Serial analysis of gene expression in HIV-1-infected T cell lines

The biomolecular mechanisms controlling latent HIV-1 infection, despite their importance for the development of a cure for HIV-1 infection, are only partially understood. For example, ex vivo studies have recently shown that T cell activation only triggered HIV-1 reactivation in a fraction of the latently infected CD4+ T cell reservoir, but the molecular biology of this phenomenon is unclear. We demonstrate that HIV-1 infection of primary T cells and T cell lines indeed generates a substantial amount of T cell receptor (TCR)/CD3 activation-inert latently infected T cells. RNA-level analysis identified extensive transcriptomic differences between uninfected, TCR/CD3 activation-responsive and -inert T cells, but did not reveal a gene expression signature that could functionally explain TCR/CD3 signaling inertness. Network analysis suggested a largely stochastic nature of these gene expression changes (transcriptomic noise), raising the possibility that widespread gene dysregulation could provide a reactivation threshold by impairing overall signal transduction efficacy. Indeed, compounds that are known to induce genetic noise, such as HDAC inhibitors impeded the ability of TCR/CD3 activation to trigger HIV-1 reactivation. Unlike for transcriptomic data, pathway enrichment analysis based on phospho-proteomic data directly identified an altered TCR signaling motif. Network analysis of this data set identified drug targets that would promote TCR/CD3-mediated HIV-1 reactivation in the fraction of otherwise TCR/CD3-reactivation inert latently HIV-1 infected T cells, regardless of whether the latency models were based on T cell lines or primary T cells. The data emphasize that latent HIV-1 infection is largely the result of extensive, stable biomolecular changes to the signaling network of the host T cells harboring latent HIV-1 infection events. In extension, the data imply that therapeutic restoration of host cell responsiveness prior to the use of any activating stimulus will likely have to be an element of future HIV-1 cure therapies.

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Cellular Gene Expression upon Human Immunodeficiency Virus Type 1 Infection of CD4+-T-Cell Lines

Journal of Virology ◽

10.1128/jvi.77.2.1392-1402.2003 ◽

2003 ◽

Vol 77 (2) ◽

pp. 1392-1402 ◽

Cited By ~ 126

Author(s):

Angélique B. van 't Wout ◽

Ginger K. Lehrman ◽

Svetlana A. Mikheeva ◽

Gemma C. O'Keeffe ◽

Michael G. Katze ◽

...

Keyword(s):

Gene Expression ◽

Human Immunodeficiency Virus ◽

T Cell ◽

Cell Lines ◽

Human Immunodeficiency Virus Type ◽

Immunodeficiency Virus ◽

Infected Cells ◽

T Cell Lines ◽

Hiv 1

ABSTRACT The expression levels of ∼4,600 cellular RNA transcripts were assessed in CD4+-T-cell lines at different times after infection with human immunodeficiency virus type 1 strain BRU (HIV-1BRU) using DNA microarrays. We found that several classes of genes were inhibited by HIV-1BRU infection, consistent with the G2 arrest of HIV-1-infected cells induced by Vpr. These included genes involved in cell division and transcription, a family of DEAD-box proteins (RNA helicases), and all genes involved in translation and splicing. However, the overall level of cell activation and signaling was increased in infected cells, consistent with strong virus production. These included a subgroup of transcription factors, including EGR1 and JUN, suggesting they play a specific role in the HIV-1 life cycle. Some regulatory changes were cell line specific; however, the majority, including enzymes involved in cholesterol biosynthesis, of changes were regulated in most infected cell lines. Compendium analysis comparing gene expression profiles of our HIV-1 infection experiments to those of cells exposed to heat shock, interferon, or influenza A virus indicated that HIV-1 infection largely induced specific changes rather than simply activating stress response or cytokine response pathways. Thus, microarray analysis confirmed several known HIV-1 host cell interactions and permitted identification of specific cellular pathways not previously implicated in HIV-1 infection. Continuing analyses are expected to suggest strategies for impacting HIV-1 replication in vivo by targeting these pathways.

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A Murine Leukemia Virus (MuLV) Long Terminal Repeat Derived from Rhesus Macaques in the Context of a Lentivirus Vector and MuLVgag Sequence Results in High-Level Gene Expression in Human T Lymphocytes

Journal of Virology ◽

10.1128/jvi.74.8.3668-3681.2000 ◽

2000 ◽

Vol 74 (8) ◽

pp. 3668-3681 ◽

Cited By ~ 42

Author(s):

Sam K. P. Kung ◽

Dong Sung An ◽

Irvin S. Y. Chen

Keyword(s):

