| Literature DB >> 33328540 |
Jéssica D Petrilli1, Luana E Araújo1, Luciane Sussuchi da Silva2, Ana Carolina Laus2, Igor Müller1, Rui Manuel Reis2,3,4, Eduardo Martins Netto5, Lee W Riley6, Sérgio Arruda1, Adriano Queiroz7.
Abstract
Current diagnostic tests for tuberculosis (TB) are not able to predict reactivation disease progression from latent TB infection (LTBI). The main barrier to predicting reactivation disease is the lack of our understanding of host biomarkers associated with progression from latent infection to active disease. Here, we applied an immune-based gene expression profile by NanoString platform to identify whole blood markers that can distinguish active TB from other lung diseases (OPD), and that could be further evaluated as a reactivation TB predictor. Among 23 candidate genes that differentiated patients with active TB from those with OPD, nine genes (CD274, CEACAM1, CR1, FCGR1A/B, IFITM1, IRAK3, LILRA6, MAPK14, PDCD1LG2) demonstrated sensitivity and specificity of 100%. Seven genes (C1QB, C2, CCR2, CCRL2, LILRB4, MAPK14, MSR1) distinguished TB from LTBI with sensitivity and specificity between 82 and 100%. This study identified single gene candidates that distinguished TB from OPD and LTBI with high sensitivity and specificity (both > 82%), which may be further evaluated as diagnostic for disease and as predictive markers for reactivation TB.Entities:
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Year: 2020 PMID: 33328540 PMCID: PMC7745039 DOI: 10.1038/s41598-020-78793-2
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Demographic and clinical data of study population.
| Active TB | LTBI | OPD | HC | |
|---|---|---|---|---|
| Men | 11 (68.75) | 4 (57.14) | 2 (40) | 1 (20) |
| Women | 5 (31.25) | 3 (42.86) | 3 (60) | 4 (80) |
| Age ± SDc | 41.93 ± 14.04 | 42.67 ± 17.06 | 43.8 ± 9.70 | 32.5 ± 3.53 |
| Sputum Smear | ||||
| Pos | 13 (76.5) | – | 0 | |
| Neg | 3 (23.5) | – | 5 (100) | – |
| Culture | ||||
| Pos | 8 (47.1) | – | 0 | – |
| Neg | 0 | – | 5 (100) | – |
| N/S | 9 (52.9) | – | – | – |
| Xpert MTB/RIF | 1 (5.9) | – | – | – |
| Pos | – | 7 (100) | – | 0 |
| Neg | – | 0 | – | 6 (100) |
TB tuberculosis, LTBI latent tuberculosis infection, OPD other pulmonary disease, HC health communicants, SD standard deviation, N/S not screened.
aMissing data: gender (TB = 1 and HC = 1) and age (TB = 1, TBL = 1 and HC = 1).
Figure 1Heatmap showing different expression pattern of 46 proinflammatory genes out of 549 genes. Heatmap of gene expression levels in patients diagnosed with active TB (red), LTBI subjects (green), OPD patients (yellow) and uninfected donors HC (blue). Expression levels are scaled from dark blue (low expression) to dark red (high expression). Heatmap was generated in R (version 3.6.3) with the ComplexHeatmap package (version 2.0.0, https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html).
Figure 2Identification of markers for TB diagnosis. (A) Heatmap of 23 gene expression levels of TB (red) and OPD (yellow) patients. (B) PCA score plot of TB and OPD patients. (C) Volcano plots showing the distribution of the gene expression fold changes in TB patients relative to OPD patients. Genes with absolute fold change ≥ 4 and p-value ≤ 0.05 are indicated in orange. Expression levels are scaled from dark blue (low expression) to dark red (high expression). Figures were generated with R (version 3.6.3) using ComplexHeatmap package (version 2.0.0, https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html), prcomp function from stats package (version 3.6.3, https://www.r-project.org/), and NanoStringNorm package (version 1.2.1.1, https://cran.r-project.org/web/packages/NanoStringNorm/index.html) for heatmap, pca and Volcano plot, respectively.
Figure 3Identification of markers for TB progression. (A) Heatmap of seven gene expression levels of TB (red) and LTBI (green) subjects. (B) PCA score plot of TB and LTBI subjects. (C) Volcano plot showing the distribution of the gene expression fold changes in TB patients relative to LTBI. Genes with absolute fold change ≥ 4 and p-value ≤ 0.05 are indicated in orange. Expression levels are scaled from dark blue (low expression) to dark red (high expression). Figures were generated with R (version 3.6.3) using ComplexHeatmap package (version 2.0.0, https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html), prcomp function from stats package (version 3.6.3, https://www.r-project.org/), and NanoStringNorm package (version 1.2.1.1, https://cran.r-project.org/web/packages/NanoStringNorm/index.html) for heatmap, pca and Volcano plot, respectively.
