1
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Buck AM, LaFranchi BH, Henrich TJ. Gaining momentum: stem cell therapies for HIV cure. Curr Opin HIV AIDS 2024; 19:194-200. [PMID: 38686850 PMCID: PMC11155292 DOI: 10.1097/coh.0000000000000859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
PURPOSE OF REVIEW Durable HIV-1 remission has been reported in a person who received allogeneic stem cell transplants (SCTs) involving CCR5 Δ32/Δ32 donor cells. Much of the reduction in HIV-1 burden following allogeneic SCT with or without donor cells inherently resistant to HIV-1 infection is likely due to cytotoxic graft-versus-host effects on residual recipient immune cells. Nonetheless, there has been growing momentum to develop and implement stem cell therapies that lead to durable long-term antiretroviral therapy (ART)-free remission without the need for SCT. RECENT FINDINGS Most current research leverages gene editing techniques to modify hematopoietic stem cells which differentiate into immune cells capable of harboring HIV-1. Approaches include targeting genes that encode HIV-1 co-receptors using Zinc Finger Nucleases (ZFN) or CRISPR-Cas-9 to render a pool of adult or progenitor cells resistant to de-novo infection. Other strategies involve harnessing multipotent mesenchymal stromal cells to foster immune environments that can more efficiently recognize and target HIV-1 while promoting tissue homeostasis. SUMMARY Many of these strategies are currently in a state of infancy or adolescence; nonetheless, promising preclinical and first-in-human studies have been performed, providing further rationale to focus resources on stem cell therapies.
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Affiliation(s)
- Amanda M Buck
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, USA
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2
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Banda A, Impomeni O, Singh A, Baloch AR, Hu W, Jaijyan DK. Precision in Action: The Role of Clustered Regularly Interspaced Short Palindromic Repeats/Cas in Gene Therapies. Vaccines (Basel) 2024; 12:636. [PMID: 38932365 PMCID: PMC11209408 DOI: 10.3390/vaccines12060636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated enzyme-CAS holds great promise for treating many uncured human diseases and illnesses by precisely correcting harmful point mutations and disrupting disease-causing genes. The recent Food and Drug Association (FDA) approval of the first CRISPR-based gene therapy for sickle cell anemia marks the beginning of a new era in gene editing. However, delivering CRISPR specifically into diseased cells in vivo is a significant challenge and an area of intense research. The identification of new CRISPR/Cas variants, particularly ultra-compact CAS systems with robust gene editing activities, paves the way for the low-capacity delivery vectors to be used in gene therapies. CRISPR/Cas technology has evolved beyond editing DNA to cover a wide spectrum of functionalities, including RNA targeting, disease diagnosis, transcriptional/epigenetic regulation, chromatin imaging, high-throughput screening, and new disease modeling. CRISPR/Cas can be used to engineer B-cells to produce potent antibodies for more effective vaccines and enhance CAR T-cells for the more precise and efficient targeting of tumor cells. However, CRISPR/Cas technology has challenges, including off-target effects, toxicity, immune responses, and inadequate tissue-specific delivery. Overcoming these challenges necessitates the development of a more effective and specific CRISPR/Cas delivery system. This entails strategically utilizing specific gRNAs in conjunction with robust CRISPR/Cas variants to mitigate off-target effects. This review seeks to delve into the intricacies of the CRISPR/Cas mechanism, explore progress in gene therapies, evaluate gene delivery systems, highlight limitations, outline necessary precautions, and scrutinize the ethical considerations associated with its application.
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Affiliation(s)
- Amrutha Banda
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Olivia Impomeni
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Aparana Singh
- Department of Chemistry, National Institute of Technology Agartala, Agartala 799046, India;
| | - Abdul Rasheed Baloch
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Wenhui Hu
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Dabbu Kumar Jaijyan
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
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Gurrola TE, Effah SN, Sariyer IK, Dampier W, Nonnemacher MR, Wigdahl B. Delivering CRISPR to the HIV-1 reservoirs. Front Microbiol 2024; 15:1393974. [PMID: 38812680 PMCID: PMC11133543 DOI: 10.3389/fmicb.2024.1393974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/22/2024] [Indexed: 05/31/2024] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is well known as one of the most complex and difficult viral infections to cure. The difficulty in developing curative strategies arises in large part from the development of latent viral reservoirs (LVRs) within anatomical and cellular compartments of a host. The clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) system shows remarkable potential for the inactivation and/or elimination of integrated proviral DNA within host cells, however, delivery of the CRISPR/Cas9 system to infected cells is still a challenge. In this review, the main factors impacting delivery, the challenges for delivery to each of the LVRs, and the current successes for delivery to each reservoir will be discussed.
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Affiliation(s)
- Theodore E. Gurrola
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Samuel N. Effah
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Microbiology, Immunology, and Inflammation and Center for Neurovirology and Gene Editing, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
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Stevens CS, Carmichael J, Watkinson R, Kowdle S, Reis RA, Hamane K, Jang J, Park A, Pernet O, Khamaikawin W, Hong P, Thibault P, Gowlikar A, An DS, Lee B. A temperature-sensitive and interferon-silent Sendai virus vector for CRISPR-Cas9 delivery and gene editing in primary human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592383. [PMID: 38746439 PMCID: PMC11092779 DOI: 10.1101/2024.05.03.592383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The transformative potential of gene editing technologies hinges on the development of safe and effective delivery methods. In this study, we developed a temperature-sensitive and interferon-silent Sendai virus (ts SeV) as a novel delivery vector for CRISPR-Cas9 and for efficient gene editing in sensitive human cell types without inducing IFN responses. ts SeV demonstrates unprecedented transduction efficiency in human CD34+ hematopoietic stem and progenitor cells (HSPCs) including transduction of the CD34+/CD38-/CD45RA-/CD90+(Thy1+)/CD49fhigh stem cell enriched subpopulation. The frequency of CCR5 editing exceeded 90% and bi-allelic CCR5 editing exceeded 70% resulting in significant inhibition of HIV-1 infection in primary human CD14+ monocytes. These results demonstrate the potential of the ts SeV platform as a safe, efficient, and flexible addition to the current gene-editing tool delivery methods, which may help to further expand the possibilities in personalized medicine and the treatment of genetic disorders.
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Affiliation(s)
- Christian S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jillian Carmichael
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ruth Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Shreyas Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rebecca A Reis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kory Hamane
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Jason Jang
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Arnold Park
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Olivier Pernet
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Wannisa Khamaikawin
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Patrick Hong
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Patricia Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aditya Gowlikar
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Dong Sung An
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Berman RE, Dampier W, Nonnemacher MR, Wigdahl B. What's in a cure: designing a broad-spectrum HIV gene therapy. Curr Opin HIV AIDS 2024; 19:150-156. [PMID: 38547339 PMCID: PMC11188629 DOI: 10.1097/coh.0000000000000846] [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] [Indexed: 04/04/2024]
Abstract
PURPOSE OF REVIEW The leading gene editing strategy for a human immunodeficiency virus type 1 (HIV-1) cure involves the delivery of SaCas9 and two guide RNAs (gRNAs) in an adeno-associated viral (AAV) vector. As a dual-component system, CRISPR is targeted to a genetic locus through the choice of a Cas effector and gRNA protospacer design pair. As CRISPR research has expanded in recent years, these components have been investigated for utilization in cure strategies, which will be discussed in this article. RECENT FINDINGS Type II SpCas9 and SaCas9 have been the leading Cas effectors across gene editing therapeutics to date. Additionally, extensive research has expanded the potential to multiplex gRNAs and target them effectively to the highly genetically diverse HIV-1 provirus. More recently, the Type V family of Cas12 effectors opens a new opportunity to use a smaller Cas protein for packaging into an AAV vector with multiplexed gRNAs. SUMMARY In understanding the individual components of a CRISPR/Cas therapeutic cure for HIV-1, it is important to know that the currently used strategies can be improved upon. Future areas will include alternative smaller Cas effectors, multiplexed gRNAs designs, and/or alternative delivery modalities.
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Affiliation(s)
- Rachel E. Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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6
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Mastrangelo A, Gama L, Cinque P. Strategies to target the central nervous system HIV reservoir. Curr Opin HIV AIDS 2024; 19:133-140. [PMID: 38457227 DOI: 10.1097/coh.0000000000000847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
PURPOSE OF THE REVIEW The central nervous system (CNS) is an hotspot for HIV persistence and may be a major obstacle to overcome for curative strategies. The peculiar anatomical, tissular and cellular characteristics of the HIV reservoir in the CNS may need to be specifically addressed to achieve a long-term HIV control without ART. In this review, we will discuss the critical challenges that currently explored curative strategies may face in crossing the blood-brain barrier (BBB), targeting latent HIV in brain-resident myeloid reservoirs, and eliminating the virus without eliciting dangerous neurological adverse events. RECENT FINDINGS Latency reversing agents (LRA), broadly neutralizing monoclonal antibodies (bNabs), chimeric antigen receptor (CAR) T-cells, and adeno-associated virus 9-vectored gene-therapies cross the BBB with varying efficiency. Although brain penetration is poor for bNAbs, viral vectors for in vivo gene-editing, certain LRAs, and CAR T-cells may reach the cerebral compartment more efficiently. All these approaches, however, may encounter difficulties in eliminating HIV-infected perivascular macrophages and microglia. Safety, including local neurological adverse effects, may also be a concern, especially if high doses are required to achieve optimal brain penetration and efficient brain cell targeting. SUMMARY Targeting the CNS remains a potential problem for the currently investigated HIV curing strategies. In vivo evidence on CNS effectiveness is limited for most of the investigated strategies, and additional studies should be focused on evaluating the interplay between the cerebral HIV reservoir and treatment aiming to achieve an ART-free cure.
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Affiliation(s)
- Andrea Mastrangelo
- Department of Allergy and Clinical Immunology, Centre Hopitalier Universitaire Vaudoise (CHUV), Lausanne, Switzerland
| | - Lucio Gama
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Paola Cinque
- Unit of Infectious Diseases and Neurovirology Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
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7
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Zhang ML, Li HB, Jin Y. Application and perspective of CRISPR/Cas9 genome editing technology in human diseases modeling and gene therapy. Front Genet 2024; 15:1364742. [PMID: 38666293 PMCID: PMC11043577 DOI: 10.3389/fgene.2024.1364742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) mediated Cas9 nuclease system has been extensively used for genome editing and gene modification in eukaryotic cells. CRISPR/Cas9 technology holds great potential for various applications, including the correction of genetic defects or mutations within the human genome. The application of CRISPR/Cas9 genome editing system in human disease research is anticipated to solve a multitude of intricate molecular biology challenges encountered in life science research. Here, we review the fundamental principles underlying CRISPR/Cas9 technology and its recent application in neurodegenerative diseases, cardiovascular diseases, autoimmune related diseases, and cancer, focusing on the disease modeling and gene therapy potential of CRISPR/Cas9 in these diseases. Finally, we provide an overview of the limitations and future prospects associated with employing CRISPR/Cas9 technology for diseases study and treatment.
