Cross-Strand Chimeric RNA Signature Predicts Prognosis and Identifies Tumor Immune Microenvironment Associations in...

Cross-strand chimeric RNAs (cscRNAs) represent an emerging class of noncanonical fusion transcripts arising from bidirectional transcription, yet their landscape and functional significance in gastric cancer remain unexplored. Here, we systematically investigated cscRNA expression patterns, prognostic relevance, and tumor immune microenvironment associations in gastric cancer through integrated computational and experimental approaches. Analysis of 372 TCGA-STAD samples revealed tumor-specific cscRNA enrichment that was independent of clinicopathological variables including tumor stage, histological grade, and lymph node metastasis status. Through a three-layer machine learning pipeline integrating univariate screening, multivariate feature selection, and bootstrap stability validation, we identified six cscRNA-enriched genomic regions that collectively formed a reproducible prognostic signature. Patients stratified by the risk score model showed significantly divergent survival outcomes (median survival: 18.9 vs. 69.0 months; univariate HR = 2.54, p < 0.001), and the risk score retained independent prognostic value after adjusting for clinical covariates (multivariable HR = 2.86, p < 0.001). In an exploratory analysis of an independent validation cohort (GSE122401, n = 26), high-risk tumors showed features consistent with an immunosuppressive microenvironment, including reduced CD8+ T-cell infiltration (p = 0.042), elevated regulatory T-cell proportions (p = 0.028), and lower immune scores (p = 0.006). Subgroup analyses by microsatellite instability and Epstein-Barr virus status (n = 4 and n = 6, respectively) suggested differential immune patterns warranting confirmation in larger cohorts. Experimental validation confirmed cscR-819 as a bona fide posttranscriptional cscRNA product, whose knockdown significantly inhibited gastric cancer cell proliferation, migration, and colony formation while promoting apoptosis. Mechanistically, cscR-819 was predominantly localized in the cytoplasm and functioned as a translational regulator, selectively enhancing the translation efficiency of genes involved in cell cycle progression, DNA replication, and antiapoptotic pathways, as demonstrated by polyribosome profiling. In conclusion, our study establishes cscRNAs as functionally relevant contributors to gastric cancer pathogenesis and identifies exploratory associations with tumor immune microenvironment features, positioning cscRNA-based signatures as promising candidate biomarkers for risk stratification and motivating further investigation of cscRNA-immune interactions.