Blood Transcriptomic Stratification of Short-term Risk in Contacts of Tuberculosis

Abstract

Background: The highest risk of tuberculosis arises in the first few months after exposure. We reasoned that this risk reflects incipient disease among tuberculosis contacts. Blood transcriptional biomarkers of tuberculosis may predate clinical diagnosis, suggesting they offer improved sensitivity to detect subclinical incipient disease. Therefore, we sought to test the hypothesis that refined blood transcriptional biomarkers of active tuberculosis will improve stratification of short-term disease risk in tuberculosis contacts.

Methods: We combined analysis of previously published blood transcriptomic data with new data from a prospective human immunodeficiency virus (HIV)-negative UK cohort of 333 tuberculosis contacts. We used stability selection as an alternative computational approach to identify an optimal signature for short-term risk of active tuberculosis and evaluated its predictive value in independent cohorts.

Results: In a previously published HIV-negative South African case-control study of patients with asymptomatic Mycobacterium tuberculosis infection, a novel 3-gene transcriptional signature comprising BATF2, GBP5, and SCARF1 achieved a positive predictive value (PPV) of 23% for progression to active tuberculosis within 90 days. In a new UK cohort of 333 HIV-negative tuberculosis contacts with a median follow-up of 346 days, this signature achieved a PPV of 50% (95% confidence interval [CI], 15.7-84.3) and negative predictive value of 99.3% (95% CI, 97.5-99.9). By comparison, peripheral blood interferon gamma release assays in the same cohort achieved a PPV of 5.6% (95% CI, 2.1-11.8).

Conclusions: This blood transcriptional signature provides unprecedented opportunities to target therapy among tuberculosis contacts with greatest risk of incident disease.

Keywords: biomarker; blood transcriptome; diagnosis; tuberculosis.

Figure 1. Identification of incipient TB by measurement of blood BATF2 transcript levels.

(A) BATF2 transcript levels (TPM) are shown for blood samples from all patients in the Zak cohort (with at least 12 months follow up after the time of sampling) who did not progress to TB (NP), and for samples from patients who progressed to a diagnosis of TB within the time intervals indicated. (B) Receiver operating characteristic (ROC) curves for discriminating between NP and progressors in each time interval shown using the BATF2 transcript level. (C) Positive predictive value for a diagnosis of TB (PPV_TB) for patients who progress to TB within 90 days, using sensitivity and specificity values derived from the optimal Youden Index (dotted line in (A)) of the ROC curve in (B) and a range of pre-test (PT) probabilities. Arrows highlight the PPV_TB of 13% for PT probability of 1.5%.

Figure 2. Identification of incipient TB by a novel 3-gene model incorporating blood transcript levels of BATF2, GBP5 and SCARF1.

(A) Three-gene scores derived from the SVM model to discriminate between active and treated TB, are shown for blood samples from all patients in the Zak cohort (with at least 12 months follow up) who did not progress to TB (NP), and for samples from patients who progressed to a diagnosis of TB within the time intervals indicated. (B) ROC curves for discriminating between NP and progressors in each time interval shown using the three-gene scores. (C) Positive predictive value for a diagnosis of TB (PPV_TB) for patients who progress to TB within 90 days, using sensitivity and specificity values derived from the optimal Youden Index of the ROC curve in (B) and a range of pre-test (PT) probabilities. Arrows highlight the PPV_TB of 23% for PT probability of 1.5%.

Figure 3. Blood transcriptomic 3-gene score at recruitment in contacts of active TB.

(A) Frequency distribution of 3-gene scores in IGRA negative contacts of active TB showing threshold (dashed lines) for identification of a high 3-gene score based on the mean+2 SD (Z₂) or +3 SD (Z₃) of the scores among IGRA negative cases. (B) Individual 3-gene scores for untreated IGRA positive and negative contacts who developed active TB or remained healthy on follow up.