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Idris A, Shrivastava S, Supramaniam A, Ray RM, Shevchenko G, Acharya D, McMillan NAJ, Morris KV. Extracellular Vesicles Loaded with Long Antisense RNAs Repress Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Nucleic Acid Ther 2024. [PMID: 38530082 DOI: 10.1089/nat.2023.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Long antisense RNAs (asRNAs) have been observed to repress HIV and other virus expression in a manner that is refractory to viral evolution. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) disease, has a distinct ability to evolve resistance around antibody targeting, as was evident from the emergence of various SARS-CoV-2 spike antibody variants. Importantly, the effectiveness of current antivirals is waning due to the rapid emergence of new variants of concern, more recently the omicron variant. One means of avoiding the emergence of viral resistance is by using long asRNA to target SARS-CoV-2. Similar work has proven successful with HIV targeting by long asRNA. In this study, we describe a long asRNA targeting SARS-CoV-2 RNA-dependent RNA polymerase gene and the ability to deliver this RNA in extracellular vesicles (EVs) to repress virus expression. The observations presented in this study suggest that EV-delivered asRNAs are one means to targeting SARS-CoV-2 infection, which is both effective and broadly applicable as a means to control viral expression in the absence of mutation. This is the first demonstration of the use of engineered EVs to deliver long asRNA payloads for antiviral therapy.
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Affiliation(s)
- Adi Idris
- School of Pharmacy and Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Brisbane, Australia
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Surya Shrivastava
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, Duarte, California, USA
| | - Aroon Supramaniam
- School of Pharmacy and Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Brisbane, Australia
| | - Roslyn M Ray
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, Duarte, California, USA
| | - Galina Shevchenko
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, Duarte, California, USA
| | - Dhruba Acharya
- School of Pharmacy and Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Brisbane, Australia
| | - Nigel A J McMillan
- School of Pharmacy and Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Brisbane, Australia
| | - Kevin V Morris
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Brisbane, Australia
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Muskan M, Abeysinghe P, Cecchin R, Branscome H, Morris KV, Kashanchi F. Therapeutic potential of RNA-enriched extracellular vesicles: The next generation in RNA delivery via biogenic nanoparticles. Mol Ther 2024:S1525-0016(24)00094-7. [PMID: 38414242 DOI: 10.1016/j.ymthe.2024.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/21/2024] [Accepted: 02/24/2024] [Indexed: 02/29/2024] Open
Abstract
Exosomes are extracellular vesicles (EVs) (∼50-150 nm) that have emerged as promising vehicles for therapeutic applications and drug delivery. These membrane-bound particles, released by all actively dividing cells, have the ability to transfer effector molecules, including proteins, RNA, and even DNA, from donor cells to recipient cells, thereby modulating cellular responses. RNA-based therapeutics, including microRNAs, messenger RNAs, long non-coding RNAs, and circular RNAs, hold great potential in controlling gene expression and treating a spectrum of medical conditions. RNAs encapsulated in EVs are protected from extracellular degradation, making them attractive for therapeutic applications. Understanding the intricate biology of cargo loading and transfer within EVs is pivotal to unlocking their therapeutic potential. This review discusses the biogenesis and classification of EVs, methods for loading RNA into EVs, their advantages as drug carriers over synthetic-lipid-based systems, and the potential applications in treating neurodegenerative diseases, cancer, and viral infections. Notably, EVs show promise in delivering RNA cargo across the blood-brain barrier and targeting tumor cells, offering a safe and effective approach to RNA-based therapy in these contexts.
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Affiliation(s)
- Muskan Muskan
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia
| | - Pevindu Abeysinghe
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Riccardo Cecchin
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia
| | - Heather Branscome
- George Mason University, School of Systems Biology, Fairfax, VA 22030, USA
| | - Kevin V Morris
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia.
| | - Fatah Kashanchi
- George Mason University, School of Systems Biology, Fairfax, VA 22030, USA.
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Idris A, Supramaniam A, Tayyar Y, Kelly G, McMillan NAJ, Morris KV. An intranasally delivered ultra-conserved siRNA prophylactically represses SARS-CoV-2 infection in the lung and nasal cavity. Antiviral Res 2024; 222:105815. [PMID: 38246206 DOI: 10.1016/j.antiviral.2024.105815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/15/2023] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
There remains a striking overall mortality burden of COVID-19 worldwide. Given the waning effectiveness of current SARS-CoV-2 antivirals due to the rapid emergence of new variants of concern (VOC), we employed a direct-acting molecular therapy approach using gene silencing RNA interference (RNAi) technology. In this study, we developed and screened several ultra-conserved small-interfering RNAs (siRNAs) before selecting one potent siRNA candidate for pre-clinical in vivo testing. This non-immunostimulatory, anti-SARS-CoV-2 siRNA candidate maintains its antiviral activity against all tested SARS-CoV-2 VOC and works effectively as a single agent. For the first time, significant antiviral effects in both the lungs and nasal cavities of SARS-CoV-2 infected mice were observed when this siRNA candidate was delivered intranasally (IN) as a prophylactic agent with the aid of lipid nanoparticles (LNPs). Importantly, a pre-exposure prophylactic IN-delivered anti-SARS-CoV-2 siRNA antiviral that can ameliorate viral replication in the nasal cavity could potentially prevent aerosol spread of respiratory viruses. An IN delivery approach would allow for the development of a direct-acting nasal spray approach that could be self-administered prophylactically.
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Affiliation(s)
- Adi Idris
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; Centre for Immunlogy and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia.
| | - Aroon Supramaniam
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Yaman Tayyar
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; Prorenata Biotech, Molendinar, Queensland, Australia
| | - Gabrielle Kelly
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Nigel A J McMillan
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Kevin V Morris
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; Centre for Genomics and Personalized Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia
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Urak R, Gittins B, Soemardy C, Grepo N, Goldberg L, Maker M, Shevchenko G, Davis A, Li S, Scott T, Morris KV, Forman SJ, Wang X. Evaluation of the Elements of Short Hairpin RNAs in Developing shRNA-Containing CAR T Cells. Cancers (Basel) 2023; 15:2848. [PMID: 37345185 DOI: 10.3390/cancers15102848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/23/2023] Open
Abstract
Short hairpin RNAs (shRNAs) have emerged as a powerful tool for gene knockdown in various cellular systems, including chimeric antigen receptor (CAR) T cells. However, the elements of shRNAs that are crucial for their efficacy in developing shRNA-containing CAR T cells remain unclear. In this study, we evaluated the impact of different shRNA elements, including promoter strength, orientation, multiple shRNAs, self-targeting, and sense and antisense sequence composition on the knockdown efficiency of the target gene in CAR T cells. Our findings highlight the importance of considering multiple shRNAs and their orientation to achieve effective knockdown. Moreover, we demonstrate that using a strong promoter and avoiding self-targeting can enhance CAR T cell functionality. These results provide a framework for the rational design of CAR T cells with shRNA-mediated knockdown capabilities, which could improve the therapeutic efficacy of CAR T cell-based immunotherapy.
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Affiliation(s)
- Ryan Urak
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
- Center for Gene Therapy, Beckman Research Institute, Duarte, CA 91010, USA
| | - Brenna Gittins
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, Beckman Research Institute, Duarte, CA 91010, USA
| | - Nicole Grepo
- Center for Gene Therapy, Beckman Research Institute, Duarte, CA 91010, USA
| | - Lior Goldberg
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Madeleine Maker
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Galina Shevchenko
- Center for Gene Therapy, Beckman Research Institute, Duarte, CA 91010, USA
| | - Alicia Davis
- Center for Gene Therapy, Beckman Research Institute, Duarte, CA 91010, USA
| | - Shirley Li
- Center for Gene Therapy, Beckman Research Institute, Duarte, CA 91010, USA
| | - Tristan Scott
- Center for Gene Therapy, Beckman Research Institute, Duarte, CA 91010, USA
| | - Kevin V Morris
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4215, Australia
| | - Stephen J Forman
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Xiuli Wang
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA
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Frederickson R, Ritter T, Morris KV. Extracellular vesicles: Expanding the landscape for next-generation delivery strategies in gene and cell therapy. Mol Ther 2023; 31:1189-1190. [PMID: 37054709 PMCID: PMC10188908 DOI: 10.1016/j.ymthe.2023.03.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/15/2023] Open
Affiliation(s)
| | - Thomas Ritter
- Regenerative Medicine Institute, National University of Ireland Galway, Galway, Ireland.
| | - Kevin V Morris
- Menzies Health Institute Queensland and Griffith University, Southport, QLD, Australia.