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Affiliation(s)
- Man-Ling Zhang
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Hong-Bin Li
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yong Jin
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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8
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Stranford DM, Simons LM, Berman KE, Cheng L, DiBiase BN, Hung ME, Lucks JB, Hultquist JF, Leonard JN. Genetically encoding multiple functionalities into extracellular vesicles for the targeted delivery of biologics to T cells. Nat Biomed Eng 2024; 8:397-414. [PMID: 38012307 PMCID: PMC11088532 DOI: 10.1038/s41551-023-01142-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
The genetic modification of T cells has advanced cellular immunotherapies, yet the delivery of biologics specifically to T cells remains challenging. Here we report a suite of methods for the genetic engineering of cells to produce extracellular vesicles (EVs)-which naturally encapsulate and transfer proteins and nucleic acids between cells-for the targeted delivery of biologics to T cells without the need for chemical modifications. Specifically, the engineered cells secreted EVs that actively loaded protein cargo via a protein tag and that displayed high-affinity T-cell-targeting domains and fusogenic glycoproteins. We validated the methods by engineering EVs that delivered Cas9-single-guide-RNA complexes to ablate the gene encoding the C-X-C chemokine co-receptor type 4 in primary human CD4+ T cells. The strategy is amenable to the targeted delivery of biologics to other cell types.
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Affiliation(s)
- Devin M Stranford
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Katherine E Berman
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
| | - Luyi Cheng
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
| | - Beth N DiBiase
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Michelle E Hung
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, USA.
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9
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Chen K, Ernst P, Kim S, Si Y, Varadkar T, Ringel MD, Liu X“M, Zhou L. An Innovative Mitochondrial-targeted Gene Therapy for Cancer Treatment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.584499. [PMID: 38585739 PMCID: PMC10996521 DOI: 10.1101/2024.03.24.584499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Targeting cancer cell mitochondria holds great therapeutic promise, yet current strategies to specifically and effectively destroy cancer mitochondria in vivo are limited. Here, we introduce mLumiOpto, an innovative mitochondrial-targeted luminoptogenetics gene therapy designed to directly disrupt the inner mitochondrial membrane (IMM) potential and induce cancer cell death. We synthesize a blue light-gated channelrhodopsin (CoChR) in the IMM and co-express a blue bioluminescence-emitting Nanoluciferase (NLuc) in the cytosol of the same cells. The mLumiOpto genes are selectively delivered to cancer cells in vivo by using adeno-associated virus (AAV) carrying a cancer-specific promoter or cancer-targeted monoclonal antibody-tagged exosome-associated AAV. Induction with NLuc luciferin elicits robust endogenous bioluminescence, which activates mitochondrial CoChR, triggering cancer cell IMM permeability disruption, mitochondrial damage, and subsequent cell death. Importantly, mLumiOpto demonstrates remarkable efficacy in reducing tumor burden and killing tumor cells in glioblastoma or triple-negative breast cancer xenografted mouse models. These findings establish mLumiOpto as a novel and promising therapeutic strategy by targeting cancer cell mitochondria in vivo.
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Affiliation(s)
- Kai Chen
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Patrick Ernst
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Seulhee Kim
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Yingnan Si
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Tanvi Varadkar
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Matthew D. Ringel
- Department of Molecular Medicine and Therapeutics, The Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Xiaoguang “Margaret” Liu
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Lufang Zhou
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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10
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McLaurin KA, Li H, Khalili K, Mactutus CF, Booze RM. HIV-1 mRNA knockdown with CRISPR/CAS9 enhances neurocognitive function. J Neurovirol 2024; 30:71-85. [PMID: 38355914 PMCID: PMC11035469 DOI: 10.1007/s13365-024-01193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
Mixed glia are infiltrated with HIV-1 virus early in the course of infection leading to the development of a persistent viral reservoir in the central nervous system. Modification of the HIV-1 genome using gene editing techniques, including CRISPR/Cas9, has shown great promise towards eliminating HIV-1 viral reservoirs; whether these techniques are capable of removing HIV-1 viral proteins from mixed glia, however, has not been systematically evaluated. Herein, the efficacy of adeno-associated virus 9 (AAV9)-CRISPR/Cas9 gene editing for eliminating HIV-1 messenger RNA (mRNA) from cortical mixed glia was evaluated in vitro and in vivo. In vitro, a within-subjects experimental design was utilized to treat mixed glia isolated from neonatal HIV-1 transgenic (Tg) rats with varying doses (0, 0.9, 1.8, 2.7, 3.6, 4.5, or 5.4 µL corresponding to a physical titer of 0, 4.23 × 109, 8.46 × 109, 1.269 × 1010, 1.692 × 1010, 2.115 × 1010, and 2.538 × 1010 gc/µL) of CRISPR/Cas9 for 72 h. Dose-dependent decreases in the number of HIV-1 mRNA, quantified using an innovative in situ hybridization technique, were observed in a subset (i.e., n = 5 out of 8) of primary mixed glia. In vivo, HIV-1 Tg rats were retro-orbitally inoculated with CRISPR/Cas9 for two weeks, whereby treatment resulted in profound excision (i.e., approximately 53.2%) of HIV-1 mRNA from the medial prefrontal cortex. Given incomplete excision of the HIV-1 viral genome, the clinical relevance of HIV-1 mRNA knockdown for eliminating neurocognitive impairments was evaluated via examination of temporal processing, a putative neurobehavioral mechanism underlying HIV-1-associated neurocognitive disorders (HAND). Indeed, treatment with CRISPR/Cas9 protractedly, albeit not permanently, restored the developmental trajectory of temporal processing. Proof-of-concept studies, therefore, support the susceptibility of mixed glia to gene editing and the potential of CRISPR/Cas9 to serve as a novel therapeutic strategy for HAND, even in the absence of full viral eradication.
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Affiliation(s)
- Kristen A McLaurin
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S Limestone Street, Lexington, KY, 40508, USA
| | - Hailong Li
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
| | - Kamel Khalili
- Center for Neurovirology and Gene Editing, Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, 3500 N. Broad Street, 7th Floor, Philadelphia, PA, 19140, USA
| | - Charles F Mactutus
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
| | - Rosemarie M Booze
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA.
- Department of Psychology, Carolina Trustees Professor and Bicentennial Endowed Chair of Behavioral Neuroscience, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA.
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11
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Bouzidi MS, Dossani ZY, Di Benedetto C, Raymond KA, Desai S, Chavez LR, Betancur P, Pillai SK. High-resolution Inference of Multiplexed Anti-HIV Gene Editing using Single-Cell Targeted DNA Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.576921. [PMID: 38328062 PMCID: PMC10849705 DOI: 10.1101/2024.01.24.576921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Gene therapy-based HIV cure strategies typically aim to excise the HIV provirus directly, or target host dependency factors (HDFs) that support viral persistence. Cure approaches will likely require simultaneous co-targeting of multiple sites within the HIV genome to prevent evolution of resistance, and/or co-targeting of multiple HDFs to fully render host cells refractory to HIV infection. Bulk cell-based methods do not enable inference of co-editing within individual viral or target cell genomes, and do not discriminate between monoallelic and biallelic gene disruption. Here, we describe a targeted single-cell DNA sequencing (scDNA-seq) platform characterizing the near full-length HIV genome and 50 established HDF genes, designed to evaluate anti-HIV gene therapy strategies. We implemented the platform to investigate the capacity of multiplexed CRISPR-Cas9 ribonucleoprotein complexes (Cas9-RNPs) to simultaneously 1) inactivate the HIV provirus, and 2) knockout the CCR5 and CXCR4 HDF (entry co-receptor) genes in microglia and primary monocyte-derived macrophages (MDMs). Our scDNA-seq pipeline revealed that antiviral gene editing is rarely observed at multiple loci (or both alleles of a locus) within an individual cell, and editing probabilities across sites are linked. Our results demonstrate that single-cell sequencing is critical to evaluate the true efficacy and therapeutic potential of HIV gene therapy.
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Affiliation(s)
- Mohamed S. Bouzidi
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Zain Y. Dossani
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | - Kyle A. Raymond
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR3569, Paris, France
| | | | - Leonard R. Chavez
- Vitalant Research Institute, San Francisco, CA, USA
- Rewrite Therapeutics, Berkeley, CA, USA
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Satish K. Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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12
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Dampier W, Berman R, Nonnemacher MR, Wigdahl B. Computational analysis of cas proteins unlocks new potential in HIV-1 targeted gene therapy. Front Genome Ed 2024; 5:1248982. [PMID: 38239625 PMCID: PMC10794619 DOI: 10.3389/fgeed.2023.1248982] [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: 06/27/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction: The human immunodeficiency virus type 1 (HIV-1) pandemic has been slowed with the advent of anti-retroviral therapy (ART). However, ART is not a cure and as such has pushed the disease into a chronic infection. One potential cure strategy that has shown promise is the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas gene editing system. It has recently been shown to successfully edit and/or excise the integrated provirus from infected cells and inhibit HIV-1 in vitro, ex vivo, and in vivo. These studies have primarily been conducted with SpCas9 or SaCas9. However, additional Cas proteins are discovered regularly and modifications to these known proteins are being engineered. The alternative Cas molecules have different requirements for protospacer adjacent motifs (PAMs) which impact the possible targetable regions of HIV-1. Other modifications to the Cas protein or gRNA handle impact the tolerance for mismatches between gRNA and the target. While reducing off-target risk, this impacts the ability to fully account for HIV-1 genetic variability. Methods: This manuscript strives to examine these parameter choices using a computational approach for surveying the suitability of a Cas editor for HIV-1 gene editing. The Nominate, Diversify, Narrow, Filter (NDNF) pipeline measures the safety, broadness, and effectiveness of a pool of potential gRNAs for any PAM. This technique was used to evaluate 46 different potential Cas editors for their HIV therapeutic potential. Results: Our examination revealed that broader PAMs that improve the targeting potential of editors like SaCas9 and LbCas12a have larger pools of useful gRNAs, while broader PAMs reduced the pool of useful SpCas9 gRNAs yet increased the breadth of targetable locations. Investigation of the mismatch tolerance of Cas editors indicates a 2-missmatch tolerance is an ideal balance between on-target sensitivity and off-target specificity. Of all of the Cas editors examined, SpCas-NG and SPRY-Cas9 had the highest number of overall safe, broad, and effective gRNAs against HIV. Discussion: Currently, larger proteins and wider PAMs lead to better targeting capacity. This implies that research should either be targeted towards delivering longer payloads or towards increasing the breadth of currently available small Cas editors. With the discovery and adoption of additional Cas editors, it is important for researchers in the HIV-1 gene editing field to explore the wider world of Cas editors.
