Integrated genome-wide high-throughput screening and functional validation identifies Sm proteins as essential...

Alternative splicing mediated by Smith antigen (Sm) proteins involving seven small nuclear ribonucleoprotein polypeptides (SNRPs), plays a critical role in cancer progression. Our previous work identified Sm protein B (SNRPB) as an essential gene in gastric cancer (GC) cells. However, the functional roles of the broader Sm proteins and their regulatory mechanisms in GC progression remain unclear. Integrating genome-wide CRISPR-Cas9 and RNA interference proliferation screening data from human GC cell lines, we identified Sm proteins as essential genes for GC growth. Analysis of RNA-seq data from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas revealed elevated Sm proteins mRNA levels in GC. Further Single-cell RNA sequencing data from the GSE183904 dataset further confirmed Sm proteins overexpression in GC malignant epithelial cells. Functional validation demonstrated that knockdown of SNRPB, SNRPD1, SNRPD2, or SNRPD3 suppressed GC cell proliferation. Specifically, scRNA-seq data analysis and in vitro assays showed that SNRPB depletion modulated the expression of apoptosis-related proteins, thereby impairing cell proliferation and migration while promoting apoptosis. Consistently, SNRPB knockdown markedly inhibited tumor growth in xenograft models. Mechanistically, SNRPB depletion mediated exon skipping in CASP6 pre-mRNA, upregulating CASP6 transcript variant ENST00000352981, which restrained proliferation and induced apoptosis. Clinical analysis of four independent cohorts revealed that SNRPB overexpression in GC tissues was significantly associated with poor patient prognosis. In conclusion, our integrated approach defines the Sm proteins as essential for GC progression. Specifically, SNRPB mediated exon skipping of CASP6 facilitates tumor progression, highlighting the therapeutic potential of targeting this splicing pathway.