| Literature DB >> 32533832 |
Clare Eckold1, Vinod Kumar2,3, January Weiner4, Bachti Alisjahbana5,6, Anca-Lelia Riza3,7,8, Katharina Ronacher9,10, Jorge Coronel11, Sarah Kerry-Barnard12, Stephanus T Malherbe10, Leanie Kleynhans10, Kim Stanley10, Rovina Ruslami5, Mihai Ioana7,8, Cesar Ugarte-Gil1,13, Gerhard Walzl10, Reinout van Crevel3, Cisca Wijmenga2, Julia A Critchley12, Hazel M Dockrell1, Jacqueline M Cliff1.
Abstract
BACKGROUND: People with diabetes have an increased risk of developing active tuberculosis (TB) and are more likely to have poor TB-treatment outcomes, which may impact on control of TB as the prevalence of diabetes is increasing worldwide. Blood transcriptomes are altered in patients with active TB relative to healthy individuals. The effects of diabetes and intermediate hyperglycemia (IH) on this transcriptomic signature were investigated to enhance understanding of immunological susceptibility in diabetes-TB comorbidity.Entities:
Keywords: diabetes; hyperglycemia; inflammation; tuberculosis
Mesh:
Year: 2021 PMID: 32533832 PMCID: PMC7823074 DOI: 10.1093/cid/ciaa751
Source DB: PubMed Journal: Clin Infect Dis ISSN: 1058-4838 Impact factor: 9.079
Characteristics of Study Participants
| Characteristic | Country | TB Only | IH-TB | DM-TB | T2DM Only | Healthy Controls |
|
|---|---|---|---|---|---|---|---|
| No. of study participants | South Africa | 11 | 20 | 15 | 33 | 24 | |
| Romania | 10 | 10 | 15 | 19 | 12 | ||
| Indonesia | 14 | 5 | 19 | … | … | ||
| Peru | 11 | 9 | 12 | … | … | ||
| All sites | 46 | 44 | 61 | … | … | ||
| Age, y, median (range) | South Africa | 48 (31–56) | 44.5 (25–57) | 46 (27–57) | 49 (29–64) | 42 (30–70) | .168 |
| Romania | 43 (30–64) | 48.5 (22–63) | 47 (22–64) | 55 (38–65) | 46 (38–61) | .329 | |
| Indonesia | 47 (28–62) | 51 (37–54) | 52 (33–66) | … | … | .430 | |
| Peru | 55 (31–69) | 52 (31–68) | 50.5 (42–58) | … | … | .928 | |
| All sites | 46 (28–69) | 46 (22–68) | 49 (22–66) | … | … | .2645 | |
| Sex, % (No. male/female) | South Africa | 18 (2/9) | 60 (12/8) | 47 (7/8) | 45 (15/18) | 50 (12/12) | |
| Romania | 60 (6/4) | 90 (9/1) | 87 (13/2) | 73 (14/5) | 83 (10/2) | ||
| Indonesia | 50 (7/7) | 80 (4/1) | 58 (11/8) | … | … | ||
| Peru | 45 (5/6) | 55 (5/4) | 50 (6/6) | … | … | ||
| All sites | 43 (26/20) | 68 (30/14) | 60 (37/24) | … | … | ||
| BMI, kg/m2, median (range) | South Africa | 20.1 (14.6–24.1) | 18.4 (13.7–27.1) | 19.1 (13.9–32.3) | 29 (20.52–52.54) | 23.7 (17.37–45.20) | 1.43x10[-8] |
| Romania | 20.65 (17.7–25.5) | 21 (15.5–22) | 21.5 (15.3–36.1) | 28.7 (13.1–37.8) | … | 6.73x10[-4] | |
| Indonesia | 19.8 (13.76–33.27) | 18.67 (13.9–20.09) | 19.52 (16.10–31.73) | … | … | .242 | |
| Peru | 23.98 (17.35–28.96) | 21.94 (18.67–25.56) | 22.7 (20.55–33.33) | … | … | .207 | |
| All sites | 20.94 (13.76–33.27) | 19.44 (13.7–27.1) | 21.5 (13.9–36.1) | … | … | 1.67x10[-3] | |
| HbA1c, %, median (range) | South Africa | 5.3 (4.8–5.7) | 6 (5.7–6.3) | 10.8 (6.5–14.3) | 10.1 (4.7–14.9) | 5.3 (4.8–5.6) | 2.2x10[-16] |
| Romania | 5.5 (5.2–5.7) | 6 (5.7–6.4) | 10.4 (6.6–15) | 9 (7.1–14) | 5.4 (5.2–5.6) | 1.2x10[-13] | |
| Indonesia | 5.55 (5–5.7) | 5.9 (5.8–6) | 11.9 (7.5–15.9) | … | … | 3.2x10[-12] | |
| Peru | 5.3 (5.1–5.7) | 5.8 (5.7–6.1) | 11.4 (7.1–15.2) | … | … | 8.33x10[-9] | |
| All sites | 5.5 (4.8–5.7) | 5.95 (5.7–6.4) | 11 (6.5–15.9) | … | … | 2.2x10[-16] |
Abbreviations: ANOVA, analysis of variance; BMI, body mass index; DM-TB, diabetes mellitus–tuberculosis; HbA1c, glycated hemoglobin; IH-TB, intermediate hyperglycemia–tuberculosis; T2DM, type 2 diabetes mellitus; TB, tuberculosis.
