1
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Khetan N, Zuckerman B, Calia GP, Chen X, Arceo XG, Weinberger LS. Quantitative comparison of single-cell RNA sequencing versus single-molecule RNA imaging for quantifying transcriptional noise. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607289. [PMID: 39149226 PMCID: PMC11326230 DOI: 10.1101/2024.08.09.607289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability. However, how best to quantify genome-wide noise, remains unclear. Here we utilize a small-molecule perturbation (IdU) to amplify noise and assess noise quantification from numerous scRNA-seq algorithms on human and mouse datasets, and then compare to noise quantification from single-molecule RNA FISH (smFISH) for a panel of representative genes. We find that various scRNA-seq analyses report amplified noise, without altered mean-expression levels, for ~90% of genes and that smFISH analysis verifies noise amplification for the vast majority of genes tested. Collectively, the analyses suggest that most scRNA-seq algorithms are appropriate for quantifying noise including a simple normalization approach, although all of these systematically underestimate noise compared to smFISH. From a practical standpoint, this analysis argues that IdU is a globally penetrant noise-enhancer molecule-amplifying noise without altering mean-expression levels-which could enable investigations of the physiological impacts of transcriptional noise.
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Affiliation(s)
- Neha Khetan
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Binyamin Zuckerman
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Giuliana P. Calia
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Xinyue Chen
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Ximena Garcia Arceo
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
| | - Leor S. Weinberger
- Gladstone|UCSF Center for Cell Circuitry, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Lead contact
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2
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Pitchai FNN, Tanner EJ, Khetan N, Vasen G, Levrel C, Kumar AJ, Pandey S, Ordonez T, Barnette P, Spencer D, Jung SY, Glazier J, Thompson C, Harvey-Vera A, Son HI, Son HI, Strathdee SA, Holguin L, Urak R, Burnett J, Burgess W, Busman-Sahay K, Estes JD, Hessell A, Fennessey CM, Keele BF, Haigwood NL, Weinberger LS. Engineered deletions of HIV replicate conditionally to reduce disease in nonhuman primates. Science 2024; 385:eadn5866. [PMID: 39116226 DOI: 10.1126/science.adn5866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 06/06/2024] [Indexed: 08/10/2024]
Abstract
Antiviral therapies with reduced frequencies of administration and high barriers to resistance remain a major goal. For HIV, theories have proposed that viral-deletion variants, which conditionally replicate with a basic reproductive ratio [R0] > 1 (termed "therapeutic interfering particles" or "TIPs"), could parasitize wild-type virus to constitute single-administration, escape-resistant antiviral therapies. We report the engineering of a TIP that, in rhesus macaques, reduces viremia of a highly pathogenic model of HIV by >3log10 following a single intravenous injection. Animal lifespan was significantly extended, TIPs conditionally replicated and were continually detected for >6 months, and sequencing data showed no evidence of viral escape. A single TIP injection also suppressed virus replication in humanized mice and cells from persons living with HIV. These data provide proof of concept for a potential new class of single-administration antiviral therapies.
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Affiliation(s)
- Fathima N Nagoor Pitchai
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Elizabeth J Tanner
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Neha Khetan
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Gustavo Vasen
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Clara Levrel
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
| | - Arjun J Kumar
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Shilpi Pandey
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Tracy Ordonez
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Philip Barnette
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - David Spencer
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
- Absci Corporation, Vancouver, WA, USA
| | - Seung-Yong Jung
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Joshua Glazier
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Cassandra Thompson
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Hye-In Son
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- US-Mexico Border Health Commission, Tijuana, Mexico
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Hye-In Son
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
| | - Steffanie A Strathdee
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Leo Holguin
- Global Health Sciences, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ryan Urak
- Center for Gene Therapy, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - John Burnett
- Center for Gene Therapy, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William Burgess
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
- Faculty of Health, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- School of Health and Biomedical Sciences College of Science, Engineering and Health RMIT University, Melbourne, Australia
| | - Ann Hessell
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nancy L Haigwood
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Leor S Weinberger
- Gladstone Center for Cell Circuitry, University of California, San Francisco, CA, USA
- Gladstone Institute of Virology, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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3
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D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
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Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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4
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Grandi C, Emmaneel M, Nelissen FHT, Roosenboom LWM, Petrova Y, Elzokla O, Hansen MMK. Decoupled degradation and translation enables noise modulation by poly(A) tails. Cell Syst 2024; 15:526-543.e7. [PMID: 38901403 DOI: 10.1016/j.cels.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/24/2023] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Poly(A) tails are crucial for mRNA translation and degradation, but the exact relationship between tail length and mRNA kinetics remains unclear. Here, we employ a small library of identical mRNAs that differ only in their poly(A)-tail length to examine their behavior in human embryonic kidney cells. We find that tail length strongly correlates with mRNA degradation rates but is decoupled from translation. Interestingly, an optimal tail length of ∼100 nt displays the highest translation rate, which is identical to the average endogenous tail length measured by nanopore sequencing. Furthermore, poly(A)-tail length variability-a feature of endogenous mRNAs-impacts translation efficiency but not mRNA degradation rates. Stochastic modeling combined with single-cell tracking reveals that poly(A) tails provide cells with an independent handle to tune gene expression fluctuations by decoupling mRNA degradation and translation. Together, this work contributes to the basic understanding of gene expression regulation and has potential applications in nucleic acid therapeutics.
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Affiliation(s)
- Carmen Grandi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Martin Emmaneel
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands
| | - Laura W M Roosenboom
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Yoanna Petrova
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Omnia Elzokla
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Oncode Institute, Nijmegen, the Netherlands.
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5
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Ordway AJ, Helt RN, Johnston RJ. Transcriptional priming and chromatin regulation during stochastic cell fate specification. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230046. [PMID: 38432315 PMCID: PMC10909510 DOI: 10.1098/rstb.2023.0046] [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: 08/21/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024] Open
Abstract
Stochastic cell fate specification, in which a cell chooses between two or more fates with a set probability, diversifies cell subtypes in development. Although this is a vital process across species, a common mechanism for these cell fate decisions remains elusive. This review examines two well-characterized stochastic cell fate decisions to identify commonalities between their developmental programmes. In the fly eye, two subtypes of R7 photoreceptors are specified by the stochastic ON/OFF expression of a transcription factor, spineless. In the mouse olfactory system, olfactory sensory neurons (OSNs) randomly select to express one copy of an olfactory receptor (OR) gene out of a pool of 2800 alleles. Despite the differences in these sensory systems, both stochastic fate choices rely on the dynamic interplay between transcriptional priming, chromatin regulation and terminal gene expression. The coupling of transcription and chromatin modifications primes gene loci in undifferentiated neurons, enabling later expression during terminal differentiation. Here, we compare these mechanisms, examine broader implications for gene regulation during development and posit key challenges moving forward. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Alison J. Ordway
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Rina N. Helt
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Robert J. Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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6
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Reda O, Monde K, Sugata K, Rahman A, Sakhor W, Rajib SA, Sithi SN, Tan BJY, Niimura K, Motozono C, Maeda K, Ono M, Takeuchi H, Satou Y. HIV-Tocky system to visualize proviral expression dynamics. Commun Biol 2024; 7:344. [PMID: 38509308 PMCID: PMC10954732 DOI: 10.1038/s42003-024-06025-8] [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: 09/05/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
Determinants of HIV-1 latency establishment are yet to be elucidated. HIV reservoir comprises a rare fraction of infected cells that can survive host and virus-mediated killing. In vitro reporter models so far offered a feasible means to inspect this population, but with limited capabilities to dissect provirus silencing dynamics. Here, we describe a new HIV reporter model, HIV-Timer of cell kinetics and activity (HIV-Tocky) with dual fluorescence spontaneous shifting to reveal provirus silencing and reactivation dynamics. This unique feature allows, for the first time, identifying two latent populations: a directly latent, and a recently silenced subset, with the latter having integration features suggestive of stable latency. Our proposed model can help address the heterogeneous nature of HIV reservoirs and offers new possibilities for evaluating eradication strategies.
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Affiliation(s)
- Omnia Reda
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Microbiology Department, High Institute of Public Health, Alexandria University, Alexandria, Egypt
| | - Kazuaki Monde
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenji Sugata
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Akhinur Rahman
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Wajihah Sakhor
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Sharmin Nahar Sithi
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Benjy Jek Yang Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Koki Niimura
- School of Medicine, Kumamoto University, Kumamoto, Japan
| | - Chihiro Motozono
- Division of Infection and Immunology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Kenji Maeda
- Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, London, UK
| | - Hiroaki Takeuchi
- Department of High-risk Infectious Disease Control, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
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7
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Ranga U, Panchapakesan A, Saini C. HIV-1 subtypes and latent reservoirs. Curr Opin HIV AIDS 2024; 19:87-92. [PMID: 38169308 DOI: 10.1097/coh.0000000000000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW We explore the current status of research on HIV-1 subtype-specific variations and their impact on HIV-1 latency. We also briefly address the controversy surrounding the decision-making process governing the ON/OFF states of HIV-1 transcription, specifically focusing on the regulatory elements, the long terminal repeat (LTR), and Tat. Understanding the decision-making process is crucial for developing effective intervention strategies, such as the 'shock-and-kill' approach, to reactivate latent HIV-1. RECENT FINDINGS Attention has been drawn to subtype-specific transcription factor binding site (TFBS) variations and the possible impact of these variations on viral latency. Further, diverse subtype-specific assays have been developed to quantify the latent viral reservoirs. One interesting observation is the relatively larger latent reservoirs in HIV-1B infection than those of other viral subtypes, which needs rigorous validation. The emergence of LTR-variant viral strains in HIV-1C demonstrating significantly higher levels of latency reversal has been reported. SUMMARY Despite persistent and substantial efforts, latent HIV-1 remains a formidable challenge to a functional cure. Determined and continued commitment is needed to understand the ON/OFF decision-making process of HIV-1 latency, develop rigorous assays for accurately quantifying the latent reservoirs, and identify potent latency-reversing agents and cocktails targeting multiple latency stages. The review emphasizes the importance of including diverse viral subtypes in future latency research.
