Elsevier

Tuberculosis

Volume 109, March 2018, Pages 41-51
Tuberculosis

Diagnostics
Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in individuals from south India

https://doi.org/10.1016/j.tube.2018.01.002Get rights and content

Abstract

Several studies have identified blood transcriptomic signatures that can distinguish active from latent Tuberculosis (TB). The purpose of this study was to assess how well these existing gene profiles classify TB disease in a South Indian population. RNA sequencing was performed on whole blood PAXgene samples collected from 28 TB patients and 16 latently TB infected (LTBI) subjects enrolled as part of an ongoing household contact study. Differential gene expression and clustering analyses were performed and compared with explicit predictive testing of TB and LTBI individuals based on established gene signatures. We observed strong predictive performance of TB disease states based on expression of known gene sets (ROC AUC 0.9007–0.9879). Together, our findings indicate that previously reported classifiers generated from different ethnic populations can accurately discriminate active TB from LTBI in South Indian patients. Future work should focus on converting existing gene signatures into a universal TB gene signature for diagnosis, monitoring TB treatment, and evaluating new drug regimens.

Introduction

Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (Mtb), is a global health concern with 10.4 million new cases estimated in 2015 [1]. Untreated TB has a high mortality rate, estimated at a 70% 10-year case fatality rate in smear-positive pulmonary tuberculosis [2]. The WHO estimates that depending on context, 15–50% of TB cases are unreported or undiagnosed [1]. Further, the limitations of bacterial diagnosis in paucibacillary TB that is pediatric, extrapulmonary, or smear-negative pulmonary TB, often lead to empirical treatment. This approach exposes some individuals unnecessarily to side effects of the TB treatment while delaying effective therapy of the actual cause of the disease. Further, patients with TB may be denied appropriate treatment if bacteriologic testing is negative.

Currently, though nucleic acid amplification tests approach the sensitivity of Mtb culture [3], more sensitive diagnostics may need to be based on host biomarkers. These tests are inherently nonspecific, and it is unclear how they will perform in different populations. Several transcriptomic studies of TB cases and individuals infected with Mtb have been performed to characterize systemic gene expression (reviewed in Ref. [4]). Jacobsen et al. (2007) performed a microarray analysis and identified a minimal set of three genes in peripheral blood mononuclear cells that allowed distinction between TB disease and healthy individuals with latent TB infection (LTBI) [5]. The Berry et al. (2010) microarray studies demonstrated a 393-gene whole blood signature that discriminated subjects with active TB disease from those with LTBI, as well as an 86-gene set discriminating TB disease from other inflammatory and infectious diseases [6]. In this study, they also noted that this active TB signature was extinguished in patients following anti-TB treatment [6]. Kaforou et al. (2013) proposed a 27-gene whole blood signature that could distinguish TB and latent TB, regardless of HIV infection status [7]. Zak et al. (2016) recently identified a 16-gene signature for predicting TB disease risk through sequencing analysis of whole blood PAXgene samples from a prospective cohort [8]. Given this recent proliferation of transcriptional studies in the field of TB, Sweeney et al. (2016) performed a meta-analysis of 14 publicly available TB transcriptomic datasets to identify a 3-gene set that they determined was robustly diagnostic for active TB disease [9].

Strikingly, although India accounts for more than one-quarter of the world's TB cases and deaths, transcriptomic studies in an Indian Mtb-infected populations have been limited [1,[10], [11], [12]]. TB is hyperendemic in India with an incidence of 217 per 100,000 and a mortality rate of 36 per 100,000 individuals as estimated in 2015 [1]. Furthermore, there is a high prevalence of other non-communicable confounding conditions and risk factors complicating TB disease cases in India, including diabetes, smoking, and alcohol consumption [[13], [14], [15]]. Presence of such comorbidities in patients with TB can impact their disease courses and treatment responses [[16], [17], [18], [19]]. Thus, while two studies have proposed TB disease gene signatures (Maertzdorf et al. 4-gene signature and Sambarey et al. 10-gene signature) that were evaluated in Indian populations, additional studies are required [10,11]. Thus, the overall goal of this study was to assess how well the published gene signatures of active TB disease classified subjects in patients from South India.

Section snippets

Study subjects and inclusion criteria

Subjects were recruited into the current cross-sectional sub-study from an ongoing observational household contact study being conducted at Jawarharlal Institute of Postgraduate Medical Education and Research (JIPMER). TB cases were recruited through the Revised National TB Control Programme (RNTCP) network of clinics in the city of Pondicherry (Puducherry union territory) and the districts of Villupuram and Cuddalore (Tamil Nadu state) in South India. Through the RNTCP, symptomatic individuals

Differentially expressed genes in Indian subjects with TB versus LTBI overlap with existing TB signatures

The DEGs were identified between patients with active TB disease and asymptomatic individuals with latent TB infection (LTBI) in the Indian study. More than 1200 genes were differentially expressed between TB and LTBI individuals at a 0.00001 adjusted p-value (FDR) cutoff. For visualization and discussion purposes of a shorter DEG list, a more stringent adjusted p-value (FDR) cutoff of <10−11 was used resulting in a list of 76 DEGs (Fig. 1, Supplementary Table S2). Many DEGs identified from

Discussion

The results of this study suggest that gene expression of existing transcriptional signatures can accurately classify TB and LTBI individuals within the South Indian subjects in our study. Distinct patterns of gene expression were observed in active TB patients versus LTBI individuals for each of the eight published gene sets evaluated. Whereas seven of the tested signatures were designed to characterize an active TB profile, the Zak et al. (2016) 16-gene signature was described as a predictor

Funding

This publication is based on work supported by Award No. USB1-31150-XX-13 of the U.S. Civilian Research & Development Foundation (CRDF Global), Department of Biotechnology BT/PR8941/MED/15/108/2013 and by the National Science Foundation under Cooperative Agreement No. OISE-9531011.

Conflicts of interest

None.

Author contributions

PS, JJE, NSH, SS and CRH contributed to cohort design; SL and YZ performed the experiments and analyzed the data; PS and WEJ designed experiment and interpreted the data; NJ, SS, JP, NSH, DH, SL, GR contributed to subject recruitment and sample collection, storage and shipping, and data management; SL, YZ, PS and WEJ wrote the manuscript; PS, JJE and WEJ contributed to discussion and conclusions of the study.

Acknowledgements

We thank all of the participants who made the study possible. We also acknowledge the dedication and hard work of the field staff and study team. We thank Rachel Kubiak and Astrid Loomans for help with data management, and Laura White for help with statistics. This work was performed under the auspices of the RePORT India Program. We wish to acknowledge the support of Sudha Srinivasan and Peter Kim from DAIDS/NIAID/NIH and Jyoti M. Logani from Department of Biotechnology, Ministry of Science

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