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Oliveira BC, Bari S, Melenhorst JJ. Leveraging Vector-Based Gene Disruptions to Enhance CAR T-Cell Effectiveness. Cancers (Basel) 2025; 17:383. [PMID: 39941752 PMCID: PMC11815729 DOI: 10.3390/cancers17030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 01/21/2025] [Accepted: 01/21/2025] [Indexed: 02/16/2025] Open
Abstract
Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy represents a breakthrough in the treatment of relapsed and refractory B-cell malignancies, such as chronic lymphocytic leukemia (CLL), inducing long-term, sometimes curative, responses. However, fewer than 30% of CLL patients achieve such outcomes. It has been shown that a smaller subset of T cells capable of expansion and persistence is crucial for treatment effectiveness. Notably, a pre-existing mutation in the epigenetic regulator TET2, combined with CAR vector-induced disruption of the other intact allele, significantly enhanced the potency of the CAR-engineered T-cell clone in one CLL patient. This finding aligns with independent research, suggesting that the CAR gene's genomic insertion site influences tumor-targeting capability. Thus, it is plausible that vector-induced gene disruptions affect CAR T-cell function. This review synthesizes existing knowledge on vector integration into the host genome and its impact on clinical outcomes in CAR T-cell therapy patients. Our aim is to inform the development of improved therapies and enhance their overall efficacy.
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Affiliation(s)
| | | | - J. Joseph Melenhorst
- Cell Therapy & Immuno-Engineering Program, Center for Immunotherapy and Precision Immuno-Oncology, Lerner College of Medicine, Cleveland Clinic, Cleveland, OH 44016, USA; (B.C.O.); (S.B.)
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2
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Zorina A, Zorin V, Isaev A, Kudlay D, Manturova N, Ustugov A, Kopnin P. Current Status of Biomedical Products for Gene and Cell Therapy of Recessive Dystrophic Epidermolysis Bullosa. Int J Mol Sci 2024; 25:10270. [PMID: 39408598 PMCID: PMC11476579 DOI: 10.3390/ijms251910270] [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: 07/30/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 10/20/2024] Open
Abstract
This detailed review describes innovative strategies and current products for gene and cell therapy at different stages of research and development to treat recessive dystrophic epidermolysis bullosa (RDEB) which is associated with the functional deficiency of collagen type VII alpha 1 (C7) caused by defects in the COL7A1 gene. The use of allogenic mesenchymal stem/stromal cells, which can be injected intradermally and intravenously, appears to be the most promising approach in the field of RDEB cell therapy. Injections of genetically modified autologous dermal fibroblasts are also worth mentioning under this framework. The most common methods of RDEB gene therapy are gene replacement using viral vectors and gene editing using programmable nucleases. Ex vivo epidermal transplants (ETs) based on autologous keratinocytes (Ks) have been developed using gene therapy methods; one such ET successively passed phase III clinical trials. Products based on the use of two-layer transplants have also been developed with both types of skin cells producing C7. Gene products have also been developed for local use. To date, significant progress has been achieved in the development of efficient biomedical products to treat RDEB, one of the most severe hereditary diseases.
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Affiliation(s)
- Alla Zorina
- Artgen Biotech, Moscow 119333, Russia; (A.Z.)
- Skincell LLC, Moscow 119333, Russia
| | - Vadim Zorin
- Artgen Biotech, Moscow 119333, Russia; (A.Z.)
- Skincell LLC, Moscow 119333, Russia
| | - Artur Isaev
- Artgen Biotech, Moscow 119333, Russia; (A.Z.)
| | - Dmitry Kudlay
- Department of Pharmacology, The I. M. Sechenov First Moscow State Medical University (The Sechenov University), Moscow 119991, Russia
- Department of Pharmacognosy and Industrial Pharmacy, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Natalia Manturova
- Department of Plastic and Reconstructive surgery, Cosmetology and Cell Technologies, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- JSC Plastic Surgery and Cosmetology Institute, Moscow 125047, Russia
| | - Andrei Ustugov
- Department of Plastic and Reconstructive surgery, Cosmetology and Cell Technologies, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- JSC Plastic Surgery and Cosmetology Institute, Moscow 125047, Russia
| | - Pavel Kopnin
- Scientific Research Institute of Carcinogenesis, N. N. Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia
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3
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Duggan NN, Dragic T, Chanda SK, Pache L. Breaking the Silence: Regulation of HIV Transcription and Latency on the Road to a Cure. Viruses 2023; 15:2435. [PMID: 38140676 PMCID: PMC10747579 DOI: 10.3390/v15122435] [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: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Antiretroviral therapy (ART) has brought the HIV/AIDS epidemic under control, but a curative strategy for viral eradication is still needed. The cessation of ART results in rapid viral rebound from latently infected CD4+ T cells, showing that control of viral replication alone does not fully restore immune function, nor does it eradicate viral reservoirs. With a better understanding of factors and mechanisms that promote viral latency, current approaches are primarily focused on the permanent silencing of latently infected cells ("block and lock") or reactivating HIV-1 gene expression in latently infected cells, in combination with immune restoration strategies to eliminate HIV infected cells from the host ("shock and kill"). In this review, we provide a summary of the current, most promising approaches for HIV-1 cure strategies, including an analysis of both latency-promoting agents (LPA) and latency-reversing agents (LRA) that have shown promise in vitro, ex vivo, and in human clinical trials to reduce the HIV-1 reservoir.
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Affiliation(s)
- Natasha N. Duggan
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Tatjana Dragic
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Sumit K. Chanda
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Lars Pache
- NCI Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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4
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Nasiri F, Muhammadnejad S, Rahbarizadeh F. Effects of polybrene and retronectin as transduction enhancers on the development and phenotypic characteristics of VHH-based CD19-redirected CAR T cells: a comparative investigation. Clin Exp Med 2023; 23:2535-2549. [PMID: 36434173 DOI: 10.1007/s10238-022-00928-8] [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: 06/04/2022] [Accepted: 10/15/2022] [Indexed: 11/26/2022]
Abstract
Chimeric antigen receptor T cells (CAR T cells) have improved the prognosis of patients with certain hematologic malignancies. However, broader clinical application of this type of therapy is dependent on production protocols. We characterized VHH-based CD19-redirected CAR T cells generated using the transduction enhancers (TEs) polybrene or retronectin. The proliferation rate of activated T cells transduced using polybrene concentrations > 6 mg/mL decreased compared with untreated group. There was a direct relationship between polybrene concentration and transduction efficacy. Moreover, we demonstrated the proliferation of retronectin-transduced T cells increased in a dose-dependent manner (4-20 μg/mL). Whereas, different retronectin concentrations did not mediate a significant increase in T cell transduction rate. Moreover, lentiviral transduction rate was also dependent on the concentration of lentiviruses. At optimized TE concentrations, multiplicity of infection (MOI) of > 10 decreased living T cell transduction rate. Additionally, we demonstrated that CAR T cell phenotype is highly affected by TE type. Naïve T cell differentiation to central memory T cell was observed in the beginning of the expansion process and effector memory T cells became the predominant subset in the second week of expansion. Importantly, retronectin increased the proliferation of CAR T cells alongside medicating higher transduction rates, resulting in more naïve and central memory T cells. We demonstrated that a higher percentage of CAR T cells were generated using retronectin (with a less differentiated phenotype) making retronectin a more effective TE than polybrene for long-term CAR T cell processing in preclinical or clinical studies.
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Affiliation(s)
- Fatemeh Nasiri
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box: 14115-331, Tehran, Iran
| | - Samad Muhammadnejad
- Gene Therapy Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box: 14115-331, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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5
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Couto PS, Stibbs DJ, Rotondi MC, Takeuchi Y, Rafiq QA. Scalable manufacturing of gene-modified human mesenchymal stromal cells with microcarriers in spinner flasks. Appl Microbiol Biotechnol 2023; 107:5669-5685. [PMID: 37470820 PMCID: PMC10439856 DOI: 10.1007/s00253-023-12634-w] [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: 02/06/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 07/21/2023]
Abstract
Due to their immunomodulatory properties and in vitro differentiation ability, human mesenchymal stromal cells (hMSCs) have been investigated in more than 1000 clinical trials over the last decade. Multiple studies that have explored the development of gene-modified hMSC-based products are now reaching early stages of clinical trial programmes. From an engineering perspective, the challenge lies in developing manufacturing methods capable of producing sufficient doses of ex vivo gene-modified hMSCs for clinical applications. This work demonstrates, for the first time, a scalable manufacturing process using a microcarrier-bioreactor system for the expansion of gene-modified hMSCs. Upon isolation, umbilical cord tissue mesenchymal stromal cells (UCT-hMSCs) were transduced using a lentiviral vector (LV) with green fluorescent protein (GFP) or vascular endothelial growth factor (VEGF) transgenes. The cells were then seeded in 100 mL spinner flasks using Spherecol microcarriers and expanded for seven days. After six days in culture, both non-transduced and transduced cell populations attained comparable maximum cell concentrations (≈1.8 × 105 cell/mL). Analysis of the culture supernatant identified that glucose was fully depleted after day five across the cell populations. Lactate concentrations observed throughout the culture reached a maximum of 7.5 mM on day seven. Immunophenotype analysis revealed that the transduction followed by an expansion step was not responsible for the downregulation of the cell surface receptors used to identify hMSCs. The levels of CD73, CD90, and CD105 expressing cells were above 90% for the non-transduced and transduced cells. In addition, the expression of negative markers (CD11b, CD19, CD34, CD45, and HLA-DR) was also shown to be below 5%, which is aligned with the criteria established for hMSCs by the International Society for Cell and Gene Therapy (ISCT). This work provides a foundation for the scalable manufacturing of gene-modified hMSCs which will overcome a significant translational and commercial bottleneck. KEY POINTS: • hMSCs were successfully transduced by lentiviral vectors carrying two different transgenes: GFP and VEGF • Transduced hMSCs were successfully expanded on microcarriers using spinner flasks during a period of 7 days • The genetic modification step did not cause any detrimental impact on the hMSC immunophenotype characteristics.