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Affiliation(s)
- Udaykumar Ranga
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
| | - Arun Panchapakesan
- Molecular Biology Laboratory, Y R Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, Tamil Nadu, India
| | - Chhavi Saini
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
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8
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Cafaro A, Schietroma I, Sernicola L, Belli R, Campagna M, Mancini F, Farcomeni S, Pavone-Cossut MR, Borsetti A, Monini P, Ensoli B. Role of HIV-1 Tat Protein Interactions with Host Receptors in HIV Infection and Pathogenesis. Int J Mol Sci 2024; 25:1704. [PMID: 38338977 PMCID: PMC10855115 DOI: 10.3390/ijms25031704] [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: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Each time the virus starts a new round of expression/replication, even under effective antiretroviral therapy (ART), the transactivator of viral transcription Tat is one of the first HIV-1 protein to be produced, as it is strictly required for HIV replication and spreading. At this stage, most of the Tat protein exits infected cells, accumulates in the extracellular matrix and exerts profound effects on both the virus and neighbor cells, mostly of the innate and adaptive immune systems. Through these effects, extracellular Tat contributes to the acquisition of infection, spreading and progression to AIDS in untreated patients, or to non-AIDS co-morbidities in ART-treated individuals, who experience inflammation and immune activation despite virus suppression. Here, we review the role of extracellular Tat in both the virus life cycle and on cells of the innate and adaptive immune system, and we provide epidemiological and experimental evidence of the importance of targeting Tat to block residual HIV expression and replication. Finally, we briefly review vaccine studies showing that a therapeutic Tat vaccine intensifies ART, while its inclusion in a preventative vaccine may blunt escape from neutralizing antibodies and block early events in HIV acquisition.
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Affiliation(s)
- Aurelio Cafaro
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy; (I.S.); (L.S.); (R.B.); (M.C.); (F.M.); (S.F.); (M.R.P.-C.); (A.B.); (P.M.)
| | | | | | | | | | | | | | | | | | | | - Barbara Ensoli
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00161 Rome, Italy; (I.S.); (L.S.); (R.B.); (M.C.); (F.M.); (S.F.); (M.R.P.-C.); (A.B.); (P.M.)
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9
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Rausch JW, Parvez S, Pathak S, Capoferri AA, Kearney MF. HIV Expression in Infected T Cell Clones. Viruses 2024; 16:108. [PMID: 38257808 PMCID: PMC10820123 DOI: 10.3390/v16010108] [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: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among persistence determinants, as it allows infected cells to evade the cytopathic effects of virion production and killing by cytotoxic T lymphocytes (CTL) and other immune factors. HIV-1 persistence is also governed by cellular proliferation, an innate and essential capacity of CD4+ T cells that both sustains cell populations over time and enables a robust directed response to immunological threats. However, when HIV-1 infects CD4+ T cells, this capacity for proliferation can enable surreptitious HIV-1 propagation without the deleterious effects of viral gene expression in latently infected cells. Over time on ART, the HIV-1 reservoir is shaped by both persistence determinants, with selective forces most often favoring clonally expanded infected cell populations harboring transcriptionally quiescent proviruses. Moreover, if HIV latency is incomplete or sporadically reversed in clonal infected cell populations that are replenished faster than they are depleted, such populations could both persist indefinitely and contribute to low-level persistent viremia during ART and viremic rebound if treatment is withdrawn. In this review, select genetic, epigenetic, cellular, and immunological determinants of viral transcriptional suppression and clonal expansion of HIV-1 reservoir T cells, interdependencies among these determinants, and implications for HIV-1 persistence will be presented and discussed.
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Affiliation(s)
- Jason W. Rausch
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.P.); (S.P.); (A.A.C.); (M.F.K.)
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10
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Van Gulck E, Pardons M, Nijs E, Verheyen N, Dockx K, Van Den Eynde C, Battivelli E, Vega J, Florence E, Autran B, Archin NM, Margolis DM, Katlama C, Hamimi C, Van Den Wyngaert I, Eyassu F, Vandekerckhove L, Boden D. A truncated HIV Tat demonstrates potent and specific latency reversal activity. Antimicrob Agents Chemother 2023; 67:e0041723. [PMID: 37874295 PMCID: PMC10649039 DOI: 10.1128/aac.00417-23] [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: 03/28/2023] [Accepted: 08/09/2023] [Indexed: 10/25/2023] Open
Abstract
A major barrier to HIV-1 cure is caused by the pool of latently infected CD4 T-cells that persist under combination antiretroviral therapy (cART). This latent reservoir is capable of producing replication-competent infectious viruses once prolonged suppressive cART is withdrawn. Inducing the reactivation of HIV-1 gene expression in T-cells harboring a latent provirus in people living with HIV-1 under cART may result in depletion of this latent reservoir due to cytopathic effects or immune clearance. Studies have investigated molecules that reactivate HIV-1 gene expression, but to date, no latency reversal agent has been identified to eliminate latently infected cells harboring replication-competent HIV in cART-treated individuals. Stochastic fluctuations in HIV-1 tat gene expression have been described and hypothesized to allow the progression into proviral latency. We hypothesized that exposing latently infected CD4+ T-cells to Tat would result in effective latency reversal. Our results indicate the capacity of a truncated Tat protein and mRNA to reactivate HIV-1 in latently infected T-cells ex vivo to a similar degree as the protein kinase C agonist: phorbol 12-myristate 13-acetate, without T-cell activation or any significant transcriptome perturbation.
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Affiliation(s)
- Ellen Van Gulck
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Erik Nijs
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Nick Verheyen
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Koen Dockx
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Christel Van Den Eynde
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Emilie Battivelli
- Janssen Infectious Diseases, A Division of Janssen Pharmaceutica NV, Brisbane, California, USA
| | - Jerel Vega
- Arcturus Therapeutics, Science Center Drive, San Diego, California, USA
| | | | - Brigitte Autran
- Faculty of Medicine Sorbonne-University, CIMI-Paris, UPMC/Inserm, Paris, France
| | - Nancie M. Archin
- University of North Carolina School of Medicine and UNC, HIV Cure Center, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- University of North Carolina School of Medicine and UNC, HIV Cure Center, Chapel Hill, North Carolina, USA
| | - Christine Katlama
- Department Infectious Diseases, Hospital Pitié Salpetière, Sorbonne-University and IPLESP, Paris, France
| | - Chiraz Hamimi
- Faculty of Medicine Sorbonne-University, CIMI-Paris, UPMC/Inserm, Paris, France
| | - Ilse Van Den Wyngaert
- Discovery Sciences, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Filmon Eyassu
- Discovery Sciences, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Daniel Boden
- Janssen Infectious Diseases, A Division of Janssen Pharmaceutica NV, Brisbane, California, USA
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11
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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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12
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Biondo M, Singh A, Caselle M, Osella M. Out-of-equilibrium gene expression fluctuations in the presence of extrinsic noise. Phys Biol 2023; 20:10.1088/1478-3975/acea4e. [PMID: 37489881 PMCID: PMC10680095 DOI: 10.1088/1478-3975/acea4e] [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: 03/13/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Cell-to-cell variability in protein concentrations is strongly affected by extrinsic noise, especially for highly expressed genes. Extrinsic noise can be due to fluctuations of several possible cellular factors connected to cell physiology and to the level of key enzymes in the expression process. However, how to identify the predominant sources of extrinsic noise in a biological system is still an open question. This work considers a general stochastic model of gene expression with extrinsic noise represented as fluctuations of the different model rates, and focuses on the out-of-equilibrium expression dynamics. Combining analytical calculations with stochastic simulations, we characterize how extrinsic noise shapes the protein variability during gene activation or inactivation, depending on the prevailing source of extrinsic variability, on its intensity and timescale. In particular, we show that qualitatively different noise profiles can be identified depending on which are the fluctuating parameters. This indicates an experimentally accessible way to pinpoint the dominant sources of extrinsic noise using time-coarse experiments.
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Affiliation(s)
- Marta Biondo
- Department of Physics, University of Turin and INFN, via P. Giuria 1, I-10125 Turin, Italy
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, Department of Biomedical Engineering, Department of Mathematical Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, United States of America
| | - Michele Caselle
- Department of Physics, University of Turin and INFN, via P. Giuria 1, I-10125 Turin, Italy
| | - Matteo Osella
- Department of Physics, University of Turin and INFN, via P. Giuria 1, I-10125 Turin, Italy
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13
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Enhanced Transcriptional Strength of HIV-1 Subtype C Minimizes Gene Expression Noise and Confers Stability to the Viral Latent State. J Virol 2023; 97:e0137622. [PMID: 36533949 PMCID: PMC9888270 DOI: 10.1128/jvi.01376-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Stochastic fluctuations in gene expression emanating from the HIV-1 long terminal repeat (LTR), amplified by the Tat positive feedback circuit, determine the choice between viral infection fates: active transcription (ON) or transcriptional silence (OFF). The emergence of several transcription factor binding site (TFBS) variant strains in HIV-1 subtype C (HIV-1C), especially those containing the duplication of the NF-κB motif, mandates the evaluation of the effect of enhanced transcriptional strength on gene expression noise and its influence on viral fate selection switch. Using a panel of subgenomic LTR-variant strains containing different copy numbers of the NF-κB motif (ranging from 0 to 4), we used flow cytometry, mRNA quantification, and pharmacological perturbations to demonstrate an inverse correlation between promoter strength and gene expression noise in Jurkat T cells and primary CD4+ T cells. The inverse correlation is consistent in clonal cell populations at constant intracellular concentrations of Tat and when NF-κB levels were regulated pharmacologically. Further, we show that strong LTRs containing at least two copies of the NF-κB motif in the enhancer establish a more stable latent state and demonstrate more rapid latency reversal than weak LTRs containing fewer motifs. We also demonstrate a cooperative binding of NF-κB to the motif cluster in HIV-1C LTRs containing two, three, or four NF-κB motifs (Hill coefficient [H] = 2.61, 3.56, and 3.75, respectively). The present work alludes to a possible evolution of the HIV-1C LTR toward gaining transcriptional strength associated with attenuated gene expression noise with implications for viral latency. IMPORTANCE Over the past two consecutive decades, HIV-1 subtype C (HIV-1C) has been undergoing directional evolution toward augmenting the transcriptional strength of the long terminal repeat (LTR) by adding more copies of the existing transcription factor binding site (TFBS) by sequence duplication. Additionally, the duplicated elements are genetically diverse, suggesting broader-range signal receptivity by variant LTRs. The HIV-1 promoter is inherently noisy, and the stochastic fluctuations in gene expression of variant LTRs may influence the active transcription (ON)/transcriptional silence (OFF) latency decisions. The evolving NF-κB motif variations of HIV-1C offer a powerful opportunity to examine how the transcriptional strength of the LTR might influence gene expression noise. Our work here shows that the augmented transcriptional strength of the HIV-1C LTR leads to concomitantly reduced gene expression noise, consequently leading to stabler latency maintenance and rapid latency reversal. The present work offers a novel lead toward appreciating the molecular mechanisms governing HIV-1 latency.
