PTBP1-dependent regulation of USP5 alternative RNA splicing plays a role in glioblastoma tumorigenesis.

in Molecular carcinogenesis by Daisy I Izaguirre, Wen Zhu, Tao Hai, Hannah C Cheung, Ralf Krahe, Gilbert J Cote

TLDR

  • The study investigates how abnormal changes in the way our cells make a type of RNA called messenger RNA (mRNA) can contribute to the development of brain tumors called glioblastoma (GBM). The researchers used a type of test called a microarray to compare the way mRNA is made in GBM tumor samples and cells. They found a specific change in the way the USP5 gene is made in GBM that may be important for the development of the tumor. The researchers then tested how changing this specific change in the USP5 gene affected the growth and movement of GBM cells. They found that changing the USP5 gene in this way slowed down the growth and movement of the GBM cells. This suggests that changes in the way mRNA is made in GBM may be important for the development of the tumor and that these changes could be targeted with new treatments.

Abstract

Aberrant RNA splicing is thought to play a key role in tumorigenesis. The assessment of its specific contributions is limited by the complexity of information derived from genome-wide array-based approaches. We describe how performing splicing factor-specific comparisons using both tumor and cell line data sets may more readily identify physiologically relevant tumor-specific splicing events. Affymetrix exon array data derived from glioblastoma (GBM) tumor samples with defined polypyrimidine tract-binding protein 1 (PTBP1) levels were compared with data from U251 GBM cells with and without PTBP1 knockdown. This comparison yielded overlapping gene sets that comprised only a minor fraction of each data set. The identification of a novel GBM-specific splicing event involving the USP5 gene led us to further examine its role in tumorigenesis. In GBM, USP5 generates a shorter isoform 2 through recognition of a 5' splice site within exon 15. Production of the USP5 isoform 2 was strongly correlated with PTBP1 expression in GBM tumor samples and cell lines. Splicing regulation was consistent with the presence of an intronic PTBP1 binding site and could be modulated through antisense targeting of the isoform 2 splice site to force expression of isoform 1 in GBM cells. The forced expression of USP5 isoform 1 in two GBM cell lines inhibited cell growth and migration, implying an important role for USP5 splicing in gliomagenesis. These results support a role for aberrant RNA splicing in tumorigenesis and suggest that changes in relatively few genes may be sufficient to drive the process.

Overview

  • The study investigates the role of aberrant RNA splicing in tumorigenesis using genome-wide array-based approaches. The authors compare splicing factor-specific gene sets in glioblastoma (GBM) tumor samples and cell lines to identify GBM-specific splicing events. The study focuses on the USP5 gene and its role in tumorigenesis, specifically the production of a shorter isoform 2 through recognition of a 5' splice site within exon 15. The study aims to identify the specific contributions of aberrant RNA splicing to tumorigenesis and to explore potential therapeutic targets for GBM.

Comparative Analysis & Findings

  • The study compares splicing factor-specific gene sets in GBM tumor samples and cell lines. The authors identify a novel GBM-specific splicing event involving the USP5 gene, which generates a shorter isoform 2 through recognition of a 5' splice site within exon 15. The production of the USP5 isoform 2 is strongly correlated with PTBP1 expression in GBM tumor samples and cell lines. The study finds that splicing regulation is consistent with the presence of an intronic PTBP1 binding site and can be modulated through antisense targeting of the isoform 2 splice site to force expression of isoform 1 in GBM cells. The forced expression of USP5 isoform 1 in two GBM cell lines inhibits cell growth and migration, implying an important role for USP5 splicing in gliomagenesis.

Implications and Future Directions

  • The study's findings suggest that changes in relatively few genes may be sufficient to drive the process of aberrant RNA splicing in tumorigenesis. The identification of GBM-specific splicing events and their role in tumorigenesis may lead to the development of targeted therapies for GBM. The study highlights the importance of splicing regulation in tumorigenesis and suggests that splicing factors may be potential therapeutic targets for GBM. Future research could explore the role of other splicing factors in GBM and the potential of splicing-based therapies for other cancers.
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