Tumor suppressor properties of the splicing regulatory factor RBM10

Abstract

RBM10 is an RNA binding protein and alternative splicing regulator frequently mutated in lung adenocarcinomas. Recent results indicate that RBM10 inhibits proliferation of lung cancer cells by promoting skipping of exon 9 of the gene NUMB, a frequent alternative splicing change in lung cancer generating a negative regulator of Notch signaling. Complementing these observations, we show that knock down of RBM10 in human cancer cells enhances growth of mouse tumor xenografts, confirming that RBM10 acts as a tumor suppressor, while knock down of an oncogenic mutant version of RBM10 reduces xenograft tumor growth. A RBM10 mutation found in lung cancer cells, V354E, disrupts RBM10-mediated regulation of NUMB alternative splicing, inducing the cell proliferation-promoting isoform. We now show that 2 natural RBM10 isoforms that differ by the presence or absence of V354 in the second RNA Recognition Motif (RRM2), display similar regulatory effects on NUMB alternative splicing, suggesting that V354E actively disrupts RBM10 activity. Structural modeling localizes V354 in the outside surface of one α-helix opposite to the RNA binding surface of RBM10, and we show that the mutation does not compromise binding of the RRM2 domain to NUMB RNA regulatory sequences. We further show that other RBM10 mutations found in lung adenocarcinomas also compromise regulation of NUMB exon 9. Collectively, our previous and current results reveal that RBM10 is a tumor suppressor that represses Notch signaling and cell proliferation through the regulation of NUMB alternative splicing.

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

“…Our pathway analysis suggests that, in certain solid tumors, splicing factor mutations are associated with reduced immune infiltration and, therefore, may provide selective advantage to cancer cells through immune evasion. Unlike SF3B1 and U2AF1, RBM10 has been reported to regulate splicing of apoptosis and notch pathway genes, and functional studies of cancer cell lines in vitro and in vivo show that LoF mutations lead to enhanced colony formation or accelerated tumor growth (Bechara et al, 2013; Hernández et al, 2016; Zhao et al, 2017). Our analysis comparing RBM10 LoF mutations in tumor samples and in cancer cell lines complements the existing studies, and it proposes that loss of this splicing factor has an immunosuppressive role in addition to its cell-autonomous growth-promoting role.…”

Genomic Alterations in Fatal Forms of Non-Anaplastic Thyroid Cancer: Identification of MED12 and RBM10 as Novel Thyroid Cancer Genes Associated with Tumor Virulence

“…Most frequent mutations occur in SF3B1, U2AF1, SRSF2 and ZRSR2 and are generally mutually exclusive (38). With regards to RBM10 , mutations have been reported in lung adenocarcinomas (39,40), where it acts as an alternative splicing regulator (41) modulating the product of NUMB , a NOTCH pathway regulator gene (42) critical for progression of lung adenocarcinomas. Studies point to loss of tumor suppressor properties of wild type RBM10 and oncogenic function of mutated RBM10 as possible mechanisms for causing uncontrolled growth (40).…”

“…With regards to RBM10 , mutations have been reported in lung adenocarcinomas (39,40), where it acts as an alternative splicing regulator (41) modulating the product of NUMB , a NOTCH pathway regulator gene (42) critical for progression of lung adenocarcinomas. Studies point to loss of tumor suppressor properties of wild type RBM10 and oncogenic function of mutated RBM10 as possible mechanisms for causing uncontrolled growth (40). RBM10 knockdown ( RBM10KD ) in human cancer cells enhanced tumor growth of xenografts in nude mice with similar results in lung adenocarcinoma cells expressing an RBM10 valine to glutamic acid (V354E) substitution (40).…”

“…Studies point to loss of tumor suppressor properties of wild type RBM10 and oncogenic function of mutated RBM10 as possible mechanisms for causing uncontrolled growth (40). RBM10 knockdown ( RBM10KD ) in human cancer cells enhanced tumor growth of xenografts in nude mice with similar results in lung adenocarcinoma cells expressing an RBM10 valine to glutamic acid (V354E) substitution (40). In addition to missense mutations, truncation mutations also occur in RBM10 .…”

Splicing-factor alterations in cancers

“…Finally, RBM10 is also among the most frequently mutated genes in lung adenocarcinoma (Imielinski et al 2012). The RBM10 mutations identified in patients disrupt NUMB splicing regulation and promote proliferation of cancer cell lines (Bechara et al 2013;Hernandez et al 2016).…”