sites under replication stress has a function to suppress R‐loop levels.…”

Mutations in spliceosome genes and therapeutic opportunities in myeloid malignancies

“…These findings suggest that the pathological effects of spliceosome mutations are imparted through multiple mis‐spliced products simultaneously. In parallel, pathway analyses followed by functional validation revealed that splicing factor mutations distinctly converge on key cellular pathways to drive disease pathogenesis, including defects in DNA damage response and aberrant innate immune signaling . Further studies will be required to systematically address these fundamental questions, and more importantly, to identify the key players and pathways that can potentially be exploited for therapeutic purposes.…”