Identifying quantitative sncRNAs signature using global sequencing as a potential biomarker for tuberculosis diagnosis and their role in regulating host response

• Published in: International journal of biological macromolecules Vol. 271; no. Pt 2; p. 132714
• Main Authors: Kaul, Sheetal, Nair, Vivek, Gcanga, Lorna, Lakshmanan, Vairavan, Kalamuddin, M., Anang, Vandana, Rathore, Sumit, Dhawan, Shikha, Alam, Tanvir, Khanna, Vishal, Lohiya, Sheelu, Ali, Shakir, Mannan, Shamim, Rade, Kirankumar, Parihar, Suraj P., Khanna, Ashwani, Malhotra, Pawan, Brombacher, Frank, Dasaradhi, Palakodeti VN, Guler, Reto, Mohmmed, Asif
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2024
• Subjects: Adult; AntagomiRs; Biomarker; biomarkers; Biomarkers - blood; Case-Control Studies; CFU assay; Cross-Sectional Studies; diagnostic techniques; disease progression; drug resistance; Female; High-Throughput Nucleotide Sequencing - methods; Host-Pathogen Interactions - genetics; Humans; In-silico target identification; interleukin-6; interleukin-8; Male; microRNA; MicroRNAs - blood; MicroRNAs - genetics; Middle Aged; Mycobacterium tuberculosis; Mycobacterium tuberculosis - genetics; pathogenesis; Pro-inflammatory cytokines; RNA, Small Untranslated - genetics; ROC Curve; Small non-coding RNAs (sncRNAs); Tuberculosis; Tuberculosis - blood; Tuberculosis - diagnosis; Tuberculosis - genetics; Tuberculosis - microbiology; Tuberculosis, Pulmonary - blood; Tuberculosis, Pulmonary - diagnosis; Tuberculosis, Pulmonary - genetics; Tuberculosis, Pulmonary - microbiology; Biomarker; Tuberculosis; In-silico target identification; Pro-inflammatory cytokines; AntagomiRs; Small non-coding RNAs (sncRNAs); CFU assay
• ISSN: 0141-8130; 1879-0003; 1879-0003
• DOI: 10.1016/j.ijbiomac.2024.132714

The study aimed to identify a quantitative signature of circulating small non-coding RNAs (sncRNAs) as a biomarker for pulmonary tuberculosis disease (active-TB/ATB) and explore their regulatory roles in host-pathogen interactions and disease progression. We conducted a cross-sectional study recruiting subjects diagnosed with active-TB (drug-sensitive and drug-resistant) and healthy controls. Sera samples were collected and utilized for preparing small RNA libraries. Quantitative patterns of circulating sncRNAs (miRNAs, piRNAs and tRFs) were identified via high-throughput sequencing and DeSeq2 analysis and validated in independent active-TB cohorts. Functional knockdown for two selected miRNAs were also performed. A diagnostic signature of four sncRNAs for both drug-sensitive and drug-resistant active-TB cases was validated, exhibiting an AUC of 0.96 (95% CI: 0.937–0.996, p < 0.001) with 86.7% sensitivity (95% CI: 0.775–0.932) and 91.7% specificity (95% CI: 0.730–0.990) in ROC analysis. Functional knockdown demonstrated regulatory roles of hsa-miR-223-5p and hsa-miR-10b-5p in Mycobacterium tuberculosis (Mtb) growth and pro-inflammatory cytokine expression (IL-6 and IL-8). The study identified a diagnostic tool utilizing a signature of four sncRNAs with high specificity and sensitivity, enhancing our understanding of sncRNAs as ATB diagnostic biomarker. Additionally, hsa-miR-223-5p and hsa-miR-10b-5p demonstrated potential roles in Mtb pathogenesis and host-response to infection.