Distinct splicing signatures affect converged pathways in myelodysplastic syndrome patients carrying mutations in different splicing regulators

Abstract

Myelodysplastic syndromes (MDS) are heterogeneous myeloid disorders with prevalent mutations in several splicing factors, but the splicing programs linked to specific mutations or MDS in general remain to be systematically defined. We applied RASL-seq, a sensitive and cost-effective platform, to interrogate 5502 annotated splicing events in 169 samples from MDS patients or healthy individuals. We found that splicing signatures associated with normal hematopoietic lineages are largely related to cell signaling and differentiation programs, whereas MDS-linked signatures are primarily involved in cell cycle control and DNA damage responses. Despite the shared roles of affected splicing factors in the 3 ′ splice site definition, mutations in U2AF1, SRSF2, and SF3B1 affect divergent splicing programs, and interestingly, the affected genes fall into converging cancer-related pathways. A risk score derived from 11 splicing events appears to be independently associated with an MDS prognosis and AML transformation, suggesting potential clinical relevance of altered splicing patterns in MDS.

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

“…Given distinct splicing responses, this has brought up the appealing hypothesis that these mutations may affect distinct molecular defects, but in some converging biological pathways, as we recently observed via analysis of splicing signatures in MDS patients (Qiu et al, 2016), which is in line with the synergistic effects of mutations in SRSF2 and SF3B1 in the mouse (Lee et al, 2016a). We now provide another potential converging mechanism, which is the induction of R-loops.…”

“…Taking advantage of all mutations in the same cellular background, we first revisited an important problem with respect to diverse splicing responses induced by different splicing factor mutations (Ilagan et al, 2015; Qiu et al, 2016). We extracted total RNA from individual cell lines and used highly quantitative RNA annealing selection ligation followed by deep sequencing (RASL-seq), which we developed in the lab, to measure a large number (>5,000) of annotated alternative splicing events in humans (Li et al, 2012).…”

“…In particular, disease development has been functionally linked to the inclusion of a “toxic” exon in the Ezh2 gene in Srsf2 (P95H) knockin mice (Kim et al, 2015) and a polyadenylation switch event in the autophagy gene Atg7 caused by U2af1 (S34F) overexpression on a murine pro-B cell model (Park et al, 2016). Puzzling, however, is the observation that each splicing factor mutation appears to cause a rather unique set of splicing changes in both cellular models and patients (Ilagan et al, 2015; Kim et al, 2015; Qiu et al, 2016; Shirai et al, 2015). Even the same mutation, such as that in SF3B1 , induced largely non-overlapping splicing changes in mouse versus human cells (Mupo et al, 2017).…”

Distinct and convergent consequences of splice factor mutations in myelodysplastic syndromes

“…29 Recently, CD34 + bone marrow cells from MDS patients carrying different spliceosome mutations were interrogated in a single cohort using RNA-sequencing. Direct comparison of differential splicing Although only 5500 splicing events were interrogated, the study concluded that MDS-linked splicing signatures are primarily involved in cell cycle control and DNA damage responses.…”

“…Although only 5500 splicing events were interrogated, the study concluded that MDS-linked splicing signatures are primarily involved in cell cycle control and DNA damage responses. 29 Recently, CD34 + bone marrow cells from MDS patients carrying different spliceosome mutations were interrogated in a single cohort using RNA-sequencing.…”