ROC analysis, sensibility and specificity of candidate genes to TB diagnosis.
| Gene | ROC AUC (95% CI) | ROC p-value | Sensitivity % (95% CI) | Specificity % (95% CI) | Cut-off |
|---|---|---|---|---|---|
| C1QA | 0.98 (0.95–1.02) | < 0.0001 | 88.24 (63.56–98.54) | 100 (66.37–100) | > 3.74 |
| CD274 | 1.00 | < 0.0001 | 100 (80.49–100) | 100 (66.37–100) | > 5.71 |
| CD59 | 0.98 (0.95–1.02) | < 0.0001 | 94.12 (71.31–99.85) | 100 (66.37–100) | > 8.63 |
| CEACAM1 | 1.00 | < 0.0001 | 100 (80.49–100) | 100 (66.37–100) | > 6.02 |
| CR1 | 1.00 | < 0.0001 | 100 (80.49–100) | 100 (66.37–100) | > 10.02 |
| FCGR1A/B | 1.00 | < 0.0001 | 100 (80.49–100) | 100 (66.37–100) | > 7.83 |
| ICAM1 | 0.98 (0.95–1.02) | < 0.0001 | 88.24 (63.56–98.54) | 100 (66.37–100) | > 7.54 |
| IFITM1 | 1.00 | < 0.0001 | 100 (80.49–100) | 100 (66.37–100) | > 12.86 |
| IL18RAP | 0.98 (0.95–1.02) | < 0.0001 | 88.24 (63.56–98.54) | 100 (66.37–100) | > 8.97 |
| IL4R | 0.98 (0.95–1.02) | < 0.0001 | 94.12 (71.31–99.85) | 100 (66.37–100) | > 9.08 |
| IRAK3 | 1.00 | < 0.0001 | 100 (80.49–100) | 100 (66.37–100) | > 6.86 |
| JAK2 | 0.99 (0.97–1.01) | < 0.0001 | 94.12 (71.31–99.85) | 100 (66.37–100) | > 9.86 |
| JAK3 | 0.99 (0.97–1.01) | < 0.0001 | 94.12 (71.31–99.85) | 100 (66.37–100) | > 8.59 |
| LILRA5 | 0.97 (0.92–1.02) | < 0.0001 | 88.24 (63.56–98.54) | 100 (66.37–100) | > 9.87 |
| LILRA6 | 1.00 | < 0.0001 | 100 (80.49–100) | 100 (66.37–100) | > 7.79 |
| LY96 | 0.99 (0.97–1.01) | < 0.0001 | 94.12 (71.31–99.85) | 100 (66.37–100) | > 7.69 |
| MAPK14 | 1.00 | 0.0008757 | 100 (80.49–100) | 100 (47.82–100) | > 10.03 |
| NOD2 | 0.92 (0.81–1.04) | 0.004259 | 82.35 (56.57–96.20) | 100 (47.82–100) | > 8.79 |
| PDCD1LG2 | 1.00 | 0.0008757 | 100 (80.49–100) | 100 (47.82–100) | > 4.13 |
| PML | 0.98 (0.95–1.02) | 0.001156 | 94.12 (71.31–99.85) | 100 (47.82–100) | > 7.72 |
| SOCS3 | 0.96 (0.88–1.04) | 0.001981 | 94.12 (71.31–99.85) | 100 (47.82–100) | > 7.40 |
| TAP1 | 0.97 (0.92–1.03) | 0.001518 | 88.24 (63.56–98.54) | 100 (47.82–100) | > 8.63 |
| TNFAIP6 | 0.98 (0.95–1.02) | 0.001156 | 94.12 (71.31–99.85) | 100 (47.82–100) | > 6.02 |
ROC analysis, sensibility and specificity of candidate genes to predict TB reactivation.
| Gene | ROC AUC (95% CI) | ROC p-value | Sensitivity % (95% CI) | Specificity % (95% CI) | Cut-off |
|---|---|---|---|---|---|
| C1QB | 0.97 (0.92–1.02) | 0.0003360 | 88.24 (63.56–98.54) | 100 (59.04–100) | > 4.15 |
| C2 | 0.92 (0.82–1.02) | 0.001348 | 82.35(56.57–100) | 100 (59.04–100) | > 4.16 |
| CCR2 | 1.00 | 0.0001594 | 100 (80.49–100) | 100 (59.04–100) | > 8.61 |
| CCRL2 | 0.86 (0.71–1.01) | 0.005753 | 82.35 (56.57–96.20) | 85.71 (42.13–99.64) | > 5.31 |
| LILRB4 | 0.94 (0.82–1.05) | 0.0008613 | 94.12 (71.31–99.85) | 100 (59.04–100) | > 6.56 |
| MAPK14 | 0.95 (0.88–1.03) | 0.0005420 | 88.24 (63.56–98.54) | 100 (59.04–100) | > 10.54 |
| MSR1 | 0.99 (0.96–1.01) | 0.0002051 | 94.12 (71.31–99.85) | 100 (59.04–100) | > 4.72 |
Annotation of selected genes based on ROC curve analysis.
