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Jerome A Zack

Publications and source records attributed to Jerome A Zack.

At least 19 recordsLinked to original sources
PubMed2004

Expression-based monitoring of transcription factor activity: the TELiS database.

MOTIVATION: In microarray studies it is often of interest to identify upstream transcription control pathways mediating observed changes in gene expression. The Transcription Element Listening System (TELiS) combines sequence-based analysis of gene regulatory regions with statistical prevalence analyses to identify transcription-factor binding motifs (TFBMs) that are over-represented among the promoters of up- or down-regulated genes. Efficiency is maximized by decomposing the problem into two steps: (1) a priori compilation of prevalence matrices specifying the number of putative binding sites for a variety of transcription factors in promoters from all genes assayed by a given microarray, and (2) real-time statistical analysis of pre-compiled prevalence matrices to identify TFBMs that are over- or under-represented in promoters of differentially expressed genes. The interlocking JAVA applications namely, PromoterScan and PromoterStats carry out these tasks, and together constitute the TELiS database for reverse inference of transcription factor activity. RESULTS: In two validation studies, TELiS accurately detected in vivo activation of NF-kappaB and the Type I interferon system by HIV-1 infection and pharmacologic activation of the glucocorticoid receptor in peripheral blood mononuclear cells. The population-based statistical inference underlying TELiS out-performed conventional statistical tests in analytic sensitivity, with parametric studies demonstrating accurate identification of transcription factor activity from as few as 20 differentially expressed genes. TELiS thus provides a simple, rapid and sensitive tool for identifying transcription control pathways mediating observed gene expression dynamics.

Algorithms↗
PubMed2004

CD4 on CD8(+) T cells directly enhances effector function and is a target for HIV infection.

Costimulation of purified CD8(+) T lymphocytes induces de novo expression of CD4, suggesting a previously unrecognized function for this molecule in the immune response. Here, we report that the CD4 molecule plays a direct role in CD8(+) T cell function by modulating expression of IFN-gamma and Fas ligand, two important CD8(+) T cell effector molecules. CD4 expression also allows infection of CD8 cells by HIV, which results in down-regulation of the CD4 molecule and impairs the induction of IFN-gamma, Fas ligand, and the cytotoxic responses of activated CD8(+) T cells. Thus, the CD4 molecule plays a direct role in CD8 T cell function, and infection of these cells by HIV provides an additional reservoir for the virus and also may contribute to the immunodeficiency seen in HIV disease.

CD4 Antigens↗
PubMed2004

Stress-induced enhancement of NF-kappaB DNA-binding in the peripheral blood leukocyte pool: effects of lymphocyte redistribution.

To identify signaling pathways by which the sympathetic nervous system (SNS) might alter gene expression in the immune system, we assayed activation of the inflammatory transcription factor NF-kappaB in peripheral blood mononuclear cells (PBMC) from 13 healthy young adults at rest and following 5 min of intense exercise. SNS activation was verified by changes in cardiovascular parameters and mobilization of NK cells into circulating blood. Electrophoretic mobility shift assays (EMSA) of nuclear protein extracts confirmed previous findings that SNS activation increased NF-kappaB DNA-binding activity in bulk PBMC. However, analyses of isolated leukocyte subsets failed to indicate any increase on a per-cell basis in NK cells (the major carriers of NF-kappaB activity in circulating PBMC), in the residual CD56- leukocyte pool, or in CD14+ monocytes. Regression analyses indicated a strong correlation between increasing NK cell prevalence and changes in NF-kappaB DNA-binding activity in bulk PBMC, and suggested that no change in EMSA activity would be observed in the absence of NK cell mobilization. Such results imply that SNS-induced mobilization of NK cells can rapidly (< 10 min) alter NF-kappaB DNA-binding activity in the circulating PBMC pool without generating any true change in NF-kappaB activity on a per-cell basis. Implications for future efforts to analyze stress effects on leukocyte gene expression are considered.