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Cecchin R, Troyer Z, Witwer K, Morris KV. Extracellular vesicles: The next generation in gene therapy delivery. Mol Ther 2023; 31:1225-1230. [PMID: 36698310 PMCID: PMC10188631 DOI: 10.1016/j.ymthe.2023.01.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/30/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Extracellular vesicles (EVs) are esteemed as a promising delivery vehicle for various genetic therapeutics. They are relatively inert, non-immunogenic, biodegradable, and biocompatible. At least in rodents, they can even transit challenging bodily hurdles such as the blood-brain barrier. Constitutively shed by all cells and with the potential to interact specifically with neighboring and distant targets, EVs can be engineered to carry and deliver therapeutic molecules such as proteins and RNAs. EVs are thus emerging as an elegant in vivo gene therapy vector. Deeper understanding of basic EV biology-including cellular production, EV loading, systemic distribution, and cell delivery-is still needed for effective harnessing of these endogenous cellular nanoparticles as next-generation nanodelivery tools. However, even a perfect EV product will be challenging to produce at clinical scale. In this regard, we propose that vector transduction technologies can be used to convert cells either ex vivo or directly in vivo into EV factories for stable, safe modulation of gene expression and function. Here, we extrapolate from the current EV state of the art to a bright potential future using EVs to treat genetic diseases that are refractory to current therapeutics.
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Affiliation(s)
- Riccardo Cecchin
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia
| | - Zach Troyer
- Departments of Molecular and Comparative Pathobiology and Neurology, and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ken Witwer
- Departments of Molecular and Comparative Pathobiology and Neurology, and Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Kevin V Morris
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia.
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7
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Supramaniam A, Tayyar Y, Clarke DTW, Kelly G, Acharya D, Morris KV, McMillan NAJ, Idris A. Prophylactic intranasal administration of lipid nanoparticle formulated siRNAs reduce SARS-CoV-2 and RSV lung infection. J Microbiol Immunol Infect 2023:S1684-1182(23)00068-3. [PMID: 36934064 PMCID: PMC9991324 DOI: 10.1016/j.jmii.2023.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/17/2022] [Accepted: 02/28/2023] [Indexed: 03/09/2023]
Abstract
RNA interference (RNAi) is an emerging and promising therapy for a wide range of respiratory viral infections. This highly specific suppression can be achieved by the introduction of short-interfering RNA (siRNA) into mammalian systems, resulting in the effective reduction of viral load. Unfortunately, this has been hindered by the lack of a good delivery system, especially via the intranasal (IN) route. Here, we have developed an IN siRNA encapsulated lipid nanoparticle (LNP) in vivo delivery system that is highly efficient at targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and respiratory syncytial virus (RSV) lung infection in vivo. Importantly, IN siRNA delivery without the aid of LNPs abolishes anti-SARS-CoV-2 activity in vivo. Our approach using LNPs as the delivery vehicle overcomes the significant barriers seen with IN delivery of siRNA therapeutics and is a significant advancement in our ability to delivery siRNAs. The study presented here demonstrates an attractive alternate delivery strategy for the prophylactic treatment of both future and emerging respiratory viral diseases.
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Affiliation(s)
- Aroon Supramaniam
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Yaman Tayyar
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; Prorenata Biotech, Molendinar, Queensland, Australia
| | - Daniel T W Clarke
- School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Gabrielle Kelly
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Dhruba Acharya
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia
| | - Kevin V Morris
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Nigel A J McMillan
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia
| | - Adi Idris
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; School of Pharmacy and Medical Science, Griffith University, Southport, Queensland, Australia; School of Biomedical Sciences, Queensland University of Technology, Gardens Point, Queensland, Australia.
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8
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Scott T, Morris KV. From amputations to antibiotics: A future beyond "hacksaw" gene editing. Mol Ther 2022; 30:3505-3506. [PMID: 36417912 PMCID: PMC9734074 DOI: 10.1016/j.ymthe.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Tristan Scott
- Center for Gene Therapy, City of Hope – Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA,Corresponding author: Tristan Scott, Center for Gene Therapy, City of Hope – Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
| | - Kevin V. Morris
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4215, Australia,Corresponding author: Kevin Morris, Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4215, Australia.
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9
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Davis AM, Scott TA, Morris KV. Harnessing Rift Valley fever virus NSs gene for cancer gene therapy. Cancer Gene Ther 2022; 29:1477-1486. [PMID: 35393569 PMCID: PMC8988100 DOI: 10.1038/s41417-022-00463-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/01/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022]
Abstract
One of the greatest challenges in the treatment of cancer is tumor heterogeneity which results in differential responses to chemotherapy and drugs that work through a single pathway. A therapeutic agent that targets cancer cells for death through multiple mechanisms could be advantageous as a broad inhibitor for many types of cancers and the heterogeneous alterations they possess. Several viral proteins have been exploited for antiproliferative and apoptotic effect in cancer cells by disrupting critical survival pathways. Here, we report the use of the non-structural protein on the S segment (NSs) gene from the Rift Valley fever virus (RVFV) to induce cancer cell death. NSs has immune evasion functions in the context of RVFV with many of these functions affecting proliferation pathways and DNA damage signaling, which could be leveraged against cancer cells. We find that expression of NSs in multiple cancer cell lines leads to a rapid decline in cell viability and induction of apoptosis. Interestingly, we observed reduced toxicity in normal cells suggesting cancer cells may be more susceptible to NSs-mediated cell death. To enhance specificity of NSs for use in hepatocellular carcinoma, we incorporated four miR-122 binding sites in the 3' untranslated region (UTR) of the NSs mRNA to achieve cell type specific expression. Observations presented here collectively suggest that delivery of the NSs gene may provide a unique therapeutic approach in a broad range of cancers.
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Affiliation(s)
- Alicia M Davis
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA
| | - Tristan A Scott
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, USA.
| | - Kevin V Morris
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science Griffith University, Gold Coast Campus, QLD 4222, Brisbane, Australia.
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Morris KV, Witwer KW. The evolving paradigm of extracellular vesicles in intercellular signaling and delivery of therapeutic RNAs. Mol Ther 2022; 30:2393-2394. [PMID: 35643080 PMCID: PMC9263283 DOI: 10.1016/j.ymthe.2022.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 01/11/2023] Open
Affiliation(s)
- Kevin V. Morris
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast Campus, Menzies Health Institute Queensland, 4222, Australia,Corresponding author: Kevin V. Morris, School of Pharmacy and Medical Sciences, Griffith University, Gold Coast Campus, Menzies Health Institute Queensland, 4222, Australia.
| | - Kenneth W. Witwer
- Departments of Molecular and Comparative Pathobiology and Neurology, and Richman Family Precision Medicine Center of Excellence in Alzheimer’s Disease, Johns Hopkins University, Baltimore, MD 21205, USA
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11
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Davis A, Morris KV, Shevchenko G. Hypoxia-directed tumor targeting of CRISPR-Cas9 and HSV-TK suicide gene therapy using lipid nanoparticles. Mol Ther Methods Clin Dev 2022; 25:158-169. [PMID: 35402634 PMCID: PMC8971340 DOI: 10.1016/j.omtm.2022.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/13/2022] [Indexed: 12/13/2022]
Abstract
Hypoxia is a characteristic feature of solid tumors that contributes to tumor aggressiveness and is associated with resistance to cancer therapy. The hypoxia inducible factor-1 (HIF-1) transcription factor complex mediates hypoxia-specific gene expression by binding to hypoxia-responsive element (HRE) sequences within the promoter of target genes. HRE-driven expression of therapeutic cargo has been widely explored as a strategy to achieve cancer-specific gene expression. By utilizing this system, we achieve hypoxia-specific expression of two therapeutically relevant cargo elements: the herpes simplex virus thymidine kinase (HSV-tk) suicide gene and the CRISPR-Cas9 nuclease. Using an expression vector containing five copies of the HRE derived from the vascular endothelial growth factor gene, we are able to show high transgene expression in cells in a hypoxic environment, similar to levels achieved using the cytomegalovirus (CMV) and CBh promoters. Furthermore, we are able to deliver our therapeutic cargo to tumor cells with high efficiency using plasmid-packaged lipid nanoparticles (LNPs) to achieve specific killing of tumor cells in hypoxic conditions while maintaining tight regulation with no significant changes to cell viability in normoxia.
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Affiliation(s)
- Alicia Davis
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Kevin V. Morris
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia
| | - Galina Shevchenko
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
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12
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Guan M, Lim L, Holguin L, Han T, Vyas V, Urak R, Miller A, Browning DL, Echavarria L, Li S, Li S, Chang WC, Scott T, Yazaki P, Morris KV, Cardoso AA, Blanchard MS, Le Verche V, Forman SJ, Zaia JA, Burnett JC, Wang X. Pre-clinical data supporting immunotherapy for HIV using CMV-HIV-specific CAR T cells with CMV vaccine. Mol Ther Methods Clin Dev 2022; 25:344-359. [PMID: 35573050 PMCID: PMC9062763 DOI: 10.1016/j.omtm.2022.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/10/2022] [Indexed: 01/22/2023]
Abstract
T cells engineered to express HIV-specific chimeric antigen receptors (CARs) represent a promising strategy to clear HIV-infected cells, but to date have not achieved clinical benefits. A likely hurdle is the limited T cell activation and persistence when HIV antigenemia is low, particularly during antiretroviral therapy (ART). To overcome this issue, we propose to use a cytomegalovirus (CMV) vaccine to stimulate CMV-specific T cells that express CARs directed against the HIV-1 envelope protein gp120. In this study, we use a GMP-compliant platform to engineer CMV-specific T cells to express a second-generation CAR derived from the N6 broadly neutralizing antibody, one of the broadest anti-gp120 neutralizing antibodies. These CMV-HIV CAR T cells exhibit dual effector functions upon in vitro stimulation through their endogenous CMV-specific T cell receptors or the introduced CARs. Using a humanized HIV mouse model, we show that CMV vaccination during ART accelerates CMV-HIV CAR T cell expansion in the peripheral blood and that higher numbers of CMV-HIV CAR T cells were associated with a better control of HIV viral load and fewer HIV antigen p24+ cells in the bone marrow upon ART interruption. Collectively, these data support the clinical development of CMV-HIV CAR T cells in combination with a CMV vaccine in HIV-infected individuals.
