An In Silico and In vitro Study Examining the Links between T-Cells, MicroRNA, and mRNA Targets/Pathways Associated with Immune-Related Pathogenesis in Acquired Aplastic Anemia.

Abstract

Introduction: MicroRNA and mRNA profiling of T cells from Acquired Aplastic Anaemia (AA) patients using both in-silico and in-vitro methods identified molecular changes, including altered immune-regulatory gene expression, linked to T-cell dysregulation and AA pathobiology.

Methods: MicroRNA (GSE82095) and mRNA (GSE3807) profiles of T cells were obtained from patients with aplastic anaemia and controls using the GEO database. Differential expression was analyzed using GEO2R and TAC 4.0, selecting miRNAs and mRNAs with fold change >2 and an adjusted p-value <0.05. Enrichment analysis of significant miRNAs was conducted via miEAA2.0, while their gene targets were predicted using miRNet and validated with MiRTarBase, TargetScan, miRanda, and MiRDB. Functional enrichment of these targets was assessed using GSEA (FDR < 0.25). This workflow enabled a thorough evaluation of miRNA-mRNA interactions in AA.

Result: The T-cell dataset identified 41 miRNAs and 944 mRNA targets that were significantly altered in Aplastic Anemia (AA) cases versus controls (P<0.05). Venn diagram analysis showed all 944 differentially expressed genes overlapped with the 8305 possible mRNA targets of T-cell miRNAs, which were then used for GSEA to identify enriched gene ontology and pathways. Twenty top mRNA targets underwent further PPI network and hub gene analysis, highlighting 10 key pathways, including Interleukin-13, PI3K-Akt, IFN gamma, MAPK, hematopoietic lineage, mTOR, Interleukin- 4/13, TGF-beta, haemostasis, and cytokine receptor interaction. Network analysis identified 10 hub genes (e.g., EP300, CREBBP, CEBPB, CEBPA, FOS, NCOA3, ESR1, RUNX1, PPARG, and NCOR1) and common transcription factors (e.g., EP300, CREBBP, CEBPB, RUNX1, etc.). GSEA and DAVID analyses indicate these genes and pathways are closely involved in the immune pathogenesis of acquired AA.

Discussion: This study of miRNA and mRNA expression in T cells from acquired aplastic anemia patients shows significant molecular changes linked to immune dysregulation. Key miRNAs, hub genes, and pathways like IL-13, PI3K-Akt, and NOTCH may play a role in AA pathobiology. Analysis of protein interactions and transcription factors identified further regulatory nodes involved in abnormal immune responses. These findings reveal miRNA-mRNA networks in acquired aplastic anaemia and propose them as potential biomarkers or therapeutic targets, pending further experimental validation of their clinical significance.

Conclusion: Computational analysis shows that miRNAs regulate key T-cell mRNA and signalling pathways in AA patients. Following experimental validation, these microRNA-target interactions could be explored for potential diagnostic or therapeutic roles in AA.