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Affiliation(s)
- Pedro Silva Couto
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT UK
| | - Dale J. Stibbs
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT UK
| | - Marco C. Rotondi
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT UK
| | - Yasuhiro Takeuchi
- Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT UK
- Biotherapeutics and Advanced Therapies, Scientific Research and Innovation, Medicines, and Healthcare Products Regulatory Agency, South Mimms, EN6 3QG UK
| | - Qasim A. Rafiq
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT UK
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6
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Tang PZ, Ding B, Reyes C, Papp D, Potter J. Target-seq: single workflow for detection of genome integration site, DNA translocation and off-target events. Biotechniques 2023. [PMID: 37161298 DOI: 10.2144/btn-2023-0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Designed donor DNA delivery through viral or nonviral systems to target loci in the host genome is a critical step for gene therapy. Adeno-associated virus and lentivirus are leading vehicles for in vivo and ex vivo delivery of therapeutic genes due to their high delivery and editing efficiency. Nonviral editing tools, such as CRISPR/Cas9, are getting more attention for gene modification. However, there are safety concerns; for example, tumorigenesis due to off-target effects and DNA rearrangement. Analysis tools to detect and characterize on-target and off-target genome modification post editing in the host genome are pivotal for evaluating the success and safety of gene therapy. We developed Target-seq combined with different analysis tools to detect the genome integration site, DNA translocation and off-target events.
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Affiliation(s)
| | - Bo Ding
- Thermo Fisher Scientific, Inc., MA, USA
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7
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Boehm D, Lam V, Schnolzer M, Ott M. The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11. Cell Rep 2023; 42:112234. [PMID: 36897778 PMCID: PMC10124996 DOI: 10.1016/j.celrep.2023.112234] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/22/2022] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
A successful HIV-1 cure strategy may require enhancing HIV-1 latency to silence HIV-1 transcription. Modulators of gene expression show promise as latency-promoting agents in vitro and in vivo. Here, we identify Su(var)3-9, enhancer-of-zeste, and trithorax (SET) and myeloid, Nervy, and DEAF-1 (MYND) domain-containing protein 5 (SMYD5) as a host factor required for HIV-1 transcription. SMYD5 is expressed in CD4+ T cells and activates the HIV-1 promoter with or without the viral Tat protein, while knockdown of SMYD5 decreases HIV-1 transcription in cell lines and primary T cells. SMYD5 associates in vivo with the HIV-1 promoter and binds the HIV trans-activation response (TAR) element RNA and Tat. Tat is methylated by SMYD5 in vitro, and in cells expressing Tat, SMYD5 protein levels are increased. The latter requires expression of the Tat cofactor and ubiquitin-specific peptidase 11 (USP11). We propose that SMYD5 is a host activator of HIV-1 transcription stabilized by Tat and USP11 and, together with USP11, a possible target for latency-promoting therapy.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Victor Lam
- Tetrad Graduate Program, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martina Schnolzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Melanie Ott
- Gladstone Institute of Virology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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8
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Chameettachal A, Mustafa F, Rizvi TA. Understanding Retroviral Life Cycle and its Genomic RNA Packaging. J Mol Biol 2023; 435:167924. [PMID: 36535429 DOI: 10.1016/j.jmb.2022.167924] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Members of the family Retroviridae are important animal and human pathogens. Being obligate parasites, their replication involves a series of steps during which the virus hijacks the cellular machinery. Additionally, many of the steps of retrovirus replication are unique among viruses, including reverse transcription, integration, and specific packaging of their genomic RNA (gRNA) as a dimer. Progress in retrovirology has helped identify several molecular mechanisms involved in each of these steps, but many are still unknown or remain controversial. This review summarizes our present understanding of the molecular mechanisms involved in various stages of retrovirus replication. Furthermore, it provides a comprehensive analysis of our current understanding of how different retroviruses package their gRNA into the assembling virions. RNA packaging in retroviruses holds a special interest because of the uniqueness of packaging a dimeric genome. Dimerization and packaging are highly regulated and interlinked events, critical for the virus to decide whether its unspliced RNA will be packaged as a "genome" or translated into proteins. Finally, some of the outstanding areas of exploration in the field of RNA packaging are highlighted, such as the role of epitranscriptomics, heterogeneity of transcript start sites, and the necessity of functional polyA sequences. An in-depth knowledge of mechanisms that interplay between viral and cellular factors during virus replication is critical in understanding not only the virus life cycle, but also its pathogenesis, and development of new antiretroviral compounds, vaccines, as well as retroviral-based vectors for human gene therapy.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates. https://twitter.com/chameettachal
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
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9
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Pais G, Spinozzi G, Cesana D, Benedicenti F, Albertini A, Bernardo ME, Gentner B, Montini E, Calabria A. ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications. Brief Bioinform 2023; 24:bbac551. [PMID: 36545803 PMCID: PMC9910212 DOI: 10.1093/bib/bbac551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Longitudinal clonal tracking studies based on high-throughput sequencing technologies supported safety and long-term efficacy and unraveled hematopoietic reconstitution in many gene therapy applications with unprecedented resolution. However, monitoring patients over a decade-long follow-up entails a constant increase of large data volume with the emergence of critical computational challenges, unfortunately not addressed by currently available tools. Here we present ISAnalytics, a new R package for comprehensive and high-throughput clonal tracking studies using vector integration sites as markers of cellular identity. Once identified the clones externally from ISAnalytics and imported in the package, a wide range of implemented functionalities are available to users for assessing the safety and long-term efficacy of the treatment, here described in a clinical trial use case for Hurler disease, and for supporting hematopoietic stem cell biology in vivo with longitudinal analysis of clones over time, proliferation and differentiation. ISAnalytics is conceived to be metadata-driven, enabling users to focus on biological questions and hypotheses rather than on computational aspects. ISAnalytics can be fully integrated within laboratory workflows and standard procedures. Moreover, ISAnalytics is designed with efficient and scalable data structures, benchmarked with previous methods, and grants reproducibility and full analytical control through interactive web-reports and a module with Shiny interface. The implemented functionalities are flexible for all viral vector-based clonal tracking applications as well as genetic barcoding or cancer immunotherapies.
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Affiliation(s)
- Giulia Pais
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Giulio Spinozzi
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Daniela Cesana
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Fabrizio Benedicenti
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Alessandra Albertini
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Maria Ester Bernardo
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
- IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Bernhard Gentner
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Eugenio Montini
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Andrea Calabria
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
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10
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Solomon M, Liang C. Pseudotyped Viruses for Retroviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1407:61-84. [PMID: 36920692 DOI: 10.1007/978-981-99-0113-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Since the discovery of retroviruses, their genome and replication strategies have been extensively studied, leading to the discovery of several unique features that make them invaluable vectors for virus pseudotyping, gene delivery, and gene therapy. Notably, retroviral vectors enable the integration of a gene of interest into the host genome, they can be used to stably transduce both dividing and nondividing cells, and they can deliver relatively large genes. Today, retroviral vectors are commonly used for many research applications and have become an active tool in gene therapy and clinical trials. This chapter will discuss the important features of the retroviral genome and replication cycle that are crucial for the development of retroviral vectors, the different retrovirus-based vector systems that are commonly used, and finally the research and clinical applications of retroviral vectors.
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Affiliation(s)
- Magan Solomon
- Lady Davis Institute, Jewish General Hospital, McGill Centre for Viral Diseases, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Chen Liang
- Lady Davis Institute, Jewish General Hospital, McGill Centre for Viral Diseases, Montreal, QC, Canada. .,Department of Medicine, McGill University, Montreal, QC, Canada.
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11
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Pellaers E, Bhat A, Christ F, Debyser Z. Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection. Viruses 2022; 15:32. [PMID: 36680071 PMCID: PMC9861059 DOI: 10.3390/v15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.
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Affiliation(s)
| | | | | | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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12
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Suleman S, Payne A, Bowden J, Haque SA, Zahn M, Fawaz S, Khalifa MS, Jobling S, Hay D, Franco M, Fronza R, Wang W, Strobel-Freidekind O, Deichmann A, Takeuchi Y, Waddington SN, Gil-Farina I, Schmidt M, Themis M. HIV- 1 lentivirus tethering to the genome is associated with transcription factor binding sites found in genes that favour virus survival. Gene Ther 2022; 29:720-729. [PMID: 35513551 PMCID: PMC9750860 DOI: 10.1038/s41434-022-00335-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 01/09/2023]
Abstract
Lentiviral vectors (LV) are attractive for permanent and effective gene therapy. However, integration into the host genome can cause insertional mutagenesis highlighting the importance of understanding of LV integration. Insertion site (IS) tethering is believed to involve cellular proteins such as PSIP1/LEDGF/p75, which binds to the virus pre-integration complexes (PICs) helping to target the virus genome. Transcription factors (TF) that bind both the vector LTR and host genome are also suspected influential to this. To determine the role of TF in the tethering process, we mapped predicted transcription factor binding sites (pTFBS) near to IS chosen by HIV-1 LV using a narrow 20 bp window in infected human induced pluripotent stem cells (iPSCs) and their hepatocyte-like cell (HLC) derivatives. We then aligned the pTFBS with these sequences found in the LTRs of native and self-inactivated LTRs. We found significant enrichment of these sequences for pTFBS essential to HIV-1 life cycle and virus survival. These same sites also appear in HIV-1 patient IS and in mice infected with HIV-1 based LV. This in silco data analysis suggests pTFBS present in the virus LTR and IS sites selected by HIV-1 LV are important to virus survival and propagation.
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Affiliation(s)
- Saqlain Suleman
- Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
- Testavec Ltd, Queensgate House, Maidenhead, UK
| | - Annette Payne
- Testavec Ltd, Queensgate House, Maidenhead, UK
- Department of Computer Science, College of Engineering Design and Physical Sciences, Brunel University London, Uxbridge, UK
| | - Johnathan Bowden
- Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Sharmin Al Haque
- Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Marco Zahn
- Genewerk GmbH, Heidelberg, Germany
- University Heidelberg, Medical Faculty, Heidelberg, Germany
| | - Serena Fawaz
- Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Mohammad S Khalifa
- Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Susan Jobling
- Testavec Ltd, Queensgate House, Maidenhead, UK
- Institute of Environment, Health and Societies, College of Business, Arts and Social Sciences, Brunel University London, Uxbridge, UK
| | - David Hay
- Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | | | | | - Wei Wang
- Genewerk GmbH, Heidelberg, Germany
| | | | | | - Yasuhiro Takeuchi
- Division of Infection and Immunity, University College London, London, UK
- Division of Advanced Therapies, National Institute for Biological Standards and Control, Potters Bar, UK
| | - Simon N Waddington
- Gene Transfer Technology, EGA Institute for Women's Health, University College London, London, UK
- MRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | | | - Manfred Schmidt
- Genewerk GmbH, Heidelberg, Germany
- Department of Translational Oncology, NCT and DKFZ, Heidelberg, Germany
| | - Michael Themis
- Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK.
