Current HIV Research

ISSN: 1570-162X

Current HIV Research
Volume 5, Number 1, January 2007

Contents


Review Articles

Editorial Pp. 1


Regulation of HIV-1 Transcription by Protein Phosphatase 1 Pp. 3-9
Sergei Nekhai, Marina Jerebtsova, Angela Jackson and William Southerland
[Abstract] [Full text article]


Exploiting Structurally Diverse Nucleoside Analogs as Probes of Reverse Transcription Complexes Pp. 11-22
Jason W. Rausch and Stuart F.J. Le Grice
[Abstract] [Full text article]


HIV Genetic Diversity: Biological and Public Health Consequences Pp. 23-45
Isolde F. Butler, Ivona Pandrea, Preston A. Marx and Cristian Apetrei
[Abstract] [Full text article]


Immune Responses to HIV gp120 that Facilitate Viral Escape Pp. 47-54
Liljana Stevceva, Victor Yoon, Daphne Anastasiades and Mark C. Poznansky
[Abstract] [Full text article]


Impact of Human Immune Deficiency Virus Infection on Hepatitis C Virus Infection and Replication Pp. 55-67
Cecilia Parodi, Liliana Belmonte, Patricia Baré, María M.E. de Bracco and Beatriz Ruibal-Ares
[Abstract] [Full text article]


Original Research Papers


Alteration of the Proline at Position 7 of the HIV-1 Spacer Peptide p1 Suppresses Viral Infectivity in a Strain Dependent Manner Pp. 69-78
Melissa K. Hill, Anna Bellamy-McIntyre, Laura J. Vella, Shahan M. Campbel, John A. Marshall, Gilda Tachedjian and Johnson Mak
[Abstract] [Full text article]


Herpesvirus Saimiri Terminal Membrane Proteins Modulate HIV-1 Replication by Altering Nef and Tat Functions Pp. 79-86
Andrea D. Raymond, Muneer Hasham, Alexander Y. Tsygankov and Earl E. Henderson
[Abstract] [Full text article]


Identification of Cross-Neutralization Determinants by GAP Analysis: A Mutational Behavior Approach Pp. 87-96
Fusheng Li, Peter B. Gilbert and Steve G. Self
[Abstract] [Full text article]


HIV-1 CTL-Based Vaccine Immunogen Selection: Antigen Diversity and Cellular Response Features Pp. 97-107
Fusheng Li, Helen Horton, Peter B. Gilbert, Juliana M. McElrath, Lawrence Corey and Steve G. Self
[Abstract] [Full text article]


Routine Collection of Patient-Reported Outcomes in an HIV Clinic Setting: The First 100 Patients Pp. 109-118
Heidi M. Crane, William Lober, Eric Webster, Robert D. Harrington, Paul K. Crane, Thomas E. Davis and Mari M. Kitahata
[Abstract] [Full text article]


Identification of HLA-A11-Restricted HIV-1-Specific Cytotoxic T-Lymphocyte Epitopes in China Pp. 119-128
Shaoyang Wang, Yongtao Sun Song Zhai, Yan Zhuang, Shuguang Zhao, Whenzhen Kang, Xinhong Li, Dedong Huang,Xu G. Yu, Bruce D. Walker and Marcus A. Altfeld
[Abstract] [Full text article]


Prevalence of Dilated Cardiomyopathy in HIV-Infected African Patients Not Receiving HAART: A Multicenter, Observational, Prospective, Cohort Study in Rwanda Pp. 129-137
Marc Twagirumukiza, Emmanuel Nkeramihigo, Benoit Seminega, Emmanuel Gasakure, Franck Boccara and Giusseppe Barbaro
[Abstract] [Full text article]




Abstracts


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Editorial

Current HIV Research begins its fifth volume providing our readers with stimulating, timely, and in-depth articles on current HIV and AIDS research. As the Editor-in-Chief, I take this opportunity to thank the authors who contributed their ideas and insights into each article. The manuscripts in previously published volumes highlight a wide array of innovative scientific and medical research on HIV/AIDS.