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Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
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13
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McCutcheon SR, Swartz AM, Brown MC, Barrera A, McRoberts Amador C, Siklenka K, Humayun L, Ter Weele MA, Isaacs JM, Reddy TE, Allen AS, Nair SK, Antonia SJ, Gersbach CA. Transcriptional and epigenetic regulators of human CD8 + T cell function identified through orthogonal CRISPR screens. Nat Genet 2023; 55:2211-2223. [PMID: 37945901 PMCID: PMC10703699 DOI: 10.1038/s41588-023-01554-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 11/12/2023]
Abstract
Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phenotypes has potential to improve T cell therapies. Here we developed pooled, epigenetic CRISPR screening approaches to systematically profile the effects of activating or repressing 120 transcriptional and epigenetic regulators on human CD8+ T cell state. We found that BATF3 overexpression promoted specific features of memory T cells and attenuated gene programs associated with cytotoxicity, regulatory T cell function, and exhaustion. Upon chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. Moreover, BATF3 enhanced the potency of CAR T cells in both in vitro and in vivo tumor models and programmed a transcriptional profile that correlates with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens that defined cofactors and downstream mediators of the BATF3 gene network.
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Affiliation(s)
- Sean R McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Adam M Swartz
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Michael C Brown
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Christian McRoberts Amador
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Durham, NC, USA
| | - Keith Siklenka
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Lucas Humayun
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Maria A Ter Weele
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - James M Isaacs
- Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC, USA
| | - Timothy E Reddy
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Andrew S Allen
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Smita K Nair
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
- Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Scott J Antonia
- Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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14
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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [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: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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15
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Lyons DE, Kumar P, Roan NR, Defechereux PA, Feschotte C, Lange UC, Murthy N, Sameshima P, Verdin E, Ake JA, Parsons MS, Nath A, Gianella S, Smith DM, Kallas EG, Villa TJ, Strange R, Mwesigwa B, Furler O’Brien RL, Nixon DF, Ndhlovu LC, Valente ST, Ott M. HIV-1 Remission: Accelerating the Path to Permanent HIV-1 Silencing. Viruses 2023; 15:2171. [PMID: 38005849 PMCID: PMC10674359 DOI: 10.3390/v15112171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Despite remarkable progress, a cure for HIV-1 infection remains elusive. Rebound competent latent and transcriptionally active reservoir cells persevere despite antiretroviral therapy and rekindle infection due to inefficient proviral silencing. We propose a novel "block-lock-stop" approach, entailing long term durable silencing of viral expression towards an irreversible transcriptionally inactive latent provirus to achieve long term antiretroviral free control of the virus. A graded transformation of remnant HIV-1 in PLWH from persistent into silent to permanently defective proviruses is proposed, emulating and accelerating the natural path that human endogenous retroviruses (HERVs) take over millions of years. This hypothesis was based on research into delineating the mechanisms of HIV-1 latency, lessons from latency reversing agents and advances of Tat inhibitors, as well as expertise in the biology of HERVs. Insights from elite controllers and the availability of advanced genome engineering technologies for the direct excision of remnant virus set the stage for a rapid path to an HIV-1 cure.
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Affiliation(s)
- Danielle E. Lyons
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA;
| | - Nadia R. Roan
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Patricia A. Defechereux
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | | | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA;
- Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - Pauline Sameshima
- Faculty of Education, Lakehead University, Thunder Bay, ON P7B 5E1, Canada;
| | - Eric Verdin
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Julie A. Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (M.S.P.)
| | - Matthew S. Parsons
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA (M.S.P.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD 20824, USA;
| | - Sara Gianella
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Davey M. Smith
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Esper G. Kallas
- Department of Infectious and Parasitic Diseases, University of Sao Paulo, São Paulo 04023-900, Brazil
| | - Thomas J. Villa
- HOPE Martin Delaney Collaboratory for HIV Cure Research Community Engagement Ambassador, Washinton, DC 20004, USA (R.S.)
- National HIV & Aging Advocacy Network, Washington, DC 20004, USA
| | - Richard Strange
- HOPE Martin Delaney Collaboratory for HIV Cure Research Community Engagement Ambassador, Washinton, DC 20004, USA (R.S.)
| | - Betty Mwesigwa
- Research Department, Makerere University Walter Reed Project, Kampala P.O Box 7062, Uganda
| | - Robert L. Furler O’Brien
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Susana T. Valente
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, USA
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
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16
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McLaurin KA, Li H, Khalili K, Mactutus CF, Booze RM. HIV-1 mRNA Knockdown with CRISPR/Cas9 Enhances Neurocognitive Function. RESEARCH SQUARE 2023:rs.3.rs-3266933. [PMID: 37886577 PMCID: PMC10602171 DOI: 10.21203/rs.3.rs-3266933/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Mixed glia are infiltrated with HIV-1 virus early in the course of infection leading to the development of a persistent viral reservoir in the central nervous system. Modification of the HIV-1 genome using gene editing techniques, including CRISPR/Cas9, has shown great promise towards eliminating HIV-1 viral reservoirs; whether these techniques are capable of removing HIV-1 viral proteins from mixed glia, however, has not been systematically evaluated. Herein, the efficacy of adeno-associated virus 9 (AAV9)-CRISPR/Cas9 gene editing for eliminating HIV-1 mRNA from cortical mixed glia was evaluated in vitro and in vivo. In vitro, a within-subjects experimental design was utilized to treat mixed glia isolated from neonatal HIV-1 transgenic (Tg) rats with varying doses (0, 0.9, 1.8, 2.7, 3.6, 4.5, or 5.4 μL) of CRISPR/Cas9 for 72 hours. Dose-dependent decreases in the number of HIV-1 mRNA, quantified using an innovative in situ hybridization technique, were observed in a subset (i.e., n=5 out of 8) of primary mixed glia. In vivo, HIV-1 Tg rats were retro-orbitally inoculated with CRISPR/Cas9 for two weeks, whereby treatment resulted in profound excision (i.e., approximately 53.2%) of HIV-1 mRNA from the mPFC. Given incomplete excision of the HIV-1 viral genome, the clinical relevance of HIV-1 mRNA knockdown for eliminating neurocognitive impairments was evaluated via examination of temporal processing, a putative neurobehavioral mechanism underlying HIV-1 associated neurocognitive disorders (HAND). Indeed, treatment with CRISPR/Cas9 partially restored the developmental trajectory of temporal processing. Proof-of-concept studies, therefore, support the susceptibility of mixed glia to gene editing and the potential of CRISPR/Cas9 to serve as a novel therapeutic strategy for HAND, even in the absence of full viral eradication.
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17
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Hryhorowicz M, Lipiński D, Zeyland J. Evolution of CRISPR/Cas Systems for Precise Genome Editing. Int J Mol Sci 2023; 24:14233. [PMID: 37762535 PMCID: PMC10532350 DOI: 10.3390/ijms241814233] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
The bacteria-derived CRISPR/Cas (an acronym for regularly interspaced short palindromic repeats/CRISPR-associated protein) system is currently the most widely used, versatile, and convenient tool for genome engineering. CRISPR/Cas-based technologies have been applied to disease modeling, gene therapies, transcriptional modulation, and diagnostics. Nevertheless, some challenges remain, such as the risk of immunological reactions or off-target effects. To overcome these problems, many new methods and CRISPR/Cas-based tools have been developed. In this review, we describe the current classification of CRISPR systems and new precise genome-editing technologies, summarize the latest applications of this technique in several fields of research, and, finally, discuss CRISPR/Cas system limitations, ethical issues, and challenges.
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Affiliation(s)
- Magdalena Hryhorowicz
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (D.L.); (J.Z.)
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18
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Fan M, Bao Y, Berkhout B, Herrera-Carrillo E. CRISPR-Cas12b enables a highly efficient attack on HIV proviral DNA in T cell cultures. Biomed Pharmacother 2023; 165:115046. [PMID: 37379644 DOI: 10.1016/j.biopha.2023.115046] [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: 02/24/2023] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND The novel endonuclease Cas12b was engineered for targeted genome editing in mammalian cells and is a promising tool for certain applications because of its small size, high sequence specificity and ability to generate relatively large deletions. We previously reported inhibition of the human immunodeficiency virus (HIV) in cell culture infections upon attack of the integrated viral DNA genome by spCas9 and Cas12a. METHODS We now tested the ability of the Cas12b endonuclease to suppress a spreading HIV infection in cell culture with anti-HIV gRNAs. Virus inhibition was tested in long-term HIV replication studies, which allowed us to test for viral escape and the potential for reaching a CURE of the infected T cells. FINDINGS We demonstrate that Cas12b can achieve complete HIV inactivation with only a single gRNA, a result for which Cas9 required two gRNAs. When the Cas12b system is programmed with two antiviral gRNAs, the overall anti-HIV potency is improved and more grossly mutated HIV proviruses are generated as a result of multiple cut-repair actions. Such "hypermutated" HIV proviruses are more likely to be defective due to mutation of multiple essential parts of the HIV genome. We report that the mutational profiles of the Cas9, Cas12a and Cas12b endonucleases differ significantly, which may have an impact on the level of virus inactivation. These combined results make Cas12b the preferred editing system for HIV-inactivation. INTERPRETATION These results provide in vitro "proof of concept' for CRISPR-Cas12b mediated HIV-1 inactivation.
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Affiliation(s)
- Minghui Fan
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Yuanling Bao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
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19
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Stahl EC, Sabo JK, Kang MH, Allen R, Applegate E, Kim SE, Kwon Y, Seth A, Lemus N, Salinas-Rios V, Soczek KM, Trinidad M, Vo LT, Jeans C, Wozniak A, Morris T, Kimberlin A, Foti T, Savage DF, Doudna JA. Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs. Mol Ther 2023; 31:2422-2438. [PMID: 37403358 PMCID: PMC10422012 DOI: 10.1016/j.ymthe.2023.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/18/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023] Open
Abstract
Transient delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) into the central nervous system (CNS) for therapeutic genome editing could avoid limitations of viral vector-based delivery including cargo capacity, immunogenicity, and cost. Here, we tested the ability of cell-penetrant Cas9 RNPs to edit the mouse striatum when introduced using a convection-enhanced delivery system. These transient Cas9 RNPs showed comparable editing of neurons and reduced adaptive immune responses relative to one formulation of Cas9 delivered using AAV serotype 9. The production of ultra-low endotoxin Cas9 protein manufactured at scale further improved innate immunity. We conclude that injection-based delivery of minimally immunogenic CRISPR genome editing RNPs into the CNS provides a valuable alternative to virus-mediated genome editing.