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Affiliation(s)
- Min Guan
- T Cell Therapeutics Research Laboratory, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Laura Lim
- T Cell Therapeutics Research Laboratory, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Leo Holguin
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Tianxu Han
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Vibhuti Vyas
- T Cell Therapeutics Research Laboratory, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Ryan Urak
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Aaron Miller
- Department of Molecular Imaging and Therapy, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Diana L. Browning
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Liliana Echavarria
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Shasha Li
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Shirley Li
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Wen-Chung Chang
- T Cell Therapeutics Research Laboratory, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Tristan Scott
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Paul Yazaki
- Department of Molecular Imaging and Therapy, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Kevin V. Morris
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Angelo A. Cardoso
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - M. Suzette Blanchard
- Division of Biostatistics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Virginia Le Verche
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Stephen J. Forman
- T Cell Therapeutics Research Laboratory, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - John A. Zaia
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - John C. Burnett
- Center for Gene Therapy, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Xiuli Wang
- T Cell Therapeutics Research Laboratory, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
- Corresponding author Xiuli Wang, T Cell Therapeutics Research Laboratory, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010-3000, USA.
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13
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Laitinen P, Väänänen MA, Kolari IL, Mäkinen PI, Kaikkonen MU, Weinberg MS, Morris KV, Korhonen P, Malm T, Ylä-Herttuala S, Roberts TC, Turunen MP, Turunen TA. Nuclear microRNA-466c regulates Vegfa expression in response to hypoxia. PLoS One 2022; 17:e0265948. [PMID: 35358280 PMCID: PMC8975276 DOI: 10.1371/journal.pone.0265948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 03/10/2022] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs are well characterized in their role in silencing gene expression by targeting 3´-UTR of mRNAs in cytoplasm. However, recent studies have shown that miRNAs have a role in the regulation of genes in the nucleus, where they are abundantly located. We show here that in mouse endothelial cell line (C166), nuclear microRNA miR-466c participates in the regulation of vascular endothelial growth factor a (Vegfa) gene expression in hypoxia. Upregulation of Vegfa expression in response to hypoxia was significantly compromised after removal of miR-466c with CRISPR-Cas9 genomic deletion. We identified a promoter-associated long non-coding RNA on mouse Vegfa promoter and show that miR-466c directly binds to this transcript to modulate Vegfa expression. Collectively, these observations suggest that miR-466c regulates Vegfa gene transcription in the nucleus by targeting the promoter, and expands on our understanding of the role of miRNAs well beyond their canonical role.
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Affiliation(s)
- Pia Laitinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- RNatives Oy, Kuopio, Finland
| | - Mari-Anna Väänänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ida-Liisa Kolari
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petri I. Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U. Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Marc S. Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwaterstrand, Witwaterstrand, South Africa
| | - Kevin V. Morris
- Center for Gene Therapy, City of Hope–Beckman Research Institute at the City of Hope, Duarte, California, United States of America
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, Queensland, Australia
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Thomas C. Roberts
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MDUK Oxford Neuromuscular Centre, Oxford, United Kingdom
| | - Mikko P. Turunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- RNatives Oy, Kuopio, Finland
- * E-mail:
| | - Tiia A. Turunen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- RNatives Oy, Kuopio, Finland
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McMillan NAJ, Morris KV, Idris A. RNAi to treat SARS-CoV-2-variant proofing the next generation of therapies. EMBO Mol Med 2022; 14:e15811. [PMID: 35285158 PMCID: PMC8988212 DOI: 10.15252/emmm.202215811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 01/18/2023] Open
Abstract
There is an urgent need to bring new antivirals to SARS‐CoV‐2 to the market. Indeed, in the last 3 months, we have seen at least two new antivirals approved, molnupiravir and paxlovid. Both are older established antivirals that show some efficacy against SARS‐CoV‐2. The work by Chang et al (2022) in the current issue of EMBO Molecular Medicine explores the use of short interfering RNAs to directly target SARS‐CoV‐2 and shows that RNAi is an effective approach to reducing, or even eliminating viral replication, depending on the experimental setting. This antiviral effect results in significant prevention of infection‐related pathology in animals. The key feature of this approach, besides its simplicity as naked siRNAs, is that all current variants are covered by this treatment.
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Affiliation(s)
- Nigel A J McMillan
- Centre for Cell and Gene Medicine, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Kevin V Morris
- Centre for Cell and Gene Medicine, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Adi Idris
- Centre for Cell and Gene Medicine, Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
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15
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Scott TA, Supramaniam A, Idris A, Cardoso AA, Shrivastava S, Kelly G, Grepo NA, Soemardy C, Ray RM, McMillan NA, Morris KV. Engineered extracellular vesicles directed to the spike protein inhibit SARS-CoV-2. Mol Ther Methods Clin Dev 2022; 24:355-366. [PMID: 35127966 PMCID: PMC8806709 DOI: 10.1016/j.omtm.2022.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/28/2022] [Indexed: 12/28/2022]
Abstract
SARS-CoV-2 (CoV-2) viral infection results in COVID-19 disease, which has caused significant morbidity and mortality worldwide. A vaccine is crucial to curtail the spread of SARS-CoV-2, while therapeutics will be required to treat ongoing and reemerging infections of SARS-CoV-2 and COVID-19 disease. There are currently no commercially available effective anti-viral therapies for COVID-19, urging the development of novel modalities. Here, we describe a molecular therapy specifically targeted to neutralize SARS-CoV-2, which consists of extracellular vesicles (EVs) containing a novel fusion tetraspanin protein, CD63, embedded within an anti-CoV-2 nanobody. These anti-CoV-2-enriched EVs bind SARS-CoV-2 spike protein at the receptor-binding domain (RBD) site and can functionally neutralize SARS-CoV-2. This work demonstrates an innovative EV-targeting platform that can be employed to target and inhibit the early stages of SARS-CoV-2 infection.
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Affiliation(s)
- Tristan A. Scott
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Aroon Supramaniam
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Brisbane 4222, Australia
| | - Adi Idris
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Brisbane 4222, Australia
| | - Angelo A. Cardoso
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Surya Shrivastava
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Gabrielle Kelly
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Brisbane 4222, Australia
| | - Nicole A. Grepo
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Roslyn M. Ray
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Nigel A.J. McMillan
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Brisbane 4222, Australia
| | - Kevin V. Morris
- Menzies Health Institute Queensland, School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Brisbane 4222, Australia
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Wei CH, O'Meally D, Kirschenbaum M, Mao A, Kancharla C, Morris KV, Stewart D. Abstract P3-10-05: Feasibility of detecting long noncoding RNAs in clinical FFPE specimens using clinical grade RNA-sequencing pipeline. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p3-10-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND: RNA-based predictive biomarkers are not assessed in the clinical diagnostic setting. Potential biomarkers include long noncoding RNAs (lncRNAs), a class of molecules emerging as critical regulators of diverse cellular functions, including therapy resistance. Advances in sequencing technologies have made whole transcriptome profiling (RNA-seq) possible in formalin fixed, paraffin embedded (FFPE) tissue. In this study, we assessed the feasibility of detecting lncRNAs in clinical FFPE specimens, using clinical grade RNA-seq technology offered at a CLIA-certified laboratory. Our second aim was to investigate expression of lncRNAs contributing to endocrine resistance in a cohort of metastatic breast cancer patients. METHODS: RNA-seq was performed on clinical FFPE specimens as a physician-ordered diagnostic test in a CLIA-certified laboratory. RNA-seq libraries were constructed using ribosomal RNA depletion method and > 100 M reads were sequenced for each library. We checked for contaminating sequences using fastqScreen against multiple genomes, including human and E. coli among others. To assess the quality of the sequencing libraries, we used the nf-core RNASeq pipeline. Trimmed reads were mapped to the GRCh38 reference and abundance of transcripts from the Gencode comprehensive annotation (v33) was estimated. Each library was assessed for quality control (QC). Mapped reads were merged into a matrix of counts per gene for each sample. Differential expression was assessed between metastatic breast cancers with and without endocrine resistance. RESULTS: We obtained twenty-five cases (23 patients) of ER-positive, HER2 negative metastatic breast carcinoma that had undergone whole transcriptome sequencing at a CLIA-certified molecular laboratory. Of these, 6 (24%) cases had failed QC: 5 patients’ specimens had low RNA content (all core biopsies); 1 patient had total RNA content comprised of less than 75% human reads (lumpectomy). The mean age for specimens that failed sequencing QC was significantly different from those that passed (637.2 days vs 193.7 days, t-test, p = 0.04). After QC, a total of 19 cases were analyzed for differentially expressed lncRNA profiles. Of these, 5 cases were clinically annotated as hormone sensitive; 14 cases had acquired secondary hormone resistance. Thirty-six lncRNAs were identified as differentially expressed (7 antisense; 25 intergenic; 3 intronic; 1 sense-overlapping). Of these, lncRNAs which were found to be over-expressed in endocrine resistant tumors compared to endocrine sensitive tumors are involved in various oncogenic pathways such as cell cycle regulation (Linc0051, MIR205HG, ST8SOA6-AS1), tumor progression (LINC00885, LINC00319), and chemoresistance (SIRLNT). LncRNAs which were downregulated in endocrine resistant tumors compared to endocrine sensitive tumors are involved in stem cell state (CCDC144NL.AS1) and endocrine resistance (MIR2052HG). CONCLUSION: It is feasible to detect lncRNA biomarkers in clinical FFPE tissue specimens, using a laboratory-developed RNA sequencing pipeline in a CLIA-certified genomic laboratory. FFPE-RNA-seq pipeline can potentially expand the molecular information that could be gleamed from clinical FFPE specimens to answer pertinent clinical questions, such as therapy resistance.