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14
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Whelan M, Pelchat M. Role of RNA Polymerase II Promoter-Proximal Pausing in Viral Transcription. Viruses 2022; 14:v14092029. [PMID: 36146833 PMCID: PMC9503719 DOI: 10.3390/v14092029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
The promoter-proximal pause induced by the binding of the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) to RNAP II is a key step in the regulation of metazoan gene expression. It helps maintain a permissive chromatin landscape and ensures a quick transcriptional response from stimulus-responsive pathways such as the innate immune response. It is also involved in the biology of several RNA viruses such as the human immunodeficiency virus (HIV), the influenza A virus (IAV) and the hepatitis delta virus (HDV). HIV uses the pause as one of its mechanisms to enter and maintain latency, leading to the creation of viral reservoirs resistant to antiretrovirals. IAV, on the other hand, uses the pause to acquire the capped primers necessary to initiate viral transcription through cap-snatching. Finally, the HDV RNA genome is transcribed directly by RNAP II and requires the small hepatitis delta antigen to displace NELF from the polymerase and overcome the transcriptional block caused by RNAP II promoter-proximal pausing. In this review, we will discuss the RNAP II promoter-proximal pause and the roles it plays in the life cycle of RNA viruses such as HIV, IAV and HDV.
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15
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Voortman L, Anderson C, Urban E, Yuan L, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston RJ. Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Dev Cell 2022; 57:1817-1832.e5. [PMID: 35835116 PMCID: PMC9378680 DOI: 10.1016/j.devcel.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). We investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. The ss locus is in a compact state in undifferentiated cells. An early enhancer drives transcription in all R7 precursors, and the locus opens. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact, and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives large-scale decompaction and then compaction represses transcription, controls stochastic fate specification.
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Affiliation(s)
- Lukas Voortman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Caitlin Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Urban
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Luorongxin Yuan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sang Tran
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Josh Derrick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Joseph Henry Laboratories of Physics, the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, 75015 Paris, France
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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16
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Loell K, Wu Y, Staller MV, Cohen B. Activation domains can decouple the mean and noise of gene expression. Cell Rep 2022; 40:111118. [PMID: 35858548 PMCID: PMC9912357 DOI: 10.1016/j.celrep.2022.111118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/18/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022] Open
Abstract
Regulatory mechanisms set a gene's average level of expression, but a gene's expression constantly fluctuates around that average. These stochastic fluctuations, or expression noise, play a role in cell-fate transitions, bet hedging in microbes, and the development of chemotherapeutic resistance in cancer. An outstanding question is what regulatory mechanisms contribute to noise. Here, we demonstrate that, for a fixed mean level of expression, strong activation domains (ADs) at low abundance produce high expression noise, while weak ADs at high abundance generate lower expression noise. We conclude that differences in noise can be explained by the interplay between a TF's nuclear concentration and the strength of its AD's effect on mean expression, without invoking differences between classes of ADs. These results raise the possibility of engineering gene expression noise independently of mean levels in synthetic biology contexts and provide a potential mechanism for natural selection to tune the noisiness of gene expression.
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Affiliation(s)
- Kaiser Loell
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA,The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Yawei Wu
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA,The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Max V. Staller
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Barak Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA.
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17
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Kim EH, Manganaro L, Schotsaert M, Brown BD, Mulder LC, Simon V. Development of an HIV reporter virus that identifies latently infected CD4 + T cells. CELL REPORTS METHODS 2022; 2:100238. [PMID: 35784650 PMCID: PMC9243624 DOI: 10.1016/j.crmeth.2022.100238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/26/2022] [Accepted: 05/24/2022] [Indexed: 04/23/2023]
Abstract
There is no cure for HIV infection, as the virus establishes a latent reservoir, which escapes highly active antiretroviral treatments. One major obstacle is the difficulty identifying cells that harbor latent proviruses. We devised a single-round viral vector that carries a series of versatile reporter molecules that are expressed in an LTR-dependent or LTR-independent manner and make it possible to accurately distinguish productive from latent infection. Using primary human CD4+ T cells, we show that transcriptionally silent proviruses are found in more than 50% of infected cells. The latently infected cells harbor proviruses but lack evidence for multiple spliced transcripts. LTR-silent integrations occurred to variable degrees in all CD4+ T subsets examined, with CD4+ TEM and CD4+ TREG displaying the highest frequency of latent infections. This viral vector permits the interrogation of HIV latency at single-cell resolution, revealing mechanisms of latency establishment and allowing the characterization of effective latency-reversing agents.
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Affiliation(s)
- Eun Hye Kim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lara Manganaro
- INGM, Istituto Nazionale di Genetica Molecolare, ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian D. Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lubbertus C.F. Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine at Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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18
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Ciechonska M, Sturrock M, Grob A, Larrouy-Maumus G, Shahrezaei V, Isalan M. Emergent expression of fitness-conferring genes by phenotypic selection. PNAS NEXUS 2022; 1:pgac069. [PMID: 36741458 PMCID: PMC9896880 DOI: 10.1093/pnasnexus/pgac069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/23/2022] [Indexed: 02/07/2023]
Abstract
Genotypic and phenotypic adaptation is the consequence of ongoing natural selection in populations and is key to predicting and preventing drug resistance. Whereas classic antibiotic persistence is all-or-nothing, here we demonstrate that an antibiotic resistance gene displays linear dose-responsive selection for increased expression in proportion to rising antibiotic concentration in growing Escherichia coli populations. Furthermore, we report the potentially wide-spread nature of this form of emergent gene expression (EGE) by instantaneous phenotypic selection process under bactericidal and bacteriostatic antibiotic treatment, as well as an amino acid synthesis pathway enzyme under a range of auxotrophic conditions. We propose an analogy to Ohm's law in electricity (V = IR), where selection pressure acts similarly to voltage (V), gene expression to current (I), and resistance (R) to cellular machinery constraints and costs. Lastly, mathematical modeling using agent-based models of stochastic gene expression in growing populations and Bayesian model selection reveal that the EGE mechanism requires variability in gene expression within an isogenic population, and a cellular "memory" from positive feedbacks between growth and expression of any fitness-conferring gene. Finally, we discuss the connection of the observed phenomenon to a previously described general fluctuation-response relationship in biology.
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Affiliation(s)
| | | | - Alice Grob
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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19
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Chaturvedi S, Pablo M, Wolf M, Rosas-Rivera D, Calia G, Kumar AJ, Vardi N, Du K, Glazier J, Ke R, Chan MF, Perelson AS, Weinberger LS. Disrupting autorepression circuitry generates "open-loop lethality" to yield escape-resistant antiviral agents. Cell 2022; 185:2086-2102.e22. [PMID: 35561685 PMCID: PMC9097017 DOI: 10.1016/j.cell.2022.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 03/01/2022] [Accepted: 04/14/2022] [Indexed: 12/27/2022]
Abstract
Across biological scales, gene-regulatory networks employ autorepression (negative feedback) to maintain homeostasis and minimize failure from aberrant expression. Here, we present a proof of concept that disrupting transcriptional negative feedback dysregulates viral gene expression to therapeutically inhibit replication and confers a high evolutionary barrier to resistance. We find that nucleic-acid decoys mimicking cis-regulatory sites act as "feedback disruptors," break homeostasis, and increase viral transcription factors to cytotoxic levels (termed "open-loop lethality"). Feedback disruptors against herpesviruses reduced viral replication >2-logs without activating innate immunity, showed sub-nM IC50, synergized with standard-of-care antivirals, and inhibited virus replication in mice. In contrast to approved antivirals where resistance rapidly emerged, no feedback-disruptor escape mutants evolved in long-term cultures. For SARS-CoV-2, disruption of a putative feedback circuit also generated open-loop lethality, reducing viral titers by >1-log. These results demonstrate that generating open-loop lethality, via negative-feedback disruption, may yield a class of antimicrobials with a high genetic barrier to resistance.
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Affiliation(s)
- Sonali Chaturvedi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA.
| | - Michael Pablo
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marie Wolf
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Daniel Rosas-Rivera
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Giuliana Calia
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Arjun J Kumar
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Noam Vardi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelvin Du
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joshua Glazier
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Matilda F Chan
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Leor S Weinberger
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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20
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Guo X, Tang T, Duan M, Zhang L, Ge H. The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation. iScience 2022; 25:104358. [PMID: 35620426 PMCID: PMC9127169 DOI: 10.1016/j.isci.2022.104358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/04/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022] Open
Abstract
Noise-modulating chemicals can synergize with transcriptional activators in reactivating latent HIV to eliminate latent HIV reservoirs. To understand the underlying biomolecular mechanism, we investigate a previous two-gene-state model and identify two necessary conditions for the synergy: an assumption of the inhibition effect of transcription activators on noise enhancers; and frequent transitions to the gene non-transcription-permissive state. We then develop a loop-four-gene-state model with Tat transcription/translation and find that drug synergy is mainly determined by the magnitude and direction of energy input into the genetic regulatory kinetics of the HIV promoter. The inhibition effect of transcription activators is actually a phenomenon of energy dissipation in the nonequilibrium gene transition system. Overall, the loop-four-state model demonstrates that energy dissipation plays a crucial role in HIV latency reactivation, which might be useful for improving drug effects and identifying other synergies on lentivirus latency reactivation. The inhibition of Activator on Noise enhancer is necessary for their synergy in reactivating HIV The drug synergy is a nonequilibrium phenomenon in the gene regulatory system The magnitude and direction of energy input determine the drug synergy This nonequilibrium mechanism is general without regarding molecular details
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21
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Mori L, Valente ST. Cure and Long-Term Remission Strategies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2407:391-428. [PMID: 34985678 DOI: 10.1007/978-1-0716-1871-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.