Figure 1.Differential expression analysis of all the disease phenotypes in South Africa compared to healthy controls before the initiation of tuberculosis (TB) treatment. Gene expression profiles of TB only (n = 11, A), diabetes mellitus (DM) only (n = 33, B), DM-TB (n = 15, C), and intermediate hyperglycemia (IH)–TB (n = 20, D), each relative to healthy controls (n = 24). Genes that were deemed statistically significantly differentially expressed had an adjusted P < .05 after multiple testing correction (Benjamini-Hochberg). Black corresponds to the genes whose expression was significantly changed, and gray shows genes without significant expression change. Abbreviation: FDR, false discovery rate.
Figure 2.Concordance and discordance of gene expression between the comparisons of each disease group and healthy controls in South Africa. Log fold change (FC) and P value between groups was calculated with R-package DESeq2. A disco.score was calculated for each pair of corresponding genes. The axes show log2 FC between the conditions indicated by the labels. For example, on the top left plot the x-axis corresponds to the comparison between tuberculosis (TB) and healthy controls (HC), and the y-axis shows the log2 FC between diabetes mellitus (DM)-TB and HC. Red dots show genes that are significantly different from the controls in the same direction (concordant genes), and blue dots show genes that are significantly different in both comparisons, but in opposite directions. Intensity of color indicates the strength of concordance/discordance as measured by the disco.score.
Figure 3.Principal component analysis (PCA) of South African participants. The list of all genes that were significantly differentially expressed in any patient group comparison with healthy controls was used in a PCA of all the samples obtained from participants recruited in South Africa. Abbreviations: DM, diabetes mellitus; IH, intermediate hyperglycemia; PC, principal component; TB, tuberculosis.
Figure 4.Transcriptional modules that were significantly differentially expressed in tuberculosis (TB)-only, diabetes mellitus (DM)-TB, intermediate hyperglycemia (IH)-TB, and DM only compared to healthy controls in South Africa before initiation of TB treatment. Transcripts were evaluated using a preexisting modular framework. Significantly up-regulated (red) and down-regulated (blue) modules are shown: the length of each bar corresponds to the effect size (magnitude of change) of that module, and the color saturation represents the adjusted P value (<.0001). The amount of color represents the proportion of genes within that module that were differentially expressed.
Figure 5.Differential gene expression analysis of diabetes mellitus (DM)–tuberculosis (TB) and intermediate hyperglycemia (IH)–TB patients relative to TB-only patients, in the combined dataset from all 4 field sites. Samples collected in South Africa, Romania, Peru, and Indonesia from DM-TB (A) patients and IH-TB patients (B) were compared with patients with TB only in a combined analysis. Genes significantly differentially expressed after multiple testing correction are shown in black (P < .05). Genes in gray are not statistically significantly altered compared to patients with untreated TB only. Abbreviation: FDR, false discovery rate.
Figure 6.Summary of modular analysis in all 4 field sites. The fold changes of the genes within the top significantly differentially expressed modules are shown (adjusted P < .05). Inside: intermediate hyperglycemia–tuberculosis (TB) compared to TB only. Outside: diabetes mellitus–TB compared to TB only. Up-regulated genes are shown in red, and down-regulated genes are in blue. The saturation of color represents the magnitude of differential expression.
Figure 7.Predictive model of known signature in predictive model of known signature in TANDEM data. Receiver operating characteristic curves are based on a machine learning model generated from 2 different external datasets of transcriptome profiles of patients with tuberculosis and healthy controls (Kaforou et al [29] and Sweeney et al [30] training set). The random forest model was applied to the TANDEM cohort (test set), separately to individuals with and without diabetes mellitus. Abbreviations: AUC, area under the curve; CI, confidence interval; DM, diabetes mellitus; ROC, receiver operating characteristic.