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Affiliation(s)
- Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer K Sabo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Min Hyung Kang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Allen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth Applegate
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shin Eui Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yoonjin Kwon
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anmol Seth
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Lemus
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Viviana Salinas-Rios
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Linda T Vo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chris Jeans
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | | | | | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, Berkeley, San Francisco, CA 94114, USA.
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20
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Zhang C, Zaman LA, Poluektova LY, Gorantla S, Gendelman HE, Dash PK. Humanized Mice for Studies of HIV-1 Persistence and Elimination. Pathogens 2023; 12:879. [PMID: 37513726 PMCID: PMC10383313 DOI: 10.3390/pathogens12070879] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
A major roadblock to achieving a cure for human immunodeficiency virus type one (HIV-1) is the persistence of latent viral infections in the cells and tissue compartments of an infected human host. Latent HIV-1 proviral DNA persists in resting memory CD4+ T cells and mononuclear phagocytes (MPs; macrophages, microglia, and dendritic cells). Tissue viral reservoirs of both cell types reside in the gut, lymph nodes, bone marrow, spleen, liver, kidney, skin, adipose tissue, reproductive organs, and brain. However, despite the identification of virus-susceptible cells, several limitations persist in identifying broad latent reservoirs in infected persons. The major limitations include their relatively low abundance, the precise identification of latently infected cells, and the lack of biomarkers for identifying latent cells. While primary MP and CD4+ T cells and transformed cell lines are used to interrogate mechanisms of HIV-1 persistence, they often fail to accurately reflect the host cells and tissue environments that carry latent infections. Given the host specificity of HIV-1, there are few animal models that replicate the natural course of viral infection with any precision. These needs underlie the importance of humanized mouse models as both valuable and cost-effective tools for studying viral latency and subsequently identifying means of eliminating it. In this review, we discuss the advantages and limitations of humanized mice for studies of viral persistence and latency with an eye toward using these models to test antiretroviral and excision therapeutics. The goals of this research are to use the models to address how and under which circumstances HIV-1 latency can be detected and eliminated. Targeting latent reservoirs for an ultimate HIV-1 cure is the task at hand.
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Affiliation(s)
| | | | | | | | | | - Prasanta K. Dash
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA (S.G.)
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21
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Javed MU, Hayat MT, Mukhtar H, Imre K. CRISPR-Cas9 System: A Prospective Pathway toward Combatting Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1075. [PMID: 37370394 DOI: 10.3390/antibiotics12061075] [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: 03/14/2023] [Revised: 05/05/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic resistance is rising to dangerously high levels throughout the world. To cope with this problem, scientists are working on CRISPR-based research so that antibiotic-resistant bacteria can be killed and attacked almost as quickly as antibiotic-sensitive bacteria. Nuclease activity is found in Cas9, which can be programmed with a specific target sequence. This mechanism will only attack pathogens in the microbiota while preserving commensal bacteria. This article portrays the delivery methods used in the CRISPR-Cas system, which are both viral and non-viral, along with its implications and challenges, such as microbial dysbiosis, off-target effects, and failure to counteract intracellular infections. CRISPR-based systems have a lot of applications, such as correcting mutations, developing diagnostics for infectious diseases, improving crops productions, improving breeding techniques, etc. In the future, CRISPR-based systems will revolutionize the world by curing diseases, improving agriculture, and repairing genetic disorders. Though all the drawbacks of the technology, CRISPR carries great potential; thus, the modification and consideration of some aspects could result in a mind-blowing technique to attain all the applications listed and present a game-changing potential.
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Affiliation(s)
| | | | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Kalman Imre
- Department of Animal Production and Veterinary Public Health, Faculty of Veterinary Medicine, University of Life Sciences "King Mihai I" from Timişoara, 300645 Timișoara, Romania
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22
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Dash PK, Chen C, Kaminski R, Su H, Mancuso P, Sillman B, Zhang C, Liao S, Sravanam S, Liu H, Waight E, Guo L, Mathews S, Sariyer R, Mosley RL, Poluektova LY, Caocci M, Amini S, Gorantla S, Burdo TH, Edagwa B, Gendelman HE, Khalili K. CRISPR editing of CCR5 and HIV-1 facilitates viral elimination in antiretroviral drug-suppressed virus-infected humanized mice. Proc Natl Acad Sci U S A 2023; 120:e2217887120. [PMID: 37126704 PMCID: PMC10175831 DOI: 10.1073/pnas.2217887120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/14/2023] [Indexed: 05/03/2023] Open
Abstract
Treatment of HIV-1ADA-infected CD34+ NSG-humanized mice with long-acting ester prodrugs of cabotegravir, lamivudine, and abacavir in combination with native rilpivirine was followed by dual CRISPR-Cas9 C-C chemokine receptor type five (CCR5) and HIV-1 proviral DNA gene editing. This led to sequential viral suppression, restoration of absolute human CD4+ T cell numbers, then elimination of replication-competent virus in 58% of infected mice. Dual CRISPR therapies enabled the excision of integrated proviral DNA in infected human cells contained within live infected animals. Highly sensitive nucleic acid nested and droplet digital PCR, RNAscope, and viral outgrowth assays affirmed viral elimination. HIV-1 was not detected in the blood, spleen, lung, kidney, liver, gut, bone marrow, and brain of virus-free animals. Progeny virus from adoptively transferred and CRISPR-treated virus-free mice was neither detected nor recovered. Residual HIV-1 DNA fragments were easily seen in untreated and viral-rebounded animals. No evidence of off-target toxicities was recorded in any of the treated animals. Importantly, the dual CRISPR therapy demonstrated statistically significant improvements in HIV-1 cure percentages compared to single treatments. Taken together, these observations underscore a pivotal role of combinatorial CRISPR gene editing in achieving the elimination of HIV-1 infection.
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Affiliation(s)
- Prasanta K. Dash
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Chen Chen
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - Rafal Kaminski
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - Hang Su
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Pietro Mancuso
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - Brady Sillman
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Chen Zhang
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Shuren Liao
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - Sruthi Sravanam
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Hong Liu
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - Emiko Waight
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Lili Guo
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Saumi Mathews
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Rahsan Sariyer
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - R. Lee Mosley
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Larisa Y. Poluektova
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Maurizio Caocci
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - Shohreh Amini
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA19122
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Tricia H. Burdo
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
| | - Benson Edagwa
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Howard E. Gendelman
- Department of Pharmacology and Experimental Neuroscience, Center for Neurodegenerative Diseases, University of Nebraska Medical Center, Omaha, NE68198-5880
| | - Kamel Khalili
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA19140
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23
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McCutcheon SR, Swartz AM, Brown MC, Barrera A, Amador CM, Siklenka K, Humayun L, Isaacs JM, Reddy TE, Nair S, Antonia S, Gersbach CA. Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538906. [PMID: 37205457 PMCID: PMC10187198 DOI: 10.1101/2023.05.01.538906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The clinical response to adoptive T cell therapies is strongly associated with transcriptional and epigenetic state. Thus, technologies to discover regulators of T cell gene networks and their corresponding phenotypes have great potential to improve the efficacy of T cell therapies. We developed pooled CRISPR screening approaches with compact epigenome editors to systematically profile the effects of activation and repression of 120 transcription factors and epigenetic modifiers on human CD8+ T cell state. These screens nominated known and novel regulators of T cell phenotypes with BATF3 emerging as a high confidence gene in both screens. We found that BATF3 overexpression promoted specific features of memory T cells such as increased IL7R expression and glycolytic capacity, while attenuating gene programs associated with cytotoxicity, regulatory T cell function, and T cell exhaustion. In the context of chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. CAR T cells overexpressing BATF3 significantly outperformed control CAR T cells in both in vitro and in vivo tumor models. Moreover, we found that BATF3 programmed a transcriptional profile that correlated with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens with and without BATF3 overexpression to define co-factors and downstream factors of BATF3, as well as other therapeutic targets. These screens pointed to a model where BATF3 interacts with JUNB and IRF4 to regulate gene expression and illuminated several other novel targets for further investigation.
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Affiliation(s)
- Sean R. McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Adam M. Swartz
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael C. Brown
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Christian McRoberts Amador
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Pharmacology and Cancer Biology, Durham, NC 27710, USA
| | - Keith Siklenka
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Lucas Humayun
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - James M. Isaacs
- Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC 27710, USA
| | - Timothy E. Reddy
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Smita Nair
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Scott Antonia
- Duke Cancer Institute Center for Cancer Immunotherapy, Duke University School of Medicine, Durham, NC 27710, USA
| | - Charles A. Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
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24
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Allen AG, Chung CH, Worrell SD, Nwaozo G, Madrid R, Mele AR, Dampier W, Nonnemacher MR, Wigdahl B. Assessment of anti-HIV-1 guide RNA efficacy in cells containing the viral target sequence, corresponding gRNA, and CRISPR/Cas9. Front Genome Ed 2023; 5:1101483. [PMID: 37124096 PMCID: PMC10134072 DOI: 10.3389/fgeed.2023.1101483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 gene editing system has been shown to be effective at inhibiting human immunodeficiency virus type 1 (HIV-1). Studies have not consistently used a trackable dual reporter system to determine what cells received the Cas9/gRNA to determine the overall knockdown of HIV. Some studies have used stably transduced cells under drug selection to accomplish this goal. Here a two-color system was used that allows tracking of viral protein expression and which cells received the CRISPR/Cas9 system. These experiments ensured that each gRNA used was a perfect match to the intended target to remove this variable. The data showed that gRNAs targeting the transactivation response element (TAR) region or other highly conserved regions of the HIV-1 genome were effective at stopping viral gene expression, with multiple assays demonstrating greater than 95 percent reduction. Conversely, gRNAs targeting conserved sites of the 5' portion of the U3 region were largely ineffective, demonstrating that the location of edits in the long terminal repeat (LTR) matter with respect to function. In addition, it was observed that a gRNA targeting Tat was effective in a T-cell model of HIV-1 latency. Taken together, these studies demonstrated gRNAs designed to highly conserved functional regions have near 100% efficacy in vitro in cells known to have received the Cas9/gRNA pair.