In 2007, (Volume 5), Current HIV Research will expand the number of published issues to 6. The journal will continue to publish both original scientific articles and in-depth reviews on all areas of HIV and AIDS research. In 2006, Current HIV Research began publishing a series of HOT TOPIC issues focusing on research from leading HIV/AIDS researchers on a specialized area of HIV research. Each issue is edited by a distinguished leader in the HIV/AIDS field. In Volume 4, Dr. Jon Marsh from the National Institute of Mental Health, in Bethesda, Maryland, USA edited an outstanding issue (Volume 4-3) on NeuroAIDS. This issue has been the most requested issue for reprints from Current HIV Research. The success of this issue has promoted me to continue this program to include at least one HOT TOPIC issue in each future volume of Current HIV Research. In addition, the journal continues to welcome the submission of novel and pioneering work in the basic and clinical fields of virus replication and gene expression, HIV assembly, virus-cell interaction, viral pathogenesis, epidemiology and transmission, anti-retroviral therapy and adherence, drug discovery, the latest developments in HIV/AIDS vaccines and animal models, and prevention of viral infection. Current HIV Research aims to be the international journal for both comprehensive review articles and cutting-edge scientific findings on HIV research. The Editorial Advisory Board reflects the international representation of scientists and clinicians located in 16 different nations from some of the leading institutions in the world. We are proud that a similar diversity is reflected in the published and submitted articles as well. The journal fills a special void in the existing biomedical literature, publishing manuscripts focused on all areas of HIV/AIDS research including molecular biology, biochemistry, immunology, pharmacology, epidemiology, prevention of transmission, antiviral agents and vaccine development, as well as clinical research, which should be of interest to both basic and clinical investigators. We will continue to be responsive to our readers in order to build one of the leading research journal on HIV and AIDS research and we welcome your comments.


Ted M. Ross
(Editor-in-Chief)
Center for Vaccine Research
University of Pittsburgh
9047 Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh
PA 15261
USA
E-mail: rosst@dom.pitt.edu


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Regulation of HIV-1 Transcription by Protein Phosphatase 1
Sergei Nekhai, Marina Jerebtsova, Angela Jackson and William Southerland

[Full text article]

The emergence of drug-resistant HIV-1 strains presents a challenge for the design of new drugs. Targeting host cell factors involved in the regulation of HIV-1 replication might be one way to overcome the resistance of HIV-1 to anti-viral agents. Our recent studies identified protein phosphatase-1 (PP1) as an important regulator of HIV-1 transcription. Transcription of HIV-1 genes is activated by HIV-1 Tat protein that induces phosphorylation of the C-terminal domain of RNA polymerase-II by CDK9/cyclin T1. We have shown that HIV-1 Tat binds PP1 in vitro; targets PP1 to the nucleus; and that Tat interaction with PP1 is important for HIV-1 transcription. In this review, we discuss two potential targets of PP1 in Tat-induced HIV-1 transcription: the C-terminal domain of RNA polymerase-II and CDK9. We also present a computer model of Tat-PP1 complex that might be useful for future drug design in anti-HIV-1 therapeutics.


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Exploiting Structurally Diverse Nucleoside Analogs as Probes of Reverse Transcription Complexes
Jason W. Rausch and Stuart F.J. Le Grice

[Full text article]

Crystal structures of HIV-1 reverse transcriptase (RT) in complex with either duplex DNA or an RNA/DNA hybrid have provided significant insights into the manner in which this highly versatile enzyme accommodates the conformationally-distinct nucleic acid substrates encountered during the reverse transcription cycle. Biochemical data likewise suggest that unique structural features of the nucleic acid substrates contribute towards recognition by their cognate RT. While site-directed mutagenesis of catalytically- and structurally-critical protein motifs is relatively facile, understanding how nucleic acid structure contributes to its recognition presents a greater challenge. The relative ease with which large DNA and RNA fragments can now be chemically synthesized, in conjunction with the increased availability of ribo- and deoxyribonucleoside analogs, allows nucleic acid structure to be examined with respect to the role of hydrogen bonding, nucleobase stacking, sugar ring geometry and charge of the phosphodiester backbone. This review summarizes our use of nucleoside analogs to understand how the structure of cis-acting regulatory signals mediates their recognition by structurally diverse retroviral and retrotransposon enzymes.


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HIV Genetic Diversity: Biological and Public Health Consequences
Isolde F. Butler, Ivona Pandrea, Preston A. Marx and Cristian Apetrei

[Full text article]

The devastating consequences of AIDS pandemic will probably only be controlled when a vaccine is developed that is safe, effective, affordable, and simple enough to permit implementation in developing countries where the impact of AIDS is most severe. However, the major obstacle for the control of the spread of AIDS lies in the diversity of HIV and its enormous evolutionary potential. Numerous HIV forms contribute to the AIDS pandemic. Two viral types (HIV-1 and HIV-2), numerous groups (M, N and O for HIV-1 and A through H for HIV-2) and numerous subtypes, sub-subtypes and circulating recombinant forms (CRF) have emerged during the last 50 years. At least nine different genetic HIV-1 sub-types and over 20 CRFs were defined within group M, which accounts for the majority of cases in the AIDS pandemic. Even though HIV-1 subtype C and A predominate globally, the other viral forms co-circulate all over the world and may have a major impact for the strategies of pandemic control. Here we discuss the distribution of these divergent viral forms worldwide and the potential consequences of such a tremendous viral diversity for diagnostic, monitoring, treatment and the development of an effective vaccine.


