Multi-omics Profiling of Post-translational Modifications in RNA-binding Proteins in Colorectal Cancer

Abstract Background/Aim: Post-translational modifications (PTMs) play a pivotal role in regulating RNA-binding proteins (RBPs), which are crucial in the progression of colorectal cancer (CRC). This study aims to explore the role of PTMs in modulating RBPs and their implications for CRC pathogenesis. Materials and Methods: We characterized phosphorylation, ubiquitination, and malonylation of RBPs in CRC using previously generated post-translational multi-omics datasets from paired CRC and adjacent non-tumor tissues in our previous studies. Functional enrichment analysis was conducted to identify pathways associated with RBPs carrying different PTMs in CRC. Protein-protein interaction (PPI) networks were generated using STRING, and hub genes were identified with the Cytoscape plugin CytoHubba. We also investigated the intersection of RBPs with distinct PTMs and evaluated the expression and prognostic relevance of FLNA (filamin A). Results: Our findings revealed aberrant PTMs of RBPs in CRC, with ubiquitination sites showing the most frequent alterations, followed by phosphorylation, while malonylation exhibited the fewest changes. Functional enrichment analysis indicated that these PTMs contribute to distinct biological processes, including RNA metabolism, protein synthesis, and translation regulation. PPI network analysis showed that RBPs with different PTMs were interconnected in complex networks, identifying several potential RBPs closely related to CRC. Notably, FLNA emerged as a unique RBP modified by all three PTMs. FLNA mRNA and protein abundance were reduced in CRC, and phosphorylation of FLNA at S2319 was also decreased. Higher FLNA expression was associated with worse overall survival. FLNA-associated genes were enriched in pathways related to epithelial-mesenchymal transition (EMT) and KRAS signaling. Conclusion: Multi-PTM profiling revealed distinct and convergent modification patterns among CRC-associated RBPs. FLNA emerged as a potential multi-PTM candidate associated with CRC-related molecular and clinical features. These findings provide a framework for further investigating the biological relevance of PTM-regulated RBPs and their potential implications for the development of molecularly targeted strategies in CRC.