Table 1.Summary data of metastatic ER+ breast cancer evaluated in this studyFailed RNA QC Success RNA QCNumber of samples (%)6 (24%)19 (76%)Mean specimen age (range)27 days (11-44)194 days (3-1331)Number of specimens which are biopsies (%)5 (83%)17 (89%)Number of specimens derived from bone source (%)2 (33%)1 (5%)Number of specimens derived from visceral organs (%)2 (33%)12 (63%)Number of specimens derived from soft tissue or lymphoid sources (%)2 (33%)6 (32%)Acquired endocrine resistance5 (83%)14 (74%)Endocrine sensitive1 (17%)5 (26%)
Citation Format: Christina H. Wei, Denis O'Meally, Michele Kirschenbaum, Allen Mao, Chetan Kancharla, Kevin V. Morris, Daphne Stewart. Feasibility of detecting long noncoding RNAs in clinical FFPE specimens using clinical grade RNA-sequencing pipeline [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-10-05.
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Affiliation(s)
| | | | | | - Allen Mao
- City of Hope Comprehensive Cancer Center, Duarte, CA
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17
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Shrivastava S, Ray RM, Holguin L, Echavarria L, Grepo N, Scott TA, Burnett J, Morris KV. Exosome-mediated stable epigenetic repression of HIV-1. Nat Commun 2021; 12:5541. [PMID: 34545097 PMCID: PMC8452652 DOI: 10.1038/s41467-021-25839-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 08/31/2021] [Indexed: 11/25/2022] Open
Abstract
Human Immunodeficiency Virus (HIV-1) produces a persistent latent infection. Control of HIV-1 using combination antiretroviral therapy (cART) comes at the cost of life-shortening side effects and development of drug-resistant HIV-1. An ideal and safer therapy should be deliverable in vivo and target the stable epigenetic repression of the virus, inducing a stable "block and lock" of virus expression. Towards this goal, we developed an HIV-1 promoter-targeting Zinc Finger Protein (ZFP-362) fused to active domains of DNA methyltransferase 3 A to induce long-term stable epigenetic repression of HIV-1. Cells were engineered to produce exosomes packaged with RNAs encoding this HIV-1 repressor protein. We find here that the repressor loaded anti-HIV-1 exosomes suppress virus expression and that this suppression is mechanistically driven by DNA methylation of HIV-1 in humanized NSG mouse models. The observations presented here pave the way for an exosome-mediated systemic delivery platform of therapeutic cargo to epigenetically repress HIV-1 infection.
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Affiliation(s)
- Surya Shrivastava
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Roslyn M Ray
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Leo Holguin
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Lilliana Echavarria
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Nicole Grepo
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Tristan A Scott
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - John Burnett
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
- Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, Duarte, CA, USA
| | - Kevin V Morris
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA.
- Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, Duarte, CA, USA.
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, Brisbane, Australia.
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18
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Idris A, Davis A, Supramaniam A, Acharya D, Kelly G, Tayyar Y, West N, Zhang P, McMillan CLD, Soemardy C, Ray R, O'Meally D, Scott TA, McMillan NAJ, Morris KV. A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19. Mol Ther 2021; 29:2219-2226. [PMID: 33992805 PMCID: PMC8118699 DOI: 10.1016/j.ymthe.2021.05.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 01/16/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in humans. Despite several emerging vaccines, there remains no verifiable therapeutic targeted specifically to the virus. Here we present a highly effective small interfering RNA (siRNA) therapeutic against SARS-CoV-2 infection using a novel lipid nanoparticle (LNP) delivery system. Multiple siRNAs targeting highly conserved regions of the SARS-CoV-2 virus were screened, and three candidate siRNAs emerged that effectively inhibit the virus by greater than 90% either alone or in combination with one another. We simultaneously developed and screened two novel LNP formulations for the delivery of these candidate siRNA therapeutics to the lungs, an organ that incurs immense damage during SARS-CoV-2 infection. Encapsulation of siRNAs in these LNPs followed by in vivo injection demonstrated robust repression of virus in the lungs and a pronounced survival advantage to the treated mice. Our LNP-siRNA approaches are scalable and can be administered upon the first sign of SARS-CoV-2 infection in humans. We suggest that an siRNA-LNP therapeutic approach could prove highly useful in treating COVID-19 disease as an adjunctive therapy to current vaccine strategies.
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Affiliation(s)
- Adi Idris
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Alicia Davis
- Center for Gene Therapy, Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope and City of Hope Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences at the City of Hope, Duarte, CA 91010, USA
| | - Aroon Supramaniam
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Dhruba Acharya
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Gabrielle Kelly
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Yaman Tayyar
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Nic West
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Ping Zhang
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia
| | - Christopher L D McMillan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Citradewi Soemardy
- Center for Gene Therapy, Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope and City of Hope Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Roslyn Ray
- Center for Gene Therapy, Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope and City of Hope Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Denis O'Meally
- Center for Gene Therapy, Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope and City of Hope Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Tristan A Scott
- Center for Gene Therapy, Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope and City of Hope Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Nigel A J McMillan
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia.
| | - Kevin V Morris
- Menzies Health Institute Queensland, School of Medical Science Griffith University, Gold Coast Campus, QLD 4222, Australia; Center for Gene Therapy, Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope and City of Hope Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA 91010, USA.
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19
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Ray RM, Lang L, Pokharel SP, O'Meally D, Scott TA, Chen CW, Morris KV. Abstract 2393: The systematic evaluation of the oncogenic lncRNA LINC00963 using a CRISPRScan technique. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Long non-coding RNAs (LncRNAs) have been found to play important roles in maintaining and promoting cellular proliferation in cancerous cells. One such lncRNA, LINC00963 has been found to promote cellular proliferation, migration and tumorigenesis in prostate, ovarian, breast and non-small cell lung (NSCLC) cancer. In this study, we aim to identify important functional regions of this lncRNA with a view to identify unique regions for targeted drug therapy. In order to achieve this, we sought to investigate this lncRNA in the A549 NSCLC cell line. We found that LINC00963 was highly expressed and when targeted with either siRNAs or antisense oligonucleotides, cells rapidly undergo apoptosis. Using cell death as a proxy for loss-of-function, we characterized LINC00963 at the genomic level using a CRIPSRScan approach. CRISPRScan is a novel way of determining lncRNA functional domains through the introduction of local mutations. These mutations could potentially disrupt lncRNA function, which for LINC00963 would lead to apoptosis of the cell. We created a unique lentivirus library comprised of 1784 single guide RNAs spanning the length of LINC00963 in order to precisely identify regions of functional importance. Upon transduction in a stably expressing Cas9-A549 cell line, we collected cellular fractions over time, and using high-throughput sequencing (NextSeq, Illumina), evaluated the depletion of these sgRNAs as a proxy for their importance in LINC00963 function. The identification of these key genomic regions that may render LINC00963 non-functional may offer new lncRNA target sites for anti-cancer therapies in the future. Additionally, the utilization of an in-depth CRISPR-Cas9 approach to determine important lncRNA domains provides a novel and precise way in which to evaluate lncRNA function.
Citation Format: Roslyn M. Ray, Lu Lang, Sheela P. Pokharel, Denis O'Meally, Tristan A. Scott, Chun-Wei Chen, Kevin V. Morris. The systematic evaluation of the oncogenic lncRNA LINC00963 using a CRISPRScan technique [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2393.
