1
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D’Orso I, Forst CV. Mathematical Models of HIV-1 Dynamics, Transcription, and Latency. Viruses 2023; 15:2119. [PMID: 37896896 PMCID: PMC10612035 DOI: 10.3390/v15102119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
HIV-1 latency is a major barrier to curing infections with antiretroviral therapy and, consequently, to eliminating the disease globally. The establishment, maintenance, and potential clearance of latent infection are complex dynamic processes and can be best described with the help of mathematical models followed by experimental validation. Here, we review the use of viral dynamics models for HIV-1, with a focus on applications to the latent reservoir. Such models have been used to explain the multi-phasic decay of viral load during antiretroviral therapy, the early seeding of the latent reservoir during acute infection and the limited inflow during treatment, the dynamics of viral blips, and the phenomenon of post-treatment control. Finally, we discuss that mathematical models have been used to predict the efficacy of potential HIV-1 cure strategies, such as latency-reversing agents, early treatment initiation, or gene therapies, and to provide guidance for designing trials of these novel interventions.
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Affiliation(s)
- Iván D’Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Christian V. Forst
- Department of Genetics and Genomic Sciences, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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2
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Damour A, Slaninova V, Radulescu O, Bertrand E, Basyuk E. Transcriptional Stochasticity as a Key Aspect of HIV-1 Latency. Viruses 2023; 15:1969. [PMID: 37766375 PMCID: PMC10535884 DOI: 10.3390/v15091969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
This review summarizes current advances in the role of transcriptional stochasticity in HIV-1 latency, which were possible in a large part due to the development of single-cell approaches. HIV-1 transcription proceeds in bursts of RNA production, which stem from the stochastic switching of the viral promoter between ON and OFF states. This switching is caused by random binding dynamics of transcription factors and nucleosomes to the viral promoter and occurs at several time scales from minutes to hours. Transcriptional bursts are mainly controlled by the core transcription factors TBP, SP1 and NF-κb, the chromatin status of the viral promoter and RNA polymerase II pausing. In particular, spontaneous variability in the promoter chromatin creates heterogeneity in the response to activators such as TNF-α, which is then amplified by the Tat feedback loop to generate high and low viral transcriptional states. This phenomenon is likely at the basis of the partial and stochastic response of latent T cells from HIV-1 patients to latency-reversing agents, which is a barrier for the development of shock-and-kill strategies of viral eradication. A detailed understanding of the transcriptional stochasticity of HIV-1 and the possibility to precisely model this phenomenon will be important assets to develop more effective therapeutic strategies.
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Affiliation(s)
- Alexia Damour
- MFP UMR 5234 CNRS, Université de Bordeaux, 33076 Bordeaux, France;
| | - Vera Slaninova
- IGH UMR 9002 CNRS, Université de Montpellier, 34094 Montpellier, France;
| | - Ovidiu Radulescu
- LPHI, UMR 5294 CNRS, University of Montpellier, 34095 Montpellier, France;
| | - Edouard Bertrand
- IGH UMR 9002 CNRS, Université de Montpellier, 34094 Montpellier, France;
| | - Eugenia Basyuk
- MFP UMR 5234 CNRS, Université de Bordeaux, 33076 Bordeaux, France;
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3
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Vo HD, Forero-Quintero LS, Aguilera LU, Munsky B. Analysis and design of single-cell experiments to harvest fluctuation information while rejecting measurement noise. Front Cell Dev Biol 2023; 11:1133994. [PMID: 37305680 PMCID: PMC10250612 DOI: 10.3389/fcell.2023.1133994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction: Despite continued technological improvements, measurement errors always reduce or distort the information that any real experiment can provide to quantify cellular dynamics. This problem is particularly serious for cell signaling studies to quantify heterogeneity in single-cell gene regulation, where important RNA and protein copy numbers are themselves subject to the inherently random fluctuations of biochemical reactions. Until now, it has not been clear how measurement noise should be managed in addition to other experiment design variables (e.g., sampling size, measurement times, or perturbation levels) to ensure that collected data will provide useful insights on signaling or gene expression mechanisms of interest. Methods: We propose a computational framework that takes explicit consideration of measurement errors to analyze single-cell observations, and we derive Fisher Information Matrix (FIM)-based criteria to quantify the information value of distorted experiments. Results and Discussion: We apply this framework to analyze multiple models in the context of simulated and experimental single-cell data for a reporter gene controlled by an HIV promoter. We show that the proposed approach quantitatively predicts how different types of measurement distortions affect the accuracy and precision of model identification, and we demonstrate that the effects of these distortions can be mitigated through explicit consideration during model inference. We conclude that this reformulation of the FIM could be used effectively to design single-cell experiments to optimally harvest fluctuation information while mitigating the effects of image distortion.
