RBM10 loss promotes metastases by aberrant splicing of cytoskeletal and extracellular matrix mRNAs.

RBM10 modulates transcriptome-wide cassette exon splicing. Loss-of-function RBM10 mutations are enriched in thyroid cancers with distant metastases. Analysis of transcriptomes and genes mis-spliced by RBM10 loss showed pro-migratory and RHO/RAC signaling signatures. RBM10 loss increases cell velocity. Cytoskeletal and ECM transcripts subject to exon-inclusion events included vinculin (VCL), tenascin C (TNC) and CD44. Knockdown of the VCL exon inclusion transcript in RBM10-null cells reduced cell velocity, whereas knockdown of TNC and CD44 exon-inclusion isoforms reduced invasiveness. RAC1-GTP levels were increased in RBM10-null cells. Mouse HrasG12V/Rbm1OKO thyrocytes develop metastases that are reversed by RBM10 or by combined knockdown of VCL, CD44 and TNC inclusion isoforms. Thus, RBM10 loss generates exon inclusion in transcripts regulating ECM-cytoskeletal interactions, leading to RAC1 activation and metastatic competency. Moreover, a CRISPR-Cas9 screen for synthetic lethality with RBM10 loss identified NFkB effectors as central to viability, providing a therapeutic target for these lethal thyroid cancers. Overall design: Differential splicing analysis was performed as previously described (Dvinge et al., 2014), from RNA-sequencing of the following isogenic RBM10-overexpressing or -Knockdown (KD) thyroid cancer cell lines: KTC1, KTC1-RBM10, PE121410, PE121410-RBM10, 8305C-sh.Ctrl, 8305C-sh.RBM10, SW1736-sh.Ctrl, SW1736-sh.RBM10 and HTH83-sh.Ctrl, HTH83-sh.RBM10.