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Affiliation(s)
- Luisa Mori
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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22
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Monitoring reactivation of latent HIV by label-free gradient light interference microscopy. iScience 2021; 24:102940. [PMID: 34430819 PMCID: PMC8367845 DOI: 10.1016/j.isci.2021.102940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/24/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Human immunodeficiency virus (HIV) can infect cells and take a quiescent and nonexpressive state called latency. In this study, we report insights provided by label-free, gradient light interference microscopy (GLIM) about the changes in dry mass, diameter, and dry mass density associated with infected cells that occur upon reactivation. We discovered that the mean cell dry mass and mean diameter of latently infected cells treated with reactivating drug, TNF-α, are higher for latent cells that reactivate than those of the cells that did not reactivate. Cells with mean dry mass and diameter less than approximately 10 pg and 8 μm, respectively, remain exclusively in the latent state. Also, cells with mean dry mass greater than approximately 28-30 pg and mean diameter greater than 11–12 μm have a higher probability of reactivating. This study is significant as it presents a new label-free approach to quantify latent reactivation of a virus in single cells. GLIM imaging reveals differences between latent and reactivated HIV in JLat cells Cells with reactivated HIV have higher dry mass and diameter
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23
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Blanco A, Mahajan T, Coronado RA, Ma K, Demma DR, Dar RD. Synergistic Chromatin-Modifying Treatments Reactivate Latent HIV and Decrease Migration of Multiple Host-Cell Types. Viruses 2021; 13:v13061097. [PMID: 34201394 PMCID: PMC8228244 DOI: 10.3390/v13061097] [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: 04/19/2021] [Revised: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022] Open
Abstract
Upon infection of its host cell, human immunodeficiency virus (HIV) establishes a quiescent and non-productive state capable of spontaneous reactivation. Diverse cell types harboring the provirus form a latent reservoir, constituting a major obstacle to curing HIV. Here, we investigate the effects of latency reversal agents (LRAs) in an HIV-infected THP-1 monocyte cell line in vitro. We demonstrate that leading drug treatments synergize activation of the HIV long terminal repeat (LTR) promoter. We establish a latency model in THP-1 monocytes using a replication incompetent HIV reporter vector with functional Tat, and show that chromatin modifiers synergize with a potent transcriptional activator to enhance HIV reactivation, similar to T-cells. Furthermore, leading reactivation cocktails are shown to differentially affect latency reactivation and surface expression of chemokine receptor type 4 (CXCR4), leading to altered host cell migration. This study investigates the effect of chromatin-modifying LRA treatments on HIV latent reactivation and cell migration in monocytes. As previously reported in T-cells, epigenetic mechanisms in monocytes contribute to controlling the relationship between latent reactivation and cell migration. Ultimately, advanced “Shock and Kill” therapy needs to successfully target and account for all host cell types represented in a complex and composite latency milieu.
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Affiliation(s)
- Alexandra Blanco
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.B.); (T.M.); (R.A.C.); (K.M.); (D.R.D.)
| | - Tarun Mahajan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.B.); (T.M.); (R.A.C.); (K.M.); (D.R.D.)
| | - Robert A. Coronado
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.B.); (T.M.); (R.A.C.); (K.M.); (D.R.D.)
| | - Kelly Ma
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.B.); (T.M.); (R.A.C.); (K.M.); (D.R.D.)
| | - Dominic R. Demma
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.B.); (T.M.); (R.A.C.); (K.M.); (D.R.D.)
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (A.B.); (T.M.); (R.A.C.); (K.M.); (D.R.D.)
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: ; Tel.: +1-(217)-265-0708
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Lu Y, Singh H, Singh A, Dar RD. A transient heritable memory regulates HIV reactivation from latency. iScience 2021; 24:102291. [PMID: 33889814 PMCID: PMC8050369 DOI: 10.1016/j.isci.2021.102291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/04/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
Reactivation of human immunodeficiency virus 1 (HIV-1) from latently infected T cells is a critical barrier to cure patients. It remains unknown whether reactivation of individual latent cells occurs stochastically in response to latency reversal agents (LRAs) or is a deterministic outcome of an underlying cell state. To characterize these single-cell responses, we leverage the classical Luria-Delbrück fluctuation test where single cells are isolated from a clonal population and exposed to LRAs after colony expansion. Data show considerable colony-to-colony fluctuations with the fraction of reactivating cells following a skewed distribution. Modeling systematic measurements of fluctuations over time uncovers a transient heritable memory that regulates HIV-1 reactivation, where single cells are in an LRA-responsive state for a few weeks before switching back to an irresponsive state. These results have enormous implications for designing therapies to purge the latent reservoir and further utilize fluctuation-based assays to uncover hidden transient cellular states underlying phenotypic heterogeneity.
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Affiliation(s)
- Yiyang Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Harpal Singh
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
- Corresponding author
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
- Corresponding author
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Abstract
Strategies to stabilize and suppress the latent cell reservoir of HIV have been proposed and need to be carefully examined. We demonstrate the use of time-lapse fluorescence microscopy to quantify HIV gene-expression dynamics and detect several latency-promoting agents (LPAs) that would be overlooked when screening for mean gene expression alone. These LPAs are structurally and functionally related to inhibitors of the thioredoxin/thioredoxin reductase redox pathway, which has been suggested as a promising HIV target. Some LPAs are Food and Drug Administration–approved and commercially available and can expand the currently limited LPA repertoire. This study provides a foundation to research suppression mechanisms of HIV gene expression, alternative latency-promoting therapies, and ultimately remove the need for antiretroviral therapy in patients. Upon treatment removal, spontaneous reactivation of latently infected T cells remains a major barrier toward curing HIV. Therapies that reactivate and clear the latent reservoir are only partially effective, while latency-promoting agents (LPAs) used to suppress reactivation and stabilize latency are understudied and lack diversity in their mechanisms of action. Here, we identify additional LPAs using a screen for gene-expression fluctuations (or “noise”) that drive cell-fate specification and control HIV reactivation from latency. Single-cell protein dynamics of a minimal HIV gene circuit were monitored with time-lapse fluorescence microscopy. We screened 1,806 drugs, out of which 279 modulate noise magnitude or half autocorrelation time. Next, we tested the strongest noise modulators in a Jurkat T cell latency model and discovered three LPAs that would be overlooked by quantifying their mean expression levels alone. The LPAs reduced reactivation of latency in both Jurkat and primary cell models when challenged by synergistic and potent combinations of HIV activators. The two strongest LPAs, NSC 401005 and NSC 400938, are structurally and functionally related to inhibitors of thioredoxin reductase, a protein involved in maintaining redox balance in host cells. Experiments with multiple functional analogs revealed two additional LPAs, PX12 and tiopronin, and suggest a potential LPA family, within which some are commercially available and Food and Drug Administration–approved. The LPAs presented here may provide new strategies to complement antiretroviral treatments. Screening for gene expression noise holds the potential for drug discovery in other diseases.
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A Stronger Transcription Regulatory Circuit of HIV-1C Drives the Rapid Establishment of Latency with Implications for the Direct Involvement of Tat. J Virol 2020; 94:JVI.00503-20. [PMID: 32669338 DOI: 10.1128/jvi.00503-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
The magnitude of transcription factor binding site variation emerging in HIV-1 subtype C (HIV-1C), especially the addition of NF-κB motifs by sequence duplication, makes the examination of transcriptional silence challenging. How can HIV-1 establish and maintain latency despite having a strong long terminal repeat (LTR)? We constructed panels of subgenomic reporter viral vectors with varying copy numbers of NF-κB motifs (0 to 4 copies) and examined the profile of latency establishment in Jurkat cells. Surprisingly, we found that the stronger the viral promoter, the faster the latency establishment. Importantly, at the time of commitment to latency and subsequent points, Tat levels in the cell were not limiting. Using highly sensitive strategies, we demonstrate the presence of Tat in the latent cell, recruited to the latent LTR. Our data allude, for the first time, to Tat establishing a negative feedback loop during the late phases of viral infection, leading to the rapid silencing of the viral promoter.IMPORTANCE Over the past 10 to 15 years, HIV-1 subtype C (HIV-1C) has been evolving rapidly toward gaining stronger transcriptional activity by sequence duplication of major transcription factor binding sites. The duplication of NF-κB motifs is unique and exclusive to HIV-1C, a property not shared with any of the other eight HIV-1 genetic families. What mechanism(s) does HIV-1C employ to establish and maintain transcriptional silence despite the presence of a strong promoter and concomitant strong, positive transcriptional feedback is the primary question that we attempted to address in the present manuscript. The role that Tat plays in latency reversal is well established. Our work with the most common HIV-1 subtype, HIV-1C, offers crucial leads toward Tat possessing a dual role in serving as both a transcriptional activator and repressor at different phases of viral infection of the cell. The leads that we offer through the present work have significant implications for HIV-1 cure research.