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Affiliation(s)
- Huy D. Vo
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Linda S. Forero-Quintero
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Luis U. Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
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4
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A Higher-Order Galerkin Time Discretization and Numerical Comparisons for Two Models of HIV Infection. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3599827. [DOI: 10.1155/2022/3599827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/10/2022] [Accepted: 09/20/2022] [Indexed: 11/11/2022]
Abstract
Human immunodeficiency virus (HIV) infection affects the immune system, particularly white blood cells known as CD4+ T-cells. HIV destroys CD4+ T-cells and significantly reduces a human’s resistance to viral infectious diseases as well as severe bacterial infections, which can lead to certain illnesses. The HIV framework is defined as a system of nonlinear first-order ordinary differential equations, and the innovative Galerkin technique is used to approximate the solutions of the model. To validate the findings, solve the model employing the Runge-Kutta (RK) technique of order four. The findings of the suggested techniques are compared with the results obtained from conventional schemes such as MuHPM, MVIM, and HPM that exist in the literature. Furthermore, the simulations are performed with different time step sizes, and the accuracy is measured at various time intervals. The numerical computations clearly demonstrate that the Galerkin scheme, in contrast to the Runge-Kutta scheme, provides incredibly precise solutions at relatively large time step sizes. A comparison of the solutions reveals that the obtained results through the Galerkin scheme are in fairly good agreement with the RK4 scheme in a given time interval as compared to other conventional schemes. Moreover, having performed various numerical tests for assessing the efficiency and computational cost (in terms of time) of the suggested schemes, it is observed that the Galerkin scheme is noticeably slower than the Runge-Kutta scheme. On the other hand, this work is also concerned with the path tracking and damped oscillatory behaviour of the model with a variable supply rate for the generation of new CD4+ T-cells (based on viral load concentration) and the HIV infection incidence rate. Additionally, we investigate the influence of various physical characteristics by varying their values and analysing them using graphs. The investigations indicate that the lateral system ensured more accurate predictions than the previous model.
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5
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Qiao L, Zhang ZB, Zhao W, Wei P, Zhang L. Network design principle for robust oscillatory behaviors with respect to biological noise. eLife 2022; 11:76188. [PMID: 36125857 PMCID: PMC9489215 DOI: 10.7554/elife.76188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Oscillatory behaviors, which are ubiquitous in transcriptional regulatory networks, are often subject to inevitable biological noise. Thus, a natural question is how transcriptional regulatory networks can robustly achieve accurate oscillation in the presence of biological noise. Here, we search all two- and three-node transcriptional regulatory network topologies for those robustly capable of accurate oscillation against the parameter variability (extrinsic noise) or stochasticity of chemical reactions (intrinsic noise). We find that, no matter what source of the noise is applied, the topologies containing the repressilator with positive autoregulation show higher robustness of accurate oscillation than those containing the activator-inhibitor oscillator, and additional positive autoregulation enhances the robustness against noise. Nevertheless, the attenuation of different sources of noise is governed by distinct mechanisms: the parameter variability is buffered by the long period, while the stochasticity of chemical reactions is filtered by the high amplitude. Furthermore, we analyze the noise of a synthetic human nuclear factor κB (NF-κB) signaling network by varying three different topologies and verify that the addition of a repressilator to the activator-inhibitor oscillator, which leads to the emergence of high-robustness motif—the repressilator with positive autoregulation—improves the oscillation accuracy in comparison to the topology with only an activator-inhibitor oscillator. These design principles may be applicable to other oscillatory circuits.