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Affiliation(s)
- Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Stephen D. Worrell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Glad Nwaozo
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rebekah Madrid
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Anthony R. Mele
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
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25
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Zhou L, Yao S. Recent advances in therapeutic CRISPR-Cas9 genome editing: mechanisms and applications. MOLECULAR BIOMEDICINE 2023; 4:10. [PMID: 37027099 PMCID: PMC10080534 DOI: 10.1186/s43556-023-00115-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/04/2023] [Indexed: 04/08/2023] Open
Abstract
Recently, clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 derived editing tools had significantly improved our ability to make desired changes in the genome. Wild-type Cas9 protein recognizes the target genomic loci and induced local double strand breaks (DSBs) in the guidance of small RNA molecule. In mammalian cells, the DSBs are mainly repaired by endogenous non-homologous end joining (NHEJ) pathway, which is error prone and results in the formation of indels. The indels can be harnessed to interrupt gene coding sequences or regulation elements. The DSBs can also be fixed by homology directed repair (HDR) pathway to introduce desired changes, such as base substitution and fragment insertion, when proper donor templates are provided, albeit in a less efficient manner. Besides making DSBs, Cas9 protein can be mutated to serve as a DNA binding platform to recruit functional modulators to the target loci, performing local transcriptional regulation, epigenetic remolding, base editing or prime editing. These Cas9 derived editing tools, especially base editors and prime editors, can introduce precise changes into the target loci at a single-base resolution and in an efficient and irreversible manner. Such features make these editing tools very promising for therapeutic applications. This review focuses on the evolution and mechanisms of CRISPR-Cas9 derived editing tools and their applications in the field of gene therapy.
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Affiliation(s)
- Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
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26
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Tang Y, Jiang G. Eradication of human immunodeficiency virus-1 reservoir in the brain microglia. Neural Regen Res 2023; 18:552-553. [PMID: 36018174 PMCID: PMC9727433 DOI: 10.4103/1673-5374.350198] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Yuyang Tang
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guochun Jiang
- University of North Carolina HIV Cure Center, Institute of Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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27
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Hussein M, Molina MA, Berkhout B, Herrera-Carrillo E. A CRISPR-Cas Cure for HIV/AIDS. Int J Mol Sci 2023; 24:1563. [PMID: 36675077 PMCID: PMC9863116 DOI: 10.3390/ijms24021563] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Human immunodeficiency virus (HIV) infections and HIV-induced acquired immunodeficiency syndrome (AIDS) continue to represent a global health burden. There is currently no effective vaccine, nor any cure, for HIV infections; existing antiretroviral therapy can suppress viral replication, but only as long as antiviral drugs are taken. HIV infects cells of the host immune system, and it can establish a long-lived viral reservoir, which can be targeted and edited through gene therapy. Gene editing platforms based on the clustered regularly interspaced palindromic repeat-Cas system (CRISPR-Cas) have been recognized as promising tools in the development of gene therapies for HIV infections. In this review, we evaluate the current landscape of CRISPR-Cas-based therapies against HIV, with an emphasis on the infection biology of the virus as well as the activity of host restriction factors. We discuss the potential of a combined CRISPR-Cas approach that targets host and viral genes to activate antiviral host factors and inhibit viral replication simultaneously. Lastly, we focus on the challenges and potential solutions of CRISPR-Cas gene editing approaches in achieving an HIV cure.
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Affiliation(s)
| | | | | | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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28
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Mohammadian Gol T, Ureña-Bailén G, Hou Y, Sinn R, Antony JS, Handgretinger R, Mezger M. CRISPR medicine for blood disorders: Progress and challenges in delivery. Front Genome Ed 2023; 4:1037290. [PMID: 36687779 PMCID: PMC9853164 DOI: 10.3389/fgeed.2022.1037290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Blood disorders are a group of diseases including hematological neoplasms, clotting disorders and orphan immune deficiency diseases that affects human health. Current improvements in genome editing based therapeutics demonstrated preclinical and clinical proof to treat different blood disorders. Genome editing components such as Cas nucleases, guide RNAs and base editors are supplied in the form of either a plasmid, an mRNA, or a ribonucleoprotein complex. The most common delivery vehicles for such components include viral vectors (e.g., AAVs and RV), non-viral vectors (e.g., LNPs and polymers) and physical delivery methods (e.g., electroporation and microinjection). Each of the delivery vehicles specified above has its own advantages and disadvantages and the development of a safe transferring method for ex vivo and in vivo application of genome editing components is still a big challenge. Moreover, the delivery of genome editing payload to the target blood cells possess key challenges to provide a possible cure for patients with inherited monogenic blood diseases and hematological neoplastic tumors. Here, we critically review and summarize the progress and challenges related to the delivery of genome editing elements to relevant blood cells in an ex vivo or in vivo setting. In addition, we have attempted to provide a future clinical perspective of genome editing to treat blood disorders with possible clinical grade improvements in delivery methods.
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Affiliation(s)
- Tahereh Mohammadian Gol
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Guillermo Ureña-Bailén
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Yujuan Hou
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Ralph Sinn
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Justin S. Antony
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Rupert Handgretinger
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany,Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
| | - Markus Mezger
- Department of Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany,*Correspondence: Markus Mezger,
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29
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Bhowmik R, Chaubey B. CRISPR/Cas9: a tool to eradicate HIV-1. AIDS Res Ther 2022; 19:58. [PMID: 36457057 PMCID: PMC9713993 DOI: 10.1186/s12981-022-00483-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022] Open
Abstract
The development of antiretroviral therapy (ART) has been effective in suppressing HIV replication. However, severe drug toxicities due to the therapy and its failure in targeting the integrated proviral genome have led to the introduction of a new paradigm of gene-based therapies. With its effective inhibition and high precision, clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein-9 nuclease (Cas9) or CRISPR/Cas9 has emerged as an effective genome editing tool in the last decade. Mediated by guide RNAs (gRNAs), Cas9 endonuclease acts like genetic scissors that can modify specific target sites. With this concept, CRISPR/Cas9 has been used to target the integrated proviral HIV-1 genome both in in vitro as well as in vivo studies including non-human primates. The CRISPR has also been tested for targeting latent HIV-1 by modulating the proviral transcription with the help of a specialized Cas9 mutant. Overcoming the limitations of the current therapy, CRISPR has the potential to become the primary genome editing tool for eradicating HIV-1 infection. In this review, we summarize the recent advancements of CRISPR to target the proviral HIV-1 genome, the challenges and future prospects.
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Affiliation(s)
- Ruchira Bhowmik
- grid.59056.3f0000 0001 0664 9773Virology Lab, Centre for Advance Study, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Binay Chaubey
- grid.59056.3f0000 0001 0664 9773Virology Lab, Centre for Advance Study, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
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30
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Fraker S, Atkinson B, Heredia A. Humanized mouse models for preclinical evaluation of HIV cure strategies. AIDS Rev 2022; 24:139-151. [PMID: 35622983 PMCID: PMC9643647 DOI: 10.24875/aidsrev.22000013] [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: 04/04/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
Abstract
Although the world is currently focused on the COVID-19 pandemic, HIV/AIDS remains a significant threat to public health. To date, the HIV/AIDS pandemic has claimed the lives of over 36 million people, while nearly 38 million people are currently living with the virus. Despite the undeniable success of antiretroviral therapy (ART) in controlling HIV, the medications are not curative. Soon after initial infection, HIV integrates into the genome of infected cells as a provirus, primarily, within CD4+ T lymphocytes and tissue macrophages. When not actively transcribed, the provirus is referred to as a latent reservoir because it is hidden to the immune system and ART. Following ART discontinuation, HIV may emerge from the replication-competent proviruses and resumes the infection of healthy cells. Thus, these latent reservoirs are a major obstacle to an HIV cure, and their removal remains a priority. A vital aspect in the development of curative therapies is the demonstration of efficacy in an animal model, such as the humanized mouse model. Therefore, optimization, standardization, and validation of the humanized mouse model are a priority. The purpose of this review article is to provide an update on existing humanized mouse models, highlighting the advantages and disadvantages of each as they pertain to HIV cure studies and to review the approaches to curative therapies that are under investigation.
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Affiliation(s)
- Sally Fraker
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Benjamin Atkinson
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Alonso Heredia
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201
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31
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Medrano-Garcia S, Morales-Cano D, Barreira B, Vera-Zambrano A, Kumar R, Kosanovic D, Schermuly RT, Graham BB, Perez-Vizcaino F, Mathie A, Savai R, Pullamseti S, Butrous G, Fernández-Malavé E, Cogolludo A. HIV and Schistosoma Co-Exposure Leads to Exacerbated Pulmonary Endothelial Remodeling and Dysfunction Associated with Altered Cytokine Landscape. Cells 2022; 11:cells11152414. [PMID: 35954255 PMCID: PMC9368261 DOI: 10.3390/cells11152414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/19/2022] [Accepted: 07/27/2022] [Indexed: 11/27/2022] Open
Abstract
HIV and Schistosoma infections have been individually associated with pulmonary vascular disease. Co-infection with these pathogens is very common in tropical areas, with an estimate of six million people co-infected worldwide. However, the effects of HIV and Schistosoma co-exposure on the pulmonary vasculature and its impact on the development of pulmonary vascular disease are largely unknown. Here, we have approached these questions by using a non-infectious animal model based on lung embolization of Schistosoma mansoni eggs in HIV-1 transgenic (HIV) mice. Schistosome-exposed HIV mice but not wild-type (Wt) counterparts showed augmented pulmonary arterial pressure associated with markedly suppressed endothelial-dependent vasodilation, increased endothelial remodeling and vessel obliterations, formation of plexiform-like lesions and a higher degree of perivascular fibrosis. In contrast, medial wall muscularization was similarly increased in both types of mice. Moreover, HIV mice displayed an impaired immune response to parasite eggs in the lung, as suggested by decreased pulmonary leukocyte infiltration, small-sized granulomas, and augmented residual egg burden. Notably, vascular changes in co-exposed mice were associated with increased expression of proinflammatory and profibrotic cytokines, including IFN-γ and IL-17A in CD4+ and γδ T cells and IL-13 in myeloid cells. Collectively, our study shows for the first time that combined pulmonary persistence of HIV proteins and Schistosoma eggs, as it may occur in co-infected people, alters the cytokine landscape and targets the vascular endothelium for aggravated pulmonary vascular pathology. Furthermore, it provides an experimental model for the understanding of pulmonary vascular disease associated with HIV and Schistosoma co-morbidity.