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Li Y, Lv Z, Zhang S, Wang Z, He L, Tang M, Pu W, Zhao H, Zhang Z, Shi Q, Cai D, Wu M, Hu G, Lui KO, Feng J, Nieto MA, Zhou B. Genetic Fate Mapping of Transient Cell Fate Reveals N-Cadherin Activity and Function in Tumor Metastasis. Dev Cell 2020; 54:593-607.e5. [PMID: 32668208 DOI: 10.1016/j.devcel.2020.06.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/26/2020] [Accepted: 06/16/2020] [Indexed: 01/06/2023]
Abstract
Genetic lineage tracing unravels cell fate and plasticity in development, tissue homeostasis, and diseases. However, it remains technically challenging to trace temporary or transient cell fate, such as epithelial-to-mesenchymal transition (EMT) in tumor metastasis. Here, we generated a genetic fate-mapping system for temporally seamless tracing of transient cell fate. Highlighting its immediate application, we used it to study EMT gene activity from the local primary tumor to a distant metastatic site in vivo. In a spontaneous breast-to-lung metastasis model, we found that primary tumor cells activated vimentin and N-cadherin in situ, but only N-cadherin was activated and functionally required during metastasis. Tumor cells that have ever expressed N-cadherin constituted the majority of metastases in lungs, and functional deletion of N-cad significantly reduced metastasis. The seamless genetic recording system described here provides an alternative way for understanding transient cell fate and plasticity in biological processes.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zan Lv
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shaohua Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhuo Wang
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, 201100, Shanghai, China
| | - Lingjuan He
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Muxue Tang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenjuan Pu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huan Zhao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhenqian Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qihui Shi
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, 201100, Shanghai, China
| | - Dongqing Cai
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China
| | - Mingfu Wu
- Center for Cardiovascular Sciences, Albany Medical College, Albany, NY 12208, USA
| | - Guohong Hu
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR 999077, China
| | - Jing Feng
- Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai 201400, China
| | - M Angela Nieto
- Institute de Neurociencias CSIC-UMH, Avda. Ramon y Cajal s/n, 03550 San Juan de Alicante, Spain
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou 510632, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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28
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Chaturvedi S, Engel R, Weinberger L. The HSV-1 ICP4 Transcriptional Auto-Repression Circuit Functions as a Transcriptional "Accelerator" Circuit. Front Cell Infect Microbiol 2020; 10:265. [PMID: 32670890 PMCID: PMC7326776 DOI: 10.3389/fcimb.2020.00265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022] Open
Abstract
Herpes simplex virus-1 (HSV-1) is a significant human pathogen. Upon infection, HSV-1 expresses its immediate early (IE) genes, and the IE transcription factor ICP4 (infectious cell protein-4) plays a pivotal role in initiating the downstream gene-expression cascade. Using live-cell time-lapse fluorescence microscopy, flow cytometry, qPCR, and chromatin immunoprecipitation, we quantitatively monitored the expression of ICP4 in individual cells after infection. We find that extrinsic stimuli can accelerate ICP4 kinetics without increasing ICP4 protein or mRNA levels. The accelerated ICP4 kinetics-despite unchanged steady-state ICP4 protein or mRNA level-correlate with increased HSV-1 replicative fitness. Hence, the kinetics of ICP4 functionally mirror the kinetics of the human herpesvirus cytomegalovirus IE2 "accelerator" circuit, indicating that IE accelerator circuitry is shared among the alpha and beta herpesviruses. We speculate that this circuit motif is a common evolutionary countermeasure to throttle IE expression and thereby minimize the inherent cytotoxicity of these obligate viral transactivators.
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Affiliation(s)
- Sonali Chaturvedi
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Center for Cell Circuitry, University of California, San Francisco, San Francisco, CA, United States
| | - Ruth Engel
- Gladstone Center for Cell Circuitry, University of California, San Francisco, San Francisco, CA, United States
| | - Leor Weinberger
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, San Francisco, CA, United States
- Gladstone Center for Cell Circuitry, University of California, San Francisco, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
- Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
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29
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Bohn-Wippert K, Dar RD. Cell size dependent migration of T-cells latently infected with HIV. ACTA ACUST UNITED AC 2020; 2:1-10. [PMID: 32457938 DOI: 10.36069/jols/20200301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human immunodeficiency virus (HIV) preferentially infects T-lymphocytes by integrating into host DNA and forming a latent transcriptionally silent provirus. As previously shown, HIV-1 alters migration modes of T-lymphocytes by co-regulating viral gene expression with human C-X-C chemokine receptor-4 (CXCR4). Here, we show that motility of infected T-lymphocytes is cell size dependent. In cell migration assays, migrating cells are consistently larger than non-migrating cells. This effect is drug-treatment independent. The cell size dependent motility observed in a previously generated Jurkat latency model correlates with the motility of primary human CD4+ T-cells containing a modified HIV-1 full-length construct JLatd2GFP. In addition, large migrating T-cells, latently infected with HIV, show a slightly decreased rate of reactivation from latency. these results demonstrate that HIV reactivation is cell migration-dependent, where host cell size acts as a catalyst for altered migration velocity. We believe that host cell size controlled migration uncovers an additional mechanism of cellular controlled viral fate determination important for virus dissemination and reactivation from latency. This observation may provide more insights into viral-host interactions regulating cell migration and reactivation from latency and helps in the design and implementation of novel therapeutic strategies.
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Affiliation(s)
- Kathrin Bohn-Wippert
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Roy D Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206W Gregory Drive, Urbana, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA.,Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 306 North Wright St, Urbana, Illinois 61801, USA
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Bohn-Wippert K, Tevonian EN, Lu Y, Huang MY, Megaridis MR, Dar RD. Cell Size-Based Decision-Making of a Viral Gene Circuit. Cell Rep 2019; 25:3844-3857.e5. [PMID: 30590053 PMCID: PMC7050911 DOI: 10.1016/j.celrep.2018.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/23/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Latently infected T cells able to reinitiate viral propagation throughout the body remain a major barrier to curing HIV. Distinguishing between latently infected cells and uninfected cells will advance efforts for viral eradication. HIV decision-making between latency and active replication is stochastic, and drug cocktails that increase bursts of viral gene expression enhance reactivation from latency. Here, we show that a larger host-cell size provides a natural cellular mechanism for enhancing burst size of viral expression and is necessary to destabilize the latent state and bias viral decision-making. Latently infected Jurkat and primary CD4+ T cells reactivate exclusively in larger activated cells, while smaller cells remain silent. In addition, reactivation is cell-cycle dependent and can be modulated with cell-cycle-arresting compounds. Cell size and cell-cycle dependent decision-making of viral circuits may guide stochastic design strategies and applications in synthetic biology and may provide important determinants to advance diagnostics and therapies. Bohn-Wippert et al. investigate reactivation of T cells latently infected with HIV. They discover that only larger cells exit latency, while smaller cells remain silent. Viral expression bursts are cell size and cell-cycle dependent, presenting dynamic cell states, capable of active control, as sources of viral fate determination.
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Affiliation(s)
- Kathrin Bohn-Wippert
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Erin N Tevonian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Yiyang Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Meng-Yao Huang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | - Melina R Megaridis
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA
| | - Roy D Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 321 Everitt Laboratory, 1406 West Green Street, Urbana, IL 61801, USA; Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 306 North Wright St, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA.
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31
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Guillemin A, Duchesne R, Crauste F, Gonin-Giraud S, Gandrillon O. Drugs modulating stochastic gene expression affect the erythroid differentiation process. PLoS One 2019; 14:e0225166. [PMID: 31751364 PMCID: PMC6872177 DOI: 10.1371/journal.pone.0225166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022] Open
Abstract
To better understand the mechanisms behind cells decision-making to differentiate, we assessed the influence of stochastic gene expression (SGE) modulation on the erythroid differentiation process. It has been suggested that stochastic gene expression has a role in cell fate decision-making which is revealed by single-cell analyses but studies dedicated to demonstrate the consistency of this link are still lacking. Recent observations showed that SGE significantly increased during differentiation and a few showed that an increase of the level of SGE is accompanied by an increase in the differentiation process. However, a consistent relation in both increasing and decreasing directions has never been shown in the same cellular system. Such demonstration would require to be able to experimentally manipulate simultaneously the level of SGE and cell differentiation in order to observe if cell behavior matches with the current theory. We identified three drugs that modulate SGE in primary erythroid progenitor cells. Both Artemisinin and Indomethacin decreased SGE and reduced the amount of differentiated cells. On the contrary, a third component called MB-3 simultaneously increased the level of SGE and the amount of differentiated cells. We then used a dynamical modelling approach which confirmed that differentiation rates were indeed affected by the drug treatment. Using single-cell analysis and modeling tools, we provide experimental evidence that, in a physiologically relevant cellular system, SGE is linked to differentiation.
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Affiliation(s)
- Anissa Guillemin
- Laboratoire de biologie et modélisation de la cellule. LBMC - Ecole Normale Supérieure - Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique: UMR5239, Institut National de la Santé et de la Recherche Médicale: U1210 - Ecole Normale Supérieure de Lyon 46 allée d’Italie 69007 Lyon, France
| | - Ronan Duchesne
- Laboratoire de biologie et modélisation de la cellule. LBMC - Ecole Normale Supérieure - Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique: UMR5239, Institut National de la Santé et de la Recherche Médicale: U1210 - Ecole Normale Supérieure de Lyon 46 allée d’Italie 69007 Lyon, France
- Inria Dracula, Villeurbanne, France
| | - Fabien Crauste
- Inria Dracula, Villeurbanne, France
- Univ. Bordeaux, CNRS, Bordeaux INP, IMB, UMR 5251, F-33400, Talence, France
| | - Sandrine Gonin-Giraud
- Laboratoire de biologie et modélisation de la cellule. LBMC - Ecole Normale Supérieure - Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique: UMR5239, Institut National de la Santé et de la Recherche Médicale: U1210 - Ecole Normale Supérieure de Lyon 46 allée d’Italie 69007 Lyon, France
| | - Olivier Gandrillon
- Laboratoire de biologie et modélisation de la cellule. LBMC - Ecole Normale Supérieure - Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique: UMR5239, Institut National de la Santé et de la Recherche Médicale: U1210 - Ecole Normale Supérieure de Lyon 46 allée d’Italie 69007 Lyon, France
- Inria Dracula, Villeurbanne, France
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32
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Zhao L, Liu M, Ouyang J, Zhu Z, Geng W, Dong J, Xiong Y, Wang S, Zhang X, Qiao Y, Ding H, Sun H, Liang G, Shang H, Han X. The Per-1 Short Isoform Inhibits de novo HIV-1 Transcription in Resting CD4+ T-cells. Curr HIV Res 2019; 16:384-395. [PMID: 30774045 PMCID: PMC6446521 DOI: 10.2174/1570162x17666190218145048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/02/2019] [Accepted: 02/11/2019] [Indexed: 12/24/2022]
Abstract
Background: Understanding of the restriction of HIV-1 transcription in resting CD4+ T-cells is critical to find a cure for AIDS. Although many negative factors causing HIV-1 transcription blockage in resting CD4+ T-cells have been found, there are still unknown mechanisms to explore. Objective: To explore the mechanism for the suppression of de novo HIV-1 transcription in resting CD4+ T-cells. Methods: In this study, a short isoform of Per-1 expression plasmid was transfected into 293T cells with or without Tat's presence to identify Per-1 as a negative regulator for HIV-1 transcription. Silenc-ing of Per-1 was conducted in resting CD4+ T-cells or monocyte-derived macrophages (MDMs) to evaluate the antiviral activity of Per-1. Additionally, we analyzed the correlation between Per-1 expres-sion and viral loads in vivo, and silenced Per-1 by siRNA technology to investigate the potential anti-HIV-1 roles of Per-1 in vivo in untreated HIV-1-infected individuals. Results: We found that short isoform Per-1 can restrict HIV-1 replication and Tat ameliorates this in-hibitory effect. Silencing of Per-1 could upregulate HIV-1 transcription both in resting CD4+ T-cells and MDMs. Moreover, Per-1 expression is inversely correlated with viral loads in Rapid progressors (RPs) in vivo. Conclusion: These data together suggest that Per-1 is a novel negative regulator of HIV-1 transcrip-tion. This restrictive activity of Per-1 to HIV-1 replication may contribute to HIV-1 latency in resting CD4+ T-cells.