- Division of Ecology and Evolution, Department of Life Sciences, Imperial College London, London, UK.
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13
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Visualization of clonal expansion after massive depletion of cells carrying the bovine leukemia virus (BLV) integration sites during the course of disease progression in a BLV naturally-infected cow: a case report. Retrovirology 2022; 19:24. [PMID: 36329491 PMCID: PMC9635170 DOI: 10.1186/s12977-022-00609-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022] Open
Abstract
Bovine leukemia virus (BLV) infects cattle, integrates into host DNA as a provirus, and induces malignant B-cell lymphoma. Previous studies have addressed the impact of proviral integration of BLV on BLV-induced leukemogenesis. However, no studies have monitored sequential changes in integration sites in which naturally infected BLV individuals progress from the premalignant stage to the terminal disease. Here, we collected blood samples from a single, naturally infected Holstein cow at three disease progression stages (Stage I: polyclonal stage, Stage II: polyclonal toward oligoclonal stage, Stage III: oligoclonal stage) and successfully visualized the kinetics of clonal expansion of cells carrying BLV integration sites using our BLV proviral DNA-capture sequencing method. Although 24 integration sites were detected in Stages I and II, 92% of these sites experienced massive depletion in Stage III. Of these sites, 46%, 37%, and 17% were located within introns of Refseq genes, intergenic regions, and repetitive sequences, respectively. At Stage III cattle with lymphoma, only two integration sites were generated de novo in the intergenic region of Chr1, and the intron of the CHEK2 gene on Chr17 was significantly increased. Our results are the first to demonstrate clonal expansion after the massive depletion of cells carrying BLV integration sites in a naturally infected cow.
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14
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BET-Independent Murine Leukemia Virus Integration Is Retargeted
In Vivo
and Selects Distinct Genomic Elements for Lymphomagenesis. Microbiol Spectr 2022; 10:e0147822. [PMID: 35852337 PMCID: PMC9431007 DOI: 10.1128/spectrum.01478-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Moloney murine leukemia virus (MLV) infects BALB/c mice and induces T-cell lymphoma in mice. Retroviral integration is mediated by the interaction of the MLV integrase (IN) with members of the bromodomain and extraterminal motif (BET) protein family (BRD2, BRD3, and BRD4). The introduction of the W390A mutation into MLV IN abolishes the BET interaction. Here, we compared the replication of W390A MLV to that of wild-type (WT) MLV in adult BALB/c mice to study the role of BET proteins in replication, integration, and tumorigenesis in vivo. Comparing WT and W390A MLV infections revealed similar viral loads in the blood, thymus, and spleen cells. Interestingly, W390A MLV integration was retargeted away from GC-enriched genomic regions. However, both WT MLV- and W390A MLV-infected mice developed T-cell lymphoma after similar latencies represented by an enlarged thymus and spleen and multiorgan tumor infiltration. Integration site sequencing from splenic tumor cells revealed clonal expansion in all WT MLV- and W390A MLV-infected mice. However, the integration profiles of W390A MLV and WT MLV differed significantly. Integrations were enriched in enhancers and promoters, but compared to the WT, W390A MLV integrated less frequently into enhancers and more frequently into oncogene bodies such as Notch1 and Ppp1r16b. We conclude that host factors direct MLV in vivo integration site selection. Although BET proteins target WT MLV integration preferentially toward enhancers and promoters, insertional lymphomagenesis can occur independently from BET, likely due to the intrinsically strong enhancer/promoter of the MLV long terminal repeat (LTR). IMPORTANCE In this study, we have shown that the in vivo replication of murine leukemia virus happens independently of BET proteins, which are key host determinants involved in retroviral integration site selection. This finding opens a new research line in the discovery of alternative viral or host factors that may complement the dominant host factor. In addition, our results show that BET-independent murine leukemia virus uncouples insertional mutagenesis from gene enhancers, although lymphomagenesis still occurs despite the lack of an interaction with BET proteins. Our findings also have implications for the engineering of BET-independent MLV-based vectors for gene therapy, which may not be a safe alternative.
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15
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Winans S, Yu HJ, de Los Santos K, Wang GZ, KewalRamani VN, Goff SP. A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats. Nat Commun 2022; 13:1474. [PMID: 35304442 PMCID: PMC8933506 DOI: 10.1038/s41467-022-29097-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/24/2022] [Indexed: 11/25/2022] Open
Abstract
Retroviruses utilize the viral integrase (IN) protein to integrate a DNA copy of their genome into host chromosomal DNA. HIV-1 integration sites are highly biased towards actively transcribed genes, likely mediated by binding of the IN protein to specific host factors, particularly LEDGF, located at these gene regions. We here report a substantial redirection of integration site distribution induced by a single point mutation in HIV-1 IN. Viruses carrying the K258R IN mutation exhibit a high frequency of integrations into centromeric alpha satellite repeat sequences, as assessed by deep sequencing, a more than 10-fold increase over wild-type. Quantitative PCR and in situ immunofluorescence assays confirm this bias of the K258R mutant virus for integration into centromeric DNA. Immunoprecipitation studies identify host factors binding to IN that may account for the observed bias for integration into centromeres. Centromeric integration events are known to be enriched in the latent reservoir of infected memory T cells, as well as in elite controllers who limit viral replication without intervention. The K258R point mutation in HIV-1 IN is also present in databases of latent proviruses found in patients, and may reflect an unappreciated aspect of the establishment of viral latency. HIV-1 integration sites are biased towards actively transcribed genes, likely mediated by binding of the viral integrase (IN) protein to host factors. Here, Winans et al. show that the K258R point mutation in IN eredirects viral DNA integration to the centromeres of host chromosomes, which may affect HIV latency.
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Affiliation(s)
- Shelby Winans
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, USA
| | - Kenia de Los Santos
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Gary Z Wang
- Department of Pathology, Columbia University Medical Center, New York, NY, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA. .,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA. .,Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
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16
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Kleinman AJ, Pandrea I, Apetrei C. So Pathogenic or So What?-A Brief Overview of SIV Pathogenesis with an Emphasis on Cure Research. Viruses 2022; 14:135. [PMID: 35062339 PMCID: PMC8781889 DOI: 10.3390/v14010135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/10/2021] [Accepted: 12/25/2021] [Indexed: 02/07/2023] Open
Abstract
HIV infection requires lifelong antiretroviral therapy (ART) to control disease progression. Although ART has greatly extended the life expectancy of persons living with HIV (PWH), PWH nonetheless suffer from an increase in AIDS-related and non-AIDS related comorbidities resulting from HIV pathogenesis. Thus, an HIV cure is imperative to improve the quality of life of PWH. In this review, we discuss the origins of various SIV strains utilized in cure and comorbidity research as well as their respective animal species used. We briefly detail the life cycle of HIV and describe the pathogenesis of HIV/SIV and the integral role of chronic immune activation and inflammation on disease progression and comorbidities, with comparisons between pathogenic infections and nonpathogenic infections that occur in natural hosts of SIVs. We further discuss the various HIV cure strategies being explored with an emphasis on immunological therapies and "shock and kill".
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Affiliation(s)
- Adam J. Kleinman
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Ivona Pandrea
- Department of Infectious Diseases and Immunology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Infectious Diseases and Immunology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA;
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17
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Miskey C, Kesselring L, Querques I, Abrusán G, Barabas O, Ivics Z. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2807-2825. [PMID: 35188569 PMCID: PMC8934666 DOI: 10.1093/nar/gkac092] [Citation(s) in RCA: 7] [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: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
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Affiliation(s)
| | | | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - György Abrusán
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Zoltán Ivics
- To whom correspondence should be addressed. Tel: +49 6103 77 6000; Fax: +49 6103 77 1280;
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18
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Wood SR, Bigger BW. Delivering gene therapy for mucopolysaccharide diseases. Front Mol Biosci 2022; 9:965089. [PMID: 36172050 PMCID: PMC9511407 DOI: 10.3389/fmolb.2022.965089] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Mucopolysaccharide diseases are a group of paediatric inherited lysosomal storage diseases that are caused by enzyme deficiencies, leading to a build-up of glycosaminoglycans (GAGs) throughout the body. Patients have severely shortened lifespans with a wide range of symptoms including inflammation, bone and joint, cardiac, respiratory and neurological disease. Current treatment approaches for MPS disorders revolve around two main strategies. Enzyme replacement therapy (ERT) is efficacious in treating somatic symptoms but its effect is limited for neurological functions. Haematopoietic stem cell transplant (HSCT) has the potential to cross the BBB through monocyte trafficking, however delivered enzyme doses limit its use almost exclusively to MPSI Hurler. Gene therapy is an emerging therapeutic strategy for the treatment of MPS disease. In this review, we will discuss the various vectors that are being utilised for gene therapy in MPS as well as some of the most recent gene-editing approaches undergoing pre-clinical and clinical development.
