R-loop-driven molecular subtypes reveal prognostic and immunogenomic features in uterine corpus endometrial carcinoma

R-loops are three-stranded nucleic acid structures implicated in genome instability and cancer progression. However, the prognostic significance and mechanistic role of R-loops in uterine corpus endometrial carcinoma (UCEC) remain poorly understood.

Transcriptomic, clinical, mutational, and spatial data for UCEC were obtained from The Cancer Genome Atlas (TCGA) and public databases. Multiomics analyses, including prognostic modeling, survival analyses, differential expression analyses, copy number variation (CNV) profiling, somatic mutation comparisons, single-cell transcriptomics, spatial transcriptomics, and immune-related pathway exploration, were conducted to elucidate the biological implications of R-loop genes, matrix-specific CSDE1, and the associated SPP1 pathway. In vivo and in vitro functional experiments were conducted to evaluate the role of CSDE1 in UCEC.

Elevated R-loop activity was associated with advanced clinical stage, high tumor grade, and poor survival outcomes in patients with UCEC. A robust prognostic model based on R-loop genes achieved high predictive accuracy across multiple datasets. Low-risk patients had higher tumor mutation burdens and distinct mutational profiles, whereas high-risk patients had more chromosomal instability and more CNV events. CSDE1 emerged as the top predictive gene, displaying fibroblast-specific expression and copy number-driven upregulation. Single-cell and spatial transcriptomics revealed that CSDE1⁺ fibroblasts actively communicated with immune cells via the SPP1 pathway and were spatially enriched in malignant, fibroblast-dense regions. High CSDE1 expression correlated with the activation of oncogenic pathways and the suppression of multiple steps in the cancer-immunity cycle. Furthermore, CSDE1 promoted the proliferation and migration of UCEC cells in vitro and in vivo by reducing R-loop accumulation and DNA damage.

R-loop activity and CSDE1 expression define a clinically relevant molecular program in UCEC that integrates genomic instability, immunosuppression, and stromal remodeling. These findings provide a basis for stratified prognosis and potential therapeutic targeting in endometrial cancer, suggesting that CSDE1 may be a promising new therapeutic target for the treatment of UCEC in the future.