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Immune Responses to HIV gp120 that Facilitate Viral Escape
Liljana Stevceva, Victor Yoon, Daphne Anastasiades and Mark C. Poznansky

[Full text article]

The gp160 complex of the envelope of the HIV virus and its component gp120 are essential for viral entry into the host cell. Gp120 binding to its receptor CD4 and co-receptor, CXCR4 or CCR5 is required for fusion of viral and cellular membranes. The presence of gp120 facilitates immune escape of the virus through its profound effect on the immune cells. It is a polyclonal activator of B cells, causing them to differentiate into immunoglobulin producing cells while activating the complement cascade. This results in the formation of immune complexes that are unable to kill the virus but instead shield it from the attack of other immune cells. Such HIV-1 virus that is trapped within immune complexes and is bound to the B cells via CD21 is more infectious than the free virion. In addition, HIV virions are trapped on the membrane of follicular dendritic cells (FDC) processes in immune complexes or through complement receptors. Thus, FDC can serve as a ‘Trojan horse’ and transmit the trapped virus to CD4+ T lymphocytes as they migrate through the germinal centre to the follicular mantle and paracortical areas. It was demonstrated that CXCR4-binding HIV-1 X4 gp120 causes the movement of T cells, including HIV-specific CTL, away from high concentrations of the viral protein and its expression by target cells reduces CTL efficacy in vitro. Therefore, apart from the essential role in viral attachment and infection of cells, gp120 possesses several properties that affect the behavior of immune cells and skew the immune response to the virus facilitating viral escape.


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Impact of Human Immune Deficiency Virus Infection on Hepatitis C Virus Infection and Replication
Cecilia Parodi, Liliana Belmonte, Patricia Baré, María M.E. de Bracco and Beatriz Ruibal-Ares

[Full text article]

Human immune deficiency virus (HIV) and human hepatitis C virus (HCV) infection are frequent in patients who have been exposed to blood or blood-derived products. It has been suggested that HIV infection increases HCV replication altering the course of HCV-related disease. However, it is not known if HIV directly enhances HCV replication or if its effect is the consequence of HIV infection of other cell types that control HCV replication (lymphocytes, macrophages). While the main cell targets for HIV infection are mononuclear leukocytes bearing CD4 and the chemokine receptors CCR5 and CXCR4, HCV was originally thought to be strictly hepatotropic, but it is now known that HCV can also replicate in peripheral blood mononuclear cells (PBMC). Therefore, in co-infected individuals, these two different viruses could share cell targets and interact either directly or indirectly. Some membrane receptors can be used by both HCV and HIV for entry into target cells, but the intracellular mechanisms shared by these viruses are not known. Lack of experimental systems providing suitable methods for the study of HCV replication in the presence or absence of HIV co-infection has hampered advances in this research area, but recent investigations are currently going on in order to answer these questions. This is an important issue, as knowledge of HIV/HCV interactions is required for the design of effective antiviral therapies.


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Alteration of the Proline at Position 7 of the HIV-1 Spacer Peptide p1 Suppresses Viral Infectivity in a Strain Dependent Manner
Melissa K. Hill, Anna Bellamy-McIntyre, Laura J. Vella, Shahan M. Campbel, John A. Marshall, Gilda Tachedjian and Johnson Mak

[Full text article]

The HIV-1 spacer peptide p1 is located in the C-terminus of the Gag polyprotein and separates the nucleocapsid (NC) and p6^Gag. Research centered on p1 has been limited and as yet no function has been ascribed to this spacer peptide. We have previously found that the conserved p1 proline residues (position 7 and 13) are critical for replication in the HIV-1 strain HXB2-BH10. In this study we have focused on the proline rich p1-p6^Gag C-terminus of HIV-1. We individually examined the role of p1 proline’s in multiple strains of HIV-1 and investigated the role of three proline residues in p6^Gag (P24, P25 and P30). Assessment of the HXB2-BH10 based mutants revealed that Gag-Pol incorporation relative to Gag decreased in the p1 mutant virions, with the double proline mutant the most impaired. Mutating both p1 proline residues was found to abolish infectivity in multiple strains of HIV-1. Independent mutation of the p1 proline at position 7 resulted in a strain-dependent suppression of viral infectivity. This defect correlates with the presence of a tyrosine residue at position 9 of p1 and occurs in the early phase of the HIV-1 replication cycle. The p1 proline residues were found to be functionally distinct from P24, P25 and P30 in p6^Gag. This work affords novel insights into our understanding of the role of p1 in HIV-1 replication.