Adaptation, Physiological↗
PubMed2004

The CCR5 and CXCR4 coreceptors--central to understanding the transmission and pathogenesis of human immunodeficiency virus type 1 infection.

In this review, we will discuss what is known, what is suspected, and what still remains obscure about the central role played by coreceptor expression and usage in the transmission and pathogenic consequences of human immunodeficiency virus type 1 (HIV-1) infection. An emphasis will be on the HIV-1 phenotypic variants that are defined by their usage of the CCR5 or CXCR4 coreceptors, and how the different cellular tropism of these variants influences how and where HIV-1 replicates in vivo. We will also review what might happen when coreceptor antagonists are used clinically to treat HIV-1 infection.

Animals↗
PubMed2004

Alcohol enhances HIV type 1 infection in normal human oral keratinocytes by up-regulating cell-surface CXCR4 coreceptor.

Recent studies suggest that normal human oral keratinocytes (NHOKs) can be infected by HIV-1, and alcohol can enhance HIV infection and replication in lymphocytes. In this study, we examined the possibility that alcohol might facilitate HIV-1 infection of NHOKs by up-regulating cell surface expression of the coreceptor, CXCR4. Alcohol enhanced in vitro infection of NHOKs by CXCR4-tropic strains of HIV-1 as indicated by synthesis of viral reverse transcripts and production of p24gag protein. Alcohol had no effect on CXCR4 gene expression or on total cellular complements of CXCR4 protein. However, alcohol did enhance the fraction of total CXCR4 expressed on the cell surface relative to intracellular stores. Alcohol-induced up-regulation of cell surface CXCR4 expression and HIV-1 infectivity could be blocked by SDF-1alpha-mediated internalization. These data suggest that alcohol may influence oral HIV transmission by altering the cellular compartmentalization of CXCR4 in cells of the oral cavity.

Base Sequence↗
PubMed2004

Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a phase I study: myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients.

A phase I gene transfer clinical study was undertaken to examine the ability to introduce a potential anti-human immunodeficiency virus (HIV) gene therapeutic into hematopoietic progenitor cells (HPC), thereby contributing to multilineage engraftment. The potential therapeutic effect of genetically modifying HPC with protective genes in HIV-infected adults depends in part on the presence of adult thymic activity and myeloid capacity in the setting of HIV replication. Herein we report the presence and expression of a retroviral vector encoding an anti-HIV-1 ribozyme in mature hematopoietic cells of different lineages, and de novo T-lymphocyte development ensuing from genetically engineered CD34(+) HPC. Sustained output of vector-containing mature myeloid and T-lymphoid cells was detected even in patients with multidrug-resistant infection. In addition, the study showed that the degree of persistence of gene-containing cells was dependent on transduced HPC dose. These novel findings support the concept of gene therapy as a modality to effect immune reconstitution with cells engineered to inhibit HIV replication and this report represents the first demonstration of long-term maintenance of a potential therapeutic transgene in HIV disease.

Adult↗
PubMed2004

Impacts of epitope expression kinetics and class I downregulation on the antiviral activity of human immunodeficiency virus type 1-specific cytotoxic T lymphocytes.

The determinants of CD8(+) cytotoxic T-lymphocyte (CTL) antiviral activity against human immunodeficiency virus type 1 (HIV-1) remain poorly defined. Although recent technological advances have markedly enhanced the ability to detect HIV-1-specific T cells, commonly used assays do not reveal their direct interaction with virus. We investigated two determinants of CTL antiviral efficiency by manipulating HIV-1 and measuring the effects on CTL suppression of viral replication in acutely infected cells. Translocation of a Gag epitope into the early protein Nef markedly increased the activity of CTL recognizing that epitope, in comparison to HIV-1 expressing the epitope normally in the late protein Gag. Because this epitope translocation resulted not only in earlier expression but also in loss of major histocompatibility complex class I downregulation by Nef, the activities of CTL against a panel of viral constructs differing in kinetics of epitope expression and class I downmodulation were compared. The results indicated that both the timing of epitope expression and the reduction of class I have profound effects on the ability of CTL to suppress HIV-1 replication in acutely infected cells. The epitope targeting of CTL and viral control of class I therefore likely play important roles in the ability of CTL to exert pressure on HIV-1.

