Circulating MicroRNAs as diagnostic indicators in tuberculous Meningitis-A case -control study in North Indian population

Abstract

Purpose: Tuberculous meningitis (TBM), a severe and often fatal form of tuberculosis, showing high mortality and long-term neurological sequelae. Recent evidence suggests that microRNAs play a crucial role in TBM pathogenesis and may serve as potential biomarkers for diagnosis and disease progression. Methods: Eight TBM patients and three healthy controls were recruited. Whole blood samples RNA was extracted and processed. Sequencing was performed on the Illumina platform with a 50-bp single-end read configuration. Data preprocessing included quality control (FastQC), adapter trimming (Cutadapt), and alignment to the human genome (GRCh38) using mirDeep2. Differentially expressed miRNAs were identified using the edgeR package in R, applying a log₂ fold change threshold of ± 1 and a false discovery rate (FDR) ≤ 0.05. Experimentally validated miRNA–mRNA interactions were retrieved from miRTarBase, TarBase, and miRecords. Functional enrichment and pathway analyses were conducted using clusterProfiler and KEGG database resources in R. Results: hsa-miR-23b-5p and hsa-miR-27a-5p were significantly upregulated, while hsa-miR-126-5p and hsa-miR-339-5p were downregulated in TBM. Stage-specific miRNA expression patterns were observed, with hsa-let-7f-5p and hsa-miR-16-5p showing significant upregulation in Stage 2 TBM compared to Stage 1. Functional annotation of validated targets highlighted enrichment in biological processes such as cell cycle regulation, RNA splicing, and ubiquitin-mediated proteolysis, along with key pathways including autophagy and endocytosis, known to be involved in mycobacterial survival and host immune response. Conclusion: The identified differentially expressed miRNAs could serve as biomarkers for early diagnosis and disease monitoring. Further large-scale validation are warranted to translate these findings into clinical applications. © Fondazione Società Italiana di Neurologia 2025.