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19
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Huang AS, Ramos V, Oliveira TY, Gaebler C, Jankovic M, Nussenzweig MC, Cohn LB. Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence. J Exp Med 2021; 218:e20211427. [PMID: 34636876 PMCID: PMC8515646 DOI: 10.1084/jem.20211427] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/17/2021] [Accepted: 09/27/2021] [Indexed: 01/26/2023] Open
Abstract
Latent intact HIV-1 proviruses persist in a small subset of long-lived CD4+ T cells that can undergo clonal expansion in vivo. Expanded clones of CD4+ T cells dominate latent reservoirs in individuals on long-term antiretroviral therapy (ART) and represent a major barrier to HIV-1 cure. To determine how integration landscape might contribute to latency, we analyzed integration sites of near full length HIV-1 genomes from individuals on long-term ART, focusing on individuals whose reservoirs are highly clonal. We find that intact proviruses in expanded CD4+ T cell clones are preferentially integrated within Krüppel-associated box (KRAB) domain-containing zinc finger (ZNF) genes. ZNF genes are associated with heterochromatin in memory CD4+ T cells; nevertheless, they are expressed in these cells under steady-state conditions. In contrast to genes carrying unique integrations, ZNF genes carrying clonal intact integrations are down-regulated upon cellular activation. Together, the data suggest selected genomic sites, including ZNF genes, can be especially permissive for maintaining HIV-1 latency during memory CD4+ T cell expansion.
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Affiliation(s)
- Amy S. Huang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Thiago Y. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
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20
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Hackl T, Duponchel S, Barenhoff K, Weinmann A, Fischer MG. Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate. eLife 2021; 10:72674. [PMID: 34698016 PMCID: PMC8547959 DOI: 10.7554/elife.72674] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022] Open
Abstract
Virophages can parasitize giant DNA viruses and may provide adaptive anti-giant virus defense in unicellular eukaryotes. Under laboratory conditions, the virophage mavirus integrates into the nuclear genome of the marine flagellate Cafeteria burkhardae and reactivates upon superinfection with the giant virus CroV. In natural systems, however, the prevalence and diversity of host-virophage associations has not been systematically explored. Here, we report dozens of integrated virophages in four globally sampled C. burkhardae strains that constitute up to 2% of their host genomes. These endogenous mavirus-like elements (EMALEs) separated into eight types based on GC-content, nucleotide similarity, and coding potential and carried diverse promoter motifs implicating interactions with different giant viruses. Between host strains, some EMALE insertion loci were conserved indicating ancient integration events, whereas the majority of insertion sites were unique to a given host strain suggesting that EMALEs are active and mobile. Furthermore, we uncovered a unique association between EMALEs and a group of tyrosine recombinase retrotransposons, revealing yet another layer of parasitism in this nested microbial system. Our findings show that virophages are widespread and dynamic in wild Cafeteria populations, supporting their potential role in antiviral defense in protists. Viruses exist in all ecosystems in vast numbers and infect many organisms. Some of them are harmful but others can protect the organisms they infect. For example, a group of viruses called virophages protect microscopic sea creatures called plankton from deadly infections by so-called giant viruses. In fact, virophages need plankton infected with giant viruses to survive because they use enzymes from the giant viruses to turn on their own genes. A virophage called mavirus integrates its genes into the DNA of a type of plankton called Cafeteria. It lays dormant in the DNA until a giant virus called CroV infects the plankton. This suggests that the mavirus may be a built-in defense against CroV infections and laboratory studies seem to confirm this. But whether wild Cafeteria also use these defenses is unknown. Hackl et al. show that virophages are common in the DNA of wild Cafeteria and that the two appear to have a mutually beneficial relationship. In the experiments, the researchers sequenced the genomes of four Cafeteria populations from the Atlantic and Pacific Oceans and looked for virophages in their DNA. Each of the four Cafeteria genomes contained dozens of virophages, which suggests that virophages are important to these plankton. This included several relatives of the mavirus and seven new virophages. Virophage genes were often interrupted by so called jumping genes, which may take advantage of the virophages the way the virophages use giant viruses to meet their own needs. The experiments show that virophages often co-exist with marine plankton from around the world and these relationships are likely beneficial. In fact, the experiments suggest that the virophages may have played an important role in the evolution of these plankton. Further studies may help scientists learn more about virus ecology and how viruses have shaped the evolution of other creatures.
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Affiliation(s)
- Thomas Hackl
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
| | - Sarah Duponchel
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
| | - Karina Barenhoff
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
| | - Alexa Weinmann
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
| | - Matthias G Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
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21
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Suryawanshi GW, Arokium H, Kim S, Khamaikawin W, Lin S, Shimizu S, Chupradit K, Lee Y, Xie Y, Guan X, Suryawanshi V, Presson AP, An DS, Chen ISY. Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias. Stem Cell Res Ther 2021; 12:528. [PMID: 34620229 PMCID: PMC8499514 DOI: 10.1186/s13287-021-02601-5] [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: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Current understanding of hematopoiesis is largely derived from mouse models that are physiologically distant from humans. Humanized mice provide the most physiologically relevant small animal model to study human diseases, most notably preclinical gene therapy studies. However, the clonal repopulation dynamics of human hematopoietic stem and progenitor cells (HSPC) in these animal models is only partially understood. Using a new clonal tracking methodology designed for small sample volumes, we aim to reveal the underlying clonal dynamics of human cell repopulation in a mouse environment. METHODS Humanized bone marrow-liver-thymus (hu-BLT) mice were generated by transplanting lentiviral vector-transduced human fetal liver HSPC (FL-HSPC) in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice implanted with a piece of human fetal thymus. We developed a methodology to track vector integration sites (VIS) in a mere 25 µl of mouse blood for longitudinal and quantitative clonal analysis of human HSPC repopulation in mouse environment. We explored transcriptional and epigenetic features of human HSPC for possible VIS bias. RESULTS A total of 897 HSPC clones were longitudinally tracked in hu-BLT mice-providing a first-ever demonstration of clonal dynamics and coordinated expansion of therapeutic and control vector-modified human cell populations simultaneously repopulating in the same humanized mice. The polyclonal repopulation stabilized at 19 weeks post-transplant and the contribution of the largest clone doubled within 4 weeks. Moreover, 550 (~ 60%) clones persisted over 6 weeks and were highly shared between different organs. The normal clonal profiles confirmed the safety of our gene therapy vectors. Multi-omics analysis of human FL-HSPC revealed that 54% of vector integrations in repopulating clones occurred within ± 1 kb of H3K36me3-enriched regions. CONCLUSIONS Human repopulation in mice is polyclonal and stabilizes more rapidly than that previously observed in humans. VIS preference for H3K36me3 has no apparent negative effects on HSPC repopulation. Our study provides a methodology to longitudinally track clonal repopulation in small animal models extensively used for stem cell and gene therapy research and with lentiviral vectors designed for clinical applications. Results of this study provide a framework for understanding the clonal behavior of human HPSC repopulating in a mouse environment, critical for translating results from humanized mice models to the human settings.
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Affiliation(s)
- Gajendra W Suryawanshi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Hubert Arokium
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Sanggu Kim
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Wannisa Khamaikawin
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Samantha Lin
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | - Saki Shimizu
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | | | - YooJin Lee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Yiming Xie
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Xin Guan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
| | - Vasantika Suryawanshi
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Angela P Presson
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, 84108, USA
- Department of Biostatistics, University of California, Los Angeles, 90095, USA
| | - Dong-Sung An
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA
- School of Nursing, University of California, Los Angeles, CA, 90095, USA
| | - Irvin S Y Chen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 615 Charles E. Young Dr. South, BSRB, Rm 173, Los Angeles, CA, 90095, USA.
- UCLA AIDS Institute, Los Angeles, CA, 90095, USA.
- Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
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22
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GS-9822, a preclinical LEDGIN candidate, displays a block-and-lock phenotype in cell culture. Antimicrob Agents Chemother 2021; 65:AAC.02328-20. [PMID: 33619061 PMCID: PMC8092873 DOI: 10.1128/aac.02328-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ability of HIV to integrate into the host genome and establish latent reservoirs is the main hurdle preventing an HIV cure. LEDGINs are small-molecule integrase inhibitors that target the binding pocket of LEDGF/p75, a cellular cofactor that substantially contributes to HIV integration site selection. They are potent antivirals that inhibit HIV integration and maturation. In addition, they retarget residual integrants away from transcription units and towards a more repressive chromatin environment. As a result, treatment with the LEDGIN CX14442 yielded residual provirus that proved more latent and more refractory to reactivation, supporting the use of LEDGINs as research tools to study HIV latency and a functional cure strategy. In this study we compared GS-9822, a potent, pre-clinical lead compound, with CX14442 with respect to antiviral potency, integration site selection, latency and reactivation. GS-9822 was more potent than CX14442 in most assays. For the first time, the combined effects on viral replication, integrase-LEDGF/p75 interaction, integration sites, epigenetic landscape, immediate latency and latency reversal was demonstrated at nanomolar concentrations achievable in the clinic. GS-9822 profiles as a preclinical candidate for future functional cure research.
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23
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Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy. PLoS Pathog 2021; 17:e1009141. [PMID: 33826675 PMCID: PMC8055010 DOI: 10.1371/journal.ppat.1009141] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/19/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
HIV persists during antiretroviral therapy (ART) as integrated proviruses in cells descended from a small fraction of the CD4+ T cells infected prior to the initiation of ART. To better understand what controls HIV persistence and the distribution of integration sites (IS), we compared about 15,000 and 54,000 IS from individuals pre-ART and on ART, respectively, with approximately 395,000 IS from PBMC infected in vitro. The distribution of IS in vivo is quite similar to the distribution in PBMC, but modified by selection against proviruses in expressed genes, by selection for proviruses integrated into one of 7 specific genes, and by clonal expansion. Clones in which a provirus integrated in an oncogene contributed to cell survival comprised only a small fraction of the clones persisting in on ART. Mechanisms that do not involve the provirus, or its location in the host genome, are more important in determining which clones expand and persist. In HIV-infected individuals, a small fraction of the infected cells persist and divide. This reservoir persists during fully suppressive ART and can rekindle the infection if ART is discontinued. Because the number of possible sites of HIV DNA integration is very large, each infected cell, and all of its descendants, can be identified by the site where the provirus is integrated (IS). To understand the selective forces that determine the fates of infected cells in vivo, we compared the distribution of HIV IS in freshly-infected cells to cells from HIV-infected donors sampled both before and during ART. We found that, as previously reported, integration favors highly-expressed genes. However, over time, the fraction of cells with proviruses integrated in highly-expressed genes decreases, implying that they grow less well. There are exceptions to this broad negative selection. When a provirus is integrated in a specific region in one of seven genes, the proviruses affect the expression of the target gene, promoting growth and/or survival of the cell. Although this effect is striking, it is only a minor component of the forces that promote the growth and survival of the population of infected cells during ART.