Amino Acid Sequence↗
PubMed2003

Psychological risk factors for HIV pathogenesis: mediation by the autonomic nervous system.

BACKGROUND: Epidemiologic studies have identified psychological risk factors for specific physical diseases, but the biological mechanisms mediating these relationships remain poorly defined. METHODS: Social inhibition and autonomic nervous system (ANS) activity were assessed on multiple occasions in 54 gay men with asymptomatic human immunodeficiency virus (HIV) infection. Following baseline ANS assessment, plasma HIV-1 viral load and CD4+ T cell levels were monitored for 12-18 months to assess relationships between ANS activity and HIV pathogenesis. RESULTS: We confirmed the previously reported relationship between socially inhibited temperament and vulnerability to viral pathology. Plasma viral load set-point was elevated eight-fold in socially inhibited individuals, and these individuals showed poorer virologic and immunologic response to initiation of highly active antiretroviral therapy (HAART). Effects were independent of duration of infection, HAART regimen, demographic characteristics, and health-relevant behavior. Neurophysiologic assessments documented elevated ANS activity in socially inhibited individuals, and mediational analyses showed that such differences could account for 64%-92% of the covariance between social inhibition and virologic parameters. CONCLUSIONS: These data provide the first clinical evidence that differential neural activity mediates relationships between psychological risk factors and infectious disease pathogenesis. Such findings also suggest novel targets for adjunctive therapy in long-term control of HIV-1 disease.

Adult↗
PubMed2003

Identification of T cell-signaling pathways that stimulate latent HIV in primary cells.

Eradication of HIV infection depends on the elimination of a small, but stable population of latently infected T cells. After the discontinuation of therapy, activation of latent virus can rekindle infection. To purge this reservoir, it is necessary to define cellular signaling pathways that lead to activation of latent HIV. We used the SCID-hu (Thy/Liv) mouse model of HIV latency to analyze a broad array of T cell-signaling pathways and show in primary, quiescent cells that viral induction depends on the activation of two primary intracellular signaling pathways, protein kinase C or nuclear factor of activated T cells (NF-AT). In contrast, inhibition or activation of other important T cell stimulatory pathways (such as mitogen-activated protein kinase, calcium flux, or histone deacetylation) do not significantly induce virus expression. We found that the activation of NF-kappaB is critical to viral reactivation; however, all pathways that stimulate NF-kappaBdonot reactivate latent virus. Our studies further show that inhibition of NF-kappaB does not prevent activation of HIV by NF-AT, indicating that these pathways can function independently to activate the HIV LTR. Thus, we define several molecular pathways that trigger HIV reactivation from latency and provide evidence that latent HIV infection is maintained by the functional lack of particular transcription factors in quiescent cells.

Animals↗
PubMed2003

Controlling false-negative errors in microarray differential expression analysis: a PRIM approach.

MOTIVATION: Theoretical considerations suggest that current microarray screening algorithms may fail to detect many true differences in gene expression (Type II analytic errors). We assessed 'false negative' error rates in differential expression analyses by conventional linear statistical models (e.g. t-test), microarray-adapted variants (e.g. SAM, Cyber-T), and a novel strategy based on hold-out cross-validation. The latter approach employs the machine-learning algorithm Patient Rule Induction Method (PRIM) to infer minimum thresholds for reliable change in gene expression from Boolean conjunctions of fold-induction and raw fluorescence measurements. RESULTS: Monte Carlo analyses based on four empirical data sets show that conventional statistical models and their microarray-adapted variants overlook more than 50% of genes showing significant up-regulation. Conjoint PRIM prediction rules recover approximately twice as many differentially expressed transcripts while maintaining strong control over false-positive (Type I) errors. As a result, experimental replication rates increase and total analytic error rates decline. RT-PCR studies confirm that gene inductions detected by PRIM but overlooked by other methods represent true changes in mRNA levels. PRIM-based conjoint inference rules thus represent an improved strategy for high-sensitivity screening of DNA microarrays. AVAILABILITY: Freestanding JAVA application at http://microarray.crump.ucla.edu/focus

Algorithms↗
PubMed2003

HIV-1 infection in peripheral blood lymphocytes (PBLs) exposed to alcohol.