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Affiliation(s)
- Sandra Medrano-Garcia
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35305 Giessen, Germany
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine and Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28040 Madrid, Spain
| | - Daniel Morales-Cano
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, 28040 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28040 Madrid, Spain
- Correspondence: (D.M.-C.); (A.C.); Tel.: +34-913947120 (A.C.)
| | - Bianca Barreira
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, 28040 Madrid, Spain
| | - Alba Vera-Zambrano
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, 28040 Madrid, Spain
| | - Rahul Kumar
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Djuro Kosanovic
- Department of Pulmonology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Ralph Theo Schermuly
- Department of internal Medicine, Justus-Liebig University, Member of the German Center for Lung Research (DZL), 35305 Giessen, Germany
| | - Brian B. Graham
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Francisco Perez-Vizcaino
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, 28040 Madrid, Spain
| | - Alistair Mathie
- Medway School of Pharmacy, University of Kent and University of Greenwich, Chatham ME4 4BF, UK
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35305 Giessen, Germany
- Department of internal Medicine, Justus-Liebig University, Member of the German Center for Lung Research (DZL), 35305 Giessen, Germany
| | - Soni Pullamseti
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35305 Giessen, Germany
- Department of internal Medicine, Justus-Liebig University, Member of the German Center for Lung Research (DZL), 35305 Giessen, Germany
| | - Ghazwan Butrous
- Medway School of Pharmacy, University of Kent and University of Greenwich, Chatham ME4 4BF, UK
| | - Edgar Fernández-Malavé
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine and Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28040 Madrid, Spain
| | - Angel Cogolludo
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, 28040 Madrid, Spain
- Correspondence: (D.M.-C.); (A.C.); Tel.: +34-913947120 (A.C.)
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A Novel Approach of Antiviral Drugs Targeting Viral Genomes. Microorganisms 2022; 10:microorganisms10081552. [PMID: 36013970 PMCID: PMC9414836 DOI: 10.3390/microorganisms10081552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Outbreaks of viral diseases, which cause morbidity and mortality in animals and humans, are increasing annually worldwide. Vaccines, antiviral drugs, and antibody therapeutics are the most effective tools for combating viral infection. The ongoing coronavirus disease 2019 pandemic, in particular, raises an urgent need for the development of rapid and broad-spectrum therapeutics. Current antiviral drugs and antiviral antibodies, which are mostly specific at protein levels, have encountered difficulties because the rapid evolution of mutant viral strains resulted in drug resistance. Therefore, degrading viral genomes is considered a novel approach for developing antiviral drugs. The current article highlights all potent candidates that exhibit antiviral activity by digesting viral genomes such as RNases, RNA interference, interferon-stimulated genes 20, and CRISPR/Cas systems. Besides that, we introduce a potential single-chain variable fragment (scFv) that presents antiviral activity against various DNA and RNA viruses due to its unique nucleic acid hydrolyzing characteristic, promoting it as a promising candidate for broad-spectrum antiviral therapeutics.
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Peng Y, Lv J, Ding L, Gong X, Zhou Q. Responsible governance of human germline genome editing in China. Biol Reprod 2022; 107:261-268. [PMID: 35640230 PMCID: PMC9310509 DOI: 10.1093/biolre/ioac114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/20/2022] [Accepted: 05/26/2022] [Indexed: 11/29/2022] Open
Abstract
Considerable improvements have been made to gene editing technology, which has been increasingly applied to research involving humans. Nevertheless, human heritable germline genome editing is associated with a series of potential ethical, legal, and social risks, which have generated major controversies and discussions worldwide, especially after the “gene-edited babies” incident. Influenced by this incident, China has realized the importance of ethical governance in the field of life science and technology, has accelerated legislative and policy efforts in this field, and has gradually moved toward the direction of “precautionary” ethical governance. Black letter analysis, big data public opinion analysis, and other research methods are used in this paper. This paper explores the scientific background, ethical debates, and latest developments regarding China’s regulatory framework for human germline gene editing after the “gene-edited babies” controversy and provides several recommendations on the future governance system of human germline gene editing in China. This paper argues that in recent years, the ethics governance of germline genome editing in China has been accelerated and great changes have been made. However, the regulatory system for germline genome editing requires further improvement in three aspects: coordination of legislation and agencies, establishment of an ethics review system at high levels, and public participation and education.
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Affiliation(s)
- Yaojin Peng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jianwei Lv
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Lulu Ding
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Gong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
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Maslennikova A, Mazurov D. Application of CRISPR/Cas Genomic Editing Tools for HIV Therapy: Toward Precise Modifications and Multilevel Protection. Front Cell Infect Microbiol 2022; 12:880030. [PMID: 35694537 PMCID: PMC9177041 DOI: 10.3389/fcimb.2022.880030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
Although highly active antiretroviral therapy (HAART) can robustly control human immunodeficiency virus (HIV) infection, the existence of latent HIV in a form of proviral DNA integrated into the host genome makes the virus insensitive to HAART. This requires patients to adhere to HAART for a lifetime, often leading to drug toxicity or viral resistance to therapy. Current genome-editing technologies offer different strategies to reduce the latent HIV reservoir in the body. In this review, we systematize the research on CRISPR/Cas-based anti-HIV therapeutic methods, discuss problems related to viral escape and gene editing, and try to focus on the technologies that effectively and precisely introduce genetic modifications and confer strong resistance to HIV infection. Particularly, knock-in (KI) approaches, such as mature B cells engineered to produce broadly neutralizing antibodies, T cells expressing fusion inhibitory peptides in the context of inactivated viral coreceptors, or provirus excision using base editors, look very promising. Current and future advancements in the precision of CRISPR/Cas editing and its delivery will help extend its applicability to clinical HIV therapy.
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Affiliation(s)
- Alexandra Maslennikova
- Cell and Gene Technology Group, Institute of Gene Biology of Russian Academy of Science, Moscow, Russia
| | - Dmitriy Mazurov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology of Russian Academy of Science, Moscow, Russia
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35
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Kim TH, Lee SW. Therapeutic Application of Genome Editing Technologies in Viral Diseases. Int J Mol Sci 2022; 23:5399. [PMID: 35628210 PMCID: PMC9140762 DOI: 10.3390/ijms23105399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022] Open
Abstract
Viral infections can be fatal and consequently, they are a serious threat to human health. Therefore, the development of vaccines and appropriate antiviral therapeutic agents is essential. Depending on the virus, it can cause an acute or a chronic infection. The characteristics of viruses can act as inhibiting factors for the development of appropriate treatment methods. Genome editing technology, including the use of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) proteins, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), is a technology that can directly target and modify genomic sequences in almost all eukaryotic cells. The development of this technology has greatly expanded its applicability in life science research and gene therapy development. Research on the use of this technology to develop therapeutics for viral diseases is being conducted for various purposes, such as eliminating latent infections or providing resistance to new infections. In this review, we will look at the current status of the development of viral therapeutic agents using genome editing technology and discuss how this technology can be used as a new treatment approach for viral diseases.
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Affiliation(s)
- Tae Hyeong Kim
- Department of Molecular Biology, Dankook University, Cheonan 31116, Korea;
| | - Seong-Wook Lee
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin 16890, Korea
- R&D Center, Rznomics Inc., Seongnam 13486, Korea
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36
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Sugawara S, Reeves RK, Jost S. Learning to Be Elite: Lessons From HIV-1 Controllers and Animal Models on Trained Innate Immunity and Virus Suppression. Front Immunol 2022; 13:858383. [PMID: 35572502 PMCID: PMC9094575 DOI: 10.3389/fimmu.2022.858383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/18/2022] [Indexed: 12/23/2022] Open
Abstract
Although antiretroviral therapy (ART) has drastically changed the lives of people living with human immunodeficiency virus-1 (HIV-1), long-term treatment has been associated with a vast array of comorbidities. Therefore, a cure for HIV-1 remains the best option to globally eradicate HIV-1/acquired immunodeficiency syndrome (AIDS). However, development of strategies to achieve complete eradication of HIV-1 has been extremely challenging. Thus, the control of HIV-1 replication by the host immune system, namely functional cure, has long been studied as an alternative approach for HIV-1 cure. HIV-1 elite controllers (ECs) are rare individuals who naturally maintain undetectable HIV-1 replication levels in the absence of ART and whose immune repertoire might be a desirable blueprint for a functional cure. While the role(s) played by distinct human leukocyte antigen (HLA) expression and CD8+ T cell responses expressing cognate ligands in controlling HIV-1 has been widely characterized in ECs, the innate immune phenotype has been decidedly understudied. Comparably, in animal models such as HIV-1-infected humanized mice and simian Immunodeficiency Virus (SIV)-infected non-human primates (NHP), viremic control is known to be associated with specific major histocompatibility complex (MHC) alleles and CD8+ T cell activity, but the innate immune response remains incompletely characterized. Notably, recent work demonstrating the existence of trained innate immunity may provide new complementary approaches to achieve an HIV-1 cure. Herein, we review the known characteristics of innate immune responses in ECs and available animal models, identify gaps of knowledge regarding responses by adaptive or trained innate immune cells, and speculate on potential strategies to induce EC-like responses in HIV-1 non-controllers.
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37
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Ta TM, Malik S, Anderson EM, Jones AD, Perchik J, Freylikh M, Sardo L, Klase ZA, Izumi T. Insights Into Persistent HIV-1 Infection and Functional Cure: Novel Capabilities and Strategies. Front Microbiol 2022; 13:862270. [PMID: 35572626 PMCID: PMC9093714 DOI: 10.3389/fmicb.2022.862270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/23/2022] Open
Abstract
Although HIV-1 replication can be efficiently suppressed to undetectable levels in peripheral blood by combination antiretroviral therapy (cART), lifelong medication is still required in people living with HIV (PLWH). Life expectancies have been extended by cART, but age-related comorbidities have increased which are associated with heavy physiological and economic burdens on PLWH. The obstacle to a functional HIV cure can be ascribed to the formation of latent reservoir establishment at the time of acute infection that persists during cART. Recent studies suggest that some HIV reservoirs are established in the early acute stages of HIV infection within multiple immune cells that are gradually shaped by various host and viral mechanisms and may undergo clonal expansion. Early cART initiation has been shown to reduce the reservoir size in HIV-infected individuals. Memory CD4+ T cell subsets are regarded as the predominant cellular compartment of the HIV reservoir, but monocytes and derivative macrophages or dendritic cells also play a role in the persistent virus infection. HIV latency is regulated at multiple molecular levels in transcriptional and post-transcriptional processes. Epigenetic regulation of the proviral promoter can profoundly regulate the viral transcription. In addition, transcriptional elongation, RNA splicing, and nuclear export pathways are also involved in maintaining HIV latency. Although most proviruses contain large internal deletions, some defective proviruses may induce immune activation by expressing viral proteins or producing replication-defective viral-like particles. In this review article, we discuss the state of the art on mechanisms of virus persistence in the periphery and tissue and summarize interdisciplinary approaches toward a functional HIV cure, including novel capabilities and strategies to measure and eliminate the infected reservoirs and induce immune control.