| Symbol | Name | Annotation | Target for |
|---|---|---|---|
| C1QA | Complement C1q A chain | Complement system, host pathogen interaction, innate immune system | TB diagnosis |
| C1QB | Complement C1q B chain | Complement system, host pathogen interaction, innate immune system | TB progression |
| C2 | Complement component 2 | Complement system, host pathogen interaction, innate immune system | TB progression |
| CCR2 | C–C chemokine receptor type 2 | Chemokine signaling, cytokine signaling, innate immune system, lymphocyte activation | TB progression |
| CCRL2 | C–C chemokine ligand type 2 | Chemokine signaling | TB progression |
| CD59 | CD59 molecule | Complement system, innate immune system, lymphocyte activation | TB diagnosis |
| CD274 | CD274 molecule | Adaptive immune system, cell adhesion, lymphocyte activation | TB diagnosis |
| CEACAM1 | CEA cell adhesion molecule 1 | Hemostasis, innate immune system and lymphocyte activation | TB diagnosis |
| CR1 | Complement receptor type 1 | Complement system, host pathogen interaction, innate immune system | TB diagnosis |
| FCGR1A/B | Fc fragment of IgG receptor Ia | Adaptive immune system, cytokine signaling, host pathogen interaction, innate immune system, MHC class I antigen presentation, phagocytosis and degradation and Type II interferon signaling | TB diagnosis |
| ICAM1 | Intercellular adhesion molecule 1 | Adaptive immune system, cell adhesion, innate immune system, lymphocyte activation | TB diagnosis |
| IFITM1 | Interferon induced transmembrane protein 1 | Adaptive immune system, B cell receptor signaling, cytokine signaling and Type I interferon signaling | TB diagnosis |
| IL18RAP | Interleukin 18 receptor accessory protein | Cytokine signaling, oxidative stress | TB diagnosis |
| IL4R | Interleukin 4 receptor | Cytokine signaling, lymphocyte activation and Th2 differentiation | TB diagnosis |
| IRAK3 | Interleukin 1 receptor associated kinase 3 | Cytokine signaling, innate immune system and TLR signaling | TB diagnosis |
| JAK2 | Janus kinase 2 | Chemokine signaling, cytokine signaling, host pathogen interaction, hemostasis, oxidative stress, Th1 and Th17 differentiation, Type II interferon signaling | TB diagnosis |
| JAK3 | Janus kinase 3 | Chemokine signaling, cytokine signaling, host pathogen interaction, hemostasis, lymphocyte activation, Th2 and Th17 differentiation | TB diagnosis |
| LILRA5 | Leukocyte immunoglobulin like receptor A5 | Adaptive immune system | TB diagnosis |
| LILRA6 | Leukocyte immunoglobulin like receptor A6 | Adaptive immune system and MHC class I antigen presentation | TB diagnosis |
| LILRB4 | Leukocyte immunoglobulin like receptor B4 | Adaptive immune system | TB progression |
| LY96 | Lymphocyte antigen 96 | Adaptive immune system, apoptosis, host pathogen interaction, innate immune system, MHC class I antigen presentation, NF-κB signaling, TLR signaling | TB diagnosis |
| MAPK14 | Mitogen-activated protein kinase 14 | Cytokine signaling, hemostasis, host pathogen interaction, innate immune system, lymphocyte trafficking, NLR signaling, T cell receptor signaling, Th17 differentiation, TNF family signaling and TLR signaling | TB diagnosis and TB progression |
| NOD 2 | Nucleotide binding oligomerization domain containing 2 | Cytokine signaling, host pathogen interaction, innate immune system, lymphocyte activation, NLR signaling, TNF family signaling, TLR signaling | TB diagnosis |
| MSR1 | Macrophage scavenger receptor 1 | Phagocytosis and degradation | TB progression |
| PDCD1LG2 | Programmed cell death 1 ligand 2 | Adaptive immune system, cell adhesion and lymphocyte activation | TB diagnosis |
| PML | Promyelocytic leukemia | Cytokine signaling, host pathogen interaction, oxidative stress, Type II interferon signaling | TB diagnosis |
| SOCS3 | Suppressor of cytokine signaling 3 | Adaptive immune system, cytokine signaling, host pathogen interaction, MHC class I antigen presentation, TNF family signaling, Type I interferon signaling and Type II interferon signaling | TB diagnosis |
| TAP1 | Transporter 1, ATP binding cassette subfamily B member | Adaptive immune system, host pathogen interaction, MHC class I antigen presentation, phagocytosis and degradation | TB diagnosis |
| TNFAIP6 | Tumor necrosis factor alpha induced protein 6 | Innate immune system | TB diagnosis |
TB Tuberculosis, LTBI latent tuberculosis infection.