Table III:
Mtb-induced gene expression signature in baseline bronchoalveolar lavage cells from individuals with LTBI
| Δ – log (p-value) | |||||||
|---|---|---|---|---|---|---|---|
| -log (p-value) | LTBI unsorted vs LTBI CD4 depleted | LTBI unsorted vs. Mtb-naïve unsorted | |||||
| Symbol | Entrez Gene Name | ID | LTBI unsorted | LTBI CD4 depleted | Mtb-naïve unsorted | ||
| CXCL9 | C-X-C motif chemokine ligand 9 | 8101118 | 9.239 | 0.032 | 0.138 | 9.206 | 9.100 |
| CD40 | CD40 molecule | 8063156 | 9.221 | 0.032 | 2.846 | 9.189 | 6.375 |
| IFI35 | interferon induced protein 35 | 8007446 | 8.490 | 0.032 | 0.138 | 8.458 | 8.352 |
| TAP2 | transporter 2, ATP binding cassette subfamily B member | 8178841 | 7.097 | 0.032 | 0.138 | 7.065 | 6.959 |
| CXCL10 | C-X-C motif chemokine ligand 10 | 8101126 | 6.929 | 0.032 | 0.138 | 6.897 | 6.791 |
| UBD | ubiquitin D | 8124650 | 6.929 | 0.032 | 0.138 | 6.897 | 6.791 |
| CXCL11 | C-X-C motif chemokine ligand 11 | 8101131 | 6.612 | 0.032 | 0.138 | 6.580 | 6.474 |
| TAP1 | transporter 1, ATP binding cassette subfamily B member | 8180061 | 5.917 | 0.032 | 2.077 | 5.885 | 3.840 |
| IL15RA | interleukin 15 receptor subunit alpha | 7931899 | 7.370 | 1.771 | 5.278 | 5.599 | 2.092 |
| JAK2 | Janus kinase 2 | 8154178 | 5.305 | 0.032 | 0.138 | 5.273 | 5.167 |
| FAS | Fas cell surface death receptor | 7929032 | 4.753 | 0.032 | 0.138 | 4.721 | 4.615 |
| PNPLA3 | patatin like phospholipase domain containing 3 | 8073633 | 4.690 | 0.032 | 0.138 | 4.658 | 4.552 |
| CCL5 | C-C motif chemokine ligand 5 | 8014316 | 4.690 | 0.032 | 2.135 | 4.658 | 2.555 |
| PARP9 | poly(ADP-ribose) polymerase family member 9 | 8090018 | 4.614 | 0.032 | 0.138 | 4.582 | 4.476 |
| IFNG | interferon gamma | 7964787 | 4.593 | 0.032 | 0.138 | 4.561 | 4.455 |
| PSMB9 | proteasome subunit beta 9 | 8118571 | 4.519 | 0.032 | 0.138 | 4.487 | 4.381 |
| CD274 | CD274 molecule | 8154233 | 4.497 | 0.032 | 0.138 | 4.465 | 4.359 |
| PSME2 | proteasome activator subunit 2 | 7978123 | 4.050 | 0.032 | 0.138 | 4.018 | 3.912 |
| MX1 | MX dynamin like GTPase 1 | 8068713 | 3.861 | 0.032 | 0.138 | 3.829 | 3.723 |
| IL10RA | interleukin 10 receptor subunit alpha | 7944152 | 3.777 | 0.032 | 0.138 | 3.745 | 3.639 |
| RARRES3 | retinoic acid receptor responder 3 | 7940775 | 3.546 | 0.032 | 0.138 | 3.514 | 3.408 |
| LTA | lymphotoxin alpha | 8118137 | 3.441 | 0.032 | 0.138 | 3.409 | 3.303 |
| PARP14 | poly(ADP-ribose) polymerase family member 14 | 8082100 | 3.411 | 0.032 | 0.138 | 3.379 | 3.273 |
| RFX5 | regulatory factor X5 | 7919971 | 3.411 | 0.032 | 0.138 | 3.379 | 3.273 |
| IFIT3 | interferon induced protein with tetratricopeptide repeats 3 | 7929052 | 3.044 | 0.032 | 0.138 | 3.012 | 2.906 |
| IL15 | interleukin 15 | 8097553 | 3.000 | 0.032 | 0.138 | 2.968 | 2.862 |