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Affiliation(s)
| | - Lu Lang
- 2Systems Biology, The Beckman Research Institute, City of Hope, Monrovia, CA
| | - Sheela P. Pokharel
- 2Systems Biology, The Beckman Research Institute, City of Hope, Monrovia, CA
| | | | | | - Chun-Wei Chen
- 2Systems Biology, The Beckman Research Institute, City of Hope, Monrovia, CA
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Ray RM, Hansen AH, Taskova M, Jandl B, Hansen J, Soemardy C, Morris KV, Astakhova K. Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides. Beilstein J Org Chem 2021; 17:891-907. [PMID: 33981364 PMCID: PMC8093553 DOI: 10.3762/bjoc.17.75] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/09/2021] [Indexed: 01/28/2023] Open
Abstract
Lipid nanoparticles (LNPs) constitute a facile and scalable approach for delivery of payloads to human cells. LNPs are relatively immunologically inert and can be produced in a cost effective and scalable manner. However, targeting and delivery of LNPs across the blood–brain barrier (BBB) has proven challenging. In an effort to target LNPs composed of an ionizable cationic lipid (DLin-MC3-DMA), cholesterol, the phospholipid 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and 1,2-dimyristoyl-rac-glycero-3-methoxypolyethylene glycol-2000 (DMG-PEG 2000) to particular cell types, as well as to generate LNPs that can cross the BBB, we developed and assessed two approaches. The first was centered on the BBB-penetrating trans-activator of transcription (Tat) peptide or the peptide T7, and the other on RNA aptamers targeted to glycoprotein gp160 from human immunodeficiency virus (HIV) or C-C chemokine receptor type 5 (CCR5), a HIV-1 coreceptor. We report herein a CCR5-selective RNA aptamer that acts to facilitate entry through a simplified BBB model and that drives the uptake of LNPs into CCR5-expressing cells, while the gp160 aptamer did not. We further observed that the addition of cell-penetrating peptides, Tat and T7, did not increase BBB penetration above the aptamer-loaded LNPs alone. Moreover, we found that these targeted LNPs exhibit low immunogenic and low toxic profiles and that targeted LNPs can traverse the BBB to potentially deliver drugs into the target tissue. This approach highlights the usefulness of aptamer-loaded LNPs to increase target cell specificity and potentially deliverability of central-nervous-system-active RNAi therapeutics across the BBB.
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Affiliation(s)
- Roslyn M Ray
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
| | | | - Maria Taskova
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Bernhard Jandl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Jonas Hansen
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Citra Soemardy
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
| | - Kevin V Morris
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, United States of America.,School of Medical Sciences, Griffith University, Gold Coast, Australia 4222.,Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
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21
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Idris A, Davis A, Supramaniam A, Acharya D, Kelly G, Tayyar Y, West N, Zhang P, McMillan CLD, Soemardy C, Ray R, O'Meally D, Scott TA, McMillan NAJ, Morris KV. A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19. bioRxiv 2021. [PMID: 33907744 DOI: 10.1101/2021.04.19.440531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in humans. Despite several emerging vaccines, there remains no verifiable therapeutic targeted specifically to the virus. Here we present a highly effective siRNA therapeutic against SARS-CoV-2 infection using a novel lipid nanoparticle delivery system. Multiple small-interfering RNAs (siRNAs) targeting highly conserved regions of the SARS-CoV-2 virus were screened and three candidate siRNAs emerged that effectively inhibit virus by greater than 90% either alone or in combination with one another. We simultaneously developed and screened two novel lipid nanoparticle formulations for the delivery of these candidate siRNA therapeutics to the lungs, an organ that incurs immense damage during SARS-CoV-2 infection. Encapsulation of siRNAs in these LNPs followed by in vivo injection demonstrated robust repression of virus in the lungs and a pronounced survival advantage to the treated mice. Our LNP-siRNA approaches are scalable and can be administered upon the first sign of SARS-CoV-2 infection in humans. We suggest that an siRNA-LNP therapeutic approach could prove highly useful in treating COVID-19 disease as an adjunctive therapy to current vaccine strategies.
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22
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Scott TA, O’Meally D, Grepo NA, Soemardy C, Lazar DC, Zheng Y, Weinberg MS, Planelles V, Morris KV. Broadly active zinc finger protein-guided transcriptional activation of HIV-1. Mol Ther Methods Clin Dev 2021; 20:18-29. [PMID: 33335944 PMCID: PMC7726486 DOI: 10.1016/j.omtm.2020.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) causes a persistent viral infection resulting in the demise of immune regulatory cells. Clearance of HIV-1 infection results in integration of proviral DNA into the genome of host cells, which provides a means for evasion and long-term persistence. A therapeutic compound that specifically targets and sustainably activates a latent HIV-1 provirus could be transformative and is the goal for the "shock-and-kill" approach to a functional cure for HIV-1. Substantial progress has been made toward the development of recombinant proteins that target specific genomic loci for gene activation, repression, or inactivation by directed mutations. However, most of these modalities are too large or too complex for efficient therapeutic application. We describe here the development and testing of a novel recombinant zinc finger protein transactivator, ZFP-362-VPR, which specifically and potently enhances proviral HIV-1 transcription both in established latency models and activity across different viral clades. Additionally, ZFP-362-VPR-activated HIV-1 reporter gene expression in a well-established primary human CD4+ T cell latency model and off-target pathways were determined by transcriptome analyses. This study provides clear proof of concept for the application of a novel, therapeutically relevant, protein transactivator to purge cellular reservoirs of HIV-1.
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Affiliation(s)
- Tristan A. Scott
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Denis O’Meally
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Nicole Anne Grepo
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Daniel C. Lazar
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yue Zheng
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 92037, USA
| | - Marc S. Weinberg
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicente Planelles
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 92037, USA
| | - Kevin V. Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
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23
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Shrivastava S, Morris KV. The Multifunctionality of Exosomes; from the Garbage Bin of the Cell to a Next Generation Gene and Cellular Therapy. Genes (Basel) 2021; 12:genes12020173. [PMID: 33513776 PMCID: PMC7912150 DOI: 10.3390/genes12020173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 02/07/2023] Open
Abstract
Exosomes are packaged with a variety of cellular cargo including RNA, DNA, lipids and proteins. For several decades now there has been ongoing debate as to what extent exosomes are the garbage bin of the cell or if these entities function as a distributer of cellular cargo which acts in a meaningful mechanistic way on target cells. Are the contents of exosomes unwanted excess cellular produce or are they selective nucleic acid packaged nanoparticles used to communicate in a paracrine fashion? Overexpressed RNAs and fragments of DNA have been shown to collect into exosomes which are jettisoned from cells in response to particular stimuli to maintain homeostasis suggesting exosomes are functional trash bins of the cell. Other studies however have deciphered selective packaging of particular nucleic acids into exosomes. Nucleic acids packaged into exosomes are increasingly reported to exert transcriptional control on recipient cells, supporting the notion that exosomes may provide a role in signaling and intracellular communication. We survey the literature and conclude that exosomes are multifunctional entities, with a plethora of roles that can each be taken advantage to functionally modulate cells. We also note that the potential utility of developing exosomes as a next generation genetic therapy may in future transform cellular therapies. We also depict three models of methodologies which can be adopted by researchers intending to package nucleic acid in exosomes for developing gene and cell therapy.
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Affiliation(s)
- Surya Shrivastava
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA 91010, USA;
- Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, Duarte, CA 91010, USA
| | - Kevin V. Morris
- Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA 91010, USA;
- Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, Duarte, CA 91010, USA
- School of Medical Science, Gold Coast Campus, Griffith University, Southport 4222, Australia
- Correspondence:
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24
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Villamizar O, Waters SA, Scott T, Grepo N, Jaffe A, Morris KV. Mesenchymal Stem Cell exosome delivered Zinc Finger Protein activation of cystic fibrosis transmembrane conductance regulator. J Extracell Vesicles 2021; 10:e12053. [PMID: 33532041 PMCID: PMC7825549 DOI: 10.1002/jev2.12053] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/13/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis is a genetic disorder that results in a multi-organ disease with progressive respiratory decline which leads to premature death. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene disrupts the capacity of the protein to function as a channel, transporting chloride ions and bicarbonate across epithelial cell membranes. Small molecule treatments targeted at potentiating or correcting CFTR have shown clinical benefits, but are only effective for a small percentage of individuals with specific CFTR mutations. To overcome this limitation, we engineered stromal-derived mesenchymal stem cells (MSC) and HEK293 cells to produce exosomes containing a novel CFTR Zinc Finger Protein fusion with transcriptional activation domains VP64, P65 and Rta to target the CFTR promoter (CFZF-VPR) and activate transcription. Treatment with CFZF-VPR results in robust activation of CFTR transcription in patient derived Human Bronchial Epithelial cells (HuBEC). We also find that CFZF-VPR can be packaged into MSC and HEK293 cell exosomes and delivered to HuBEC cells to potently activate CFTR expression. Connexin 43 appeared to be required for functional release of CFZF-VPR from exosomes. The observations presented here demonstrate that MSC derived exosomes can be used to deliver a packaged zinc finger activator to target cells and activate CFTR. The novel approach presented here offers a next-generation genetic therapy that may one day prove effective in treating patients afflicted with Cystic fibrosis.
