The Association of R-Loop Binding Proteins Subtypes with CIN Implicates Therapeutic Strategies in Colorectal Cancer

SIMPLE SUMMARY: R-Loops, finely regulated by R-Loop binding proteins (RLBPs), play pivotal roles in maintaining genomic stability. By integrated proteogenomic analysis, we identified two RLBPs subtypes with distinct prognostic and therapeutic differences in colorectal cancer (CRC). Cluster-I (CI), characterized by high expression of RLBPs, was associated with chromosomal instability (CIN), better prognosis, and sensitivity to drugs targeting genome integrity and EGFR. Cluster-II (CII), characterized by low expression of RLBPs, was associated with mucinous adenocarcinoma, right-sided colon cancer, and poor prognosis. High inflammatory signaling pathway and lymphocyte infiltration enriched in CII, indicating potential application of drugs targeting inflammatory and immune response. Our research might be helpful for the precision treatment of CRC. ABSTRACT: Chromosomal instability (CIN) covers approximately 65 to 70% of colorectal cancer patients and plays an essential role in cancer progression. However, the molecular features and therapeutic strategies related to those patients are still controversial. R-loop binding proteins (RLBPs) exert significant roles in transcription and replication. Here, integrative colorectal cancer proteogenomic analysis identified two RLBPs subtypes correlated with distinct prognoses. Cluster I (CI), represented by high expression of RLBPs, was associated with the CIN phenotype. While Cluster II (CII) with the worst prognosis and low expression of RLBPs was composed of a high percentage of patients with mucinous adenocarcinoma or right-sided colon cancer. The molecular feature analysis revealed that the active RNA processing, ribosome synthesis, and aberrant DNA damage repair were shown in CI, a high inflammatory signaling pathway, and lymphocyte infiltration was enriched in CII. In addition, we revealed 42 tumor-associated RLBPs proteins. The CI with high expression of tumor-associated proteins was sensitive to drugs targeting genome integrity and EGFR in both cell and organoid models. Thus, our study unveils a significant molecular association of the CIN phenotype with RLBPs, and also provides a powerful resource for further functional exploration of RLBPs in cancer progression and therapeutic application.