Figure 3.

Blood gene expression patterns are consistent over 4 weeks of tuberculosis treatment and can be used to classify patient outcome. A, Expression patterns of genes differentially expressed between tuberculosis-relapse and cured groups in Mycobacterium tuberculosis–stimulated diluted whole-blood cultures over the first 4 weeks of tuberculosis treatment. The normalized hybridization intensity of expression of 381 genes found to be ≥2-fold differentially expressed (P < .05, with Benjamini–Hochberg false-discovery rate correction) at at least one time point is shown for the mean of each patient group at the indicated time points. Genes have been hierarchically clustered using a Euclidean algorithm in GeneSpring GX. B, Hierarchical clustering was performed, using a Euclidean similarity measure and centroid linkage rule, for both patients and genes, using the 309 genes that were on average ≥2-fold differentially expressed between tuberculosis-relapse and cured groups in diluted whole-blood samples collected after 4 weeks of treatment, following stimulation in vitro with live M. tuberculosis. The table shows the treatment outcome (C = cure and R = relapse), the disease severity at diagnosis (M = moderate or S = severe, based on chest radiography findings), the 2-month sputum smear result, and the ratio of lymphocytes to monocytes in blood at the time of tuberculosis diagnosis for each patient. C, Principal component analysis was performed for samples from the 10 patients with relapse and the 10 cured patients at the 3 time points, using the 18 genes that were highly significantly ≥2-fold differentially expressed, using the Bonferroni familywise error rate correction (Supplementary Table 4). D, Molecular signatures were derived for each sample by summing the normalized log₂-transformed hybridization intensity data for the 8 genes that were upregulated in the cured group and the 10 genes that were upregulated in the tuberculosis-relapse group, according to analysis of variance (Table 2). Receiver operating characteristic curve analyses were conducted to determine the accuracy of the molecular signatures, to determine treatment outcome. In the treatment-relapse group, 9 had data at diagnosis, 8 had data from week 2, and 10 had data from week 4. In the cured group, 10 had data at all time points. Abbreviation: AUC, area under the curve.