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24
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Spector LP, Tiffany M, Ferraro NM, Abell NS, Montgomery SB, Kay MA. Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. Mol Ther 2021; 29:1028-1046. [PMID: 33248247 PMCID: PMC7934627 DOI: 10.1016/j.ymthe.2020.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have the unique ability to promote targeted integration of transgenes via homologous recombination at specified genomic sites, reaching frequencies of 0.1%-1%. We studied genomic parameters that influence targeting efficiencies on a large scale. To do this, we generated more than 1,000 engineered, doxycycline-inducible target sites in the human HAP1 cell line and infected this polyclonal population with a library of AAV-DJ targeting vectors, with each carrying a unique barcode. The heterogeneity of barcode integration at each target site provided an assessment of targeting efficiency at that locus. We compared targeting efficiency with and without target site transcription for identical chromosomal positions. Targeting efficiency was enhanced by target site transcription, while chromatin accessibility was associated with an increased likelihood of targeting. ChromHMM chromatin states characterizing transcription and enhancers in wild-type K562 cells were also associated with increased AAV-HR efficiency with and without target site transcription, respectively. Furthermore, the amenability of a site to targeting was influenced by the endogenous transcriptional level of intersecting genes. These results define important parameters that may not only assist in designing optimal targeting vectors for genome editing, but also provide new insights into the mechanism of AAV-mediated homologous recombination.
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Affiliation(s)
- Laura P Spector
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Tiffany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole M Ferraro
- Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan S Abell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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25
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Pseudotyping Lentiviral Vectors: When the Clothes Make the Virus. Viruses 2020; 12:v12111311. [PMID: 33207797 PMCID: PMC7697029 DOI: 10.3390/v12111311] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
Delivering transgenes to human cells through transduction with viral vectors constitutes one of the most encouraging approaches in gene therapy. Lentivirus-derived vectors are among the most promising vectors for these approaches. When the genetic modification of the cell must be performed in vivo, efficient specific transduction of the cell targets of the therapy in the absence of off-targeting constitutes the Holy Grail of gene therapy. For viral therapy, this is largely determined by the characteristics of the surface proteins carried by the vector. In this regard, an important property of lentiviral vectors is the possibility of being pseudotyped by envelopes of other viruses, widening the panel of proteins with which they can be armed. Here, we discuss how this is achieved at the molecular level and what the properties and the potentialities of the different envelope proteins that can be used for pseudotyping these vectors are.
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26
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Yang Y, Lee JE, Jeong HY, Shim JY, Baek MJ, Son MJ, Kim YJ, Noh H, Lim KI. Alteration of gammaretroviral vector integration patterns by insertion of histone and leucine zipper into integrase. Biotechnol Bioeng 2020; 117:3924-3937. [PMID: 32816306 DOI: 10.1002/bit.27540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 12/19/2022]
Abstract
Retroviral vectors show long-term gene expression in gene therapy through the integration of transgenes into the human cell genome. Murine leukemia virus (MLV), a well-studied gammaretrovirus, has been often used as a representative retroviral vector. However, frequent integrations of MLV-based vectors into transcriptional start sites (TSSs) could lead to the activation of oncogenes by enhancer effects of the genetic components within the vectors. Therefore, the MLV integration preference for TSSs limits its wider use in clinical applications. To reduce the integration preference of MLV-based vectors, we attempted to perturb the structure of the viral integrase that plays a key role in determining integration sites. For this goal, we inserted histones and leucine zippers, having DNA-binding property, into internal sites of MLV integrase. This integrase engineering yielded multiple mutant vectors that showed significantly different integration patterns compared with that of wild-type vector. Some mutant vectors did not prefer the key regulatory genomic domains of human cells, TSSs. Moreover, a couple of engineered vectors did not integrate into the genomic sites near the TSSs of oncogenes. Overall, this study suggests that structural perturbation of integrase is a simple way to develop safer MLV-based retroviral vectors for use in clinical applications.
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Affiliation(s)
- Yeji Yang
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, Korea.,Division of Analytical Science Research, Research Center for Biocenvergence Analysis, Korea Basic Science Institute, Chungcheongbukdo, Korea
| | - Ji-Eun Lee
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, Korea.,Health and Environment Research Institute of Gwangju, Gwangju, Korea
| | - Hye-Young Jeong
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, Korea
| | - Ji-Yeon Shim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, Korea
| | - Min-Jeong Baek
- Bioinformatics Analysis Team, Research Institute, National Cancer Center, Goyang, Korea
| | - Min-Jeong Son
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, Korea
| | - Yeon-Ju Kim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, Korea
| | - Hohsuk Noh
- Department of Statistics, Sookmyung Women's University, Seoul, Korea
| | - Kwang-Il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, Korea.,Institute of Advanced Materials and Systems, Sookmyung Women's University, Seoul, Korea
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27
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De Rosa L, Latella MC, Secone Seconetti A, Cattelani C, Bauer JW, Bondanza S, De Luca M. Toward Combined Cell and Gene Therapy for Genodermatoses. Cold Spring Harb Perspect Biol 2020; 12:a035667. [PMID: 31653644 PMCID: PMC7197428 DOI: 10.1101/cshperspect.a035667] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
To date, more than 200 monogenic, often devastating, skin diseases have been described. Because of unmet medical needs, development of long-lasting and curative therapies has been consistently attempted, with the aim of correcting the underlying molecular defect. In this review, we will specifically address the few combined cell and gene therapy strategies that made it to the clinics. Based on these studies, what can be envisioned for the future is a patient-oriented strategy, built on the specific features of the individual in need. Most likely, a combination of different strategies, approaches, and advanced therapies will be required to reach the finish line at the end of the long and winding road hampering the achievement of definitive treatments for genodermatoses.
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Affiliation(s)
- Laura De Rosa
- Holostem Terapie Avanzate S.r.l., Center for Regenerative Medicine "Stefano Ferrari," 41125 Modena, Italy
| | - Maria Carmela Latella
- Holostem Terapie Avanzate S.r.l., Center for Regenerative Medicine "Stefano Ferrari," 41125 Modena, Italy
| | - Alessia Secone Seconetti
- Holostem Terapie Avanzate S.r.l., Center for Regenerative Medicine "Stefano Ferrari," 41125 Modena, Italy
| | - Cecilia Cattelani
- Center for Regenerative Medicine "Stefano Ferrari," Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Johann W Bauer
- EB House Austria and Department of Dermatology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Sergio Bondanza
- Holostem Terapie Avanzate S.r.l., Center for Regenerative Medicine "Stefano Ferrari," 41125 Modena, Italy
| | - Michele De Luca
- Center for Regenerative Medicine "Stefano Ferrari," Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
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Next-generation stem cells - ushering in a new era of cell-based therapies. Nat Rev Drug Discov 2020; 19:463-479. [PMID: 32612263 DOI: 10.1038/s41573-020-0064-x] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Abstract
Naturally occurring stem cells isolated from humans have been used therapeutically for decades. This has primarily involved the transplantation of primary cells such as haematopoietic and mesenchymal stem cells and, more recently, derivatives of pluripotent stem cells. However, the advent of cell-engineering approaches is ushering in a new generation of stem cell-based therapies, greatly expanding their therapeutic utility. These next-generation stem cells are being used as 'Trojan horses' to improve the delivery of drugs and oncolytic viruses to intractable tumours and are also being engineered with angiogenic, neurotrophic and anti-inflammatory molecules to accelerate the repair of injured or diseased tissues. Moreover, gene therapy and gene editing technologies are being used to create stem cell derivatives with improved functionality, specificity and responsiveness compared with their natural counterparts. Here, we review these engineering approaches and areas in which they will help broaden the utility and clinical applicability of stem cells.
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29
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Comparative analysis of CpG islands in equine infectious anemia virus strains. Virus Genes 2020; 56:339-346. [PMID: 32239368 DOI: 10.1007/s11262-020-01749-1] [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: 10/18/2019] [Accepted: 03/04/2020] [Indexed: 10/24/2022]
Abstract
Increasing evidence suggests that DNA methylation has key roles in the replication of retroviruses, including lentiviruses, and pathogenesis of diseases. However, the precise characteristics of CpG islands are not known for many retroviruses. In this study, we compared the distribution of CpG islands among strains of equine infectious anemia virus (EIAV), a lentivirus in the family Retroviridae and a model for HIV research. We identified CpG islands in 32 full-length EIAV genomic sequences obtained from the GenBank database using MethPrimer. Only one CpG island, from 100 to 120 bp, was identified in the genomes of EIAV strains DV10, DLV3-A, and DLV5-10 from China, V26 and V70 from Japan, and IRE H3, IRE F2, IRE F3, and IRE F4 from Ireland. Importantly, the CpG island was located within the Rev gene, which is required for the expression of viral cis-acting elements and the production of new virions. These results suggest that the distribution, length, and genetic properties of CpG islands differ among EIAV strains. Future research should focus on the biological significance of this CpG island within rev to improve our understanding of the precise roles of CpG islands in epigenetic regulation in the species.
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30
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Virgilio MC, Collins KL. The Impact of Cellular Proliferation on the HIV-1 Reservoir. Viruses 2020; 12:E127. [PMID: 31973022 PMCID: PMC7077244 DOI: 10.3390/v12020127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a chronic infection that destroys the immune system in infected individuals. Although antiretroviral therapy is effective at preventing infection of new cells, it is not curative. The inability to clear infection is due to the presence of a rare, but long-lasting latent cellular reservoir. These cells harboring silent integrated proviral genomes have the potential to become activated at any moment, making therapy necessary for life. Latently-infected cells can also proliferate and expand the viral reservoir through several methods including homeostatic proliferation and differentiation. The chromosomal location of HIV proviruses within cells influences the survival and proliferative potential of host cells. Proliferating, latently-infected cells can harbor proviruses that are both replication-competent and defective. Replication-competent proviral genomes contribute to viral rebound in an infected individual. The majority of available techniques can only assess the integration site or the proviral genome, but not both, preventing reliable evaluation of HIV reservoirs.
