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Co-infection with hepatitis B virus (HBV) and human immunodeficiency virus type-1 (HIV-1) is relatively common. However, the impact of this co-infection on the clinical outcome of HIV infection has not been elucidated. We herein demonstrate that the HBV X protein (HBx) superinduces ongoing HIV-1 replication and HIV-1 long terminal repeat (LTR) transcription by synergizing with Tat protein and with T-cell activation signals. Although HBx cooperated with mitogenic stimuli in the induction of reporter plasmids harboring the HIV-1 kappaB enhancer, in both a NF-kappaB-dependent manner and a NF-AT-dependent manner, deletion of this element from the LTR did not affect the HBx-mediated up-regulation in the presence of Tat and/or mitogens. In contrast, mutation of the proximal LTR Sp1-binding sites abolished the HBx-mediated synergistic activation, but only when it was accompanied by deletion of the kappaB enhancer. When HBx was targeted to the nucleus, its ability to synergize with cellular activation stimuli was maintained. Furthermore, mutations of HBx affecting its interaction with the basal transcription machinery abrogated the synergistic activation by HBx, suggesting that this protein exerts its function by acting as a nuclear co-activator. These results indicate that HBx could contribute to a faster progression to AIDS in HBV-HIV co-infected individuals.

Reverse transcription of retroviral genomes is primed by a tRNA molecule that anneals to an 18 nt primer binding site (PBS) on the viral RNA genome. Additional base pair interactions between the tRNA primer and the viral RNA have been proposed. In particular, base pairing was proposed between the anticodon loop of tRNALys3 and the 'A-rich' loop of a hairpin located immediately upstream of the PBS site in HIV-1 RNA. In order to judge the importance of this sequence/structure motif, we performed an extensive phylogenetic analysis of this genomic region in a variety of simian and human immunodeficiency viruses (SIV and HIV). Both the phylogeny of natural HIV/SIV sequences and the behaviour of U5-PBS mutant/revertant viruses support the idea that this RNA structure is critical for virus replication. Although this hairpin may play a role in tRNA annealing and/or initiation of reverse transcription, the proposed base pairing interaction between the A-rich loop of the HIV-1 hairpin and the anticodon of the initiator tRNA is not directly supported by this analysis.

Human immunodeficiency virus type 1 (HIV-1) and other lentiviridae demonstrate a strong preference for the A-nucleotide, which can account for up to 40% of the viral RNA genome. The biological mechanism responsible for this nucleotide bias is currently unknown. The increased A-content of these viral genomes corresponds to the typical use of synonymous codons by all members of the lentiviral family (HIV, SIV, BIV, FIV, CAEV, EIAV, visna) and the human spuma retrovirus, but not by other retroviruses like the human T-cell leukemia viruses HTLV-I and HTLV-II. In this article, we analyzed A-bias for all codon groups in all open reading frames of several lentiviruses. The extent of lentiviral codon bias could be related to host cellular translation. By calculating codon bias indices (CBIs), we were able to demonstrate an inverse correlation between the extent of codon bias and the rate of translation of individual reading frames in these viruses. Specifically, the shift toward A-rich codons is more pronounced in pol than in gag lentiviral genes. Since it is known that Gag synthesis exceeds Pol synthesis by a factor of 20 due to infrequent ribosomal frame-shifting during translation of the gap-pol mRNA molecule, we propose that the aminoacyl-tRNA availability in the host cell restricts the lentiviral preference for A-rich codons. In addition, less A-nucleotides were found in regions of the viral genome encoding multiple functions; e.g., overlapping reading frames (tat-rev-env) or in genes that overlap regulatory sequences (nef-LTR region). Finally, the characteristics of lentiviral codon usage are presented as a phylogenetic tree without the need for prior sequence alignment.

