Elsevier

The Lancet

Volume 387, Issue 10035, 4–10 June 2016, Pages 2312-2322
The Lancet

Articles
A blood RNA signature for tuberculosis disease risk: a prospective cohort study

https://doi.org/10.1016/S0140-6736(15)01316-1Get rights and content

Summary

Background

Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic. We aimed to assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective signatures of risk of active tuberculosis disease.

Methods

In this prospective cohort study, we followed up healthy, South African adolescents aged 12–18 years from the adolescent cohort study (ACS) who were infected with M tuberculosis for 2 years. We collected blood samples from study participants every 6 months and monitored the adolescents for progression to tuberculosis disease. A prospective signature of risk was derived from whole blood RNA sequencing data by comparing participants who developed active tuberculosis disease (progressors) with those who remained healthy (matched controls). After adaptation to multiplex quantitative real-time PCR (qRT-PCR), the signature was used to predict tuberculosis disease in untouched adolescent samples and in samples from independent cohorts of South African and Gambian adult progressors and controls. Participants of the independent cohorts were household contacts of adults with active pulmonary tuberculosis disease.

Findings

Between July 6, 2005, and April 23, 2007, we enrolled 6363 participants from the ACS study and 4466 from independent South African and Gambian cohorts. 46 progressors and 107 matched controls were identified in the ACS cohort. A 16 gene signature of risk was identified. The signature predicted tuberculosis progression with a sensitivity of 66·1% (95% CI 63·2–68·9) and a specificity of 80·6% (79·2–82·0) in the 12 months preceding tuberculosis diagnosis. The risk signature was validated in an untouched group of adolescents (p=0·018 for RNA sequencing and p=0·0095 for qRT-PCR) and in the independent South African and Gambian cohorts (p values <0·0001 by qRT-PCR) with a sensitivity of 53·7% (42·6–64·3) and a specificity of 82·8% (76·7–86) in the 12 months preceding tuberculosis.

Interpretation

The whole blood tuberculosis risk signature prospectively identified people at risk of developing active tuberculosis, opening the possibility for targeted intervention to prevent the disease.

Funding

Bill & Melinda Gates Foundation, the National Institutes of Health, Aeras, the European Union, and the South African Medical Research Council.

Introduction

A third of the population worldwide is infected with Mycobacterium tuberculosis,1 but less than 10% of these individuals will progress to have active tuberculosis disease during their lifetime; most individuals will remain healthy.2, 3, 4, 5, 6 Risk of progression is associated with age,7 comorbidities such as HIV infection and diabetes mellitus, socioeconomic and nutritional compromise, and therapy with immune modulatory drugs such as tumour necrosis factor inhibitors, among others.8, 9 Current assays for determining the presence of M tuberculosis infection, such as an interferon gamma release assay (IGRA) or tuberculin skin test (TST), cannot predict which infected individuals will develop active tuberculosis.

Previous systems biology approaches have identified diagnostic signatures that discriminate tuberculosis disease from latent M tuberculosis infection and from other disease states.10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 For example, Berry and colleagues12 identified and validated a 393 gene signature that allowed differentiation of people with active tuberculosis disease and latent infection. Anderson and colleagues14 identified and validated a 53 gene signature that distinguished active tuberculosis from other diseases in African children with or without HIV infection. By contrast with the published diagnostic studies, our focus was on prospective signatures of risk that could be identified in healthy individuals up to 2 years before clinical tuberculosis disease manifests.

Knowledge gained from this signature could lead to targeted antimicrobial therapy to prevent tuberculosis disease, as treating all people who are latently infected in endemic countries for 6–9 months is not feasible. Other potential applications of biomarkers of risk of tuberculosis disease include assessment of response to drug therapy and targeted enrolment into efficacy trials of new tuberculosis vaccines and drugs. In view of the fact that a third of the world's population is latently infected with M tuberculosis, our approach constitutes an opportunity to lessen the burden of disease. To this end, we aimed to assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective signatures of risk of active tuberculosis disease.