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Affiliation(s)
- Li Zhao
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Mei Liu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Jiayue Ouyang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Zheming Zhu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Wenqing Geng
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Jinxiu Dong
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Ying Xiong
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Shumei Wang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Xiaowei Zhang
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Ying Qiao
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Haibo Ding
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Hong Sun
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Guoxin Liang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Hong Shang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, Shenyang, China
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33
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Song S, Yang GS, Park SJ, Hong S, Kim JH, Sung J. Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics. PLoS Comput Biol 2019; 15:e1007356. [PMID: 31525182 PMCID: PMC6762214 DOI: 10.1371/journal.pcbi.1007356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/26/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022] Open
Abstract
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically, and the frequency spectrum of this chemical fluctuation carries valuable information about the dynamics of the reactions creating these biomolecules. Recent advances in single-cell techniques enable direct monitoring of the time-traces of the protein number in each cell; however, it is not yet clear how the stochastic dynamics of these time-traces is related to the reaction mechanism and dynamics. Here, we derive a rigorous relation between the frequency-spectrum of the product number fluctuation and the reaction mechanism and dynamics, starting from a generalized master equation. This relation enables us to analyze the time-traces of the protein number and extract information about dynamics of mRNA number and transcriptional regulation, which cannot be directly observed by current experimental techniques. We demonstrate our frequency spectrum analysis of protein number fluctuation, using the gene network model of luciferase expression under the control of the Bmal 1a promoter in mouse fibroblast cells. We also discuss how the dynamic heterogeneity of transcription and translation rates affects the frequency-spectra of the mRNA and protein number.
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Affiliation(s)
- Sanggeun Song
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
| | - Gil-Suk Yang
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
| | - Seong Jun Park
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
| | - Sungguan Hong
- Department of Chemistry, Chung-Ang University, Seoul, Korea
- * E-mail: (SH); (JHK); (JS)
| | - Ji-Hyun Kim
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- * E-mail: (SH); (JHK); (JS)
| | - Jaeyoung Sung
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
- * E-mail: (SH); (JHK); (JS)
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Hansen MMK, Weinberger LS. Post-Transcriptional Noise Control. Bioessays 2019; 41:e1900044. [PMID: 31222776 PMCID: PMC6637019 DOI: 10.1002/bies.201900044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/22/2019] [Indexed: 01/01/2023]
Abstract
Recent evidence indicates that transcriptional bursts are intrinsically amplified by messenger RNA cytoplasmic processing to generate large stochastic fluctuations in protein levels. These fluctuations can be exploited by cells to enable probabilistic bet-hedging decisions. But large fluctuations in gene expression can also destabilize cell-fate commitment. Thus, it is unclear if cells temporally switch from high to low noise, and what mechanisms enable this switch. Here, the discovery of a post-transcriptional mechanism that attenuates noise in HIV is reviewed. Early in its life cycle, HIV amplifies transcriptional fluctuations to probabilistically select alternate fates, whereas at late times, HIV utilizes a post-transcriptional feedback mechanism to commit to a specific fate. Reanalyzing various reported post-transcriptional negative feedback architectures reveals that they attenuate noise more efficiently than classic transcriptional autorepression, leading to the derivation of an assay to detect post-transcriptional motifs. It is hypothesized that coupling transcriptional and post-transcriptional autoregulation enables efficient temporal noise control to benefit developmental bet-hedging decisions.
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Affiliation(s)
- Maike M. K. Hansen
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Leor S. Weinberger
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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35
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Urban EA, Johnston RJ. Buffering and Amplifying Transcriptional Noise During Cell Fate Specification. Front Genet 2018; 9:591. [PMID: 30555516 PMCID: PMC6282114 DOI: 10.3389/fgene.2018.00591] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022] Open
Abstract
The molecular processes that drive gene transcription are inherently noisy. This noise often manifests in the form of transcriptional bursts, producing fluctuations in gene activity over time. During cell fate specification, this noise is often buffered to ensure reproducible developmental outcomes. However, sometimes noise is utilized as a “bet-hedging” mechanism to diversify functional roles across a population of cells. Studies of bacteria, yeast, and cultured cells have provided insights into the nature and roles of noise in transcription, yet we are only beginning to understand the mechanisms by which noise influences the development of multicellular organisms. Here we discuss the sources of transcriptional noise and the mechanisms that either buffer noise to drive reproducible fate choices or amplify noise to randomly specify fates.
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Affiliation(s)
- Elizabeth A Urban
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
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36
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Probabilistic control of HIV latency and transactivation by the Tat gene circuit. Proc Natl Acad Sci U S A 2018; 115:12453-12458. [PMID: 30455316 DOI: 10.1073/pnas.1811195115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The reservoir of HIV latently infected cells is the major obstacle for eradication of HIV infection. The "shock-and-kill" strategy proposed earlier aims to reduce the reservoir by activating cells out of latency. While the intracellular HIV Tat gene circuit is known to play important roles in controlling latency and its transactivation in HIV-infected cells, the detailed control mechanisms are not well understood. Here we study the mechanism of probabilistic control of the latent and the transactivated cell phenotypes of HIV-infected cells. We reconstructed the probability landscape, which is the probability distribution of the Tat gene circuit states, by directly computing the exact solution of the underlying chemical master equation. Results show that the Tat circuit exhibits a clear bimodal probability landscape (i.e., there are two distinct probability peaks, one associated with the latent cell phenotype and the other with the transactivated cell phenotype). We explore potential modifications to reactions in the Tat gene circuit for more effective transactivation of latent cells (i.e., the shock-and-kill strategy). Our results suggest that enhancing Tat acetylation can dramatically increase Tat and viral production, while increasing the Tat-transactivation response binding affinity can transactivate latent cells more rapidly than other manipulations. Our results further explored the "block and lock" strategy toward a functional cure for HIV. Overall, our study demonstrates a general approach toward discovery of effective therapeutic strategies and druggable targets by examining control mechanisms of cell phenotype switching via exactly computed probability landscapes of reaction networks.
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37
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Ke R, Conway JM, Margolis DM, Perelson AS. Determinants of the efficacy of HIV latency-reversing agents and implications for drug and treatment design. JCI Insight 2018; 3:123052. [PMID: 30333308 DOI: 10.1172/jci.insight.123052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/30/2018] [Indexed: 11/17/2022] Open
Abstract
HIV eradication studies have focused on developing latency-reversing agents (LRAs). However, it is not understood how the rate of latent reservoir reduction is affected by different steps in the process of latency reversal. Furthermore, as current LRAs are host-directed, LRA treatment is likely to be intermittent to avoid host toxicities. Few careful studies of the serial effects of pulsatile LRA treatment have yet been done. This lack of clarity makes it difficult to evaluate the efficacy of candidate LRAs or predict long-term treatment outcomes. We constructed a mathematical model that describes the dynamics of latently infected cells under LRA treatment. Model analysis showed that, in addition to increasing the immune recognition and clearance of infected cells, the duration of HIV antigen expression (i.e., the period of vulnerability) plays an important role in determining the efficacy of LRAs, especially if effective clearance is achieved. Patients may benefit from pulsatile LRA exposures compared with continuous LRA exposures if the period of vulnerability is long and the clearance rate is high, both in the presence and absence of an LRA. Overall, the model framework serves as a useful tool to evaluate the efficacy and the rational design of LRAs and combination strategies.
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Affiliation(s)
- Ruian Ke
- Department of Mathematics, North Carolina State University, Raleigh, North Carolina, USA.,Theoretical Biology and Biophysics Group, MS-K710, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Jessica M Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania, USA
| | - David M Margolis
- University of North Carolina (UNC) HIV Cure Center, UNC Institute of Global Health and Infectious Diseases.,Departments of Medicine, Microbiology and Immunology, UNC Chapel Hill School of Medicine, and.,Department of Epidemiology, UNC Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, MS-K710, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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38
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Vardi N, Chaturvedi S, Weinberger LS. Feedback-mediated signal conversion promotes viral fitness. Proc Natl Acad Sci U S A 2018; 115:E8803-E8810. [PMID: 30150412 PMCID: PMC6140503 DOI: 10.1073/pnas.1802905115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A fundamental signal-processing problem is how biological systems maintain phenotypic states (i.e., canalization) long after degradation of initial catalyst signals. For example, to efficiently replicate, herpesviruses (e.g., human cytomegalovirus, HCMV) rapidly counteract cell-mediated silencing using transactivators packaged in the tegument of the infecting virion particle. However, the activity of these tegument transactivators is inherently transient-they undergo immediate proteolysis but delayed synthesis-and how transient activation sustains lytic viral gene expression despite cell-mediated silencing is unclear. By constructing a two-color, conditional-feedback HCMV mutant, we find that positive feedback in HCMV's immediate-early 1 (IE1) protein is of sufficient strength to sustain HCMV lytic expression. Single-cell time-lapse imaging and mathematical modeling show that IE1 positive feedback converts transient transactivation signals from tegument pp71 proteins into sustained lytic expression, which is obligate for efficient viral replication, whereas attenuating feedback decreases fitness by promoting a reversible silenced state. Together, these results identify a regulatory mechanism enabling herpesviruses to sustain expression despite transient activation signals-akin to early electronic transistors-and expose a potential target for therapeutic intervention.
