Prediction of potential biomarkers and therapeutic targets in HIV viremic patients using immune-related circRNA-miRNA-mRNA regulatory networks

Abstract

The recent study aims to analyze the role of non-coding RNAs, particularly circRNAs, in HIV pathogenesis using construction of immune-related regulatory networks. In compliance with ethical standards and institutional guidelines, publicly available HIV-related mRNA and microRNA expression datasets were systematically retrieved from the Gene Expression Omnibus repository. These datasets underwent rigorous bioinformatics analysis employing the “limma” package in R to identify differentially expressed genes (DEGs) and microRNAs (DEmiRNAs). Validated interaction data from miRBase and ENCORI databases facilitated the construction of circRNA-DEmiRNA and DEmiRNA-DEG regulatory networks. Protein-protein interaction networks were generated through STRING database analysis, with hub genes defined as those within the highest 5% of interaction degrees. Furthermore, single-cell RNA sequencing (scRNA-seq) datasets from HIV-infected individuals were analyzed using the “Seurat” package to identify DEGs in CD4+ and CD8+ T cell subsets. Cross-validation between microarray and scRNA-seq data ensured robustness of identified hub genes. Our results revealed substantial alterations in RNA expression associated with both high viral load and low viral load HIV infections. Single-cell analyses indicated significant gene expression shifts in T cell populations: 194 upregulated and 813 downregulated genes in CD4+ T cells, and 244 upregulated and 567 downregulated genes in CD8+ T cells. Integrated analysis delineated five hub genes consistently dysregulated across T cell subsets. STAT1 and DDX39B were upregulated, whereas CXCL8, CXCL12, and PTGS2 were downregulated. The pathway enrichment analysis indicated that these genes are implicated in key regulatory pathways relevant to infectious disease mechanisms. Alongside of DEGs, our studies indicated that multiple miRNAs, such as hsa-miR-21-5p, hsa-miR-146a-5p and hsa-let-7b-5p are differentially expressed in HIV-infected samples in comparison to the normal samples. Afterward, DEmiRNA-DEGs network studies demonstrated different axes between significantly up- and down-regulated DEGs with down- and up-regulated miRNAs, respectively. Following, ceRNA regulatory network revealed circRNAs, which can interact with DEmiRNA-DEGs networks, like hsa_circ_0089761-hsa-miR-21-5p-CXCL12, hsa_circ_0003812-hsa-miR-146a-5p-PTGS2, and has_circ_0007185–has_let-7b-5p–DDX39B. Overall, this integrative analysis suggests potential circRNA-mediated regulatory mechanisms in HIV infection and highlights potential candidate circRNAs that may serve as biomarkers or therapeutic targets for further investigation.