| IL27 | interleukin 27 | 8000567 | 3.000 | 0.032 | 0.138 | 2.968 | 2.862 |
| NECTIN2 | nectin cell adhesion molecule 2 | 8029507 | 3.000 | 0.032 | 0.138 | 2.968 | 2.862 |
| IRF1 | interferon regulatory factor 1 | 8114010 | 2.975 | 0.032 | 0.138 | 2.943 | 2.836 |
| TNFSF10 | TNF superfamily member 10 | 8092169 | 2.970 | 0.032 | 0.138 | 2.938 | 2.832 |
| KL | klotho | 7968556 | 2.899 | 0.032 | 0.138 | 2.867 | 2.761 |
| IFITM3 | interferon induced transmembrane protein 3 | 7945371 | 2.890 | 0.032 | 0.138 | 2.858 | 2.752 |
| STAT2 | signal transducer and activator of transcription 2 | 7964119 | 2.890 | 0.032 | 0.138 | 2.858 | 2.752 |
| CSF2RB | colony stimulating factor 2 receptor beta common subunit | 8072757 | 2.853 | 0.032 | 0.138 | 2.821 | 2.714 |
| HLA-F | major histocompatibility complex, class I, F | 8179019 | 2.753 | 0.032 | 0.138 | 2.721 | 2.615 |
| PSMB8 | proteasome subunit beta 8 | 8125500 | 2.734 | 0.032 | 0.138 | 2.702 | 2.596 |
| CD226 | CD226 molecule | 8023757 | 2.641 | 0.032 | 0.138 | 2.609 | 2.503 |
| MAP2K1 | mitogen-activated protein kinase kinase 1 | 7984319 | 2.598 | 0.032 | 0.138 | 2.566 | 2.460 |
| GZMB | granzyme B | 7978366 | 3.887 | 1.377 | 1.657 | 2.510 | 2.230 |
| PSME1 | proteasome activator subunit 1 | 7973564 | 2.390 | 0.032 | 0.138 | 2.358 | 2.252 |
| ICOS | inducible T cell costimulator | 8047702 | 2.388 | 0.032 | 0.138 | 2.356 | 2.250 |
| AICDA | activation induced cytidine deaminase | 7960910 | 2.372 | 0.032 | 0.138 | 2.340 | 2.234 |
| USP53 | ubiquitin specific peptidase 53 | 8097098 | 2.231 | 0.032 | 0.138 | 2.199 | 2.093 |
| DNAJC7 | DnaJ heat shock protein family (Hsp40) member C7 | 8015490 | 2.217 | 0.032 | 0.138 | 2.185 | 2.079 |
| NLRC5 | NLR family CARD domain containing 5 | 7995926 | 2.199 | 0.032 | 0.138 | 2.167 | 2.061 |
| SOCS2 | suppressor of cytokine signaling 2 | 7957551 | 2.177 | 0.032 | 0.138 | 2.145 | 2.039 |
| CD80 | CD80 molecule | 8089771 | 2.146 | 0.032 | 0.138 | 2.114 | 2.008 |
Set of 47 genes identified as the signature of the impact of memory CD4+ T cells on Mtb-induced BAL cell gene expression. As detailed in the text, delineation of this gene signature was derived from evaluation of 12 canonical pathways identified with a probability of p<0.001 in unsorted BAL cells from LTBI subjects, and with a reduction in significance of at least 2 logs in both CD4+ T-cell depleted LTBI samples and BAL cells from Mtb naïve subjects (illustrated in Figure 2B). Of 68 differentially-expressed genes within these 12 pathways, the expression of the 47 genes of this signature in unsorted BAL cells of LTBI subjects also met criteria of p-value significance 2 logs greater than observed in both CD4-depleted BAL samples from LTBI subjects and unsorted BAL cells from Mtb-naïve subjects, as displayed in the two furthest right columns of Table III.