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Herpesvirus Saimiri Terminal Membrane Proteins Modulate HIV-1 Replication by Altering Nef and Tat Functions
Andrea D. Raymond, Muneer Hasham, Alexander Y. Tsygankov and Earl E. Henderson

[Full text article]

Herpesvirus saimiri (HVS)-transformed human T cells expressing terminal membrane proteins (TMPs) tyrosine kinase interacting protein (Tip) and saimiri transformation associated protein strain C (StpC) are highly permissive for R5 and X4 strains of HIV-1. StpC expression enhances replication of R5 and X4 strains of HIV-1 and induces latent reservoirs of replication competent HIV-1 in cell lines derived from T cells or monocytes. Paradoxically Tip expression restricts replication and cytopathic effects of R5 and X4 strains of HIV-1 in T cells and monocytes post-retrotransposition. Understanding the canonical pathways whereby Tip and StpC alter HIV-1 replication may uncover novel therapeutic approaches to HIV-1 infection. Here we show Tip inhibits Tat-mediated transcriptional activation of the long terminal repeat (LTR). Tip mediated inhibition of Tat transactivation is reversed by Nef. Tip also mediates restriction of late-stage replication of HIV-1 by disrupting Nef interaction with lymphocyte-specific protein-tyrosine kinase (Lck) in lipid rafts. Specifically, in the presence of Tip, Lck does not localize to lipid rafts reducing Nef interaction with Lck within the lipid rafts. Finally, the permissive phenotype conferred by StpC is the result of synergy with Tat during transcriptional activation of the HIV-1 LTR. This transcriptional synergy between StpC and Tat requires Lck and NF-κB consensus binding sequences. These findings demonstrate that the HVS TMPs influence transcriptional and post-transcriptional stages in HIV-1 replication. We propose that HVS-encoded TMPs associated with T cell transformation have evolved ability to modulate the replication of competing retroviruses. Gene based approaches utilizing Tip and StpC may provide therapeutic models for treating acute and latent HIV-1 infections, respectively.


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Identification of Cross-Neutralization Determinants by GAP Analysis: A Mutational Behavior Approach
Fusheng Li, Peter B. Gilbert and Steve G. Self

[Full text article]

Antigenic variation, which is the result of amino acid substitution and genetic evolution, poses a major challenge in the development of vaccines against pathogens with unstable genomes, such as HIV-1 and Influenza. Thus, it is highly important to characterize the relationship of genetic evolution, antigenic variation and positional mutation (GAP) from the perspective of vaccine development. For this purpose, we introduce an automatic and simple GAP analysis approach, which is based on the fundamental concept of “mutational behavior” in genomic research, to predict the specificity-determining positions in protein families. This approach identifies cross-neutralization determinants by mutational behavior correlation to antigenic and genetic changes. Correlated mutation analysis and structure mapping further refine the cross-neutralization determinants. The usability of this approach is confirmed by analysis of an Influenza H3N2 cross-reactive dataset.


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HIV-1 CTL-Based Vaccine Immunogen Selection: Antigen Diversity and Cellular Response Features
Fusheng Li, Helen Horton, Peter B. Gilbert, Juliana M. McElrath, Lawrence Corey and Steve G. Self

[Full text article]

Much of the current effort in HIV-1 vaccine design is directed at achieving T-cell immunity that will result in enough immunological memory to contain HIV-1 infection after acquisition. However, antigenic diversity, plus a lack of understanding of HIV-1 vaccine immunology, have hindered the development of a globally effective cytotoxic T-lymphocyte (CTL)-based vaccine. Cellular response, in using a finite immune system to recognize an infinite number of potential pathogens, exhibits a series of parsimonious features. These features are considered critical in modulating HIV-1 vaccine multiple specificities. We took the features into consideration when the potential epitope coverage (E_c) to circulating strains by current vaccine strategies was analyzed. Based on these analyses, several approaches are proposed to enhance the breadth of vaccine responses and, hence, the potential protective efficacy.