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Affiliation(s)
- Olga Villamizar
- Center for Gene Therapy City of Hope-Beckman Research Institute at the City of Hope Duarte California USA
| | - Shafagh A Waters
- Faculty of Medicine School of Women's & Children's Health University of New South Wales (UNSW) Sydney NSW Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC) Faculty of Medicine University of New South Wales Sydney NSW Australia.,Department of Respiratory Medicine Sydney Children's Hospital Sydney NSW Australia
| | - Tristan Scott
- Center for Gene Therapy City of Hope-Beckman Research Institute at the City of Hope Duarte California USA
| | - Nicole Grepo
- Center for Gene Therapy City of Hope-Beckman Research Institute at the City of Hope Duarte California USA
| | - Adam Jaffe
- Faculty of Medicine School of Women's & Children's Health University of New South Wales (UNSW) Sydney NSW Australia.,Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC) Faculty of Medicine University of New South Wales Sydney NSW Australia.,Department of Respiratory Medicine Sydney Children's Hospital Sydney NSW Australia
| | - Kevin V Morris
- Center for Gene Therapy City of Hope-Beckman Research Institute at the City of Hope Duarte California USA.,School of Medical Science Griffith University, Gold Coast Campus 1 Parklands Dr Southport QLD Australia
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25
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Scott TA, Morris KV. Designer nucleases to treat malignant cancers driven by viral oncogenes. Virol J 2021; 18:18. [PMID: 33441159 PMCID: PMC7805041 DOI: 10.1186/s12985-021-01488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/02/2021] [Indexed: 11/22/2022] Open
Abstract
Viral oncogenic transformation of healthy cells into a malignant state is a well-established phenomenon but took decades from the discovery of tumor-associated viruses to their accepted and established roles in oncogenesis. Viruses cause ~ 15% of know cancers and represents a significant global health burden. Beyond simply causing cellular transformation into a malignant form, a number of these cancers are augmented by a subset of viral factors that significantly enhance the tumor phenotype and, in some cases, are locked in a state of oncogenic addiction, and substantial research has elucidated the mechanisms in these cancers providing a rationale for targeted inactivation of the viral components as a treatment strategy. In many of these virus-associated cancers, the prognosis remains extremely poor, and novel drug approaches are urgently needed. Unlike non-specific small-molecule drug screens or the broad-acting toxic effects of chemo- and radiation therapy, the age of designer nucleases permits a rational approach to inactivating disease-causing targets, allowing for permanent inactivation of viral elements to inhibit tumorigenesis with growing evidence to support their efficacy in this role. Although many challenges remain for the clinical application of designer nucleases towards viral oncogenes; the uniqueness and clear molecular mechanism of these targets, combined with the distinct advantages of specific and permanent inactivation by nucleases, argues for their development as next-generation treatments for this aggressive group of cancers.
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Affiliation(s)
- Tristan A Scott
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA.
| | - Kevin V Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
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Abstract
Several recent studies support a functional role for pseudogenes, a copy of a parent gene that has lost protein-coding potential, which was for a long time thought to represent only "junk" DNA. Several hundreds of pseudogenes have now been reported as transcribed RNAs in a large variety of tissues and tumor types. Most studies have focused on pseudogenes expressed in sense direction, relative to their protein-coding gene counterpart, but some reports suggest that pseudogenes can be also transcribed as antisense RNAs (asRNAs). Key regulatory genes, such as PTEN and OCT4, have in fact been reported to be under the regulation of pseudogene-expressed asRNAs. Here, we review what is known about pseudogene-expressed asRNAs, we discuss the functional role that these transcripts may have in gene regulation and we summarize the techniques that are available to study them.
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Affiliation(s)
- Nicholas C Lister
- School of Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - Per Johnsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paul D Waters
- School of Biotechnology and Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Kevin V Morris
- Menzies Health Institute and School of Pharmacology and Medical Sciences, Griffith University, Southport, QLD, Australia
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27
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Urak RZ, Soemardy C, Ray R, Li S, Shevchenko G, Scott T, Lim L, Wang X, Morris KV. Conditionally Replicating Vectors Mobilize Chimeric Antigen Receptors against HIV. Mol Ther Methods Clin Dev 2020; 19:285-294. [PMID: 33102620 PMCID: PMC7569266 DOI: 10.1016/j.omtm.2020.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus (HIV) is an attractive target for chimeric antigen receptor (CAR) therapy. CAR T cells have proved remarkably potent in targeted killing of cancer cells, and we surmised that CAR T cells could prove useful in eradicating HIV-infected cells. Toward this goal, we interrogate several neutralizing single-chain variable fragments (scFvs) that target different regions of the HIV envelope glycoprotein, gp120. We find here that CAR T cells with scFv from NIH45-46 antibody demonstrated the highest cytotoxicity. Although NIH45-46 CAR T cells are capable of eliminating antigen-expressing cells, we wanted to address HIV reactivation from ex vivo culture of HIV patient-derived CAR T cells. In order to capitalize on the HIV reactivation, we developed a conditionally replicating lentiviral vector (crLV). The crLV can hijack HIV machinery, forming a chimeric lentivirus (LV) instead of HIV and delivered to uninfected cells. We find that CAR T cells generated with crLVs have similar CAR-mediated functionality as traditional CARs. We also demonstrate crLVs' capability of expanding CAR percentage and protecting CD4 CAR T cell in HIV donors. Collectively, we demonstrate here that the novel crLV NIH45-46 CAR can serve as a strategy to combat HIV, as well as overcome HIV reactivation in CD4+ CAR T cells.
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Affiliation(s)
- Ryan Z Urak
- Center for Gene Therapy, Beckman Research Institute at the City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, Beckman Research Institute at the City of Hope, Duarte, CA, USA
| | - Roslyn Ray
- City of Hope Center for Gene and Cell Therapy, Duarte, CA, USA
| | - Shirley Li
- City of Hope Center for Gene and Cell Therapy, Duarte, CA, USA
| | - Galina Shevchenko
- Center for Gene Therapy, Beckman Research Institute at the City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, USA
| | - Tristan Scott
- Center for Gene Therapy, Beckman Research Institute at the City of Hope, Duarte, CA, USA
| | - Laura Lim
- Department of Hematology and Hematopoietic Cell Transplantation, Duarte, CA, USA
| | - Xiuli Wang
- Department of Hematology and Hematopoietic Cell Transplantation, Duarte, CA, USA
| | - Kevin V Morris
- Center for Gene Therapy, Beckman Research Institute at the City of Hope, Duarte, CA, USA.,Hematological Malignancy and Stem Cell Transplantation Institute, City of Hope, Duarte, CA, USA.,School of Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222 Australia
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28
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Affiliation(s)
- Kevin V Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA; School of Medical Science, Griffith University, Gold Coast Campus, Southport, QSLD 4222, Australia.
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29
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Affiliation(s)
- Kevin V Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA; School of Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia.
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30
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Ray RM, Morris KV. Long Non-coding RNAs Mechanisms of Action in HIV-1 Modulation and the Identification of Novel Therapeutic Targets. Noncoding RNA 2020; 6:ncrna6010012. [PMID: 32183241 PMCID: PMC7151623 DOI: 10.3390/ncrna6010012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/01/2020] [Accepted: 03/10/2020] [Indexed: 12/17/2022] Open
Abstract
This review aims to highlight the role of long non-coding RNAs in mediating human immunodeficiency virus (HIV-1) viral replication, latency, disease susceptibility and progression. In particular, we focus on identifying possible lncRNA targets and their purported mechanisms of action for future drug design or gene therapeutics.
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31
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Scott T, Soemardy C, Morris KV. Development of a Facile Approach for Generating Chemically Modified CRISPR/Cas9 RNA. Mol Ther Nucleic Acids 2020; 19:1176-1185. [PMID: 32069700 PMCID: PMC7019045 DOI: 10.1016/j.omtn.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 02/07/2023]
Abstract
The RNA-guided, modified type II prokaryotic CRISPR with CRISPR-associated proteins (CRISPR/Cas9) system represents a simple gene-editing platform with applications in biotechnology and also potentially as a therapeutic modality. The system requires a small guide RNA (sgRNA) and a catalytic Cas9 protein to induce non-homologous end joining (NHEJ) at break sites, resulting in the formation of inactivating mutations, or through homology-directed repair (HDR) can engineer in specific sequence changes. Although CRISPR/Cas9 is a powerful technology, the effects can be limited as a result of nuclease-mediated degradation of the RNA components. Significant research has focused on the solid-phase synthesis of CRISPR RNA components with chemically modified bases, but this approach is technically challenging and expensive. Development of a simple, generic approach to generate chemically modified CRISPR RNAs may broaden applications that require nuclease-resistant CRISPR components. We report here the development of a novel, functional U-replaced trans-activating RNA (tracrRNA) that can be in vitro transcribed with chemically stabilizing 2'-fluoro (2'F)-pyrimidines. These data represent a unique and facile approach to generating chemically stabilized CRISPR RNA.
