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      Epigenetic Regulation of HIV-1 Latency by Cytosine Methylation

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          Abstract

          Human immunodeficiency virus type 1 (HIV-1) persists in a latent state within resting CD4 + T cells of infected persons treated with highly active antiretroviral therapy (HAART). This reservoir must be eliminated for the clearance of infection. Using a cDNA library screen, we have identified methyl-CpG binding domain protein 2 (MBD2) as a regulator of HIV-1 latency. Two CpG islands flank the HIV-1 transcription start site and are methylated in latently infected Jurkat cells and primary CD4 + T cells. MBD2 and histone deacetylase 2 (HDAC2) are found at one of these CpG islands during latency. Inhibition of cytosine methylation with 5-aza-2′deoxycytidine (aza-CdR) abrogates recruitment of MBD2 and HDAC2. Furthermore, aza-CdR potently synergizes with the NF-κB activators prostratin or TNF-α to reactivate latent HIV-1. These observations confirm that cytosine methylation and MBD2 are epigenetic regulators of HIV-1 latency. Clearance of HIV-1 from infected persons may be enhanced by inclusion of DNA methylation inhibitors, such as aza-CdR, and NF-κB activators into current antiviral therapies.

          Author Summary

          Current drug therapies inhibit replication of the human immunodeficiency virus (HIV). In patients undergoing these therapies, the amount of HIV is reduced to an undetectable level and HIV-related disease subsides. However, stopping antiviral drug therapy results in the quick return of HIV and of disease. One reason for this is latently infected cells, in which virus replication is temporarily halted. When drug therapy is stopped, virus from these latently infected cells can resume infection and spread to other cells in the patient, resulting in the return of disease. Here, we demonstrate that one mechanism of latency is DNA methylation, in which chemical groups called methyl groups are added to HIV DNA. We also identify a host protein called methyl-CpG binding domain protein 2 (MBD2) that binds methylated HIV DNA and is an important mediator of latency. Furthermore, we demonstrate that a drug that inhibits DNA methylation potently reactivates latent HIV. Novel strategies to eliminate or reduce the latent reservoir are necessary. Our findings may prove useful in the development of novel therapies to efficiently reactivate latent HIV-1, thus making it susceptible to current drug therapies.

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          Most cited references 67

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          Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators.

          National surveillance data show recent, marked reductions in morbidity and mortality associated with the acquired immunodeficiency syndrome (AIDS). To evaluate these declines, we analyzed data on 1255 patients, each of whom had at least one CD4+ count below 100 cells per cubic millimeter, who were seen at nine clinics specializing in the treatment of human immunodeficiency virus (HIV) infection in eight U.S. cities from January 1994 through June 1997. Mortality among the patients declined from 29.4 per 100 person-years in the first quarter of 1995 to 8.8 per 100 in the second quarter of 1997. There were reductions in mortality regardless of sex, race, age, and risk factors for transmission of HIV. The incidence of any of three major opportunistic infections (Pneumocystis carinii pneumonia, Mycobacterium avium complex disease, and cytomegalovirus retinitis) declined from 21.9 per 100 person-years in 1994 to 3.7 per 100 person-years by mid-1997. In a failure-rate model, increases in the intensity of antiretroviral therapy (classified as none, monotherapy, combination therapy without a protease inhibitor, and combination therapy with a protease inhibitor) were associated with stepwise reductions in morbidity and mortality. Combination antiretroviral therapy was associated with the most benefit; the inclusion of protease inhibitors in such regimens conferred additional benefit. Patients with private insurance were more often prescribed protease inhibitors and had lower mortality rates than those insured by Medicare or Medicaid. The recent declines in morbidity and mortality due to AIDS are attributable to the use of more intensive antiretroviral therapies.
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            Two subsets of memory T lymphocytes with distinct homing potentials and effector functions.

            Naive T lymphocytes travel to T-cell areas of secondary lymphoid organs in search of antigen presented by dendritic cells. Once activated, they proliferate vigorously, generating effector cells that can migrate to B-cell areas or to inflamed tissues. A fraction of primed T lymphocytes persists as circulating memory cells that can confer protection and give, upon secondary challenge, a qualitatively different and quantitatively enhanced response. The nature of the cells that mediate the different facets of immunological memory remains unresolved. Here we show that expression of CCR7, a chemokine receptor that controls homing to secondary lymphoid organs, divides human memory T cells into two functionally distinct subsets. CCR7- memory cells express receptors for migration to inflamed tissues and display immediate effector function. In contrast, CCR7+ memory cells express lymph-node homing receptors and lack immediate effector function, but efficiently stimulate dendritic cells and differentiate into CCR7- effector cells upon secondary stimulation. The CCR7+ and CCR7- T cells, which we have named central memory (TCM) and effector memory (TEM), differentiate in a step-wise fashion from naive T cells, persist for years after immunization and allow a division of labour in the memory response.
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              MethPrimer: designing primers for methylation PCRs.

               L.-C. Li,  R Dahiya (2002)
              DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP), remain the most commonly used techniques for methylation mapping. Existing primer design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based PCRs due to changes in DNA sequence context caused by bisulfite treatment and many special constraints both on the primers and the region to be amplified for such experiments. Therefore, the present study was designed to develop a program for such applications. MethPrimer, based on Primer 3, is a program for designing PCR primers for methylation mapping. It first takes a DNA sequence as its input and searches the sequence for potential CpG islands. Primers are then picked around the predicted CpG islands or around regions specified by users. MethPrimer can design primers for BSP and MSP. Results of primer selection are delivered through a web browser in text and in graphic view.
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                Author and article information

                Affiliations
                [1 ]Gladstone Institute of Virology and Immunology, San Francisco, California, United States of America
                [2 ]Department of Medicine, University of California, San Francisco, California, United States of America
                [3 ]Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
                [4 ]Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
                University of Pennsylvania School of Medicine, United States of America
                Author notes

                Conceived and designed the experiments: SEK AB VP EV. Performed the experiments: SEK AB. Analyzed the data: SEK AB VP EV. Contributed reagents/materials/analysis tools: AL. Wrote the paper: SEK EV.

                Contributors
                Role: Editor
                Journal
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, USA )
                1553-7366
                1553-7374
                June 2009
                June 2009
                26 June 2009
                : 5
                : 6
                2695767
                19557157
                08-PLPA-RA-1362R3
                10.1371/journal.ppat.1000495
                (Editor)
                Kauder et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                Counts
                Pages: 15
                Categories
                Research Article
                Immunology/Cellular Microbiology and Pathogenesis
                Microbiology/Cellular Microbiology and Pathogenesis
                Molecular Biology/DNA Methylation
                Molecular Biology/Transcription Initiation and Activation
                Virology/Persistence and Latency

                Infectious disease & Microbiology

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