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Affiliation(s)
- Noam Vardi
- Gladstone-University of California, San Francisco (UCSF) Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158
| | - Sonali Chaturvedi
- Gladstone-University of California, San Francisco (UCSF) Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158
| | - Leor S Weinberger
- Gladstone-University of California, San Francisco (UCSF) Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158;
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
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39
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Kessing CF, Nixon CC, Li C, Tsai P, Takata H, Mousseau G, Ho PT, Honeycutt JB, Fallahi M, Trautmann L, Garcia JV, Valente ST. In Vivo Suppression of HIV Rebound by Didehydro-Cortistatin A, a "Block-and-Lock" Strategy for HIV-1 Treatment. Cell Rep 2018; 21:600-611. [PMID: 29045830 DOI: 10.1016/j.celrep.2017.09.080] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/05/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022] Open
Abstract
HIV-1 Tat activates viral transcription and limited Tat transactivation correlates with latency establishment. We postulated a "block-and-lock" functional cure approach based on properties of the Tat inhibitor didehydro-Cortistatin A (dCA). HIV-1 transcriptional inhibitors could block ongoing viremia during antiretroviral therapy (ART), locking the HIV promoter in persistent latency. We investigated this hypothesis in human CD4+ T cells isolated from aviremic individuals. Combining dCA with ART accelerates HIV-1 suppression and prevents viral rebound after treatment interruption, even during strong cellular activation. We show that dCA mediates epigenetic silencing by increasing nucleosomal occupancy at Nucleosome-1, restricting RNAPII recruitment to the HIV-1 promoter. The efficacy of dCA was studied in the bone marrow-liver-thymus (BLT) mouse model of HIV latency and persistence. Adding dCA to ART-suppressed mice systemically reduces viral mRNA in tissues. Moreover, dCA significantly delays and reduces viral rebound levels upon treatment interruption. Altogether, this work demonstrates the potential of block-and-lock cure strategies.
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Affiliation(s)
- Cari F Kessing
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Christopher C Nixon
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, School of Medicine, Chapel Hill, NC, USA
| | - Chuan Li
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Perry Tsai
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, School of Medicine, Chapel Hill, NC, USA
| | - Hiroshi Takata
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Guillaume Mousseau
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Phong T Ho
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, School of Medicine, Chapel Hill, NC, USA
| | - Jenna B Honeycutt
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, School of Medicine, Chapel Hill, NC, USA
| | - Mohammad Fallahi
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Lydie Trautmann
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - J Victor Garcia
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, School of Medicine, Chapel Hill, NC, USA.
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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40
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The Pathway To Establishing HIV Latency Is Critical to How Latency Is Maintained and Reversed. J Virol 2018; 92:JVI.02225-17. [PMID: 29643247 DOI: 10.1128/jvi.02225-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 01/09/2023] Open
Abstract
HIV infection requires lifelong antiretroviral therapy because of the persistence of latently infected CD4+ T cells. The induction of virus expression from latently infected cells occurs following T cell receptor (TCR) activation, but not all latently infected cells respond to TCR stimulation. We compared two models of latently infected cells using an enhanced green fluorescent protein (EGFP) reporter virus to infect CCL19-treated resting CD4+ (rCD4+) T cells (preactivation latency) or activated CD4+ T cells that returned to a resting state (postactivation latency). We isolated latently infected cells by sorting for EGFP-negative (EGFP-) cells after infection. These cells were cultured with antivirals and stimulated with anti-CD3/anti-CD28, mitogens, and latency-reversing agents (LRAs) and cocultured with monocytes and anti-CD3. Spontaneous EGFP expression was more frequent in postactivation than in preactivation latency. Stimulation of latently infected cells with monocytes/anti-CD3 resulted in an increase in EGFP expression compared to that for unstimulated controls using the preactivation latency model but led to a reduction in EGFP expression in the postactivation latency model. The reduced EGFP expression was not associated with reductions in the levels of viral DNA or T cell proliferation but depended on direct contact between monocytes and T cells. Monocytes added to the postactivation latency model during the establishment of latency reduced spontaneous virus expression, suggesting that monocyte-T cell interactions at an early time point postinfection can maintain HIV latency. This direct comparison of pre- and postactivation latency suggests that effective strategies needed to reverse latency will depend on how latency is established.IMPORTANCE One strategy being evaluated to eliminate latently infected cells that persist in HIV-infected individuals on antiretroviral therapy (ART) is to activate HIV expression or production with the goal of inducing virus-mediated cytolysis or immune-mediated clearance of infected cells. The gold standard for the activation of latent virus is T cell receptor stimulation with anti-CD3/anti-CD28. However, this stimulus activates only a small proportion of latently infected cells. We show clear differences in the responses of latently infected cells to activating stimuli based on how latent infection is established, an observation that may potentially explain the persistence of noninduced intact proviruses in HIV-infected individuals on ART.
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41
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Dar RD, Weiss R. Perspective: Engineering noise in biological systems towards predictive stochastic design. APL Bioeng 2018; 2:020901. [PMID: 31069294 PMCID: PMC6481707 DOI: 10.1063/1.5025033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/16/2018] [Indexed: 01/24/2023] Open
Abstract
Significant progress has been made towards engineering both single-cell and multi-cellular systems through a combination of synthetic and systems biology, nanobiotechnology, pharmaceutical science, and computational approaches. However, our ability to engineer systems that begin to approach the complexity of natural pathways is severely limited by important challenges, e.g. due to noise, or the fluctuations in gene expression and molecular species at multiple scales (e.g. both intra- and inter-cellular fluctuations). This barrier to engineering requires that biological noise be recognized as a design element with fundamentals that can be actively controlled. Here we highlight studies of an emerging discipline that collectively strives to engineer noise towards predictive stochastic design using interdisciplinary approaches at multiple-scales in diverse living systems.
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Affiliation(s)
- Roy D. Dar
- Author to whom correspondence should be addressed:
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42
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Norred SE, Caveney PM, Chauhan G, Collier LK, Collier CP, Abel SM, Simpson ML. Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns. ACS Synth Biol 2018; 7:1251-1258. [PMID: 29687993 DOI: 10.1021/acssynbio.8b00139] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent superresolution microscopy studies in E. coli demonstrate that the cytoplasm has highly variable local concentrations where macromolecular crowding plays a central role in establishing membrane-less compartmentalization. This spatial inhomogeneity significantly influences molecular transport and association processes central to gene expression. Yet, little is known about how macromolecular crowding influences gene expression bursting-the episodic process where mRNA and proteins are produced in bursts. Here, we simultaneously measured mRNA and protein reporters in cell-free systems, showing that macromolecular crowding decoupled the well-known relationship between fluctuations in the protein population (noise) and mRNA population statistics. Crowded environments led to a 10-fold increase in protein noise even though there were only modest changes in the mRNA population and fluctuations. Instead, cell-like macromolecular crowding created an inhomogeneous spatial distribution of mRNA ("spatial noise") that led to large variability in the protein production burst size. As a result, the mRNA spatial noise created large temporal fluctuations in the protein population. These results highlight the interplay between macromolecular crowding, spatial inhomogeneities, and the resulting dynamics of gene expression, and provide insights into using these organizational principles in both cell-based and cell-free synthetic biology.
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Affiliation(s)
- S Elizabeth Norred
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee Knoxville and Oak Ridge National Laboratory , Knoxville , Tennessee 37996 , United States
| | - Patrick M Caveney
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee Knoxville and Oak Ridge National Laboratory , Knoxville , Tennessee 37996 , United States
| | - Gaurav Chauhan
- Chemical and Biomolecular Engineering Department , University of Tennessee Knoxville , Knoxville , Tennessee 37996 , United States
| | - Lauren K Collier
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Steven M Abel
- Chemical and Biomolecular Engineering Department , University of Tennessee Knoxville , Knoxville , Tennessee 37996 , United States
| | - Michael L Simpson
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee Knoxville and Oak Ridge National Laboratory , Knoxville , Tennessee 37996 , United States
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43
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Hansen MMK, Wen WY, Ingerman E, Razooky BS, Thompson CE, Dar RD, Chin CW, Simpson ML, Weinberger LS. A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization. Cell 2018; 173:1609-1621.e15. [PMID: 29754821 PMCID: PMC6044448 DOI: 10.1016/j.cell.2018.04.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/19/2018] [Accepted: 04/03/2018] [Indexed: 11/25/2022]
Abstract
Diverse biological systems utilize fluctuations ("noise") in gene expression to drive lineage-commitment decisions. However, once a commitment is made, noise becomes detrimental to reliable function, and the mechanisms enabling post-commitment noise suppression are unclear. Here, we find that architectural constraints on noise suppression are overcome to stabilize fate commitment. Using single-molecule and time-lapse imaging, we find that-after a noise-driven event-human immunodeficiency virus (HIV) strongly attenuates expression noise through a non-transcriptional negative-feedback circuit. Feedback is established through a serial cascade of post-transcriptional splicing, whereby proteins generated from spliced mRNAs auto-deplete their own precursor unspliced mRNAs. Strikingly, this auto-depletion circuitry minimizes noise to stabilize HIV's commitment decision, and a noise-suppression molecule promotes stabilization. This feedback mechanism for noise suppression suggests a functional role for delayed splicing in other systems and may represent a generalizable architecture of diverse homeostatic signaling circuits.