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Affiliation(s)
- Lingxia Qiao
- Beijing International Center for Mathematical Research, Peking University, Beijing, China
| | - Zhi-Bo Zhang
- Center for Quantitative Biology, Peking University, Beijing, China.,Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wei Zhao
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Ping Wei
- Center for Quantitative Biology, Peking University, Beijing, China.,Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lei Zhang
- Beijing International Center for Mathematical Research, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
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6
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Terebus A, Manuchehrfar F, Cao Y, Liang J. Exact Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of Multimodality. Front Genet 2021; 12:645640. [PMID: 34306004 PMCID: PMC8297706 DOI: 10.3389/fgene.2021.645640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of network phenotypes they can exhibit. In this study, we provide full characterizations of the properties of stochastic multimodality of FFLs, and how switching between different network phenotypes are controlled. We have computed the exact steady-state probability landscapes of all eight types of coherent and incoherent FFLs using the finite-butter Accurate Chemical Master Equation (ACME) algorithm, and quantified the exact topological features of their high-dimensional probability landscapes using persistent homology. Through analysis of the degree of multimodality for each of a set of 10,812 probability landscapes, where each landscape resides over 105–106 microstates, we have constructed comprehensive phase diagrams of all relevant behavior of FFL multimodality over broad ranges of input and regulation intensities, as well as different regimes of promoter binding dynamics. In addition, we have quantified the topological sensitivity of the multimodality of the landscapes to regulation intensities. Our results show that with slow binding and unbinding dynamics of transcription factor to promoter, FFLs exhibit strong stochastic behavior that is very different from what would be inferred from deterministic models. In addition, input intensity play major roles in the phenotypes of FFLs: At weak input intensity, FFL exhibit monomodality, but strong input intensity may result in up to 6 stable phenotypes. Furthermore, we found that gene duplication can enlarge stable regions of specific multimodalities and enrich the phenotypic diversity of FFL networks, providing means for cells toward better adaptation to changing environment. Our results are directly applicable to analysis of behavior of FFLs in biological processes such as stem cell differentiation and for design of synthetic networks when certain phenotypic behavior is desired.
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Affiliation(s)
- Anna Terebus
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States.,Constellation, Baltimore, MD, United States
| | - Farid Manuchehrfar
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
| | - Youfang Cao
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States.,Merck & Co., Inc., Kenilworth, NJ, United States
| | - Jie Liang
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States
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7
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Li SF, Liang X, Wu XK, Gao X, Zhang LW. Discovering the Mechanisms of Wikstroelide E as a Potential HIV-Latency-Reversing Agent by Transcriptome Profiling. JOURNAL OF NATURAL PRODUCTS 2021; 84:1022-1033. [PMID: 33721994 DOI: 10.1021/acs.jnatprod.0c01039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The discovery of efficient and specific HIV-latency-reversing agents is critical for HIV therapy. Here, we developed wikstroelide E, a daphnane diterpene from the buds of Wikstroemia chamaedaphne, as a potential HIV-latency-reversing agent that is 2500-fold more potent than the drug prostratin. Based on transcriptome analysis, the underlying mechanism was that wikstroelide E regulated the MAPK, PI3K-Akt, JAK-Stat, TNF, and NF-κB signaling pathways. We clearly demonstrated that wikstroelide E reversed latent HIV infection by activating PKC-NF-κB signals, serving as a proxy for verifying the transcriptome data. Strikingly, the Tat protein contributes to the robust activation of latent HIV in wikstroelide-E-treated cells, producing an unexpected latency-reversing effect against latent HIV. This study provides the basis for the potential development of wikstroelide E as an effective HIV-latency-reversing agent.
