An In Silico and In vitro Study Examining the Links between T-Cells, MicroRNA, and mRNA Targets/Pathways Associated
Bhuvnesh Rai1, Ghazala Sabereen1, Pragati Saxena1
1Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Rae Bareli Road, Lucknow, Uttar Pradesh 226014, India.
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.
Insights
MicroRNA and mRNA profiling in T cells from acquired aplastic anemia (AA) patients revealed significant molecular changes and immune dysregulation. These findings highlight potential diagnostic biomarkers and therapeutic targets for AA.
Area of Science:
- Immunology
- Genomics
- Molecular Biology
Background:
- Acquired aplastic anemia (AA) is characterized by T-cell dysregulation.
- Understanding the molecular underpinnings of T-cell dysfunction in AA is crucial for developing effective treatments.
Purpose of the Study:
- To investigate the differential expression of microRNAs (miRNAs) and messenger RNAs (mRNAs) in T cells from AA patients compared to healthy controls.
- To identify key miRNA-mRNA interactions and signaling pathways involved in the pathobiology of AA.
Main Methods:
- Utilized publicly available miRNA (GSE82095) and mRNA (GSE3807) datasets from T cells of AA patients and controls.
- Performed differential expression analysis, miRNA enrichment analysis, target prediction, and functional enrichment analysis (GSEA).
- Conducted network analysis to identify hub genes and key signaling pathways.
Main Results:
- Identified 41 differentially expressed miRNAs and 944 mRNA targets in T cells of AA patients.
- Network analysis highlighted 10 key pathways, including Interleukin-13, PI3K-Akt, and MAPK signaling.
- Identified 10 hub genes and common transcription factors involved in AA pathogenesis.
Conclusions:
- Significant miRNA-mRNA regulatory networks are implicated in the immune pathogenesis of acquired AA.
- Key pathways and hub genes identified may serve as potential diagnostic biomarkers or therapeutic targets for AA.
- Further experimental validation is warranted to confirm the clinical significance of these findings.
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