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Affiliation(s)
- Maike M K Hansen
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Winnie Y Wen
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elena Ingerman
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Brandon S Razooky
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Cassandra E Thompson
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Roy D Dar
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Charles W Chin
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Michael L Simpson
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Leor S Weinberger
- Gladstone
- UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
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44
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Megaridis MR, Lu Y, Tevonian EN, Junger KM, Moy JM, Bohn-Wippert K, Dar RD. Fine-tuning of noise in gene expression with nucleosome remodeling. APL Bioeng 2018; 2:026106. [PMID: 31069303 PMCID: PMC6481717 DOI: 10.1063/1.5021183] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 03/16/2018] [Indexed: 01/08/2023] Open
Abstract
Engineering stochastic fluctuations of gene expression (or “noise”) is integral to precisely bias cellular-fate decisions and statistical phenotypes in both single-cell and multi-cellular systems. Epigenetic regulation has been shown to constitute a large source of noise, and thus, engineering stochasticity is deeply intertwined with epigenetics. Here, utilizing chromatin remodeling, we report that Caffeic acid phenethyl ester (CA) and Pyrimethamine (PYR), two inhibitors of BAF250a, a subunit of the Brahma-associated factor (BAF) nucleosome remodeling complex, enable differential and tunable control of noise in transcription and translation from the human immunodeficiency virus long terminal repeat promoter in a dose and time-dependent manner. CA conserves noise levels while increasing mean abundance, resulting in direct tuning of the transcriptional burst size, while PYR strictly increases transcriptional initiation frequency while conserving a constant transcriptional burst size. Time-dependent treatment with CA reveals non-continuous tuning with noise oscillating at a constant mean abundance at early time points and the burst size increasing for treatments after 5 h. Treatments combining CA and Protein Kinase C agonists result in an even larger increase of abundance while conserving noise levels with a highly non-linear increase in variance of up to 63× untreated controls. Finally, drug combinations provide non-antagonistic combinatorial tuning of gene expression noise and map a noise phase space for future applications with viral and synthetic gene vectors. Active remodeling of nucleosomes and BAF-mediated control of gene expression noise expand a toolbox for the future design and engineering of stochasticity in living systems.
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Affiliation(s)
- Melina R Megaridis
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yiyang Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Erin N Tevonian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kendall M Junger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jennifer M Moy
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kathrin Bohn-Wippert
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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45
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Khazaei B, Sartakhti JS, Manshaei MH, Zhu Q, Sadeghi M, Mousavi SR. HIV-1-infected T-cells dynamics and prognosis: An evolutionary game model. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2017; 152:1-14. [PMID: 29054249 DOI: 10.1016/j.cmpb.2017.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 07/01/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND OBJECTIVE Understanding the dynamics of human immunodeficiency virus (HIV) is essential for depicting, developing, and investigating effective treatment strategies. HIV infects several types of immune cells, but its main target is to destroy helper T-cells. In the lymph nodes, the infected T-cells interact with each other and their environment to obtain more resources. According to infectivity and replicative capacity of T-cells in the HIV infection process, they can be divided into four phenotypes. Although genetic mutations in the reverse transcription that beget these phenotypes are random, the framework by which a phenotype become favored is affected by the environment and neighboring phenotypes. Moreover, the HIV disease has all components of an evolutionary process, including replication, mutation, and selection. METHODS We propose a novel structure-based game-theoretic model for the evolution of HIV-1-Infected CD4+T-cells and invasion of the immune system. We discuss the theoretical basis of the stable equilibrium states of the evolutionary dynamics of four T-cells types as well as its significant results to understand and control HIV infection. The results include the importance of genetic variations and the process of establishing evolutionary dynamics of the virus quasispecies. RESULTS Our results show that there is a direct dependency between some parameters such as mutation rates and the stability of equilibrium states in the HIV infection. This is an interesting result because these parameters can be changed by some pharmacotherapies and alternative treatments. Our model indicates that in an appropriate treatment the relative frequency of the wild type of virus quasispecies can be decreased in the population. Consequently, this can cause delaying the emergence of the AIDS phase. To assess the model, we investigate two new treatments for HIV. The results show that our model can predict the treatment results. CONCLUSIONS The paper shows that a structured-based evolutionary game theory can model the evolutionary dynamics of the infected T-cells and virus quasispecies. The model predicts certain aspects of the HIV infection process under several treatments.
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Affiliation(s)
- Bahareh Khazaei
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | | | - Mohammad Hossein Manshaei
- Department of Electrical and Computer Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran.
| | - Quanyan Zhu
- Department of Electrical and Computer Engineering, Polytechnic School of Engineering, New York University, NY, USA
| | - Mehdi Sadeghi
- National Institute of Genetic Engineering and Biotechnology and the School of Biological Sciences, Institute for Research in Fundamental Sciences, Tehran, Iran
| | - Seyed Rasoul Mousavi
- Computer Engineering Department, Amirkabir University of Technology and the Institute for Research in Fundamental Sciences, Tehran, Iran
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Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS. Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean. PLoS Biol 2017; 15:e2000841. [PMID: 29045398 PMCID: PMC5646755 DOI: 10.1371/journal.pbio.2000841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/19/2017] [Indexed: 12/28/2022] Open
Abstract
Fundamental to biological decision-making is the ability to generate bimodal expression patterns where 2 alternate expression states simultaneously exist. Here, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV's fate decision between active replication and viral latency. We find that the HIV transactivator of transcription (Tat) protein manipulates the intrinsic toggling of HIV's promoter, the long terminal repeat (LTR), to generate bimodal ON-OFF expression and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality. This result holds for both minimal synthetic viral circuits and full-length virus. Strikingly, computational analysis indicates that the Tat circuit's noncooperative "nonlatching" feedback architecture is optimized to slow the promoter's toggling and generate bimodality by stochastic extinction of Tat. In contrast to the standard Poisson model, theory and experiment show that nonlatching positive feedback substantially dampens the inverse noise-mean relationship to maintain stochastic bimodality despite increasing mean expression levels. Given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression appears consistent with the hypothesis that HIV's decision between active replication and latency provides a viral fitness advantage. More broadly, the results suggest that positive-feedback circuits may have evolved not only for signal amplification but also for robustly generating bimodality by decoupling expression fluctuations (noise) from mean expression levels.
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Affiliation(s)
- Brandon S. Razooky
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
- The Gladstone Institutes (Virology and Immunology), San Francisco, California, United States of America
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, California, United Sates of America
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Youfang Cao
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Maike M. K. Hansen
- The Gladstone Institutes (Virology and Immunology), San Francisco, California, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Michael L. Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (MLS); (LSW)
| | - Leor S. Weinberger
- The Gladstone Institutes (Virology and Immunology), San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
- QB3: California Institute of Quantitative Biosciences, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (MLS); (LSW)
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Abstract
Current antivirals effectively target diverse viruses at various stages of their life cycles. Nevertheless, curative therapy has remained elusive for important pathogens, such as human immunodeficiency virus type 1 (HIV-1) and herpesviruses, in large part due to viral latency and the evolution of resistance to existing therapies. Here, we review the discovery of viral master circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression programs (i.e., between active, latent, and abortive fates). These circuits offer the opportunity for a new class of antivirals that could lead to intrinsic combination-antiviral therapies within a single molecule-evolutionary escape from such circuit-disrupting antivirals would require simultaneous evolution of both the viral cis regulatory element (e.g., the DNA-binding site) and the trans element (e.g., the transcription factor) in order for the virus to recapitulate a circuit that would not be disrupted. We review the architectures of these fate-regulating master circuits in HIV-1 and the human herpesvirus cytomegalovirus along with potential circuit-disruption strategies that may ultimately enable escape-resistant antiviral therapies.
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Affiliation(s)
- Anand Pai
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158;
| | - Leor S Weinberger
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158; .,Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
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Li Q, Xue X, Li W, Wang Q, Han L, Brunson T, Xu W, Chambers-Harris I, Wang Q, Li X, Ma L, Song Q. Heterogeneous DNA methylation status in same-cell subpopulations of ovarian cancer tissues. Tumour Biol 2017; 39:1010428317701650. [PMID: 28618935 DOI: 10.1177/1010428317701650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This study aims to explore the heterogeneous DNA methylation differences between individual single ovarian cancer cells isolated from the same formalin-fixed and paraffin-embedded human ovarian cancer tissue. Single cells were isolated by laser microdissection. Whole genome amplification and polymerase chain reaction purification were performed on the converted genomic DNA. Target primers designed for checking DNA methylation were used in polymerase chain reaction reactions to amplify special fragments. Sequencing was performed to analyze the heterogeneous DNA methylation statuses of different single ovarian cancer cells. Three of nine single human ovarian cancer cells showed positive bands (33.3%) on separating gel. The methylated and unmethylated CpGs were shown at the same loci in different single cells. We show heterogeneous DNA methylation statuses in same-cell subpopulations.
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Affiliation(s)
- Qiling Li
- 1 Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xue Xue
- 1 Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wenzhi Li
- 2 Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA
| | - Qi Wang
- 1 Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Lu Han
- 1 Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Tiffany Brunson
- 2 Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA
| | - Wei Xu
- 2 Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA
| | | | - Qing Wang
- 1 Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Xu Li
- 1 Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Li Ma
- 2 Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA
| | - Qing Song
- 1 Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China.,2 Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA
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Carja O, Plotkin JB. The evolutionary advantage of heritable phenotypic heterogeneity. Sci Rep 2017; 7:5090. [PMID: 28698577 PMCID: PMC5505965 DOI: 10.1038/s41598-017-05214-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 05/25/2017] [Indexed: 11/13/2022] Open
Abstract
Phenotypic plasticity is an evolutionary driving force in diverse biological processes, including the adaptive immune system, the development of neoplasms, and the persistence of pathogens despite drug pressure. It is essential, therefore, to understand the evolutionary advantage of an allele that confers on cells the ability to express a range of phenotypes. Here, we study the fate of a new mutation that allows the expression of multiple phenotypic states, introduced into a finite population of individuals that can express only a single phenotype. We show that the advantage of such a mutation depends on the degree of phenotypic heritability between generations, called phenotypic memory. We analyze the fixation probability of the phenotypically plastic allele as a function of phenotypic memory, the variance of expressible phenotypes, the rate of environmental changes, and the population size. We find that the fate of a phenotypically plastic allele depends fundamentally on the environmental regime. In constant environments, plastic alleles are advantageous and their fixation probability increases with the degree of phenotypic memory. In periodically fluctuating environments, by contrast, there is an optimum phenotypic memory that maximizes the probability of the plastic allele's fixation. This same optimum memory also maximizes geometric mean fitness, in steady state. We interpret these results in the context of previous studies in an infinite-population framework. We also discuss the implications of our results for the design of therapies that can overcome persistence and, indirectly, drug resistance.
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Affiliation(s)
- Oana Carja
- Department of Biology, University of Pennsylvania, Philadelphia, 19104, USA.
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, 19104, USA
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