Research in context

Evidence before this study

We searched the PubMed database for studies published before July 1, 2015, using the search criteria “tuberculosis AND risk AND blood AND (RNA OR microarray OR transcriptome OR RNA-Seq)”. The resulting scientific literature included several substantial analyses comparing the blood RNA profiles of individuals with active tuberculosis disease and healthy individuals. These important studies have established that the tuberculosis disease state is reflected in the blood RNA profile of the patient with tuberculosis with ongoing disease. The resulting literature also included several small studies reporting candidate host markers for tuberculosis disease risk that have not been rigorously assessed in independent cohorts. Repeating the search without the “(RNA OR microarray OR transcriptome OR RNA-Seq)” term yielded literature with established risk factors for tuberculosis disease, which have been summarised in several reviews. Despite these important studies and known tuberculosis risk factors, it is not possible to predict which individuals infected with Mycobacterium tuberculosis will develop active tuberculosis with tools.

Added value of this study

Our study expands the previous findings by being the first large-scale search for prospective correlates of risk of tuberculosis in healthy individuals before the onset of disease. We used unbiased high-throughput screening of host blood RNA profiles to identify new signatures of risk for tuberculosis. These signatures were confirmed in the original cohort with targeted assays; these targeted assays were then successfully used to predict tuberculosis disease progression in two independent cohorts. Further meta-analyses of published datasets showed that the prognostic signatures might simultaneously serve as diagnostic signatures for tuberculosis.

Implications of all the evidence

Our study provides the first demonstration that host blood RNA signatures can be used to predict progression to active tuberculosis disease in healthy individuals that are latently infected with or exposed to the M tuberculosis pathogen. These findings will result in further follow-up studies to assess whether the prognostic signatures can be used to prevent tuberculosis disease through targeted prophylactic treatment. Additional follow-up studies might focus on optimising the practical measurement of the signatures and understanding the biological significance of the host genes implicated by the signatures.

Section snippets

Study design and participants

We included participants from several cohorts in this analysis. First, we assessed participants aged 12–18 years from the South African adolescent cohort study (ACS) who were infected with M tuberculosis to identify and validate a tuberculosis risk signature (figure 1). All adolescents whose parents or legal guardians provided written, informed consent and who provided written, informed assent themselves were enrolled. About half the participants from the ACS cohort were assessed at enrolment

Results

Between July 6, 2005, and April 23, 2007, we enrolled 6363 healthy adolescents from the ACS cohort; follow-up was completed by February, 2009 (appendix 1). Between Feb 27, 2005, and Dec 14, 2010, (South Africa) and between March 5, 2007, and Oct 21, 2010 (The Gambia), we enrolled 4466 healthy individuals from the GC6-74 cohort, of these 1197 were enrolled in the South African and 1948 enrolled in The Gambia (appendix 1).

46 ACS participants with microbiologically confirmed tuberculosis were

Discussion

Roughly one third of the world's population might harbour latent M tuberculosis infection and is at risk of active disease. We have identified a gene expression signature for predicting the risk of tuberculosis disease progression. This signature was discovered in a longitudinal analysis of South African adolescents with latent M tuberculosis infection who either developed tuberculosis disease or remained healthy. The signature was then validated in blinded samples from untouched adolescents of

References (38)

  • CE Barry et al.

    The spectrum of latent tuberculosis: rethinking the biology and intervention strategies

    Nat Rev Microbiol

    (2009)
  • G Walzl et al.

    Immunological biomarkers of tuberculosis

    Nat Rev Immunol

    (2011)
  • CI Bloom et al.

    Detectable changes in the blood transcriptome are present after two weeks of antituberculosis therapy

    PLoS One

    (2012)
  • CI Bloom et al.

    Transcriptional blood signatures distinguish pulmonary tuberculosis, pulmonary sarcoidosis, pneumonias and lung cancers

    PLoS One

    (2013)
  • MP Berry et al.

    An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

    Nature

    (2010)
  • M Kaforou et al.

    Detection of tuberculosis in HIV-infected and -uninfected African adults using whole blood RNA expression signatures: a case-control study

    PLoS Med

    (2013)
  • ST Anderson et al.

    Diagnosis of childhood tuberculosis and host RNA expression in Africa

    N Engl J Med

    (2014)
  • TH Ottenhoff et al.

    Genome-wide expression profiling identifies type 1 interferon response pathways in active tuberculosis

    PLoS One

    (2012)
  • J Maertzdorf et al.

    Common patterns and disease-related signatures in tuberculosis and sarcoidosis

    Proc Natl Acad Sci USA

    (2012)
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