Aberrant splicing in neuroblastoma generates RNA-fusion transcripts and provides vulnerability to spliceosome inhibitors

Abstract

The paucity of recurrent mutations has hampered efforts to understand and treat neuroblastoma. Alternative splicing and splicing-dependent RNA-fusions represent mechanisms able to increase the gene product repertoire but their role in neuroblastoma remains largely unexplored. Here we investigate the presence and possible roles of aberrant splicing and splicing-dependent RNA-fusion transcripts in neuroblastoma. In addition, we attend to establish whether the spliceosome can be targeted to treat neuroblastoma. Through analysis of RNA-sequenced neuroblastoma we show that elevated expression of splicing factors is a strong predictor of poor clinical outcome. Furthermore, we identified >900 primarily intrachromosomal fusions containing canonical splicing sites. Fusions included transcripts from well-known oncogenes, were enriched for proximal genes and in chromosomal regions commonly gained or lost in neuroblastoma. As a proof-of-principle that these fusions can generate altered gene products, we characterized a ZNF451-BAG2 fusion, producing a truncated BAG2-protein which inhibited retinoic acid induced differentiation. Spliceosome inhibition impeded neuroblastoma fusion expression, induced apoptosis and inhibited xenograft tumor growth. Our findings elucidate a splicing-dependent mechanism generating altered gene products in neuroblastoma and show that the spliceosome is a potential target for clinical intervention.

Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer

“…Although there is limited experimental evidence that correlates chimeric RNA formation with the onset and/or progression of brain tumours, their contribution in numerous other tumour contexts is greatly emerging [ 190 ]. However, a very recent paper by Shi and colleagues [ 191 ] clearly showed how brain tumour cells may exploit trans-splicing-mediated fusion RNAs to their own advantage in order to guarantee their proliferation and survival [ 191 ]. By analysing a cohort of 172 RNA-sequenced neuroblastoma tumours, the authors identified more than 900 primarily intra-chromosomal fusion RNAs, with most of them specifically expressed in neuroblastoma [ 191 ].…”

“…However, a very recent paper by Shi and colleagues [ 191 ] clearly showed how brain tumour cells may exploit trans-splicing-mediated fusion RNAs to their own advantage in order to guarantee their proliferation and survival [ 191 ]. By analysing a cohort of 172 RNA-sequenced neuroblastoma tumours, the authors identified more than 900 primarily intra-chromosomal fusion RNAs, with most of them specifically expressed in neuroblastoma [ 191 ]. Interestingly, the identified fusion RNAs included transcripts from well-known oncogenes, previously shown to be important for neuroblastoma biology (i.e., MYCN and LIM domain only 1 LMO1), and they involved chromosomal regions commonly gained or lost in high-risk neuroblastoma [ 191 ].…”

“…By analysing a cohort of 172 RNA-sequenced neuroblastoma tumours, the authors identified more than 900 primarily intra-chromosomal fusion RNAs, with most of them specifically expressed in neuroblastoma [ 191 ]. Interestingly, the identified fusion RNAs included transcripts from well-known oncogenes, previously shown to be important for neuroblastoma biology (i.e., MYCN and LIM domain only 1 LMO1), and they involved chromosomal regions commonly gained or lost in high-risk neuroblastoma [ 191 ]. The identified RNA chimeras contained canonical splicing donor and acceptor sites and the fusion junctions were located in chromosomic regions no larger than 100 Kb, supporting the primary role of trans-splicing events for their biogenesis [ 191 ].…”

“…Interestingly, the identified fusion RNAs included transcripts from well-known oncogenes, previously shown to be important for neuroblastoma biology (i.e., MYCN and LIM domain only 1 LMO1), and they involved chromosomal regions commonly gained or lost in high-risk neuroblastoma [ 191 ]. The identified RNA chimeras contained canonical splicing donor and acceptor sites and the fusion junctions were located in chromosomic regions no larger than 100 Kb, supporting the primary role of trans-splicing events for their biogenesis [ 191 ]. Importantly, Pladienolide B-dependent splicing inhibition strongly reduced the expression of fusion transcripts, whereas the expression of the linear and independent transcripts was largely unaffected [ 191 ].…”

Ral GEF with the PH Domain and SH3 Binding Motif 1 Regulated by Splicing Factor Junction Plakoglobin and Pyrimidine Metabolism Are Prognostic in Uterine Carcinosarcoma

“…In previous studies, various parameters including the clinical stage, epithelial component grade, performance status, expression level of CA-125, myometrial invasion, adjuvant therapy, and residual cancer were considered to be related to the survival rate of patients with UCS [ 31 ]. In recent years, anomalous ASEs related to SFs were identified to be significant in researching cancer biology and clinical treatments as potential factors [ 10 , 32 ]. ASEs and SFs have been convinced to manufacture various oncoprotein isoforms related to cancer cell proliferation, antiapoptosis, and clinical metastasis [ 33 ].…”