Complex landscape of alternative splicing in myeloid neoplasms

Abstract

Myeloid neoplasms are characterized by frequent mutations in at least seven components of the spliceosome that have distinct roles in the process of pre-mRNA splicing. Hotspot mutations in SF3B1 , SRSF2 , U2AF1 and loss of function mutations in ZRSR2 have revealed widely different aberrant splicing signatures with little overlap. However, previous studies lacked the power necessary to identify commonly mis-spliced transcripts in heterogeneous patient cohorts. By performing RNA-Seq on bone marrow samples from 1,258 myeloid neoplasm patients and 63 healthy bone marrow donors, we identified transcripts frequently mis-spliced by mutated splicing factors (SF), rare SF mutations with common alternative splicing (AS) signatures, and SF-dependent neojunctions. We characterized 17,300 dysregulated AS events using a pipeline designed to predict the impact of mis-splicing on protein function. Meta-splicing analysis revealed a pattern of reduced levels of retained introns among disease samples that was exacerbated in patients with splicing factor mutations. These introns share characteristics with “detained introns,” a class of introns that have been shown to promote differentiation by detaining pro-proliferative transcripts in the nucleus. In this study, we have functionally characterized 17,300 targets of mis-splicing by the SF mutations, identifying a common pathway by which AS may promote maintenance of a proliferative state.

Functional analyses of human LUC7-like proteins involved in splicing regulation and myeloid neoplasms

“…However, KD of LUC7L and LUC7L2 both showed increased levels of intron exclusion as opposed to intron retention (Figure 4C). This phenomenon of increased intronic splicing efficiency has also been identified in myeloid neoplastic patient bone marrow samples with LUC7L2 deficiency (Hershberger et al, 2020b). Although yeast Luc7p is known to stabilize the interaction of U1 snRNA and the 5 0 SS, the mammalian LUC7-like proteins seem to have additional functions in AS, including the repression of a subset of alternatively spliced introns and regulation of SEs.…”

“…The unique role of LUC7L2 mutations or deletions in myelodysplastic syndrome and related neoplasms distinguishes it from the other paralogs. In a large set of myeloid disease patient bone marrows, expression of LUC7L2 was reduced with or without concomitant mutation or deletion compared with normal bone marrow (Hershberger et al, 2020b). In addition, low LUC7L2 expression or mutation is associated with reduced patient survival in these diseases (Hosono et al, 2014).…”

“…For LUC7L2, however, a loss of function due to frameshift and nonsense mutations as well as deletions that encompass LUC7L2 in the q arm of chromosome 7 are common (Chen et al, 2014;Jerez et al, 2012). Low expression of LUC7L2 in myeloid neoplastic patient bone marrow was shown to cause 5 0 SS dysregulation and an increase in splicing of normally retained introns (RIs) (Hershberger et al, 2020b). Interestingly, despite the homology between the LUC7-like family of putative SFs, LUC7L and LUC7L3 are not frequently targeted by mutations and deletions in patients with myeloid neoplasms, suggesting that LUC7L2 uniquely regulates a subset of genes that are important for the initiation or progression of disease.…”

Chromatin accessibility determines intron retention in a cell type-specific manner

“…Fates of intron-retaining transcripts can be diverse and include (i) nonsense-mediated decay triggered by intronic premature termination codons, (ii) detention in the nucleus or nuclear degradation, and (iii) translation into alternative protein isoforms or creation of neoepitopes (Monteuuis et al, 2019; Smart et al, 2018; Wong et al, 2016). A better understanding of how IR is regulated is crucial to determine factors leading to aberrant IR, which has been associated with multiple diseases including cancer (Dvinge et al, 2019; Hershberger et al, 2020; Monteuuis et al, 2020)…”

Improved risk stratification in younger IDH wild-type glioblastoma patients by combining a 4-miRNA signature with MGMT promoter methylation status

“…SF3B1 is involved in alternative splicing, frequently mutated in myeloid neoplasms and appeared also as most statistically significant in the analysis of Cancer Gene Census gene and has not been published in the context of glioblastoma so far. 35 ONECUT2, a transcription factor of the onecut family, is involved in cell differentiation was shown to be down-regulated in glioblastoma. PAWR is a known tumor-suppressor gene involved in the regulation of apoptosis and has been suggested as a prognostic risk factor in glioblastoma.…”