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Affiliation(s)
- Tristan Scott
- Center for Gene Therapy, City of Hope-Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, City of Hope-Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Kevin V Morris
- Center for Gene Therapy, City of Hope-Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
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32
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Abstract
CRISPR/Cas is a transformative gene editing tool, that offers a simple and effective way to target a catalytic Cas9, the most widely used is derived from Streptococcus pyogenes (SpCas9), with a complementary small guide RNA (sgRNA) to inactivate endogenous genes resulting from insertions and deletions (indels). CRISPR/Cas9 has been rapidly applied to basic research as well as expanded for potential clinical applications. Utilization of spCas9 as an ribonuclearprotein complex (RNP) is considered the most safe and effective method to apply Cas9 technology, and the efficacy of this system is critically dependent on the ability of Cas9 to generate high levels of indels. We find here that novel sequence changes to the tracrRNA significantly improves Cas9 activity when delivered as an RNP. We demonstrate that a dual-guide RNA (dgRNA) with a modified tracrRNA can improve reporter knockdown and indel formation at several targets within the long terminal repeat (LTR) of HIV. Furthermore, the sequence-modified tracrRNAs improved Cas9-mediated reduction of CCR5 surface receptor expression in cell lines, which correlated with higher levels of indel formation. It was demonstrated that a Cas9 RNP with a sequence modified tracrRNA enhanced indel formation at the CCR5 target site in primary CD4+ T-cells. Finally, we show improved activity at two additional targets within the HBB locus and the BCL11A GATA site. Overall, the data presented here suggests that novel facile tracrRNA sequence changes could potentially be integrated with current dgRNA technology, and open up the possibility for the development of sequence modified tracrRNAs to improve Cas9 RNP activity.
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Affiliation(s)
- Tristan Scott
- Center for Gene Therapy, City of Hope - Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Ryan Urak
- Center for Gene Therapy, City of Hope - Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, City of Hope - Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Kevin V Morris
- Center for Gene Therapy, City of Hope - Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA.
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Villamizar O, Waters SA, Scott T, Saayman S, Grepo N, Urak R, Davis A, Jaffe A, Morris KV. Targeted Activation of Cystic Fibrosis Transmembrane Conductance Regulator. Mol Ther 2019; 27:1737-1748. [PMID: 31383454 PMCID: PMC6822231 DOI: 10.1016/j.ymthe.2019.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 06/24/2019] [Accepted: 07/03/2019] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The majority of CFTR mutations result in impaired chloride channel function as only a fraction of the mutated CFTR reaches the plasma membrane. The development of a therapeutic approach that facilitates increased cell-surface expression of CFTR could prove clinically relevant. Here, we evaluate and contrast two molecular approaches to activate CFTR expression. We find that an RNA-guided nuclease null Cas9 (dCas9) fused with a tripartite activator, VP64-p65-Rta can activate endogenous CFTR in cultured human nasal epithelial cells from CF patients. We also find that targeting BGas, a long non-coding RNA involved in transcriptionally modulating CFTR expression with a gapmer, induced both strong knockdown of BGas and concordant activation of CFTR. Notably, the gapmer can be delivered to target cells when generated as electrostatic particles with recombinant HIV-Tat cell penetrating peptide (CPP), when packaged into exosomes, or when loaded into lipid nanoparticles (LNPs). Treatment of patient-derived human nasal epithelial cells containing F508del with gapmer-CPP, gapmer-exosomes, or LNPs resulted in increased expression and function of CFTR. Collectively, these observations suggest that CRISPR/dCas-VPR (CRISPR) and BGas-gapmer approaches can target and specifically activate CFTR.
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Affiliation(s)
- Olga Villamizar
- Center for Gene Therapy, City of Hope-Beckman Research Institute at the City of Hope, Duarte, CA 91010, USA
| | - Shafagh A Waters
- Faculty of Medicine, School of Women's & Children's Health, University of New South Wales (UNSW), Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), School of Women's & Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Tristan Scott
- Center for Gene Therapy, City of Hope-Beckman Research Institute at the City of Hope, Duarte, CA 91010, USA
| | - Sheena Saayman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicole Grepo
- Center for Gene Therapy, City of Hope-Beckman Research Institute at the City of Hope, Duarte, CA 91010, USA
| | - Ryan Urak
- Center for Gene Therapy, City of Hope-Beckman Research Institute at the City of Hope, Duarte, CA 91010, USA
| | - Alicia Davis
- Center for Gene Therapy, City of Hope-Beckman Research Institute at the City of Hope, Duarte, CA 91010, USA
| | - Adam Jaffe
- Faculty of Medicine, School of Women's & Children's Health, University of New South Wales (UNSW), Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), School of Women's & Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Kevin V Morris
- Center for Gene Therapy, City of Hope-Beckman Research Institute at the City of Hope, Duarte, CA 91010, USA.
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34
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Ray RM, Hansen AH, Slott S, Taskova M, Astakhova K, Morris KV. Control of LDL Uptake in Human Cells by Targeting the LDLR Regulatory Long Non-coding RNA BM450697. Mol Ther Nucleic Acids 2019; 17:264-276. [PMID: 31279228 PMCID: PMC6611981 DOI: 10.1016/j.omtn.2019.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 10/31/2022]
Abstract
Hypercholesterolemia is a condition that is characterized by very high levels of cholesterol in the blood and is a major correlating factor with heart disease. Indeed, high levels of the low-density lipoprotein (LDL) have been causally linked to the development of atherosclerotic cardiovascular disease (ASCVD). A method to specifically reduce cholesterol in the blood in a long-term, stable manner could prove therapeutically relevant. Cholesterol is removed from the blood by the LDL receptor (LDLR) in the liver. Others and we have discovered that a long non-coding RNA (lncRNA; BM450697) functions as an endogenous epigenetic regulator of LDLR and that the repression of this lncRNA by the action of small interfering RNAs (siRNAs) results in the activation of LDLR. We found here, through the interrogation of two siRNAs that can target this lncRNA, both in a transcriptional and post-transcriptional manner, that BM450697 functions as a local scaffold for modulating LDLR transcription. Moreover, we found that conjugation of α-N-acetylgalactosamine (GalNAc) with two lncRNA-directed siRNAs allows for direct liver cell targeting of this lncRNA and functional enhanced uptake of cholesterol. Collectively, these data suggest that targeting the BM450697 lncRNA regulator of LDLR may result in a more specific, long-term, targeted approach to regulating cholesterol in the blood.
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Affiliation(s)
- Roslyn M Ray
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Anders Højgaard Hansen
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Sofie Slott
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Maria Taskova
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, 206 Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - Kevin V Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute, 1500 E. Duarte Rd., Duarte, CA, 91010, USA.
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Nieminen T, Scott TA, Lin FM, Chen Z, Yla-Herttuala S, Morris KV. Long Non-Coding RNA Modulation of VEGF-A during Hypoxia. Noncoding RNA 2018; 4:ncrna4040034. [PMID: 30463374 PMCID: PMC6315885 DOI: 10.3390/ncrna4040034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Abstract
The role and function of long non-coding RNAs (lncRNAs) in modulating gene expression is becoming apparent. Vascular endothelial growth factor A (VEGF-A) is a key regulator of blood vessel formation and maintenance making it a promising therapeutic target for activation in ischemic diseases. In this study, we uncover a functional role for two antisense VEGF-A lncRNAs, RP1-261G23.7 and EST AV731492, in transcriptional regulation of VEGF-A during hypoxia. We find here that both lncRNAs are polyadenylated, concordantly upregulated with VEGF-A, localize to the VEGF-A promoter and upstream elements in a hypoxia dependent manner either as a single-stranded RNA or DNA bound RNA, and are associated with enhancer marks H3K27ac and H3K9ac. Collectively, these data suggest that VEGF-A antisense lncRNAs, RP1-261G23.7 and EST AV731492, function as VEGF-A promoter enhancer-like elements, possibly by acting as a local scaffolding for proteins and also small RNAs to tether.