The efficient control of gene expression in vivo from lentiviral vectors remains technically challenging. To analyze inducible gene expression in a human setting, we generated 'human immune system' (HIS) mice by transplanting newborn BALB/c Rag2(-/-) IL-2R gamma(-/-)(c) immunodeficient mice with human hematopoietic stem cells transduced with a doxycycline-inducible lentiviral vector. We compared several methods of doxycycline delivery to mice, and could accurately measure doxycycline in vivo using a new sensitive detection assay. Two different lentiviral vector designs with constitutive (TRECMV-V14) or autoregulatory (TREAuto-V14) expression of an optimized reverse tetracycline transactivator were used to transduce human hematopoietic stem cells. After transplantation into immunodeficient mice, we analyzed the expression of the green fluorescent protein (GFP) reporter gene in the human hematopoiesis-derived cells that develop and accumulate in the generated HIS mice. We show efficient inducible GFP expression in adult HIS mice containing TREAuto-V14-transduced human cells, whereas GFP expression is poor with the TRECMV-V14 vector. Multiple cycles of doxycycline exposure in the TREAuto-V14 group result in repeated cycles of GFP expression with no loss of intensity. These findings are of major interest for gene therapy and basic research settings that require inducible gene expression. Gene Therapy (2010) 17, 14-25; doi: 10.1038/gt.2009.109; published online 3 September 2009

Background Live-attenuated SIV can induce superinfection resistance; however, the mechanism of this effect is not understood and may have implications for HIV vaccine development. To further investigate the role of virus replication in conferring protection we have analysed T cell phenotype and responses in gut tissue following infection of macaques with either SIVmac239Δnef or a doxycycline-dependent replication variant of SIVmac239 Δnef designated SIVrtTA.

Background In the SIV/macaque model of HIV in man, live attenuated virus confers the most potent protection against wild-type virus challenge. We have developed a novel live attenuated (nef deleted) vaccine SIVmac239 (SIVrtTA) that is dependent on doxycycline for replication in vivo. Withdrawal of doxycycline prevents replication of SIVrtTA. We used this virus to vaccinate rhesus macaques to investigate the role of virus replication and persistence in protection against SIVmac239 challenge.

RNA interference (RNAi) gene therapy against HIV-1 by stable expression of antiviral short hairpin RNAs (shRNAs) can potently inhibit viral replication in T cells. Recently, a mouse model with a human immune system (HIS) was developed that can be productively infected with HIV-1. In this in vivo model, in which Rag-2(-/-)gamma(c)(-/-) mice are engrafted with human CD34(+)CD38(-) hematopoietic precursor cells, we evaluated an anti-HIV RNAi gene therapy. Human hematopoietic stem cells were transduced with a lentiviral vector expressing an shRNA against the HIV-1 nef gene (shNef) or the control vector. We observed normal development of the different cell subsets of the immune system. However, although initial transduction efficiencies were similar for both vectors, a reduced percentage of transduced human immune cells was observed for the shNef vector after establishment of the HIS in vivo. Further studies are required to fully evaluate the safety implications. When we infected the mature human CD4(+) T cells from the HIS mouse ex vivo with HIV-1, potent inhibition of viral replication was scored in shNef-expressing cells, confirming efficacy. When challenged with an shNef-resistant HIV-1 variant, equal replication was scored in control and shNef-expressing cells, confirming sequence-specificity of the RNAi therapy. We thus demonstrated that an antiviral RNAi-based gene therapy on blood stem cells leads to HIV-1-resistant T cells in vivo, an important proof of concept in the clinical development of RNAi against HIV-1.

We studied sequence differences in regulatory elements of the long terminal repeat (LTR) and primer-binding site (PBS) among various human immunodeficiency virus type 1 (HIV-1) subtypes. Phylogenetic sequence analysis of a fragment of 729 base pairs (bp) covering the Gag-coding region for half of p24 and all of p17 revealed the gag subtype of all 60 viruses included in the study: A (n = 20), B (n = 12), C (n = 7), D (n = 10), E (n = 3), F (n = 4), G (n = 3), and H (n = 1). The subtype was also determined by analysis of a 689-bp fragment comprising the LTR and the PBS motif. Comparison of the LTR versus gag sequences showed a mosaic genome for seven isolates. After analysis of all sequences, we could describe subtype-specific differences in sequences encompassing the regulatory elements of the LTR and the PBS motif.