Epidemiological and in vitro studies have implied that heavy alcohol consumption may increase an individual's risk of HIV-1 infection. To examine the role of alcohol in direct infection of T-cells, viral reverse transcripts and HIV-1 receptor expression were examined in infected peripheral blood lymphocytes (PBLs) pretreated with alcohol. PCR results showed that alcohol increased HIV-1 DNA in PBLs by at least 10-fold. Alcohol enhanced the expression of the CXCR4 chemokine co-receptor but not the major HIV-1 CD4 receptor. Pretreatment with alcohol was also associated with increased intracellular cAMP. Thus, alcohol may facilitate enhanced viral infection by increasing the availability of HIV-1 co-receptor. This effect is associated with increases in intracellular cAMP.

Acquired Immunodeficiency Syndrome↗
PubMed2003

HIV type 1 infection alters cytokine mRNA expression in thymus.

We and others have previously shown that HIV infection of human thymus/liver implants in severe combined immunodeficient (SCID-hu Thy/Liv) mice results in a loss of CD4(+) thymocytes and a decreased recovery of human myeloid and erythroid colony-forming activity. Furthermore, our previous studies have shown that this decrease in colony-forming potential is due to indirect effects, rather than to massive loss of CD34(+) hematopoietic progenitor cells, suggesting that HIV infection might alter expression of hematopoietic cytokines. Herein we have investigated potential HIV-1-induced perturbations of hematolymphoid microenvironments by determining the effect of HIV-1 infection on levels of cytokine mRNAs in human stroma and thymocytes, using the reverse transcription-polymerase chain reaction (RT-PCR). The levels of interleukin 6 (IL-6), interferon gamma (IFN-gamma), and IL-2 RNAs increased and macrophage inflammatory protein 1beta (MIP-1beta) RNA decreased significantly in infected thymocytes. IL-6 RNA levels in stroma also increased somewhat with infection; however, expression of stromal cell-derived factor 1 (SDF-1) by stromal elements was not affected. IL-4 RNA levels were unaffected by infection in both stroma and thymocytes. Antiretroviral drug treatment of the infected animals, which results in restoration of colony-forming potential, tends to restore the cytokine mRNA levels in HIV-1-infected implants to those of mock-infected implants. These results indicate that HIV-1 infection can greatly distort the cytokine profiles in Thy/Liv implants, and suggest that cytokine perturbation could be involved in virus-induced inhibition of hematopoiesis.

Animals↗
PubMed2003

Molecular characterization, reactivation, and depletion of latent HIV.

Antiretroviral therapy is unable to eliminate HIV infection in a small, long-lived population of latently infected T cells, providing a source for renewed viral replication following cessation of therapy. Analysis of individual latently infected cells generated in the SCID-hu (Thy/Liv) mouse demonstrated no functional viral RNA produced in the latent state. Following reactivation viral expression was dramatically increased, rendering the infected cells susceptible to an anti-HIV immunotoxin. Treatment with the immunotoxin in conjunction with agents that activate virus expression without inducing cell division (IL-7 or the non-tumor-promoting phorbol ester prostratin) depleted the bulk of the latent reservoir and left uninfected cells able to respond to subsequent costimulation. We demonstrate that activation of latent virus is required for targeting by antiviral agents and provide the basis for future therapeutic strategies to eradicate the latent reservoir.

