Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma

Author(s)

Correa, Bruna R. ; de Araujo, Patricia Rosa ; Qiao, Mei ; Burns, Suzanne C. ; Chen, Chen ; Schlegel, Richard ; Agarwal, Seema ; Galante, Pedro A. F. ; Penalva, Luiz O. F.

• Document type: Journal article
• Source: GENOME BIOLOGY; v. 17, p. 16-pg., 2016-06-10.

Abstract

Background: Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and transcriptomic analyses have become important tools to identify new avenues for therapies. RNA-binding proteins (RBPs) are master regulators of co-and post-transcriptional events; however, their role in GBM remains poorly understood. To further our knowledge of novel regulatory pathways that could contribute to gliomagenesis, we have conducted a systematic study of RBPs in GBM. Results: By measuring expression levels of 1542 human RBPs in GBM samples and glioma stem cell samples, we identified 58 consistently upregulated RBPs. Survival analysis revealed that increased expression of 21 RBPs was also associated with a poor prognosis. To assess the functional impact of those RBPs, we modulated their expression in GBM cell lines and performed viability, proliferation, and apoptosis assays. Combined results revealed a prominent oncogenic candidate, SNRPB, which encodes core spliceosome machinery components. To reveal the impact of SNRPB on splicing and gene expression, we performed its knockdown in a GBM cell line followed by RNA sequencing. We found that the affected genes were involved in RNA processing, DNA repair, and chromatin remodeling. Additionally, genes and pathways already associated with gliomagenesis, as well as a set of general cancer genes, also presented with splicing and expression alterations. Conclusions: Our study provides new insights into how RBPs, and specifically SNRPB, regulate gene expression and directly impact GBM development. (AU)

• FAPESP's process: 13/25483-4 - Identification and functional analysis of RNA binding proteins associated with the development of glioblastoma multiform
• Grantee: Bruna Renata Silva Corrêa
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 13/07159-5 - RNA-binding proteins and post-transcriptional variations: influence on glioblastoma multiforme development
• Grantee: Bruna Renata Silva Corrêa
• Support Opportunities: Scholarships in Brazil - Doctorate