Table II:
Canonical pathways associated with Mtb-induced BAL cell gene expression in LTBI subjects
| Canonical pathways with -log p-value >3.0 (from Mtb-induced gene expression in LTBI subjects) | LTBI unsorted | LTBI CD4 depleted | Δ-log p |
|---|---|---|---|
| Interferon Signaling | 10.666 | 0.342 | 10.323 |
| Crosstalk between Dendritic Cells and Natural Killer Cells | 10.347 | 1.987 | 8.360 |
| Pathogenesis of Multiple Sclerosis | 6.057 | 0.000 | 6.057 |
| Th1 Pathway | 7.473 | 1.781 | 5.692 |
| Antigen Presentation Pathway | 5.277 | 0.000 | 5.277 |
| Type I Diabetes Mellitus Signaling | 6.294 | 1.102 | 5.192 |
| Activation of IRF by Cytosolic Pattern Recognition Receptors | 5.127 | 0.210 | 4.917 |
| CD40 Signaling | 5.694 | 0.862 | 4.833 |
| Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses | 8.772 | 4.212 | 4.560 |
| Role of Hypercytokinemia/hyperchemokinemia in the Pathogenesis of Influenza | 6.694 | 2.446 | 4.249 |
| Th1 and Th2 Activation Pathway | 6.791 | 2.614 | 4.178 |
| JAK/Stat Signaling | 5.367 | 1.301 | 4.066 |
| IL-15 Production | 4.465 | 0.437 | 4.027 |
| Altered T Cell and B Cell Signaling in Rheumatoid Arthritis | 7.441 | 3.493 | 3.948 |
| iNOS Signaling | 4.194 | 0.288 | 3.906 |
| Primary Immunodeficiency Signaling | 4.636 | 0.898 | 3.737 |
| Role of JAK1, JAK2 and TYK2 in Interferon Signaling | 3.658 | 0.000 | 3.658 |
| Dendritic Cell Maturation | 6.869 | 3.235 | 3.634 |
| Toll-like Receptor Signaling | 5.061 | 1.473 | 3.588 |
| Graft-versus-Host Disease Signaling | 7.030 | 3.571 | 3.460 |
| Communication between Innate and Adaptive Immune Cells | 9.139 | 5.680 | 3.458 |
| Atherosclerosis Signaling | 6.668 | 3.682 | 2.986 |
| IL-10 Signaling | 4.541 | 1.592 | 2.949 |
| Allograft Rejection Signaling | 3.868 | 0.959 | 2.909 |
| Hepatic Fibrosis / Hepatic Stellate Cell Activation | 5.784 | 3.025 | 2.760 |
| Role of MAPK Signaling in the Pathogenesis of Influenza | 3.640 | 0.966 | 2.674 |
| NF-κB Signaling | 3.597 | 1.163 | 2.434 |
| Agranulocyte Adhesion and Diapedesis | 5.524 | 3.255 | 2.269 |
| Acute Phase Response Signaling | 4.938 | 2.700 | 2.237 |
| T Helper Cell Differentiation | 3.871 | 1.657 | 2.214 |
| Oncostatin M Signaling | 3.868 | 1.727 | 2.142 |
| IL-6 Signaling | 4.964 | 2.881 | 2.084 |
| Autoimmune Thyroid Disease Signaling | 3.050 | 1.003 | 2.047 |
| HMGB1 Signaling | 4.818 | 2.795 | 2.023 |
| IL-17A Signaling in Airway Cells | 3.350 | 1.418 | 1.932 |
| Th2 Pathway | 3.930 | 2.071 | 1.859 |
| Granulocyte Adhesion and Diapedesis | 8.079 | 6.339 | 1.739 |
| Antioxidant Action of Vitamin C | 3.290 | 1.635 | 1.655 |
| Differential Regulation of Cytokine Production in Intestinal Epithelial Cells by IL-17A and IL-17F | 3.751 | 2.197 | 1.554 |
| IL-15 Signaling | 3.350 | 2.056 | 1.294 |
| MIF-mediated Glucocorticoid Regulation | 3.115 | 1.835 | 1.280 |
| Colorectal Cancer Metastasis Signaling | 3.135 | 2.118 | 1.017 |
| LXR/RXR Activation | 3.221 | 2.397 | 0.824 |
| Role of Macrophages, Fibroblasts and Endothelial Cells in Rheumatoid Arthritis | 3.980 | 3.296 | 0.685 |
| Role of IL-17A in Arthritis | 3.730 | 3.060 | 0.669 |
| TREM1 Signaling | 5.229 | 4.678 | 0.551 |
| Inhibition of Matrix Metalloproteases | 4.556 | 4.443 | 0.113 |
| Hepatic Cholestasis | 4.021 | 4.200 | -0.179 |
| Differential Regulation of Cytokine Production in Macrophages and T Helper Cells by IL-17A and IL-17F | 3.126 | 3.715 | -0.588 |
| Role of Cytokines in Mediating Communication between Immune Cells | 3.821 | 4.802 | -0.981 |
| Role of IL-17F in Allergic Inflammatory Airway Diseases | 3.405 | 5.335 | -1.929 |
Canonical pathways associated with Mtb-induced gene expression in LTBI subjects. Pathway analysis was based on IPA assessment of genes identified as having significant changes in expression following in vitro infection of unsorted BAL cells from individuals with LTBI, and from BAL cells from which CD4+ T cells were depleted prior to Mtb infection. Pathways are ordered by the differences in the degree to which they were identified as significant in assessments of unsorted and CD4-depleted BAL cells (as indicated by Δ -log p-value). Of the 51 pathways identified in unsorted BAL cells by the p-value cut-off of <0.001 (-log p > 3.0), 34 (shown in bold) displayed a reduction in significance of > 2 logs following CD4 depletion.