Integration of aberrant alternative splicing events and RNA binding proteins revealed their potential regulation in diabetic foot ulcers

Abstract

Abstract Background Diabetic foot ulcer (DFU) is one of the most serious complications of diabetes and the main cause of non-traumatic amputation in diabetic patients. Disruption of alternative splicing (AS) and RNA binding proteins (RBPs) has been proven to cause a variety of diseases, including DFU. But the regulatory network of RBPs-AS and its underlying functions in DFU remain unclear. Methods Whole transcriptome data of ulceration tissues were analyzed to identify dysregulated AS and RBPs, comprising ulceration tissues from thirteen DFU patients (seven patients with healed ulcers and six patients with unhealed ulcers, the DFU group) and eight normal samples (the control group). We identified the differentially expressed genes (DEGs), regulated alternative splicing events (RASEs), and changes in immune infiltration between DFU and control tissues. Finally, co-expression analysis was performed to establish the regulatory network of RBPs-AS-immune infiltration in DFU tissues. Results DEG analysis showed that 4478 and 4514 genes were differentially expressed in healed and unhealed DFU tissues, respectively. Gene functional analysis showed that many DEGs were enriched in immune and inflammatory pathways. Many RASEs were identified between unhealed DFU and control tissues. Functional analysis showed that genes with RASEs were primarily enriched in apoptosis pathways. According to immune infiltration analysis, the percentage of memory B cells and activated mast cells were higher in the DFU group than in the control group. According to the co-expression analysis, the ratio values of RASEs in apoptosis-associated genes were related to the percentage of infiltrated immune cells in DFU tissues. In addition, the co-expression network showed that differentially expressed RBPs (DE RBPs) could regulate the RASEs and affect the immune infiltration in DFU tissues. Finally, we found that the aberrant expressions of DCN, HSP90AA1, SMAD7, YWHAG, YWHAZ, KPNA2, S100A16, and DUSP14 would affect the AS of FAT1, COL12A1, UPP1, EIF5A and AKAP13 in DFU tissues. Conclusion Our results showed that DE RBPs may play a role in wound healing in DFU by regulating the AS of pre-mRNAs, especially immune inflammation- and apoptosis-related pre-mRNAs, and may continue to play a role in DFU regardless of the healing state.