Network-Based Prediction and Analysis of HIV Dependency Factors

Murali, T. M.; Dyer, Matthew D.; Badger, David; Tyler, Brett M.; Katze, Michael G.

doi:10.1007/978-3-642-29627-7_18

Cited by 24 publications

(15 citation statements)

References 68 publications

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“…RT-PCR-based gene arrays are used to determine if cellular gene expression is altered by infected cells treated with a potential inhibitor [14, 100, 101]. Data analysis requires a large data base to define potential nodules responsible for the gene expression alterations.…”

Section: Cellular Targetsmentioning

confidence: 99%

The Continuing Evolution of HIV-1 Therapy: Identification and Development of Novel Antiretroviral Agents Targeting Viral and Cellular Targets

Hartman

Buckheit

2012

Molecular Biology International

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During the past three decades, over thirty-five anti-HIV-1 therapies have been developed for use in humans and the progression from monotherapeutic treatment regimens to today’s highly active combination antiretroviral therapies has had a dramatic impact on disease progression in HIV-1-infected individuals. In spite of the success of AIDS therapies and the existence of inhibitors of HIV-1 reverse transcriptase, protease, entry and fusion, and integrase, HIV-1 therapies still have a variety of problems which require continued development efforts to improve efficacy and reduce toxicity, while making drugs that can be used throughout both the developed and developing world, in pediatric populations, and in pregnant women. Highly active antiretroviral therapies (HAARTs) have significantly delayed the progression to AIDS, and in the developed world HIV-1-infected individuals might be expected to live normal life spans while on lifelong therapies. However, the difficult treatment regimens, the presence of class-specific drug toxicities, and the emergence of drug-resistant virus isolates highlight the fact that improvements in our therapeutic regimens and the identification of new and novel viral and cellular targets for therapy are still necessary. Antiretroviral therapeutic strategies and targets continue to be explored, and the development of increasingly potent molecules within existing classes of drugs and the development of novel strategies are ongoing.

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Section: Cellular Targetsmentioning

confidence: 99%

The Continuing Evolution of HIV-1 Therapy: Identification and Development of Novel Antiretroviral Agents Targeting Viral and Cellular Targets

Hartman

Buckheit

2012

Molecular Biology International

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“…Furthermore, they also played a role as targeted and required genes of viral infections [66,67]. As a consequence, such centrality measures and the determination of control nodes may allow the computational prediction of potential viral targets based on topological measures [57,58,[68][69][70].…”

Section: What Are the Protein Targets Of Human Viruses?mentioning

confidence: 99%

Protein-protein interactions of human viruses

Goodacre

Devkota

Bae

et al. 2020

Seminars in Cell & Developmental Biology

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Viruses infect their human hosts by a series of interactions between viral and host proteins, indicating that detailed knowledge of such virus-host interaction interfaces are critical for our understanding of viral infection mechanisms, disease etiology and the development of new drugs. In this review, we primarily survey human host-virus interaction data that are available from public databases following the standardized PSI-MS format. Notably, available host-virus protein interaction information is strongly biased toward a small number of virus families including herpesviridae, papillomaviridae, orthomyxoviridae and retroviridae. While we explore the reliability and relevance of these protein interactions we also survey the current knowledge about viruses functional and topological targets. Furthermore, we assess emerging frontiers of host-virus protein interaction research, focusing on protein interaction interfaces of hosts that are infected by different viruses and viruses that infect multiple hosts. Finally, we cover the current status of research that investigates the relationships of virus-targeted host proteins to other comorbidities as well as the influence of host-virus protein interactions on human metabolism.

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“…In contrast, orthologs from nonhuman primates frequently retain anti-HIV activity, and comparisons between human and primate genes have identified single or small numbers of amino acids that could be edited into the human genes to restore anti-HIV activity. [69][70][71] In contrast, dependency factors [72][73][74] are the group of cellular factors that are essential for HIV-1 replication and that are exploited by this viral parasite. Together with information from genome-wide association studies, which can identify genetic variants associated with greater HIV control, 75 it may be possible to select candidate alleles from naturally occurring human variants that could also be engineered to inhibit HIV-1.…”

Section: Hdr-mediated Gene Editing and Addition For Anti-hiv Therapiesmentioning

confidence: 99%

The clinical applications of genome editing in HIV

Wang

Cannon

2016

Blood

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HIV/AIDS has long been at the forefront of the development of gene- and cell-based therapies. Although conventional gene therapy approaches typically involve the addition of anti-HIV genes to cells using semirandomly integrating viral vectors, newer genome editing technologies based on engineered nucleases are now allowing more precise genetic manipulations. The possible outcomes of genome editing include gene disruption, which has been most notably applied to the CCR5 coreceptor gene, or the introduction of small mutations or larger whole gene cassette insertions at a targeted locus. Disruption of CCR5 using zinc finger nucleases was the first-in-human application of genome editing and remains the most clinically advanced platform, with 7 completed or ongoing clinical trials in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we review the laboratory and clinical findings of CCR5 editing in T cells and HSPCs for HIV therapy and summarize other promising genome editing approaches for future clinical development. In particular, recent advances in the delivery of genome editing reagents and the demonstration of highly efficient homology-directed editing in both T cells and HSPCs are expected to spur the development of even more sophisticated applications of this technology for HIV therapy.

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Network-Based Prediction and Analysis of HIV Dependency Factors

Cited by 24 publications

References 68 publications

The Continuing Evolution of HIV-1 Therapy: Identification and Development of Novel Antiretroviral Agents Targeting Viral and Cellular Targets

The Continuing Evolution of HIV-1 Therapy: Identification and Development of Novel Antiretroviral Agents Targeting Viral and Cellular Targets

Protein-protein interactions of human viruses

The clinical applications of genome editing in HIV

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