Dataset: Transcription profiling by array of human lymphatic tissue from HIV-1 infected individuals
Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. While each of the three stages has well-known...
Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. While each of the three stages has well-known clinical, virologic and immunological characteristics, much less is known of the molecular mechanisms underlying each stage. Here we report lymphatic tissue microarray analyses revealing for the first time stage-specific patterns of gene expression during HIV-1 infection. We show that while there is a common set of key genes with altered expression throughout all stages, each stage has a unique gene-expression signature. The acute stage is most notably characterized by increased expression of hundreds of genes involved in immune activation, innate immune defenses (e.g.MDA-5, TLR-7 and -8, PKR, APOBEC3B, 3F, 3G), adaptive immunity, and in the pro-apoptotic Fas-Fas-L pathway. Yet, quite strikingly, the expression of nearly all acute-stage genes return to baseline levels in the asymptomatic stage, accompanying partial control of infection. In the AIDS stage, decreased expression of numerous genes involved in T cell signaling identifies genes contributing to T cell dysfunction. These common and stage-specific, gene-expression signatures provide new insights into the molecular mechanisms underlying the host response and the slow, natural course of HIV-1 infection. Experiment Overall Design: A total of 52 patients were analyzed: 10 patients unaffected, 18 patients with asymptomatic stages of AIDs, 16 patients with acute stages of AIDs, and 8 patients with AIDs.
- Species:
- human
- Samples:
- 52
- Source:
- E-GEOD-16363
- PubMed:
- 19596987
- Updated:
- Dec.12, 2014
- Registered:
- Sep.12, 2014
Factors:
(via ArrayExpress)
| Sample | CLINICAL INFORMATION | AGE | SEX | INDIVIDUAL | DISEASE STATE | ETHNICITY | CLINICAL HISTORY |
|---|---|---|---|---|---|---|---|
| GSE16363GSM410750 | plasma HIV-1 RNA level: undetectable | 28 | Female | 1476 | control | Hispanic | Peripheral Blood CD4 positive T cell level: 704 cells/ml |
| GSE16363GSM410750 | plasma HIV-1 RNA level: undetectable | 28 | Female | 1476 | control | Hispanic | Peripheral Blood CD4 positive T cell level: 704 cells/ml |
| GSE16363GSM410752 | plasma HIV-1 RNA level: 27200 copies/ml | 23 | Male | 1463 | asymptomatic HIV-1 infection | African American | Peripheral Blood CD4 positive T cell level: 259 cells/ml |
| GSE16363GSM410752 | plasma HIV-1 RNA level: 27200 copies/ml | 23 | Male | 1463 | asymptomatic HIV-1 infection | African American | Peripheral Blood CD4 positive T cell level: 259 cells/ml |
| GSE16363GSM410754 | plasma HIV-1 RNA level: undetectable | 52 | Female | 1472 | control | Caucasian | Peripheral Blood CD4 positive T cell level: 837 cells/ml |
| GSE16363GSM410754 | plasma HIV-1 RNA level: undetectable | 52 | Female | 1472 | control | Caucasian | Peripheral Blood CD4 positive T cell level: 837 cells/ml |
| GSE16363GSM410756 | plasma HIV-1 RNA level: 14696 copies/ml | 41 | Male | 1324 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 494 cells/ml |
| GSE16363GSM410756 | plasma HIV-1 RNA level: 14696 copies/ml | 41 | Male | 1324 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 494 cells/ml |
| GSE16363GSM410758 | plasma HIV-1 RNA level: 15284 copies/ml | 32 | Male | 1335 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 400 cells/ml |
| GSE16363GSM410758 | plasma HIV-1 RNA level: 15284 copies/ml | 32 | Male | 1335 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 400 cells/ml |
| GSE16363GSM410760 | plasma HIV-1 RNA level: 4960 copies/ml | 49 | Male | 1438 | AIDS | Caucasian | Peripheral Blood CD4 positive T cell level: 147 cells/ml |
| GSE16363GSM410760 | plasma HIV-1 RNA level: 4960 copies/ml | 49 | Male | 1438 | AIDS | Caucasian | Peripheral Blood CD4 positive T cell level: 147 cells/ml |
| GSE16363GSM410762 | plasma HIV-1 RNA level: 71200 copies/ml | 34 | Male | 1431 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 333 cells/ml |
| GSE16363GSM410762 | plasma HIV-1 RNA level: 71200 copies/ml | 34 | Male | 1431 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 333 cells/ml |
| GSE16363GSM410764 | plasma HIV-1 RNA level: 3610 copies/ml | 26 | Male | 1430 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 683 cells/ml |
| GSE16363GSM410764 | plasma HIV-1 RNA level: 3610 copies/ml | 26 | Male | 1430 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 683 cells/ml |
| GSE16363GSM410766 | plasma HIV-1 RNA level: undetectable | 45 | Female | 1442 | control | Caucasian | Peripheral Blood CD4 positive T cell level: 485 cells/ml |
| GSE16363GSM410766 | plasma HIV-1 RNA level: undetectable | 45 | Female | 1442 | control | Caucasian | Peripheral Blood CD4 positive T cell level: 485 cells/ml |
| GSE16363GSM410768 | plasma HIV-1 RNA level: 122000 copies/ml | 34 | Male | 1464 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 202 cells/ml |
| GSE16363GSM410768 | plasma HIV-1 RNA level: 122000 copies/ml | 34 | Male | 1464 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 202 cells/ml |