The human genome contains a large number of sequences that belong to the HERV-K family of human endogenous retroviruses. Most of these elements are likely remnants of ancient infections by ancestral exogenous retroviruses. To obtain further insight into the evolutionary history and molecular mechanisms responsible for the diversity of the human HERV-K elements, we analyzed several aspects of their genome structure. The nucleotide composition of the HERV-K genome was found to be highly biased and asymmetric, with an abundance of the A nucleotide in the viral (+) strand. A similar trend has been reported for the genomes of several exogenous retroviruses, with different nucleotides as the preferred building block. Other genome characteristics that were reported previously for actively replicating retroviruses are also apparent for the endogenous HERV-K virus. In particular, we observed suppression of the dinucleotide CpG, which represents potential methylation sites, and a strong preference for synonymous substitutions within the open reading frame of the reverse transcriptase (RT) enzyme. Furthermore, the mutational spectrum of the HERV-K RT enzyme was evaluated by nucleotide sequence comparison of 34 available elements. Interestingly, this analysis revealed a striking similarity with the mutational pattern of the HIV-1 RT enzyme, with a preference for G-to-A and C-to-T transitions. It is proposed that the mutational bias of the HERV-K RT enzyme played a role in the shaping of this retroviral genome, which was actively replicating more than 30 million years ago. This effect can still be observed in the contemporary endogenous HERV-K elements.

Publisher Summary This chapter deals with the structure and function of the leader transcript of human immunodeficiency virus (HIV-1) and HIV-2. Most of the RNA signals encoded by the untranslated leader RNA have specific nucleotide sequences critical for recognition and function, but there is accumulating evidence that their structural context can also be important. There is an intense effort to analyze the secondary structure of retroviral leader RNAs using a variety of methods, including biochemical analysis, free-energy minimization, sequence comparison, and mutant analysis. The chapter focuses primarily on the relationships between the structure of specific leader RNA motifs and their function in the retroviral life cycle. Among retroviruses, the lentiviruses have the most complex genome structure and expression strategy. The primate lentiviruses include the human and simian immunodeficiency viruses (SIV). Understanding the three-dimensional structure formed by the HIV leader RNA molecule, both free and in the ribonucleoprotein complex of virion, is crucial for analyzing its specific recognition by proteins and its interaction by other RNA molecules during virus replication. The number of HIV–SIV sequences now known is sufficiently large; hence, comparative analysis can be used effectively to deduce some of the basic design principles underlying HIV RNA structure. By understanding the molecular basis of the interactions that govern critical steps in the retroviral replication cycle, it may be possible to develop methods to intervene therapeutically in the process.

The design of novel anti-HIV vaccination and gene therapy strategies will be presented, including pilot experiments in animal models. Our gene therapy approach uses the RNA interference (RNAi) machinery to make human cells resistant to HIV-1. The problem of viral escape and the control of viral escape by means of a combination-RNAi therapy will be discussed. A humanized mouse model has been set up as pre-clinical test system to address the safety and efficacy of lentiviral vector-delivered RNAi cassettes. Our vaccination approach deals with the novel concept of a conditional-live virus that can be turned on and off at will. Live-attenuated virus confers the most potent protection against wild-type virus challenge in the SIV/macaque vaccination model. However, such a vaccine is not pursued because of safety reasons as the vaccine virus persists and may evolve into a pathogenic variant. We therefore designed an SIVmac239Δnef variant that is dependent on doxycycline for replication by replacing the natural Tat/TAR transcription mechanism by the Tet-system for inducible gene expression. Replication of this virus can be switched off after vaccination, which will prevent evolution. The first rhesus macaque test yielded a marked vaccine effect. This new conditional-live virus will be a useful tool to identify the correlates of protection by this vaccine strategy.

Thymus-derived lymphocytes (T cells) are essential in the protection of vertebrates from environmental pathogens. As effector cells, they serve to recognize and eliminate cells bearing infectious agents and tumor antigens. In addition, they play a major role in the functional regulation of the immune response. Unlike B lymphocytes, which mediate their antigen-specific functions via secreted or membrane bound immunoglobulins that can bind to soluble ligands, T cells are responsive only to cell-surface antigens. Specifically, T-lymphocyte membrane receptors recognize antigen presenting cells (APCs), which express the autologous class I or class II integral membrane protein products of the major histocompatibility complex (MHC). This interaction between cells can lead to a variety of responses by the antigen-specific T lymphocytes, including proliferation, production of lymphokines, and target cell cytolysis.