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Affiliation(s)
- Shi-Fei Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Xue Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Xing-Kang Wu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Xiang Gao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, People's Republic of China
| | - Li-Wei Zhang
- Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan 030006, People's Republic of China
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8
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Conway JM, Meily P, Li JZ, Perelson AS. Unified model of short- and long-term HIV viral rebound for clinical trial planning. J R Soc Interface 2021; 18:20201015. [PMID: 33849338 PMCID: PMC8086917 DOI: 10.1098/rsif.2020.1015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/23/2021] [Indexed: 11/12/2022] Open
Abstract
Antiretroviral therapy (ART) effectively controls HIV infection, suppressing HIV viral loads. Typically suspension of therapy is rapidly followed by rebound of viral loads to high, pre-therapy levels. Indeed, a recent study showed that approximately 90% of treatment interruption study participants show viral rebound within at most a few months of therapy suspension, but the remaining 10%, showed viral rebound some months, or years, after ART suspension. Some may even never rebound. We investigate and compare branching process models aimed at gaining insight into these viral dynamics. Specifically, we provide a theory that explains both short- and long-term viral rebounds, and post-treatment control, via a multitype branching process with time-inhomogeneous rates, validated with data from Li et al. (Li et al. 2016 AIDS30, 343-353. (doi:10.1097/QAD.0000000000000953)). We discuss the associated biological interpretation and implications of our best-fit model. To test the effectiveness of an experimental intervention in delaying or preventing rebound, the standard practice is to suspend therapy and monitor the study participants for rebound. We close with a discussion of an important application of our modelling in the design of such clinical trials.
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Affiliation(s)
- Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Paige Meily
- University of Pennsylvania School of Arts and Sciences, Philadephia, PA, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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9
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Grossman Z, Singh NJ, Simonetti FR, Lederman MM, Douek DC, Deeks SG. 'Rinse and Replace': Boosting T Cell Turnover To Reduce HIV-1 Reservoirs. Trends Immunol 2020; 41:466-480. [PMID: 32414695 DOI: 10.1016/j.it.2020.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 12/22/2022]
Abstract
Latent HIV-1 persists indefinitely during antiretroviral therapy (ART) as an integrated silent genome in long-lived memory CD4+ T cells. In untreated infections, immune activation increases the turnover of intrinsically long-lived provirus-containing CD4+ T cells. Those are 'washed out' as a result of their activation, which when coupled to viral protein expression can facilitate local inflammation and recruitment of uninfected cells to activation sites, causing latently infected cells to compete for survival. De novo infection can counter this washout. During ART, inflammation and CD4+ T cell activation wane, resulting in reduced cell turnover and a persistent reservoir. We propose accelerating reservoir washout during ART by triggering sequential waves of polyclonal CD4+ T cell activation while simultaneously enhancing virus protein expression. Reservoir reduction as an adjunct to other therapies might achieve lifelong viral control.
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Affiliation(s)
- Zvi Grossman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Nevil J Singh
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Francesco R Simonetti
- 'L. Sacco' Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | | | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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10
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Jin H, Li D, Lin MH, Li L, Harrich D. Tat-Based Therapies as an Adjuvant for an HIV-1 Functional Cure. Viruses 2020; 12:v12040415. [PMID: 32276443 PMCID: PMC7232260 DOI: 10.3390/v12040415] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 12/18/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV) establishes a chronic infection that can be well controlled, but not cured, by combined antiretroviral therapy (cART). Interventions have been explored to accomplish a functional cure, meaning that a patient remains infected but HIV is undetectable in the blood, with the aim of allowing patients to live without cART. Tat, the viral transactivator of transcription protein, plays a critical role in controlling HIV transcription, latency, and viral rebound following the interruption of cART treatment. Therefore, a logical approach for controlling HIV would be to block Tat. Tackling Tat with inhibitors has been a difficult task, but some recent discoveries hold promise. Two anti-HIV proteins, Nullbasic (a mutant of Tat) and HT1 (a fusion of HEXIM1 and Tat functional domains) inhibit viral transcription by interfering with the interaction of Tat and cellular factors. Two small molecules, didehydro-cortistatin A (dCA) and triptolide, inhibit Tat by different mechanisms: dCA through direct binding and triptolide through enhanced proteasomal degradation. Finally, two Tat-based vaccines under development elicit Tat-neutralizing antibodies. These vaccines have increased the levels of CD4+ cells and reduced viral loads in HIV-infected people, suggesting that the new vaccines are therapeutic. This review summarizes recent developments of anti-Tat agents and how they could contribute to a functional cure for HIV.
