Deciphering Immune-Related Gene Signatures in Diabetic Retinopathy: Insights from In Silico Analysis and In vitro Experiment

Title:Deciphering Immune-Related Gene Signatures in Diabetic Retinopathy: Insights from In Silico Analysis and In vitro Experiment

Volume: 25

Author(s): Nan Xia, Qingsong Zhao, Jinmei Xu and Zhifeng Cheng*

Affiliation:

• Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China

Keywords: Diabetic retinopathy, immune-related signature, gene set enrichment analysis, regulation of immune effector process, immune responses, gene.

Abstract: Background: Diabetes retinopathy (DR) is one of the most common microvascular consequences of diabetes, and the economic burden is increasing. Our aim is to decipher the relevant mechanisms of immune-related gene features in DR and explore biomarkers targeting DR. Provide a basis for the treatment and prevention of DR.

Method: The immune infiltration enrichment score of DR patients was evaluated from the single- cell RNA sequencing dataset, and the samples were divided into low immune subgroups and high immune subgroups based on this result. Through weighted gene correlation network analysis, differentially expressed genes (DEGs) between two subgroups were identified and crossed with genes with the strongest immune association, resulting in significant key genes. Then divide the DR individuals into two immune related differentially expressed gene (IDEG) clusters, A and B. Submit cross DEGs between two clusters through Gene Set Enrichment Analysis (GSEA) to further explore their functions. A protein-protein interaction (PPI) network of IDEG was established to further identify central genes associated with DR. Use the discovered central genes to predict the regulatory network involved in the pathogenesis of DR. Then, the role of the identified hub gene in the pathogenesis of DR was further studied through in vitro experiments.

Result: We found that the immune scores of DR and control groups were different, and 27 IDEGs were found in the DR subgroup. Compared with cluster A, the proportion of cytotoxic lymphocytes, B lineage, monocyte lineage, and fibroblasts in DR patients in cluster B is significantly enriched. GSEA indicates that these genes are associated with T cell activation, regulation of immune response processes, lymphocyte-mediated immunity, TNF signaling pathway, and other signaling pathways. The PPI network subsequently identified 10 hub genes in DR, including SIGLEC10, RGS10, PENK, FGD2, LILRA6, CIITA, EGR2, SIGLEC7, LILRB1, and CD300LB. The upstream regulatory network and lncRNA miRNA mRNA ceRNA network of these hub genes were ultimately constructed. The discovery and identification of these genes will provide biomarkers for targeted prediction and treatment of DR.

Conclusion: By integrating bioinformatics analysis and in vitro experiments, we have identified a set of central genes, indicating that these genes can serve as potential biomarkers for DR, which may be promising targets for future DR immunotherapy interventions.

Cite this article as:

Xia Nan, Zhao Qingsong, Xu Jinmei and Cheng Zhifeng*, Deciphering Immune-Related Gene Signatures in Diabetic Retinopathy: Insights from In Silico Analysis and In vitro Experiment, Current Pharmaceutical Biotechnology 2024; 25 () . https://dx.doi.org/10.2174/0113892010276304240103084841