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Affiliation(s)
- Tram M. Ta
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Sajjaf Malik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Elizabeth M. Anderson
- Office of the Assistant Secretary for Health, Region 3, U.S. Department of Health and Human Services, Washington, DC, United States
| | - Amber D. Jones
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jocelyn Perchik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Maryann Freylikh
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Luca Sardo
- Department of Infectious Disease and Vaccines, Merck & Co., Inc., Kenilworth, NJ, United States
| | - Zackary A. Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Neuroimmunology and CNS Therapeutics, Institute of Molecular Medicine and Infectious Diseases, Drexel University of Medicine, Philadelphia, PA, United States
| | - Taisuke Izumi
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,*Correspondence: Taisuke Izumi,
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Najafi S, Tan SC, Aghamiri S, Raee P, Ebrahimi Z, Jahromi ZK, Rahmati Y, Sadri Nahand J, Piroozmand A, Jajarmi V, Mirzaei H. Therapeutic potentials of CRISPR-Cas genome editing technology in human viral infections. Biomed Pharmacother 2022; 148:112743. [PMID: 35228065 PMCID: PMC8872819 DOI: 10.1016/j.biopha.2022.112743] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
Viral infections are a common cause of morbidity worldwide. The emergence of Coronavirus Disease 2019 (COVID-19) has led to more attention to viral infections and finding novel therapeutics. The CRISPR-Cas9 system has been recently proposed as a potential therapeutic tool for the treatment of viral diseases. Here, we review the research progress in the use of CRISPR-Cas technology for treating viral infections, as well as the strategies for improving the delivery of this gene-editing tool in vivo. Key challenges that hinder the widespread clinical application of CRISPR-Cas9 technology are also discussed, and several possible directions for future research are proposed.
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Affiliation(s)
- Sajad Najafi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Shahin Aghamiri
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Ebrahimi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Kargar Jahromi
- Central Research Laboratory, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Yazdan Rahmati
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Piroozmand
- Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Vahid Jajarmi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Correspondence to: Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19395-4818, Iran
| | - Hamed Mirzaei
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran,Corresponding author at: Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Widjaya MA, Ju JC, Lee SD. CRISPR-Edited Stem Cell Transplantation for HIV-Related Gene Modification In Vivo: A Systematic Review. Stem Cell Rev Rep 2022; 18:1743-1755. [PMID: 35169967 DOI: 10.1007/s12015-022-10345-9] [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] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND CRISPR is a novel genomic editing technology which can be useful for the treatment of immune diseases such as HIV. However, the application of CRISPR in stem cells for HIV-related research was not effective, and most of the research was done in vivo. This systematic review is to identify a new research idea about increase CRISPR-editing efficiencies in stem cell transplantation for HIV treatment, as well as its future perspective. METHOD Four databases were searched for articles published during 1952 to 2020. PRISMA method was used to select appropriate research papers. CAMARADES was used to identify the paper quality. The outcome was engraftment efficiency, gene disruption percentage, differentiation ability, HIV-resistant efficiency. RESULT Screening method showed 196 papers mentioned the topic. However, only 5 studies were reliable with the research objective. We found that (1) Two research ideas which was double gene knockout and knockout-knockin method to provide HIV-resistant cells, engraftment support and avoid cardiac disease as an HIV disease side effect. (2) Ribonucleoprotein (RNP) delivery was the best way to deliver the CRISPR/Cas9 and Adeno-Associated Virus (AAV) would be effective for knockin purpose. (3) CRISPR/SaCas9 could replace CRISPR/Cas9 role in editing HIV-related gene. CONCLUSION Potential genes to increase HIV resistance and stem cell engraftment should be explored more in the future. Double knockout and knock-in procedures should be applied to set up a better engraftment for improving HIV treatment or resistance of patients. CRISPR/SaCas9 and RNP delivery should be explored more in the future. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42020203312.
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Affiliation(s)
- Michael Anekson Widjaya
- Department of Biotechnology, College of Health Science, Asia University, Taichung, 41354, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan
| | - Jyh-Cherng Ju
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan. .,Translational Medicine Research Center, China Medical University Hospital, Taichung, 40402, Taiwan. .,Department of Bioinformatics and Medical Engineering, College of Information and Electrical Engineering, Asia University, Taichung, 41354, Taiwan. .,Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Shin-Da Lee
- Department of Physical Therapy, China Medical University, Taichung, 40402, Taiwan. .,Department of Physical Therapy, Asia University, Taichung, 41354, Taiwan. .,School of Rehabilitation Medicine, Weifang Medical University, Shandong, 261053, China.
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40
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Wu BW, Yee MB, Goldstein RS, Kinchington PR. Antiviral Targeting of Varicella Zoster Virus Replication and Neuronal Reactivation Using CRISPR/Cas9 Cleavage of the Duplicated Open Reading Frames 62/71. Viruses 2022; 14:v14020378. [PMID: 35215971 PMCID: PMC8880005 DOI: 10.3390/v14020378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/29/2022] Open
Abstract
Varicella Zoster Virus (VZV) causes Herpes Zoster (HZ), a common debilitating and complicated disease affecting up to a third of unvaccinated populations. Novel antiviral treatments for VZV reactivation and HZ are still in need. Here, we evaluated the potential of targeting the replicating and reactivating VZV genome using Clustered Regularly Interspaced Short Palindromic Repeat-Cas9 nucleases (CRISPR/Cas9) delivered by adeno-associated virus (AAV) vectors. After AAV serotype and guide RNA (gRNA) optimization, we report that a single treatment with AAV2-expressing Staphylococcus aureus CRISPR/Cas9 (saCas9) with gRNA to the duplicated and essential VZV genes ORF62/71 (AAV2-62gRsaCas9) greatly reduced VZV progeny yield and cell-to-cell spread in representative epithelial cells and in lytically infected human embryonic stem cell (hESC)-derived neurons. In contrast, AAV2-62gRsaCas9 did not reduce the replication of a recombinant virus mutated in the ORF62 targeted sequence, establishing that antiviral effects were a consequence of VZV-genome targeting. Delivery to latently infected and reactivation-induced neuron cultures also greatly reduced infectious-virus production. These results demonstrate the potential of AAV-delivered genome editors to limit VZV productive replication in epithelial cells, infected human neurons, and upon reactivation. The approach could be developed into a strategy for the treatment of VZV disease and virus spread in HZ.
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Affiliation(s)
- Betty W. Wu
- Graduate Program in Microbiology and Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
| | - Michael B. Yee
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
| | | | - Paul R. Kinchington
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- Correspondence: ; Tel.: +1-412-647-6319
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41
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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: 1.5] [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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A systematic mapping study on machine learning techniques for the prediction of CRISPR/Cas9 sgRNA target cleavage. Comput Struct Biotechnol J 2022; 20:5813-5823. [PMID: 36382194 PMCID: PMC9630617 DOI: 10.1016/j.csbj.2022.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/21/2022] [Accepted: 10/08/2022] [Indexed: 11/30/2022] Open
Abstract
CRISPR/Cas9 technology has greatly accelerated genome engineering research. The CRISPR/Cas9 complex, a bacterial immune response system, is widely adopted for RNA-driven targeted genome editing. The systematic mapping study presented in this paper examines the literature on machine learning (ML) techniques employed in the prediction of CRISPR/Cas9 sgRNA on/off-target cleavage, focusing on improving support in sgRNA design activities and identifying areas currently being researched. This area of research has greatly expanded recently, and we found it appropriate to work on a Systematic Mapping Study (SMS), an investigation that has proven to be an effective secondary study method. Unlike a classic review, in an SMS, no comparison of methods or results is made, while this task can instead be the subject of a systematic literature review that chooses one theme among those highlighted in this SMS. The study is illustrated in this paper. To the best of the authors' knowledge, no other SMS studies have been published on this topic. Fifty-seven papers published in the period 2017–2022 (April, 30) were analyzed. This study reveals that the most widely used ML model is the convolutional neural network (CNN), followed by the feedforward neural network (FNN), while the use of other models is marginal. Other interesting information has emerged, such as the wide availability of both open code and platforms dedicated to supporting the activity of researchers or the fact that there is a clear prevalence of public funds that finance research on this topic.
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Wei Hou ZZ, Chen S. Updates on CRISPR-based gene editing in HIV-1/AIDS therapy. Virol Sin 2022; 37:1-10. [PMID: 35234622 PMCID: PMC8922418 DOI: 10.1016/j.virs.2022.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022] Open
Abstract
Although tremendous efforts have been made to prevent and treat HIV-1 infection, HIV-1/AIDS remains a major threat to global human health. The combination antiretroviral therapy (cART), although able to suppress HIV-1 replication, cannot eliminate the proviral DNA integrated into the human genome and thus requires lifelong treatment that may lead to various side effects. In recent years, clustered regularly interspaced short palindromic repeat (CRISPR)-associated nuclease 9 (Cas9) related gene-editing systems have been developed and designed as effective ways to treat HIV-1 infection. However, new gene-targeting tools derived from or functioning like CRISPR/Cas9, including base editor, prime editing, SHERLOCK, DETECTR, PAC-MAN, ABACAS, pfAGO, have been developed and optimized for pathogens detection and diseases correction. Here, we summarize recent studies on HIV-1/AIDS gene therapy and provide more gene-editing targets based on studies relating to the molecular mechanism of HIV-1 infection. We also identify the strategies and potential applications of these new gene-editing technologies for HIV-1/AIDS treatment in the future. Moreover, we discuss the caveats and problems that should be addressed before the clinical use of these versatile CRISPR-based gene targeting tools. Finally, we offer alternative solutions to improve the practice of gene targeting in HIV-1/AIDS gene therapy. New gene-targeting tools derived from CRISPR/Cas9 have been introduced. Recent researches in HIV-1/AIDS gene therapy have been summarized. The strategies and potential applications of new gene editing technologies for HIV-1/AIDS treatment have been provided. The caveats and challenges in HIV-1/AIDS gene therapy have been discussed.
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Short term but highly efficient Cas9 expression mediated by excisional system using adenovirus vector and Cre. Sci Rep 2021; 11:24369. [PMID: 34934130 PMCID: PMC8692473 DOI: 10.1038/s41598-021-03803-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Genome editing techniques such as CRISPR/Cas9 have both become common gene engineering technologies and have been applied to gene therapy. However, the problems of increasing the efficiency of genome editing and reducing off-target effects that induce double-stranded breaks at unexpected sites in the genome remain. In this study, we developed a novel Cas9 transduction system, Exci-Cas9, using an adenovirus vector (AdV). Cas9 was expressed on a circular molecule excised by the site-specific recombinase Cre and succeeded in shortening the expression period compared to AdV, which expresses the gene of interest for at least 6 months. As an example, we chose hepatitis B, which currently has more than 200 million carriers in the world and frequently progresses to liver cirrhosis or hepatocellular carcinoma. The efficiencies of hepatitis B virus genome disruption by Exci-Cas9 and Cas9 expression by AdV directly (Avec) were the same, about 80–90%. Furthermore, Exci-Cas9 enabled cell- or tissue-specific genome editing by expressing Cre from a cell- or tissue-specific promoter. We believe that Exci-Cas9 developed in this study is useful not only for resolving the persistent expression of Cas9, which has been a problem in genome editing, but also for eliminating long-term DNA viruses such as human papilloma virus.