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Affiliation(s)
- Maria C. Virgilio
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathleen L. Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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31
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Kruize Z, Kootstra NA. The Role of Macrophages in HIV-1 Persistence and Pathogenesis. Front Microbiol 2019; 10:2828. [PMID: 31866988 PMCID: PMC6906147 DOI: 10.3389/fmicb.2019.02828] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/21/2019] [Indexed: 12/12/2022] Open
Abstract
Current antiretroviral therapy (ART) effectively suppresses Human Immunodeficiency Virus type 1 (HIV-1) in infected individuals. However, even long term ART does not eradicate HIV-1 infected cells and the virus persists in cellular reservoirs. Beside memory CD4+ T cells, cells of the myeloid lineage, especially macrophages, are believed to be an important sanctuary for HIV-1. Monocytes and macrophages are key players in the innate immune response to pathogens and are recruited to sites of infection and inflammation. Due to their long life span and ability to reside in virtually every tissue, macrophages have been proposed to play a critical role in the establishment and persistence of the HIV-1 reservoir. Current HIV-1 cure strategies mainly focus on the concept of “shock and kill” to purge the viral reservoir. This approach aims to reactivate viral protein production in latently infected cells, which subsequently are eliminated as a consequence of viral replication, or recognized and killed by the immune system. Macrophage susceptibility to HIV-1 infection is dependent on the local microenvironment, suggesting that molecular pathways directing differentiation and polarization are involved. Current latency reversing agents (LRA) are mainly designed to reactivate the HIV-1 provirus in CD4+ T cells, while their ability to abolish viral latency in macrophages is largely unknown. Moreover, the resistance of macrophages to HIV-1 mediated kill and the presence of infected macrophages in immune privileged regions including the central nervous system (CNS), may pose a barrier to elimination of infected cells by current “shock and kill” strategies. This review focusses on the role of monocytes/macrophages in HIV-1 persistence. We will discuss mechanisms of viral latency and persistence in monocytes/macrophages. Furthermore, the role of these cells in HIV-1 tissue distribution and pathogenesis will be discussed.
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Affiliation(s)
- Zita Kruize
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
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32
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Takashima S, Shinkuma S, Fujita Y, Nomura T, Ujiie H, Natsuga K, Iwata H, Nakamura H, Vorobyev A, Abe R, Shimizu H. Efficient Gene Reframing Therapy for Recessive Dystrophic Epidermolysis Bullosa with CRISPR/Cas9. J Invest Dermatol 2019; 139:1711-1721.e4. [DOI: 10.1016/j.jid.2019.02.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 02/01/2019] [Accepted: 02/15/2019] [Indexed: 12/21/2022]
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33
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Patterson K, Shavarebi F, Magnan C, Chang I, Qi X, Baldi P, Bilanchone V, Sandmeyer SB. Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites. Genome Res 2019; 29:1298-1309. [PMID: 31249062 PMCID: PMC6673722 DOI: 10.1101/gr.240861.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 06/12/2019] [Indexed: 12/27/2022]
Abstract
Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled genome-wide using a random barcode-tagged Ty3. Saturation transposition showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets with high frequencies of transposition. To examine potential effects of cis-acting DNA features on transposition, targeting was tested on high-copy plasmids with restricted amounts of 5′ flanking sequence plus tDNA. Relative activity of targets was reconstituted in these constructions. Weighting of genomic insertions according to frequency identified an A/T-rich sequence followed by C as the dominant site of strand transfer. This site lies immediately adjacent to the adenines previously implicated in the RNAP3 TSS motif (CAA). In silico DNA structural analysis upstream of this motif showed that targets with elevated DNA curvature coincide with reduced integration. We propose that integration mediated by the Ty3 intasome complex (IN and cDNA) is subject to inputs from a combination of host factor occupancy and insertion site architecture, and that this results in the wide range of Ty3 targeting frequencies.
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Affiliation(s)
- Kurt Patterson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Farbod Shavarebi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Christophe Magnan
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Ivan Chang
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Xiaojie Qi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Pierre Baldi
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Virginia Bilanchone
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Suzanne B Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
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34
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Villarreal LP, Witzany G. That is life: communicating RNA networks from viruses and cells in continuous interaction. Ann N Y Acad Sci 2019; 1447:5-20. [PMID: 30865312 DOI: 10.1111/nyas.14040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA-mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA networks and RNA communication can interconnect these levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact.
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Affiliation(s)
- Luis P Villarreal
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
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35
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Gene therapy targeting haematopoietic stem cells for inherited diseases: progress and challenges. Nat Rev Drug Discov 2019; 18:447-462. [DOI: 10.1038/s41573-019-0020-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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36
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Thangsunan P, Wongsaipun S, Kittiwachana S, Suree N. Effective prediction model and determination of binding residues influential for inhibitors targeting HIV-1 integrase-LEDGF/p75 interface by employing solvent accessible surface area energy as key determinant. J Biomol Struct Dyn 2019; 38:460-473. [PMID: 30744499 DOI: 10.1080/07391102.2019.1580219] [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: 10/27/2022]
Abstract
Development of a highly accurate prediction model for protein-ligand inhibition has been a major challenge in drug discovery. Herein, we describe a novel predictive model for the inhibition of HIV-1 integrase (IN)-LEDGF/p75 protein-protein interaction. The model was constructed using energy parameters approximated from molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. Chemometric analysis using partial least squares (PLS) regression revealed that solvent accessible surface area energy (ΔGSASA) is the major determinant parameter contributing greatly to the prediction accuracy. PLS prediction model on the ΔGSASA values collected from 41 complexes yielded a strong correlation between the predicted and the actual inhibitory activities (R2 = 0.9666, RMSEC of pIC50 values = 0.0890). Additionally, for the test set of 14 complexes, the model performed satisfactorily with very low pIC50 errors (Q2 = 0.5168, RMSEP = 0.3325). A strong correlation between the buried surface areas on the IN protein, when bound with IN-LEDGF/p75 inhibitors, and the respective ΔGSASA values was also obtained. Furthermore, the current method could identify 'hot spots'of amino acid residues highly influential to the inhibitory activity prediction. This could present fruitful implications in binding site determination and future inhibitor developments targeting protein-protein interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patcharapong Thangsunan
- Interdisciplinary Program in Biotechnology, Graduate School, Chiang Mai University, Muang, Chiang Mai, Thailand.,Division of Biochemistry and Biochemical Technology, Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Sakunna Wongsaipun
- Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Sila Kittiwachana
- Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Nuttee Suree
- Division of Biochemistry and Biochemical Technology, Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand.,Department of Chemistry, Faculty of Science, Chiang Mai University, Muang, Chiang Mai, Thailand.,Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, Thailand
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37
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Hashemi P, Barreto K, Bernhard W, Lomness A, Honson N, Pfeifer TA, Harrigan PR, Sadowski I. Compounds producing an effective combinatorial regimen for disruption of HIV-1 latency. EMBO Mol Med 2019; 10:160-174. [PMID: 29246970 PMCID: PMC5838563 DOI: 10.15252/emmm.201708193] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Highly active antiretroviral therapy (HAART) has improved the outlook for the HIV epidemic, but does not provide a cure. The proposed “shock‐and‐kill” strategy is directed at inducing latent HIV reservoirs, which may then be purged via boosted immune response or targeting infected cells. We describe five novel compounds that are capable of reversing HIV latency without affecting the general T‐cell activation state. The new compounds exhibit synergy for reactivation of latent provirus with other latency‐reversing agents (LRAs), in particular ingenol‐3‐angelate/PEP005. One compound, designated PH02, was efficient at reactivating viral transcription in several cell lines bearing reporter HIV‐1 at different integration sites. Furthermore, it was capable of reversing latency in resting CD4+ T lymphocytes from latently infected aviremic patient cells on HAART, while producing minimal cellular toxicity. The combination of PH02 and PEP005 produces a strong synergistic effect for reactivation, as demonstrated through a quantitative viral outgrowth assay (qVOA), on CD4+ T lymphocytes from HIV‐1‐infected individuals. We propose that the PH02/PEP005 combination may represent an effective novel treatment for abrogating persistent HIV‐1 infection.
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Affiliation(s)
- Pargol Hashemi
- Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kris Barreto
- Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Wendy Bernhard
- Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Adam Lomness
- Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Nicolette Honson
- The Centre for Drug Research and Development, Vancouver, BC, Canada
| | - Tom A Pfeifer
- The Centre for Drug Research and Development, Vancouver, BC, Canada
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada
| | - Ivan Sadowski
- Biochemistry and Molecular Biology, Molecular Epigenetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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38
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Abstract
Current antiretroviral therapy (ART) effectively suppresses Human Immunodeficiency Virus type 1 (HIV-1) in infected individuals. However, even long term ART does not eradicate HIV-1 infected cells and the virus persists in cellular reservoirs. Beside memory CD4+ T cells, cells of the myeloid lineage, especially macrophages, are believed to be an important sanctuary for HIV-1. Monocytes and macrophages are key players in the innate immune response to pathogens and are recruited to sites of infection and inflammation. Due to their long life span and ability to reside in virtually every tissue, macrophages have been proposed to play a critical role in the establishment and persistence of the HIV-1 reservoir. Current HIV-1 cure strategies mainly focus on the concept of "shock and kill" to purge the viral reservoir. This approach aims to reactivate viral protein production in latently infected cells, which subsequently are eliminated as a consequence of viral replication, or recognized and killed by the immune system. Macrophage susceptibility to HIV-1 infection is dependent on the local microenvironment, suggesting that molecular pathways directing differentiation and polarization are involved. Current latency reversing agents (LRA) are mainly designed to reactivate the HIV-1 provirus in CD4+ T cells, while their ability to abolish viral latency in macrophages is largely unknown. Moreover, the resistance of macrophages to HIV-1 mediated kill and the presence of infected macrophages in immune privileged regions including the central nervous system (CNS), may pose a barrier to elimination of infected cells by current "shock and kill" strategies. This review focusses on the role of monocytes/macrophages in HIV-1 persistence. We will discuss mechanisms of viral latency and persistence in monocytes/macrophages. Furthermore, the role of these cells in HIV-1 tissue distribution and pathogenesis will be discussed.