Adjuvants, Immunologic↗
PubMed2003

Human immunodeficiency virus type 1 infection and replication in normal human oral keratinocytes.

Recent epidemiologic studies show increasing human immunodeficiency virus type 1 (HIV-1) transmission through oral-genital contact. This paper examines the possibility that normal human oral keratinocytes (NHOKs) might be directly infected by HIV or might convey infectious HIV virions to adjacent leukocytes. PCR analysis of proviral DNA constructs showed that NHOKs can be infected by CXCR4-tropic (NL4-3 and ELI) and dualtropic (89.6) strains of HIV-1 to generate a weak but productive infection. CCR5-tropic strain Ba-L sustained minimal viral replication. Antibody inhibition studies showed that infection by CXCR4-tropic viral strains is mediated by the galactosylceramide receptor and the CXCR4 chemokine coreceptor. Coculture studies showed that infectious HIV-1 virions can also be conveyed from NHOKs to activated peripheral blood lymphocytes, suggesting a potential role of oral epithelial cells in the transmission of HIV infection.

Cells, Cultured↗
PubMed2002

Retrocyclin: a primate peptide that protects cells from infection by T- and M-tropic strains of HIV-1.

Human bone marrow expresses a pseudogene that encodes an antimicrobial peptide homologous to rhesus monkey circular minidefensins (delta-defensins). We prepared the putative ancestral human peptide by solid-phase synthesis and named it "retrocyclin." Retrocyclin did not cause direct inactivation of HIV-1, and its modest antibacterial properties resembled those of its rhesus homologs. Nevertheless, retrocyclin had a remarkable ability to inhibit proviral DNA formation and to protect immortalized and primary human CD4(+) lymphocytes from in vitro infection by both T-tropic and M-tropic strains of HIV-1. Confocal fluorescent microscopy studies performed with BODIPY-FL-labeled RC-101, a close analog of retrocyclin, showed that the peptide formed patch-like aggregates on the surface of CD4(+) cells. These findings suggest that retrocyclin interferes with an early stage of HIV-1 infection and that retrocyclin-like agents might be useful topical agents to prevent sexually acquired HIV-1 infections.

Animals↗
PubMed2002

Cocaine enhances human immunodeficiency virus replication in a model of severe combined immunodeficient mice implanted with human peripheral blood leukocytes.

Epidemiologic studies have identified cocaine as a cofactor for development of acquired immunodeficiency syndrome (AIDS). To evaluate this interaction, human peripheral blood leukocytes (PBL) were implanted into severe combined immunodeficient mice and infected with human immunodeficiency virus (HIV) in both the presence and absence of cocaine. Concurrent administration of cocaine resulted in significantly more PBL becoming infected with HIV in vivo (38.85% vs. 18.5%). The number of CD4(+) cells recovered from HIV-infected, cocaine-treated animals was significantly lower than that from mice infected with HIV in the absence of cocaine (6.5 x 10(4) vs. 19 x 10(4)) and was associated with a lower CD4:CD8 ratio and a dramatic increase in virus load. Exposure to cocaine alone did not affect the implantation of PBL, suggesting a specific interaction between cocaine and HIV. This report describes a model for evaluating HIV cofactors and supports cocaine's role in the development and progression of AIDS.

Animals↗
PubMed2002

Activation of CD8 T cells induces expression of CD4, which functions as a chemotactic receptor.

It was previously shown that costimulation of CD8(+) lymphocytes results in de novo expression of CD4. This study expanded on this observation to investigate the function of CD4 on CD8 cells. The ability of costimulated CD8 cells to respond to interleukin 16 (IL-16), a ligand that binds CD4 and induces cellular chemotaxis, was examined. IL-16-mediated ligation of CD4 expressed on CD8 T cells was found to induce an intracellular signal that directs migration of these cells in vitro. Thus, expression of CD4 on a CD8 lymphocyte has functional importance and may serve to control distribution of newly activated CD8 T cells in vivo.

CD4 Antigens↗