Host derived RNA biosignatures with diagnostic, prognostic and predictive utility for the treatment and control of tuberculosis

Delays in diagnosis and treatment of pulmonary tuberculosis (TB) can lead to more severe disease and increased transmission. Contact investigation among household contacts (HHC) of TB patients is crucial to ensure optimal outcomes. In the context of a prospective cohort study in Palamaner, Southern India, this study attempted to assess the potential of 27 different soluble immune markers to accurately assign HHC for appropriate treatment. A multiplex bead assay was applied on QuantiFERON (QFT)-nil supernatants collected from 89 HHC grouped by longitudinal QFT status; M. tuberculosis (Mtb) infected (QFT positive at baseline and follow-up), recent QFT converters (QFT-negative at baseline and converted to QFT-positivity within 6 months of exposure) and QFT consistent negatives. The 29 TB index cases represented Active TB. Active TB cases and HHCs with consistent Despite the fact that both groups were infected with Mtb, HHC with or without Mtb infection produced significantly different levels of both pro-inflammatory (IFN, IL17, IL8, IP10, MIP-1α, MIP1β and VEGF) and anti-inflammatory (IL9 and IL1RA) cytokines. We identified a 4- protein signature (bFGF, IFN, IL9, and IP10) that correctly classified Mtb infected vs. Active TB with a specificity of 92.6%, suggesting that this 4-protein signature has the potential to assign HHC for either full-length TB treatment or preventive TB treatment. We further identified a 4-protein signature (bFGF, GCSF, IFNγ, and IL1RA) that differentiated HHC with Mtb infection from QFT consistent negatives with a specificity of 62.5%, but not satisfactory to safely assign HHC to no TB treatment. QFT conversion, reflecting new Mtb infection, induced an elevated median concentration of nearly two-thirds (19/27) of the analysed soluble markers compared to the levels measured at baseline. This manuscript has been submitted in journal Frontiers in Immunology ( Oct 25th, 2021, which is in under review- 2nd revision). Title: “Improving assignments for therapeutic and prophylactic treatment within TB households. A potential for immuno-diagnosis?” Stduy Design: All household contacts were followed up for one year. Samples were collected at 0, 2, 6, and 12 months. Some people go on to develop TB (Progressors/Sub-clinical TB) where as some others do not (Non-progressors/Incipient TB). Household controls were carefully selected from the same incipient TB/non-progressors and sub-clinical TB/progressors families and age-matched to either incipient or subclinical TB cases. We used the same method as for the controls to pick the active TB cases in the adult index TB. For this study, for incipient TB baseline and 12 month or last available samples were selected, for sub-clinical TB baseline and culture-postive for Mtb time point samples or closely available time-point samples were selected, whereas for active TB and household controls baseline samples were selected and sent for RNA-sequencing. Within families/households of TB index cases, the present study aimed to i) identify differentially expressed transcriptional biomarkers associated with distinct stages of TB in samples acquired at baseline contact investigation. ii) identify transcriptional signatures with the ability to distinguish subclinical TB from incipient TB in samples acquired at baseline, iii) evaluate the performance of identified transcriptional signature(s) in active TB disease cases and asymptomatic household controls in samples acquired at baseline. Summary: Identification of blood transcriptional biomarkers linked to different phases of tuberculosis. The discovery of a transcriptional signature that distinguishes subclinical TB/progressors from incipient TB/non-progressors at baseline could lead to tuberculosis interventions that combat the tuberculosis epidemic in the context of household contacts. We have deposited our RNA-seq data in GEO bank (GEO ref no: GSE193777). This data will be publicly available when our manuscript is published. The proposed project is built on an extensive existing collaborative network that extends from Norwegian research institutes through academic collaborations in India and Africa, down to the village level in both high TB-endemic countries. The ethical approvals for the Indian TB cohort studies on which, the studies outlined in the proposals are based on, have been provided by committees whose composition includes a diverse range of professionals. Members from the national TB control program, doctors at local TB clinics, pharmacists, key private practitioners in the study area and community leaders have also been contacted in the planning of the large cohort studies conducted in Palamaner, Chittoor district, India by members of this consortium. Communication with users: key findings will be communicated with national and international research and policy-forming bodies. The results from our studies will be published in international high-impact peer-reviewed journals and results presented in relevant national and international conferences. The collaborative network for this project works closely with TBVI, the EU (through the Horizon 2020 program) and the EDCTP. The partners have experience from the conduct of large prospective population-based studies, vaccine trials and RCTs, both in Norway and with partners in South Africa, and India. Combined, the partners have a vast network which will ensure the successful conduct of this project. This would ensure rapid dissemination to international policy-making groups and increase public awareness.