Gene Expression ◽

T Cells ◽

T Cell ◽

Cell Lines ◽

Murine Leukemia Virus ◽

Leukemia Virus ◽

Retrovirus Vector ◽

T Cell Lines ◽

Hiv 1 ◽

Murine Leukemia

ABSTRACT We constructed human immunodeficiency virus type 1 (HIV-1) vectors that will allow higher levels of gene expression in T cells. Gene expression under the control of an internal cytomegalovirus (CMV) immediate-early promoter in a self-inactivating lentiviral vector (CSCG) is 4- to 15-fold lower in T-cell lines (SUPT1 and CEMX174) than in non-lymphoid-cell lines (HeLa and 293T). This is in contrast to a Moloney murine leukemia virus (MoMLV)-based retrovirus vector (SRαLEGFP). We therefore replaced the internal CMV promoter of CSCG with three different murine oncoretroviral long terminal repeat (LTR) promoters—murine sarcoma virus (MSV), MoMLV (MLV), and the LTR (termed Rh-MLV) that is derived from the ampho-mink cell focus-forming (AMP/MCF) retrovirus in the serum of one rhesus macaque monkey that developed T-cell lymphoma following autologous transplantation of enriched bone marrow stem cells transduced with a retrovirus vector preparation containing replication-competent viruses (E. F. Vanin, M. Kaloss, C. Broscius, and A. W. Nienhuis, J. Virol. 68:4241–4250, 1994). We found that the combination of Rh-MLV LTR and a partial gag sequence of MoMLV (Δgag 871–1612) in CS-Rh-MLV-E gave the highest level of enhanced green fluorescent protein (EGFP) gene expression compared with MLV, MSV LTR, phosphoglycerate kinase, and CMV promoters in T-cell lines, as well as activated primary T cells. Interestingly, there was a further two- to threefold increase in EGFP expression (thus, 10-fold-higher expression than with CMV) when the Rh-MLV promoter and Δgag 871–1612 were used in a self-inactivating-vector setting that has a further deletion in the U3 region of the HIV-1 LTR. These hybrid vectors should prove useful in gene therapy applications for T cells.

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Unique Gene Expression Patterns in Human T-cell Lines Generated from Multiple Sclerosis Patients by Stimulation with a Synthetic MOG Peptide

Clinical and Developmental Immunology ◽

10.1080/17402520500233460 ◽

2005 ◽

Vol 12 (3) ◽

pp. 203-209 ◽

Cited By ~ 4

Author(s):

Mathilda Mandel ◽

Michael Gurevich ◽

Gad Lavie ◽

Irun R. Cohen ◽

Anat Achiron

Keyword(s):

Gene Expression ◽

T Cells ◽

T Cell ◽

Cell Lines ◽

Healthy Subjects ◽

Expression Patterns ◽

Gene Expression Pattern ◽

Gene Expression Patterns ◽

T Cell Lines ◽

Myelin Antigens

Multiple sclerosis (MS) is an autoimmune disease where T-cells activated against myelin antigens are involved in myelin destruction. Yet, healthy subjects also harbor T-cells responsive to myelin antigens, suggesting that MS patient-derived autoimmune T-cells might bear functional differences from T-cells derived from healthy individuals. We addressed this issue by analyzing gene expression patterns of myelin oligodendrocytic glycoprotein (MOG) responsive T-cell lines generated from MS patients and healthy subjects. We identified 150 transcripts that were differentially expressed between MS patients and healthy controls. The most informative 43 genes exhibited >1.5-fold change in expression level. Eighteen genes were up-regulated including BCL2, lifeguard, IGFBP3 and VEGF. Twenty five genes were down-regulated, including apoptotic activators like TNF and heat shock protein genes. This gene expression pattern was unique to MOG specific T-cell lines and was not expressed in T-cell lines reactive to tetanus toxin (TTX). Our results indicate that activation in MS that promotes T-cell survival and expansion, has its own state and that the unique gene expression pattern that characterize autoreactive T-cells in MS represent a constellation of factors in which the chronicity, timing and accumulation of damage make the difference between health and disease.

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Ovine herpesvirus 2 lytic cycle replication and capsid production

Journal of General Virology ◽

10.1099/0022-1317-83-12-2999 ◽

2002 ◽

Vol 83 (12) ◽

pp. 2999-3002 ◽

Cited By ~ 14

Author(s):

Jane Rosbottom ◽

Robert G. Dalziel ◽

Hugh W. Reid ◽

James P. Stewart

Keyword(s):

Gene Expression ◽

T Cell ◽

Cell Lines ◽

Lytic Cycle ◽

Malignant Catarrhal Fever ◽

Virus Capsids ◽

Latently Infected ◽

T Cell Lines ◽

First Time

Ovine herpesvirus 2 (OvHV-2) causes malignant catarrhal fever in cattle, pigs and deer. We have observed intact circular and linear OvHV-2 genomes in infected T cell lines derived from cows and rabbits. Bovine T cell lines were predominantly latently infected but rabbit T cell lines supported OvHV-2 productive cycle gene expression and virus capsids were demonstrated for the first time.

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