Whole blood RNA-seq based Gene biomarkers differentiates active TB from latent TB
Background:Tuberculosis (TB) is one of the infectious diseases having the highest rate of mortality. Various biomarkers are being studied around the world to diagnose TB, and molecular biomarkers like the transcriptomic biomarkers can serve useful for TB diagnosis. Transcriptomic analysis reveals the molecular functions and modifications within the cells upon infection or treatment with specificity. RNA sequencing (RNA-seq) is the high throughput next-generation sequencing (NGS) technology developing in the last decades in the field of transcriptomics with the characteristics of lower detection time, higher accuracy data and cheaper cost.
Aim & Objective: To identify gene biomarker to differentiate latent infection from active TB disease.
Methodology:3mL of whole blood in RNA Tempus tube was collected from 20 pulmonary TB patients at baseline (PTB BL) and after 6 months of anti TB treatment (PTB PT) and from 20 latently infected people (LTB) positive for Interferon gamma test in South India. RNA was isolated from the blood sample by following the kit method by Applied Biosystems and performed RNA sequencing through Illumina platform. Differential Gene expression and pathway enrichment analysis was done through bioinformatics pipeline for gene expressions, available at CSI NGS Portal.
Results & Conclusion:From our preliminary differential expression gene analysis, we obtained a data of top 20 gene set (LOC100129931, C20orf118, MYH11, LOC100289511), with high significance (P=0.0000 to P<0.0001) for pulmonary TB at baseline (PTB BL, n=20) and 6 months of post-treatment (PTB PT, n=20) (Group 1) when compared with latent TB group (LTB, n=20) (Group 2). Canonical pathway revealed a set of genes to be downregulated in the pulmonary TB group, which includes genes related to translation enrichment, rRNA processing, and mitochondrial translation. Whereas, in the LTB group, a set of upregulated genes were found in the Neutrophil degranulation, Mitotic Prometaphase and Class I MHC processing pathways. Further validation of these gene set is necessary in larger population to confirm its utility as a biomarker for therapeutic monitoring and disease progression.
Kadar Moideen 1, Nathella P. Kumar 1, 2, Ramalingam Bethunaickan 2 and Subash Babu 1, 3
1 National Institutes of Health—NIRT— International Center for Excellence in Research, Chennai, India and
2 National Institute for Research in Tuberculosis, Chennai, India
3 LPD, NIAID, NIH, Bethesda, MD