| GSE16363GSM410770 | plasma HIV-1 RNA level: 439000 copies/ml | 51 | Male | 1458 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 400 cells/ml |
| GSE16363GSM410770 | plasma HIV-1 RNA level: 439000 copies/ml | 51 | Male | 1458 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 400 cells/ml |
| GSE16363GSM410772 | plasma HIV-1 RNA level: undetectable | 40 | Male | 1452 | control | Hispanic | Peripheral Blood CD4 positive T cell level: 742 cells/ml |
| GSE16363GSM410772 | plasma HIV-1 RNA level: undetectable | 40 | Male | 1452 | control | Hispanic | Peripheral Blood CD4 positive T cell level: 742 cells/ml |
| GSE16363GSM410774 | plasma HIV-1 RNA level: 10684 copies/ml | 45 | Male | 1406 | AIDS | African American | Peripheral Blood CD4 positive T cell level: 188 cells/ml |
| GSE16363GSM410774 | plasma HIV-1 RNA level: 10684 copies/ml | 45 | Male | 1406 | AIDS | African American | Peripheral Blood CD4 positive T cell level: 188 cells/ml |
| GSE16363GSM410776 | plasma HIV-1 RNA level: 484694 copies/ml | 59 | Male | 1329 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 370 cells/ml |
| GSE16363GSM410776 | plasma HIV-1 RNA level: 484694 copies/ml | 59 | Male | 1329 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 370 cells/ml |
| GSE16363GSM410778 | plasma HIV-1 RNA level: 32173 copies/ml | 32 | Male | 1389 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 824 cells/ml |
| GSE16363GSM410778 | plasma HIV-1 RNA level: 32173 copies/ml | 32 | Male | 1389 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 824 cells/ml |
| GSE16363GSM410780 | plasma HIV-1 RNA level: 174000 copies/ml | 49 | Male | 1456 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 478 cells/ml |
| GSE16363GSM410780 | plasma HIV-1 RNA level: 174000 copies/ml | 49 | Male | 1456 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 478 cells/ml |
| GSE16363GSM410782 | plasma HIV-1 RNA level: 20014 copies/ml | 39 | Male | 1408 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 685 cells/ml |
| GSE16363GSM410782 | plasma HIV-1 RNA level: 20014 copies/ml | 39 | Male | 1408 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 685 cells/ml |
| GSE16363GSM410784 | plasma HIV-1 RNA level: undetectable | 26 | Male | 1467 | control | Caucasian | Peripheral Blood CD4 positive T cell level: 326 cells/ml |
| GSE16363GSM410784 | plasma HIV-1 RNA level: undetectable | 26 | Male | 1467 | control | Caucasian | Peripheral Blood CD4 positive T cell level: 326 cells/ml |
| GSE16363GSM410786 | plasma HIV-1 RNA level: 46400 copies/ml | 63 | Male | 1436 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 248 cells/ml |
| GSE16363GSM410786 | plasma HIV-1 RNA level: 46400 copies/ml | 63 | Male | 1436 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 248 cells/ml |
| GSE16363GSM410788 | plasma HIV-1 RNA level: greater than 100 000 copies/ml | 30 | Male | 1449 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 333 cells/ml |
| GSE16363GSM410788 | plasma HIV-1 RNA level: greater than 100 000 copies/ml | 30 | Male | 1449 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 333 cells/ml |
| GSE16363GSM410790 | plasma HIV-1 RNA level: 31922 copies/ml | 35 | Male | 1407 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 372 cells/ml |
| GSE16363GSM410790 | plasma HIV-1 RNA level: 31922 copies/ml | 35 | Male | 1407 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 372 cells/ml |
| GSE16363GSM410792 | plasma HIV-1 RNA level: 35000 copies/ml | 43 | Male | 1462 | AIDS | Caucasian | Peripheral Blood CD4 positive T cell level: 81 cells/ml |
| GSE16363GSM410792 | plasma HIV-1 RNA level: 35000 copies/ml | 43 | Male | 1462 | AIDS | Caucasian | Peripheral Blood CD4 positive T cell level: 81 cells/ml |
| GSE16363GSM410794 | plasma HIV-1 RNA level: greater than 100 000 copies/ml | 42 | Male | 1435 | acute HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 410 cells/ml |
| GSE16363GSM410795 | plasma HIV-1 RNA level: 12046 copies/ml | 40 | Female | 1327 | AIDS | African American | Peripheral Blood CD4 positive T cell level: 112 cells/ml |
| GSE16363GSM410795 | plasma HIV-1 RNA level: 12046 copies/ml | 40 | Female | 1327 | AIDS | African American | Peripheral Blood CD4 positive T cell level: 112 cells/ml |
| GSE16363GSM410797 | plasma HIV-1 RNA level: 19400 copies/ml | 23 | Male | 1455 | acute HIV-1 infection | African American | Peripheral Blood CD4 positive T cell level: 209 cells/ml |
| GSE16363GSM410797 | plasma HIV-1 RNA level: 19400 copies/ml | 23 | Male | 1455 | acute HIV-1 infection | African American | Peripheral Blood CD4 positive T cell level: 209 cells/ml |
| GSE16363GSM410799 | plasma HIV-1 RNA level: 24718 copies/ml | 37 | Male | 1391 | acute HIV-1 infection | African American | Peripheral Blood CD4 positive T cell level: 414 cells/ml |
| GSE16363GSM410800 | plasma HIV-1 RNA level: greater than 100 000 copies/ml | 36 | Male | 1459 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 286 cells/ml |
| GSE16363GSM410800 | plasma HIV-1 RNA level: greater than 100 000 copies/ml | 36 | Male | 1459 | asymptomatic HIV-1 infection | Caucasian | Peripheral Blood CD4 positive T cell level: 286 cells/ml |