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Routine Collection of Patient-Reported Outcomes in an HIV Clinic Setting: The First 100 Patients
Heidi M. Crane, William Lober, Eric Webster, Robert D. Harrington, Paul K. Crane, Thomas E. Davis and Mari M. Kitahata

[Full text article]

Background: Information from patient-reported outcomes (PROs) can enhance patient-provider communication and facilitate clinical research. However, there are barriers to collecting PROs within a clinic. Recent technological advances may help overcome these barriers. We examined the feasibility of using a web-based application on tablet PCs with touch screens to collect PROs in a busy, multi-provider, outpatient HIV clinical care setting.

Methods: Patients presenting for routine care were asked to complete a touch-screen-based assessment containing 62 to 111 items depending on patient responses. The assessment included instruments measuring body morphology abnormalities, depression, symptom burden, medication adherence, drug/alcohol/tobacco use, and health-related quality of life.

Results: Of 136 patients approached to participate in the study, 106 patients (78%) completed the assessment, 6 (4%) started but did not complete it, and 24 (18%) refused. Of those who completed the assessment, the mean age was 48 years, and 29% reported a history of injection drug use. The median time to complete the assessment was 12 minutes. The prevalence of lipoatrophy was 51%, the prevalence of lipohypertrophy was 69%, and the prevalence of moderate or severe depression was 51%. We found that 25% of those receiving highly active antiretroviral therapy noted missing a dose of their antiretroviral medications in the prior 4 days.

Conclusions: Collection of PROs using touch-screen-based, internet technology was feasible in a busy HIV clinic. We found a high prevalence of body morphology abnormalities, depression, and poor adherence. Touch-screen-based collec-tion of PROs is a promising tool to facilitate research and clinical care.


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Identification of HLA-A11-Restricted HIV-1-Specific Cytotoxic T-Lymphocyte Epitopes in China
Shaoyang Wang, Yongtao Sun Song Zhai, Yan Zhuang, Shuguang Zhao, Whenzhen Kang, Xinhong Li, Dedong Huang,Xu G. Yu, Bruce D. Walker and Marcus A. Altfeld

[Full text article]

To fully define HLA-A11- restricted HIV-1- specific cytotoxic T-lymphocyte epitopes in China, a method combining the enzyme-linked immunospot (ELISPOT) assay with intracellular gamma interferon staining (ICS) of peripheral blood mononuclear cells (PBMC) was used to map the optimal epitopes targeted by ELISPOT and then to define the HLA restriction of epitopes by ICS. A novel HLA-A11-restricted CTL epitope and five other published HLA-A11-restricted epitopes previously identified by reverse immunogenetics or other methods were defined. The approach of integrating ELISPOT with ICS is both convenient and useful for the characterization of CTL responses to HIV-1 infection; this method is practical for defining novel epitopes and facilitates in developing new strategies for future vaccine design in China and other Asian countries.


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Prevalence of Dilated Cardiomyopathy in HIV-Infected African Patients Not Receiving HAART: A Multicenter, Observational, Prospective, Cohort Study in Rwanda
Marc Twagirumukiza, Emmanuel Nkeramihigo, Benoit Seminega, Emmanuel Gasakure, Franck Boccara and Giusseppe Barbaro

[Full text article]

Introduction: Several studies performed before the introduction of highly active antiretroviral therapy (HAART) have shown that HIV-1 infection is an important cause of dilated cardiomyopathy. However, factors associated with the development of HIV-associated cardiomyopathy in developing countries are still debated.

Objectives: To assess the prevalence of dilated cardiomyopathy, diagnosed by echocardiography, in HIV-infected Rwandese patients not receiving HAART and the risk factors associated with its development.

Methods: A sample of 416 HIV-infected african patients, without a previous definite history of cardiovascular disease, attending University hospitals in Rwanda, from January to December 2005, were included in a multicenter, observational, prospective, cohort study, with the collaboration of two European Clinical Centers (in France and in Italy). Clinical and laboratory tests along with echocardiographic examination were performed in all patients included in the study.

Results: Out of 416 patients included in the study, dilated cardiomyopathy was documented by echocardiography in 71 (17.7%). By both univariate and multivariate univariate analysis, low socio-economic status, estimated duration of HIV-1 infection, CD4 count, HIV-1 viral load, CDC stage B and C of HIV disease and low plasmatic level of selenium were factors significantly associated with the development of cardiomyopathy. Alcohol consumption and smoking were factors associated with the development of cardiomyopathy only by univariate analysis.

Conclusions: HIV-associated cardiomyopathy is a significant clinical problem in HIV-infected patients not receiving HAART in Rwanda. Early tracking of cardiomyopathy in african HIV-infected patients is therefore recommended. Before administering HAART, clinicians should be aware of a possible existing cardiomyopathy to ensure appropriate, comprehensive, and rational patient care.