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Affiliation(s)
- Zita Kruize
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
| | - Neeltje A Kootstra
- Laboratory for Viral Immune Pathogenesis, Department of Experimental Immunology, Amsterdam UMC, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands
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Shifting Retroviral Vector Integrations Away from Transcriptional Start Sites via DNA-Binding Protein Domain Insertion into Integrase. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 12:58-70. [PMID: 30534579 PMCID: PMC6278723 DOI: 10.1016/j.omtm.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/06/2018] [Indexed: 12/13/2022]
Abstract
The unique ability of retroviruses to integrate genes into host genomes is of great value for long-term expression in gene therapy, but only when integrations occur at safe genomic sites. To reap the benefit of using retroviruses without severe detrimental effects, we developed several murine leukemia virus (MLV)-based gammaretroviral vectors with safer integration patterns by perturbing the structure of the integrase via insertion of DNA-binding zinc-finger domains (ZFDs) into an internal position of the enzyme. ZFD insertion significantly reduced the inherent, strong MLV integration preference for genomic regions near transcriptional start sites (TSSs), which are the most dangerous spots. The altered retroviral integration pattern was related to increased formation of residual primer-binding site sequences at the 3' end of proviruses. Several ZFD insertion mutants showed lower frequencies of integrations into the TSS genome regions when having the residual primer-binding site sequences in the proviruses. Our findings not only can extend the use of retroviruses in biomedical applications, but also provide a glimpse into the mechanisms underlying retroviral integration.
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40
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Engelman AN, Singh PK. Cellular and molecular mechanisms of HIV-1 integration targeting. Cell Mol Life Sci 2018; 75:2491-2507. [PMID: 29417178 PMCID: PMC6004233 DOI: 10.1007/s00018-018-2772-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/21/2022]
Abstract
Integration is central to HIV-1 replication and helps mold the reservoir of cells that persists in AIDS patients. HIV-1 interacts with specific cellular factors to target integration to interior regions of transcriptionally active genes within gene-dense regions of chromatin. The viral capsid interacts with several proteins that are additionally implicated in virus nuclear import, including cleavage and polyadenylation specificity factor 6, to suppress integration into heterochromatin. The viral integrase protein interacts with transcriptional co-activator lens epithelium-derived growth factor p75 to principally position integration within gene bodies. The integrase additionally senses target DNA distortion and nucleotide sequence to help fine-tune the specific phosphodiester bonds that are cleaved at integration sites. Research into virus-host interactions that underlie HIV-1 integration targeting has aided the development of a novel class of integrase inhibitors and may help to improve the safety of viral-based gene therapy vectors.
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Affiliation(s)
- Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA, 02215, USA.
- Department of Medicine, Harvard Medical School, A-111, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, A-111, 25 Shattuck Street, Boston, MA, 02115, USA
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41
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Battivelli E, Dahabieh MS, Abdel-Mohsen M, Svensson JP, Tojal Da Silva I, Cohn LB, Gramatica A, Deeks S, Greene WC, Pillai SK, Verdin E. Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4 + T cells. eLife 2018; 7:e34655. [PMID: 29714165 PMCID: PMC5973828 DOI: 10.7554/elife.34655] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/18/2018] [Indexed: 12/21/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is currently incurable, due to the persistence of latently infected cells. The 'shock and kill' approach to a cure proposes to eliminate this reservoir via transcriptional activation of latent proviruses, enabling direct or indirect killing of infected cells. Currently available latency-reversing agents (LRAs) have however proven ineffective. To understand why, we used a novel HIV reporter strain in primary CD4+ T cells and determined which latently infected cells are reactivatable by current candidate LRAs. Remarkably, none of these agents reactivated more than 5% of cells carrying a latent provirus. Sequencing analysis of reactivatable vs. non-reactivatable populations revealed that the integration sites were distinguishable in terms of chromatin functional states. Our findings challenge the feasibility of 'shock and kill', and suggest the need to explore other strategies to control the latent HIV reservoir.
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Affiliation(s)
- Emilie Battivelli
- Gladstone Institute of Virology and ImmunologyGladstone InstitutesSan FranciscoUnited States
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
- Buck Institute for Research on AgingNovatoUnited States
| | - Matthew S Dahabieh
- Gladstone Institute of Virology and ImmunologyGladstone InstitutesSan FranciscoUnited States
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
| | - Mohamed Abdel-Mohsen
- University of California San FranciscoSan FranciscoUnited States
- Blood Systems Research InstituteSan FranciscoUnited States
- The Wistar InstitutePhiladelphiaUnited States
| | - J Peter Svensson
- Department of Biosciences and NutritionKarolinska InstitutetSolnaSweden
| | - Israel Tojal Da Silva
- Laboratory of Molecular ImmunologyThe Rockefeller UniversityNew YorkUnited States
- Laboratory of Computational Biology and BioinformaticsInternational Research CenterSao PauloBrazil
| | - Lillian B Cohn
- Laboratory of Molecular ImmunologyThe Rockefeller UniversityNew YorkUnited States
| | - Andrea Gramatica
- Gladstone Institute of Virology and ImmunologyGladstone InstitutesSan FranciscoUnited States
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoUnited States
| | - Steven Deeks
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
| | - Warner C Greene
- Gladstone Institute of Virology and ImmunologyGladstone InstitutesSan FranciscoUnited States
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
- Department of Cellular and Molecular PharmacologyUniversity of California San FranciscoSan FranciscoUnited States
| | - Satish K Pillai
- University of California San FranciscoSan FranciscoUnited States
- Blood Systems Research InstituteSan FranciscoUnited States
| | - Eric Verdin
- Gladstone Institute of Virology and ImmunologyGladstone InstitutesSan FranciscoUnited States
- Department of MedicineUniversity of California San FranciscoSan FranciscoUnited States
- Buck Institute for Research on AgingNovatoUnited States
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42
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Brendel C, Rothe M, Santilli G, Charrier S, Stein S, Kunkel H, Abriss D, Müller-Kuller U, Gaspar B, Modlich U, Galy A, Schambach A, Thrasher AJ, Grez M. Non-Clinical Efficacy and Safety Studies on G1XCGD, a Lentiviral Vector for Ex Vivo Gene Therapy of X-Linked Chronic Granulomatous Disease. HUM GENE THER CL DEV 2018; 29:69-79. [PMID: 29664709 DOI: 10.1089/humc.2017.245] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chronic granulomatous disease (CGD) is a debilitating primary immunodeficiency affecting phagocyte function due to the absence of nicotinamide dinucleotide phosphate (NADPH) oxidase activity. The vast majority of CGD patients in the Western world have mutations within the X-linked CYBB gene encoding for gp91phox (NOX2), the redox center of the NADPH oxidase complex (XCGD). Current treatments of XCGD are not entirely satisfactory, and prior attempts at autologous gene therapy using gammaretrovirus vectors did not provide long-term curative effects. A new strategy was developed based on the use of the lentiviral vector G1XCGD expressing high levels of the gp91phox transgene in myeloid cells. As a requisite for a clinical trial approval, standardized non-clinical studies were conducted in vitro and in mice in order to evaluate the pharmacodynamics and biosafety of the vector and the biodistribution of G1XCGD-transduced cells. Transduced CD34+ cells derived from XCGD patients engrafted and differentiated similarly to their non-transduced counterparts in xenograft mouse models and generated therapeutically relevant levels of NADPH activity in myeloid cells expressing gp91phox. Expression of functional gp91phox in hematopoietic cells did not affect their homing properties, which engrafted at high levels in mice. Extensive in vitro and in vivo genotoxicity studies found no evidence for adverse mutagenesis related to vector treatment. These studies paved the way for the approval of clinical trials in Europe and in the United States for the treatment of XCGD patients with G1XCGD gene-modified autologous hematopoietic cells.
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Affiliation(s)
- Christian Brendel
- 1 Institute for Tumor Biology and Experimental Therapy , Georg-Speyer-Haus, Frankfurt, Germany .,2 Division of Hematology/Oncology, Boston Children's Hospital , Boston, Massachusetts.,3 Harvard Medical School , Boston, Massachusetts.,4 Pediatric Oncology, Dana-Farber Cancer Institute , Boston, Massachusetts.,5 Harvard Stem Cell Institute, Harvard University , Boston, Massachusetts
| | - Michael Rothe
- 6 Hannover Medical School, Institute of Experimental Hematology , Hannover, Germany
| | - Giorgia Santilli
- 7 UCL Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital for Children NHS Trust London , United Kingdom
| | | | - Stefan Stein
- 1 Institute for Tumor Biology and Experimental Therapy , Georg-Speyer-Haus, Frankfurt, Germany
| | - Hana Kunkel
- 1 Institute for Tumor Biology and Experimental Therapy , Georg-Speyer-Haus, Frankfurt, Germany
| | - Daniela Abriss
- 1 Institute for Tumor Biology and Experimental Therapy , Georg-Speyer-Haus, Frankfurt, Germany
| | - Uta Müller-Kuller
- 1 Institute for Tumor Biology and Experimental Therapy , Georg-Speyer-Haus, Frankfurt, Germany
| | - Bobby Gaspar
- 7 UCL Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital for Children NHS Trust London , United Kingdom
| | - Ute Modlich
- 6 Hannover Medical School, Institute of Experimental Hematology , Hannover, Germany .,9 Research Group Gene Modification in Stem Cells , Paul-Ehrlich-Institute, Langen, Germany
| | | | - Axel Schambach
- 2 Division of Hematology/Oncology, Boston Children's Hospital , Boston, Massachusetts.,6 Hannover Medical School, Institute of Experimental Hematology , Hannover, Germany .,10 Hannover Medical School , Cluster of Excellence REBIRTH, Hannover, Germany
| | - Adrian J Thrasher
- 7 UCL Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital for Children NHS Trust London , United Kingdom
| | - Manuel Grez
- 1 Institute for Tumor Biology and Experimental Therapy , Georg-Speyer-Haus, Frankfurt, Germany
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43
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Abstract
Viral vectors provide an efficient means for modification of eukaryotic cells, and their use is now commonplace in academic laboratories and industry for both research and clinical gene therapy applications. Lentiviral vectors, derived from the human immunodeficiency virus, have been extensively investigated and optimized over the past two decades. Third-generation, self-inactivating lentiviral vectors have recently been used in multiple clinical trials to introduce genes into hematopoietic stem cells to correct primary immunodeficiencies and hemoglobinopathies. These vectors have also been used to introduce genes into mature T cells to generate immunity to cancer through the delivery of chimeric antigen receptors (CARs) or cloned T-cell receptors. CAR T-cell therapies engineered using lentiviral vectors have demonstrated noteworthy clinical success in patients with B-cell malignancies leading to regulatory approval of the first genetically engineered cellular therapy using lentiviral vectors. In this review, we discuss several aspects of lentiviral vectors that will be of interest to clinicians, including an overview of lentiviral vector development, the current uses of viral vectors as therapy for primary immunodeficiencies and cancers, large-scale manufacturing of lentiviral vectors, and long-term follow-up of patients treated with gene therapy products.