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Affiliation(s)
- Hongping Jin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (H.J.); (D.L.); (M.-H.L.)
| | - Dongsheng Li
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (H.J.); (D.L.); (M.-H.L.)
| | - Min-Hsuan Lin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (H.J.); (D.L.); (M.-H.L.)
| | - Li Li
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia;
| | - David Harrich
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (H.J.); (D.L.); (M.-H.L.)
- Correspondence: ; Tel.: +617-3845-3679
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11
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Abstract
A disease of more than 39.6 million people worldwide, HIV-1 infection has no curative therapy. To date, one man has achieved a sterile cure, with millions more hoping to avoid the potential pitfalls of lifelong antiretroviral therapy and other HIV-related disorders, including neurocognitive decline. Recent developments in immunotherapies and gene therapies provide renewed hope in advancing efforts toward a sterilizing or functional cure. On the horizon is research concentrated in multiple separate but potentially complementary domains: vaccine research, viral transcript editing, T-cell effector response targeting including checkpoint inhibitors, and gene editing. Here, we review the concept of targeting the HIV-1 tissue reservoirs, with an emphasis on the central nervous system, and describe relevant new work in functional cure research and strategies for HIV-1 eradication.
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12
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Wallet C, De Rovere M, Van Assche J, Daouad F, De Wit S, Gautier V, Mallon PWG, Marcello A, Van Lint C, Rohr O, Schwartz C. Microglial Cells: The Main HIV-1 Reservoir in the Brain. Front Cell Infect Microbiol 2019; 9:362. [PMID: 31709195 PMCID: PMC6821723 DOI: 10.3389/fcimb.2019.00362] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022] Open
Abstract
Despite efficient combination of the antiretroviral therapy (cART), which significantly decreased mortality and morbidity of HIV-1 infection, a definitive HIV cure has not been achieved. Hidden HIV-1 in cellular and anatomic reservoirs is the major hurdle toward a functional cure. Microglial cells, the Central Nervous system (CNS) resident macrophages, are one of the major cellular reservoirs of latent HIV-1. These cells are believed to be involved in the emergence of drugs resistance and reseeding peripheral tissues. Moreover, these long-life reservoirs are also involved in the development of HIV-1-associated neurocognitive diseases (HAND). Clearing these infected cells from the brain is therefore crucial to achieve a cure. However, many characteristics of microglial cells and the CNS hinder the eradication of these brain reservoirs. Better understandings of the specific molecular mechanisms of HIV-1 latency in microglial cells should help to design new molecules and new strategies preventing HAND and achieving HIV cure. Moreover, new strategies are needed to circumvent the limitations associated to anatomical sanctuaries with barriers such as the blood brain barrier (BBB) that reduce the access of drugs.
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Affiliation(s)
- Clementine Wallet
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Marco De Rovere
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Jeanne Van Assche
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Fadoua Daouad
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Stéphane De Wit
- Division of Infectious Diseases, Saint-Pierre University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Virginie Gautier
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Patrick W G Mallon
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Olivier Rohr
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Christian Schwartz
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
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13
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Conway JM, Perelson AS, Li JZ. Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers. PLoS Comput Biol 2019; 15:e1007229. [PMID: 31339888 PMCID: PMC6682162 DOI: 10.1371/journal.pcbi.1007229] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 08/05/2019] [Accepted: 06/30/2019] [Indexed: 01/31/2023] Open
Abstract
Antiretroviral therapy (ART) effectively controls HIV infection, suppressing HIV viral loads. Suspension of therapy is followed by rebound of viral loads to high, pre-therapy levels. However, there is significant heterogeneity in speed of rebound, with some rebounds occurring within days, weeks, or sometimes years. We present a stochastic mathematical model to gain insight into these post-treatment dynamics, specifically characterizing the dynamics of short term viral rebounds (≤ 60 days). Li et al. (2016) report that the size of the expressed HIV reservoir, i.e., cell-associated HIV RNA levels, and drug regimen correlate with the time between ART suspension and viral rebound to detectable levels. We incorporate this information and viral rebound times to parametrize our model. We then investigate insights offered by our model into the underlying dynamics of the latent reservoir. In particular, we refine previous estimates of viral recrudescence after ART interruption by accounting for heterogeneity in infection rebound dynamics, and determine a recrudescence rate of once every 2-4 days. Our parametrized model can be used to aid in design of clinical trials to study viral dynamics following analytic treatment interruption. We show how to derive informative personalized testing frequencies from our model and offer a proof-of-concept example. Our results represent first steps towards a model that can make predictions on a person living with HIV (PLWH)'s rebound time distribution based on biomarkers, and help identify PLWH with long viral rebound delays.