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Xun J, Zhang X, Guo S, Lu H, Chen J. Editing out HIV: application of gene editing technology to achieve functional cure. Retrovirology 2021; 18:39. [PMID: 34922576 PMCID: PMC8684261 DOI: 10.1186/s12977-021-00581-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 11/05/2021] [Indexed: 03/01/2023] Open
Abstract
Highly active antiretroviral therapy (HAART) successfully suppresses human immunodeficiency virus (HIV) replication and improves the quality of life of patients living with HIV. However, current HAART does not eradicate HIV infection because an HIV reservoir is established in latently infected cells and is not recognized by the immune system. The successful curative treatment of the Berlin and London patients following bone marrow transplantation inspired researchers to identify an approach for the functional cure of HIV. As a promising technology, gene editing-based strategies have attracted considerable attention and sparked much debate. Herein, we discuss the development of different gene editing strategies in the functional cure of HIV and highlight the potential for clinical applications prospects. ![]()
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Affiliation(s)
- Jingna Xun
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xinyu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China
| | - Shuyan Guo
- Shanghai Foreign Language School, Shanghai International Studies University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China.
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Transient CRISPR-Cas Treatment Can Prevent Reactivation of HIV-1 Replication in a Latently Infected T-Cell Line. Viruses 2021; 13:v13122461. [PMID: 34960730 PMCID: PMC8705111 DOI: 10.3390/v13122461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023] Open
Abstract
Novel therapeutic strategies aiming at the permanent inactivation of the HIV-1 reservoir in infected individuals are currently being explored, including approaches based on CRISPR-Cas gene editing. Extinction of all infectious HIV provirus in infected T-cell cultures was previously achieved when cells were transduced with lentiviral vectors for the stable expression of CRISPR-Cas9 or Cas12a systems targeting HIV DNA. Because lentiviral transduction and long-term CRISPR-Cas activity are less suitable for in vivo application of this antiviral strategy, we investigated whether HIV can also be completely inactivated by transient CRISPR-Cas activity. Latently infected SupT1 T-cells were repeatedly transfected with different Cas9 and Cas12a mRNA/protein sources in combination with dual gRNAs/crRNAs targeting highly conserved viral sequences. Upon repeated Cas9 protein treatment, viral replication could no longer be reactivated. We demonstrate that this was due to complete mutational inactivation of the proviral DNA, mostly through mutations at the target sites, but also through excision or inversion of the viral DNA fragment between the two target sites. These results demonstrate that repeated transient CRISPR-Cas treatment of a latently infected T-cell culture can lead to the permanent inactivation of HIV replication, indicating that transient CRISPR-Cas delivery methods can be considered for in vivo application.
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Gao M, Zhu X, Yang G, Bao J, Bu H. CRISPR/Cas9-Mediated Gene Editing in Porcine Models for Medical Research. DNA Cell Biol 2021; 40:1462-1475. [PMID: 34847741 DOI: 10.1089/dna.2020.6474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Pigs have been extensively used as the research models for human disease pathogenesis and gene therapy. They are also the optimal source of cells, tissues, and organs for xenotransplantation due to anatomical and physiological similarities to humans. Several breakthroughs in gene-editing technologies, including the advent of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9), have greatly improved the efficiency of genetic manipulation and significantly broadened the application of gene-edited large animal models. In this review, we have not only outlined the important applications of the CRISPR/Cas9 system in pigs as a means to study human diseases but also discussed the potential challenges of the use of CRISPR/Cas9 in large animals.
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Affiliation(s)
- Mengyu Gao
- Department of Pathology, West China Hospital, Sichuan University, Chendu, P.R. China.,Key Laboratory of Transplant Engineering and Immunology, Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Xinglong Zhu
- Key Laboratory of Transplant Engineering and Immunology, Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Guang Yang
- Experimental Animal Center, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Ji Bao
- Key Laboratory of Transplant Engineering and Immunology, Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
| | - Hong Bu
- Department of Pathology, West China Hospital, Sichuan University, Chendu, P.R. China.,Key Laboratory of Transplant Engineering and Immunology, Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, P.R. China
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Liu Y, Meng FZ, Wang X, Wang P, Liu JB, Hu WH, Young WB, Ho WZ. Methamphetamine facilitates HIV infection of primary human monocytes through inhibiting cellular viral restriction factors. Cell Biosci 2021; 11:194. [PMID: 34758885 PMCID: PMC8579418 DOI: 10.1186/s13578-021-00703-4] [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: 05/31/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background Methamphetamine (METH), a potent addictive psychostimulant, is highly prevalent in HIV-infected individuals. Clinically, METH use is implicated in alteration of immune system and increase of HIV spread/replication. Therefore, it is of importance to examine whether METH has direct effect on HIV infection of monocytes, the major target and reservoir cells for the virus. Results METH-treated monocytes were more susceptible to HIV infection as evidenced by increased levels of viral proteins (p24 and Pr55Gag) and expression of viral GAG gene. In addition, using HIV Bal with luciferase reporter gene (HIV Bal-eLuc), we showed that METH-treated cells expressed higher luciferase activities than untreated monocytes. Mechanistically, METH inhibited the expression of IFN-λ1, IRF7, STAT1, and the antiviral IFN-stimulated genes (ISGs: OAS2, GBP5, ISG56, Viperin and ISG15). In addition, METH down-regulated the expression of the HIV restriction microRNAs (miR-28, miR-29a, miR-125b, miR-146a, miR-155, miR-223, and miR-382). Conclusions METH compromises the intracellular anti-HIV immunity and facilitates HIV replication in primary human monocytes. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00703-4.
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Affiliation(s)
- Yu Liu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Feng-Zhen Meng
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Xu Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA.,Center for Substance Abuse Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140 USA
| | - Peng Wang
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA.,Center for Substance Abuse Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140 USA
| | - Jin-Biao Liu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Wen-Hui Hu
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Won-Bin Young
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA
| | - Wen-Zhe Ho
- Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, 3500 N Broad St., Philadelphia, PA 19140 USA.,Center for Substance Abuse Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140 USA
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Smith LM, Ladner JT, Hodara VL, Parodi LM, Harris RA, Callery JE, Lai Z, Zou Y, Raveedran M, Rogers J, Giavedoni LD. Multiplexed Simian Immunodeficiency Virus-Specific Paired RNA-Guided Cas9 Nickases Inactivate Proviral DNA. J Virol 2021; 95:e0088221. [PMID: 34549979 PMCID: PMC8577357 DOI: 10.1128/jvi.00882-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
Human and simian immunodeficiency virus (HIV and SIV) infections establish lifelong reservoirs of cells harboring an integrated proviral genome. Genome editing CRISPR-associated Cas9 nucleases, combined with SIV-specific guiding RNA (gRNA) molecules, inactivate integrated provirus DNA in vitro and in animal models. We generated RNA-guided Cas9 nucleases (RGNu) and nickases (RGNi) targeting conserved SIV regions with no homology in the human or rhesus macaque genome. Assays in cells cotransfected with SIV provirus and plasmids coding for RGNus identified SIV long terminal repeat (LTR), trans-activation response (TAR) element, and ribosome slip site (RSS) regions as the most effective at virus suppression; RGNi targeting these regions inhibited virus production significantly. Multiplex plasmids that coexpressed these three RGNu (Nu3), or six (three pairs) RGNi (Ni6), were more efficient at virus suppression than any combination of individual RGNu and RGNi plasmids. Both Nu3 and Ni6 plasmids were tested in lymphoid cells chronically infected with SIVmac239, and whole-genome sequencing was used to determine on- and off-target mutations. Treatment with these all-in-one plasmids resulted in similar levels of mutations of viral sequences from the cellular genome; Nu3 induced indels at the 3 SIV-specific sites, whereas for Ni6 indels were present at the LTR and TAR sites. Levels of off-target effects detected by two different algorithms were indistinguishable from background mutations. In summary, we demonstrate that Cas9 nickase in association with gRNA pairs can specifically eliminate parts of the integrated provirus DNA; also, we show that careful design of an all-in-one plasmid coding for 3 gRNAs and Cas9 nuclease inhibits SIV production with undetectable off-target mutations, making these tools a desirable prospect for moving into animal studies. IMPORTANCE Our approach to HIV cure, utilizing the translatable SIV/rhesus macaque model system, aims at provirus inactivation and its removal with the least possible off-target side effects. We developed single molecules that delivered either three truncated SIV-specific gRNAs along with Cas9 nuclease or three pairs of SIV-specific gRNAs (six individual gRNAs) along with Cas9 nickase to enhance efficacy of on-target mutagenesis. Whole-genome sequencing demonstrated effective SIV sequence mutation and inactivation and the absence of demonstrable off-target mutations. These results open the possibility to employ Cas9 variants that introduce single-strand DNA breaks to eliminate integrated proviral DNA.
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Affiliation(s)
- Lisa M. Smith
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UT Health San Antonio, San Antonio, Texas, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Vida L. Hodara
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura M. Parodi
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jessica E. Callery
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Zhao Lai
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, Texas, USA
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas, USA
| | - Yi Zou
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas, USA
| | - Muthuswamy Raveedran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Luis D. Giavedoni
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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Tyumentseva MA, Tyumentsev AI, Akimkin VG. Protocol for assessment of the efficiency of CRISPR/Cas RNP delivery to different types of target cells. PLoS One 2021; 16:e0259812. [PMID: 34752487 PMCID: PMC8577758 DOI: 10.1371/journal.pone.0259812] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Delivery of CRISPR/Cas RNPs to target cells still remains the biggest bottleneck to genome editing. Many efforts are made to develop efficient CRISPR/Cas RNP delivery methods that will not affect viability of target cell dramatically. Popular current methods and protocols of CRISPR/Cas RNP delivery include lipofection and electroporation, transduction by osmocytosis and reversible permeabilization and erythrocyte-based methods. METHODS In this study we will assess the efficiency and optimize current CRISPR/Cas RNP delivery protocols to target cells. We will conduct our work using molecular cloning, protein expression and purification, cell culture, flow cytometry (immunocytochemistry) and cellular imaging techniques. DISCUSSION This will be the first extensive comparative study of popular current methods and protocols of CRISPR/Cas RNP delivery to human cell lines and primary cells. All protocols will be optimized and characterized using the following criteria i) protein delivery and genome editing efficacy; ii) viability of target cells after delivery (post-transduction recovery); iii) scalability of delivery process; iv) cost-effectiveness of the delivery process and v) intellectual property rights. Some methods will be considered 'research-use only', others will be recommended for scaling and application in the development of cell-based therapies.
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