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44
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Abstract
Replication-defective retroviral vectors have been used for more than 25 years as a tool for efficient and stable insertion of therapeutic transgenes in human cells. Patients suffering from severe genetic diseases have been successfully treated by transplantation of autologous hematopoietic stem-progenitor cells (HSPCs) transduced with retroviral vectors, and the first of this class of therapies, Strimvelis, has recently received market authorization in Europe. Some clinical trials, however, resulted in severe adverse events caused by vector-induced proto-oncogene activation, which showed that retroviral vectors may retain a genotoxic potential associated to proviral integration in the human genome. The adverse events sparked a renewed interest in the biology of retroviruses, which led in a few years to a remarkable understanding of the molecular mechanisms underlying retroviral integration site selection within mammalian genomes. This review summarizes the current knowledge on retrovirus-host interactions at the genomic level, and the peculiar mechanisms by which different retroviruses, and their related gene transfer vectors, integrate in, and interact with, the human genome. This knowledge provides the basis for the development of safer and more efficacious retroviral vectors for human gene therapy.
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Affiliation(s)
| | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
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45
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Herrera-Carrillo E, Liu YP, Berkhout B. Improving miRNA Delivery by Optimizing miRNA Expression Cassettes in Diverse Virus Vectors. Hum Gene Ther Methods 2018; 28:177-190. [PMID: 28712309 DOI: 10.1089/hgtb.2017.036] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The RNA interference pathway is an evolutionary conserved post-transcriptional gene regulation mechanism that is exclusively triggered by double-stranded RNA inducers. RNAi-based methods and technologies have facilitated the discovery of many basic science findings and spurred the development of novel RNA therapeutics. Transient induction of RNAi via transfection of synthetic small interfering RNAs can trigger the selective knockdown of a target mRNA. For durable silencing of gene expression, either artificial short hairpin RNA or microRNA encoding transgene constructs were developed. These miRNAs are based on the molecules that induce the natural RNAi pathway in mammals and humans: the endogenously expressed miRNAs. Significant efforts focused on the construction and delivery of miRNA cassettes in order to solve basic biology questions or to design new therapy strategies. Several viral vectors have been developed, which are particularly useful for the delivery of miRNA expression cassettes to specific target cells. Each vector system has its own unique set of distinct properties. Thus, depending on the specific application, a particular vector may be most suitable. This field was previously reviewed for different viral vector systems, and now the recent progress in the field of miRNA-based gene-silencing approaches using lentiviral vectors is reported. The focus is on the unique properties and respective limitations of the available vector systems for miRNA delivery.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam , Amsterdam, The Netherlands
| | - Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam , Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam , Amsterdam, The Netherlands
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46
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Benleulmi MS, Matysiak J, Robert X, Miskey C, Mauro E, Lapaillerie D, Lesbats P, Chaignepain S, Henriquez DR, Calmels C, Oladosu O, Thierry E, Leon O, Lavigne M, Andreola ML, Delelis O, Ivics Z, Ruff M, Gouet P, Parissi V. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails. Retrovirology 2017; 14:54. [PMID: 29179726 PMCID: PMC5704366 DOI: 10.1186/s12977-017-0378-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/20/2017] [Indexed: 01/28/2023] Open
Abstract
Background Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein–protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. Results We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Conclusions Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin. Electronic supplementary material The online version of this article (10.1186/s12977-017-0378-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohamed S Benleulmi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Julien Matysiak
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Xavier Robert
- MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Stéphane Chaignepain
- UMR CNRS 5248 CBMN (Chimie Biologie des Membranes et Nanoobjets), Université de Bordeaux, 33076, Bordeaux, France
| | - Daniel R Henriquez
- Virology Program, ICBM, Faculty of Medicine, University of Chile, Santiago of Chile, Chile
| | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Oyindamola Oladosu
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France
| | | | - Oscar Leon
- Virology Program, ICBM, Faculty of Medicine, University of Chile, Santiago of Chile, Chile
| | - Marc Lavigne
- Dpt de Virologie, UMR 3569, CNRS, Institut Pasteur, Paris, France.,Institut Cochin-Inserm U1016-CNRS UMR8104-Université Paris Descartes, Paris, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Marie-Line Andreola
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Olivier Delelis
- LBPA, UMR8113, CNRS, ENS-Cachan, 94235, Cachan, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Marc Ruff
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Patrice Gouet
- MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France. .,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France. .,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France.
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47
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Yuen G, Khan FJ, Gao S, Stommel JM, Batchelor E, Wu X, Luo J. CRISPR/Cas9-mediated gene knockout is insensitive to target copy number but is dependent on guide RNA potency and Cas9/sgRNA threshold expression level. Nucleic Acids Res 2017; 45:12039-12053. [PMID: 29036671 PMCID: PMC5714203 DOI: 10.1093/nar/gkx843] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 is a powerful gene editing tool for gene knockout studies and functional genomic screens. Successful implementation of CRISPR often requires Cas9 to elicit efficient target knockout in a population of cells. In this study, we investigated the role of several key factors, including variation in target copy number, inherent potency of sgRNA guides, and expression level of Cas9 and sgRNA, in determining CRISPR knockout efficiency. Using isogenic, clonal cell lines with variable copy numbers of an EGFP transgene, we discovered that CRISPR knockout is relatively insensitive to target copy number, but is highly dependent on the potency of the sgRNA guide sequence. Kinetic analysis revealed that most target mutation occurs between 5 and 10 days following Cas9/sgRNA transduction, while sgRNAs with different potencies differ by their knockout time course and by their terminal-phase knockout efficiency. We showed that prolonged, low level expression of Cas9 and sgRNA often fails to elicit target mutation, particularly if the potency of the sgRNA is also low. Our findings provide new insights into the behavior of CRISPR/Cas9 in mammalian cells that could be used for future improvement of this platform.
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Affiliation(s)
- Garmen Yuen
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Fehad J. Khan
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Undergraduate Scholarship Program, National Institutes of Health, Bethesda, MD, USA
| | - Shaojian Gao
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jayne M. Stommel
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Eric Batchelor
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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48
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Boehm D, Ott M. Host Methyltransferases and Demethylases: Potential New Epigenetic Targets for HIV Cure Strategies and Beyond. AIDS Res Hum Retroviruses 2017; 33:S8-S22. [PMID: 29140109 DOI: 10.1089/aid.2017.0180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A successful HIV cure strategy may require reversing HIV latency to purge hidden viral reservoirs or enhancing HIV latency to permanently silence HIV transcription. Epigenetic modifying agents show promise as antilatency therapeutics in vitro and ex vivo, but also affect other steps in the viral life cycle. In this review, we summarize what we know about cellular DNA and protein methyltransferases (PMTs) as well as demethylases involved in HIV infection. We describe the biology and function of DNA methyltransferases, and their controversial role in HIV infection. We further explain the biology of PMTs and their effects on lysine and arginine methylation of histone and nonhistone proteins. We end with a focus on protein demethylases, their unique modes of action and their emerging influence on HIV infection. An outlook on the use of methylation-modifying agents in investigational HIV cure strategies is provided.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
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49
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Liu Q, Wang XF, Du C, Lin YZ, Ma J, Wang YH, Zhou JH, Wang X. The integration of a macrophage-adapted live vaccine strain of equine infectious anaemia virus (EIAV) in the horse genome. J Gen Virol 2017; 98:2596-2606. [PMID: 28884679 DOI: 10.1099/jgv.0.000918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Integration is an important feature of retroviruses and retrovirus-based therapeutic transfection vectors. The non-primate lentivirus equine infectious anaemia virus (EIAV) primarily targets macrophages/monocytes in vivo. Investigation of the integration features of EIAVDLV121 strains, which are adapted to donkey monocyte-derived macrophages (MDMs), is of great interest. In this study, we analysed the integration features of EIAVDLV121 in equine MDMs during in vitro infection. Our previously published integration sites (IS) for EIAVFDDV13 in fetal equine dermal (FED) cells were also analysed in parallel as references. Sequencing of the host genomic regions flanking the viral IS showed that reference sequence (RefSeq) genes were preferentially targeted for integration by EIAVDLV121. Introns, AT-rich regions, long interspersed nuclear elements (LINEs) and DNA transposons were also predominantly biased toward viral insertion, which is consistent with EIAVFDDV13 integration into the horse genome in FED cells. In addition, the most significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, specifically gag junctions for EIAVDLV121 and tight junctions for EIAVFDDV13, are regulators of metabolic function, which is consistent with the common bioprocesses, specifically cell cycle and chromosome/DNA organization, identified by gene ontology (GO) analysis. Our results demonstrate that EIAV integration occurs in regions that harbour structural and topological features of local chromatin in both macrophages and fibroblasts. Our data on EIAV will facilitate further understanding of lentivirus infection and the development of safer and more effective gene therapy vectors.
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Affiliation(s)
- Qiang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, PR China
| | - Xue-Feng Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, PR China
| | - Cheng Du
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, PR China
| | - Yue-Zhi Lin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, PR China
| | - Jian Ma
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, PR China
| | - Yu-Hong Wang
- Department of Geriatrics, The First Affiliated Clinical College of Harbin Medical University, Harbin, PR China
| | - Jian-Hua Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, PR China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, PR China
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
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