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Affiliation(s)
- Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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Aguilera LU, Rodríguez-González J. Modeling the effect of tat inhibitors on HIV latency. J Theor Biol 2019; 473:20-27. [PMID: 31004612 DOI: 10.1016/j.jtbi.2019.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/07/2019] [Accepted: 04/16/2019] [Indexed: 11/28/2022]
Abstract
Even in the presence of a successful combination therapy stalling the progress of AIDS, developing a cure for this disease is still an open question. One of the major steps towards a cure would be to be able to eradicate latent HIV reservoirs present in patients. During the last decade, multiple findings point to the dominant role of the viral protein Tat in the establishment of latency. Here we present a mathematical study to understand the potential role of Tat inhibitors as virus-suppressing agents. For this aim, we implemented a computational model that reproduces intracellular dynamics. Simulating an HIV-infected cell and its intracellular feedback we observed that removing Tat protein from the system via inhibitors resulted in a temporary and reversible viral suppression. In contrast, we observed that compounds that interact with Tat protein and disrupt the integrated viral genome produced a more permanent viral suppression.
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Affiliation(s)
- Luis U Aguilera
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Im Neuenheimer Feld 267, Heidelberg 69120, Germany; Colorado State University
| | - Jesús Rodríguez-González
- Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Unidad Monterrey, Via del Conocimiento 201, Parque PIIT, Apodaca CP 66600 NL, México.
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Wallet C, De Rovere M, Van Assche J, Daouad F, De Wit S, Gautier V, Mallon PWG, Marcello A, Van Lint C, Rohr O, Schwartz C. Microglial Cells: The Main HIV-1 Reservoir in the Brain. Front Cell Infect Microbiol 2019. [PMID: 31709195 DOI: 10.3389/fcimb.2019.00362/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
Despite efficient combination of the antiretroviral therapy (cART), which significantly decreased mortality and morbidity of HIV-1 infection, a definitive HIV cure has not been achieved. Hidden HIV-1 in cellular and anatomic reservoirs is the major hurdle toward a functional cure. Microglial cells, the Central Nervous system (CNS) resident macrophages, are one of the major cellular reservoirs of latent HIV-1. These cells are believed to be involved in the emergence of drugs resistance and reseeding peripheral tissues. Moreover, these long-life reservoirs are also involved in the development of HIV-1-associated neurocognitive diseases (HAND). Clearing these infected cells from the brain is therefore crucial to achieve a cure. However, many characteristics of microglial cells and the CNS hinder the eradication of these brain reservoirs. Better understandings of the specific molecular mechanisms of HIV-1 latency in microglial cells should help to design new molecules and new strategies preventing HAND and achieving HIV cure. Moreover, new strategies are needed to circumvent the limitations associated to anatomical sanctuaries with barriers such as the blood brain barrier (BBB) that reduce the access of drugs.
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Affiliation(s)
- Clementine Wallet
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Marco De Rovere
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Jeanne Van Assche
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Fadoua Daouad
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Stéphane De Wit
- Division of Infectious Diseases, Saint-Pierre University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Virginie Gautier
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Patrick W G Mallon
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Olivier Rohr
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Christian Schwartz
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
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