Research Article: Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures

Date Published: April 23, 2019

Publisher: Public Library of Science

Author(s): Hayley Warsinske, Rohit Vashisht, Purvesh Khatri, Richard Chaisson

Abstract: BackgroundThe World Health Organization (WHO) and Foundation for Innovative New Diagnostics (FIND) have published target product profiles (TPPs) calling for non-sputum-based diagnostic tests for the diagnosis of active tuberculosis (ATB) disease and for predicting the progression from latent tuberculosis infection (LTBI) to ATB. A large number of host-derived blood-based gene-expression biomarkers for diagnosis of patients with ATB have been proposed to date, but none have been implemented in clinical settings. The focus of this study is to directly compare published gene signatures for diagnosis of patients with ATB across a large, diverse list of publicly available gene expression datasets, and evaluate their performance against the WHO/FIND TPPs.Methods and findingsWe searched PubMed, Gene Expression Omnibus (GEO), and ArrayExpress in June 2018. We included all studies irrespective of study design and enrollment criteria. We found 16 gene signatures for the diagnosis of ATB compared to other clinical conditions in PubMed. For each signature, we implemented a classification model as described in the corresponding original publication of the signature. We identified 24 datasets containing 3,083 transcriptome profiles from whole blood or peripheral blood mononuclear cell samples of healthy controls or patients with ATB, LTBI, or other diseases from 14 countries in GEO. Using these datasets, we calculated weighted mean area under the receiver operating characteristic curve (AUROC), specificity at 90% sensitivity, and negative predictive value (NPV) for each gene signature across all datasets. We also compared the diagnostic odds ratio (DOR), heterogeneity in DOR, and false positive rate (FPR) for each signature using bivariate meta-analysis. Across 9 datasets of patients with culture-confirmed diagnosis of ATB, 11 signatures had weighted mean AUROC > 0.8, and 2 signatures had weighted mean AUROC ≤ 0.6. All but 2 signatures had high NPV (>98% at 2% prevalence). Two gene signatures achieved the minimal WHO TPP for a non-sputum-based triage test. When including datasets with clinical diagnosis of ATB, there was minimal reduction in the weighted mean AUROC and specificity of all but 3 signatures compared to when using only culture-confirmed ATB data. Only 4 signatures had homogeneous DOR and lower FPR when datasets with clinical diagnosis of ATB were included; other signatures either had heterogeneous DOR or higher FPR or both. Finally, 7 of 16 gene signatures predicted progression from LTBI to ATB 6 months prior to sputum conversion with positive predictive value > 6% at 2% prevalence. Our analyses may have under- or overestimated the performance of certain ATB diagnostic signatures because our implementation may be different from the published models for those signatures. We re-implemented published models because the exact models were not publicly available.ConclusionsWe found that host-response-based diagnostics could accurately identify patients with ATB and predict individuals with high risk of progression from LTBI to ATB prior to sputum conversion. We found that a higher number of genes in a signature did not increase the accuracy of the signature. Overall, the Sweeney3 signature performed robustly across all comparisons. Our results provide strong evidence for the potential of host-response-based diagnostics in achieving the WHO goal of ending tuberculosis by 2035, and host-response-based diagnostics should be pursued for clinical implementation.

Partial Text: The World Health Organization (WHO) has identified the need for a non-sputum-based triage test to rule out active tuberculosis (ATB) disease [1]. The WHO consensus meeting report describes that such a triage test should have 90% sensitivity and 70% specificity at minimum to end tuberculosis (TB) by 2035 [1]. In clinical practice, a triage test to rule out ATB requires high negative predictive value (NPV). WHO has also described the need for a test to predict progression from latent TB infection (LTBI) to ATB with >75% specificity and >75% sensitivity [2]. Further, the Foundation for Innovative New Diagnostics (FIND) and the New Diagnostics Working Group of the Stop TB Partnership have proposed a need for a prognostic test for TB risk that requires a positive predictive value (PPV) > 5.8% at a 2-year cumulative incidence of ATB of 2% (

Our systematic search of the literature for published transcriptional signatures diagnosing ATB against other clinical conditions identified 16 transcriptional signatures (Table 1) that distinguished patients with ATB from 1 or more of the following: healthy controls, patients with LTBI, or patients with ODs. Next, we searched 2 public data repositories (NCBI GEO and EBI ArrayExpress) for gene expression datasets that profiled whole blood or PBMC samples comparing patients with ATB to healthy controls or patients with LTBI or ODs. We identified 24 independent datasets consisting of 3,083 transcriptome profiles from 14 countries (Table 2). Note that 8 of these 24 datasets were used to derive 1 or more of the 16 gene signatures. Therefore, in order to ensure that the discovery cohort(s) of each signature did not bias its overall performance, we removed the corresponding discovery cohort(s) for each signature when computing the overall performance of each signature across all datasets. For example, for the Verhagen10 signature, we removed GSE41055 when estimating the overall AUROC and PPV, whereas for Sweeney3 we removed GSE19491, GSE37250, and GSE42834.

In this study, we compared 16 gene signatures for distinguishing patients with ATB from healthy controls or patients with LTBI or ODs using 24 independent datasets of >3,000 whole blood or PBMC transcriptome profiles from 14 countries. Collectively, these datasets represented real-world heterogeneity observed in patients with TB. For instance, the samples collected across 14 countries represented diversity in both host and pathogen genetics. Similarly, some datasets profiled samples from children whereas others profiled samples from adults, which represented heterogeneity in host response due to age. These data also represented heterogeneity in clinical practice as patients were diagnosed using different criteria (e.g., sputum culture versus sputum microscopy).



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