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Affiliation(s)
- Tiina Nieminen
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Tristan A Scott
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Feng-Mao Lin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
| | - Seppo Yla-Herttuala
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, FI-70211 Kuopio, Finland.
| | - Kevin V Morris
- The Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
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Shevchenko G, Morris KV. All I's on the RADAR: role of ADAR in gene regulation. FEBS Lett 2018; 592:2860-2873. [PMID: 29770436 DOI: 10.1002/1873-3468.13093] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/26/2018] [Accepted: 05/05/2018] [Indexed: 12/12/2022]
Abstract
Adenosine to inosine (A-to-I) editing is the most abundant form of RNA modification in mammalian cells, which is catalyzed by adenosine deaminase acting on the double-stranded RNA (ADAR) protein family. A-to-I editing is currently known to be involved in the regulation of the immune system, RNA splicing, protein recoding, microRNA biogenesis, and formation of heterochromatin. Editing occurs within regions of double-stranded RNA, particularly within inverted Alu repeats, and is associated with many diseases including cancer, neurological disorders, and metabolic syndromes. However, the significance of RNA editing in a large portion of the transcriptome remains unknown. Here, we review the current knowledge about the prevalence and function of A-to-I editing by the ADAR protein family, focusing on its role in the regulation of gene expression. Furthermore, RNA editing-independent regulation of cellular processes by ADAR and the putative role(s) of this process in gene regulation will be discussed.
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Affiliation(s)
- Galina Shevchenko
- Hematological Malignancy and Stem Cell Transplantation Institute, Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
| | - Kevin V Morris
- Hematological Malignancy and Stem Cell Transplantation Institute, Center for Gene Therapy, City of Hope-Beckman Research Institute, Duarte, CA, USA
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Shrivastava S, Charlins P, Ackley A, Embree H, Dropulic B, Akkina R, Weinberg MS, Morris KV. Stable Transcriptional Repression and Parasitism of HIV-1. Mol Ther Nucleic Acids 2018; 12:12-18. [PMID: 30195752 PMCID: PMC6019856 DOI: 10.1016/j.omtn.2018.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 01/13/2023]
Abstract
Gene-based therapies represent a promising treatment for HIV-1 infection, as they offer the potential for sustained viral inhibition and reduced treatment interventions. One approach developed here involves using conditionally replicating vectors (CR-vectors). CR-vectors utilize HIV-expressed proteins to replicate and disseminate along with HIV into the budding viral particles, thereby co-infecting target cellular reservoirs. We generated and characterized several CR-vectors carrying various therapeutic payloads of non-coding RNAs targeted to HIV-1, both transcriptionally and post-transcriptionally. Both virus and vector expression was followed in cell culture systems and T cells in the presence and absence of mycophenolic acid (MPA) selection. We find here that CR-vectors functionally suppress HIV expression in a long-term stable manner and that transcriptional targeting of and epigenetic silencing of HIV can be passaged to newly infected cells by the action of the CR-vector, ultimately establishing a sustained parasitism of HIV. Our findings suggest that CR-vectors with modulatory non-coding RNAs may be a viable approach to achieving long-term sustained suppression of HIV-1, leading ultimately to a functional cure.
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Affiliation(s)
- Surya Shrivastava
- Hematological Malignancy and Stem Cell Transplantation Institute and Center for Gene Therapy, City of Hope-Beckman Research Institute, 1500 Duarte Road, Duarte, CA 91007, USA
| | - Paige Charlins
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Amanda Ackley
- Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - Ramesh Akkina
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Marc S Weinberg
- Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin V Morris
- Hematological Malignancy and Stem Cell Transplantation Institute and Center for Gene Therapy, City of Hope-Beckman Research Institute, 1500 Duarte Road, Duarte, CA 91007, USA; Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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38
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Zhou J, Lazar D, Li H, Xia X, Satheesan S, Charlins P, O'Mealy D, Akkina R, Saayman S, Weinberg MS, Rossi JJ, Morris KV. Receptor-targeted aptamer-siRNA conjugate-directed transcriptional regulation of HIV-1. Am J Cancer Res 2018; 8:1575-1590. [PMID: 29556342 PMCID: PMC5858168 DOI: 10.7150/thno.23085] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/09/2017] [Indexed: 12/16/2022] Open
Abstract
Gene-based therapies represent a promising therapeutic paradigm for the treatment of HIV-1, as they have the potential to maintain sustained viral inhibition with reduced treatment interventions. Such an option may represent a long-term treatment alternative to highly active antiretroviral therapy. Methods: We previously described a therapeutic approach, referred to as transcriptional gene silencing (TGS), whereby small noncoding RNAs directly inhibit the transcriptional activity of HIV-1 by targeting sites within the viral promoter, specifically the 5' long terminal repeat (LTR). TGS differs from traditional RNA interference (RNAi) in that it is characterized by concomitant silent-state epigenetic marks on histones and DNA. To deliver TGS-inducing RNAs, we developed functional RNA conjugates based on the previously reported dual function of the gp120 (A-1) aptamer conjugated to 27-mer Dicer-substrate anti-HIV-1 siRNA (dsiRNA), LTR-362. Results: We demonstrate here that high levels of processed guide RNAs localize to the nucleus in infected T lymphoblastoid CEM cell line and primary human CD4+ T-cells. Treatment of the aptamer-siRNA conjugates induced TGS with an ~10-fold suppression of viral p24 levels as measured at day 12 post infection. To explore the silencing efficacy of aptamer-siRNA conjugates in vivo, HIV-1-infected humanized NOD/SCID/IL2 rγnull mice (hu-NSG) were treated with the aptamer-siRNA conjugates. Systemic delivery of the A-1-stick-LTR-362 27-mer siRNA conjugates suppressed HIV-1 infection and protected CD4+ T cell levels in viremia hu-NSG mice. Principle conclusions: Collectively these data suggest that the gp120 aptamer-dsiRNA conjugate design is suitable for systemic delivery of small RNAs that can be used to suppress HIV-1.
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Castino MR, Baker-Andresen D, Ratnu VS, Shevchenko G, Morris KV, Bredy TW, Youngson NA, Clemens KJ. Persistent histone modifications at the BDNF and Cdk-5 promoters following extinction of nicotine-seeking in rats. Genes Brain Behav 2017; 17:98-106. [PMID: 28857504 DOI: 10.1111/gbb.12421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 02/03/2023]
Abstract
Drugs of addiction lead to a wide range of epigenetic changes at the promoter regions of genes directly implicated in learning and memory processes. We have previously shown that the histone deactylase inhibitor, sodium butyrate (NaB), accelerates the extinction of nicotine-seeking and provides resistance to relapse. Here, we explore the potential molecular mechanisms underlying this effect. Rats received intravenous nicotine or saline self-administration, followed by 6 days of extinction training, with each extinction session followed immediately by treatment with NaB or vehicle. On the last day of extinction, rats were killed and the medial ventral prefrontal cortex retained for chromatin immunoprecipitation and quantitative polymerase chain reaction (qPCR). A history of nicotine exposure significantly decreased H3K14 acetylation at the brain-derived neurotrophic factor (BDNF) exon IV promoter, and this effect was abolished with NaB treatment. In contrast, nicotine self-administration alone, resulted in a significant decrease in histone methylation at the H3K27me3 and H3K9me2 marks in the promoter regions of BDNF exon IV and cyclin-dependent kinase 5 (Cdk-5). Quantitative PCR-identified changes in several genes associated with NaB treatment that were independent of nicotine exposure; however, an interaction of nicotine history and NaB treatment was detected only in the expression of BDNF IV and BDNF IX. Together these results suggest that nicotine self-administration leads to a number of epigenetic changes at both the BDNF and Cdk-5 promoters, and that these changes may contribute to the enhanced extinction of nicotine-seeking by NaB.
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Affiliation(s)
- M R Castino
- School of Psychology, University of New South Wales, Sydney, Australia
| | - D Baker-Andresen
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - V S Ratnu
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - G Shevchenko
- Center for Gene Therapy, City of Hope, Duarte, CA, USA
| | - K V Morris
- Center for Gene Therapy, City of Hope, Duarte, CA, USA
| | - T W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - N A Youngson
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - K J Clemens
- School of Psychology, University of New South Wales, Sydney, Australia
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DeWitt JJ, Hecht PM, Grepo N, Wilkinson B, Evgrafov OV, Morris KV, Knowles JA, Campbell DB. Transcriptional Gene Silencing of the Autism-Associated Long Noncoding RNA MSNP1AS in Human Neural Progenitor Cells. Dev Neurosci 2016; 38:375-383. [PMID: 28030860 DOI: 10.1159/000453258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/08/2016] [Indexed: 12/21/2022] Open
Abstract
The long noncoding RNA MSNP1AS (moesin pseudogene 1, antisense) is a functional element that was previously associated with autism spectrum disorder (ASD) with genome-wide significance. Expression of MSNP1AS was increased 12-fold in the cerebral cortex of individuals with ASD and 22-fold in individuals with a genome-wide significantly associated ASD genetic marker on chromosome 5p14.1. Overexpression of MSNP1AS in human neuronal cells caused decreased expression of moesin protein, which is involved in neuronal process stability. In this study, we hypothesize that MSNP1AS knockdown impacts global transcriptome levels. We transfected the human neural progenitor cell line SK- N-SH with constructs that caused a 50% suppression of MSNP1AS expression. After 24 h, cells were harvested for total RNA isolation. Strand-specific RNA sequencing analysis indicated altered expression of 1,352 genes, including altered expression of 318 genes following correction for multiple comparisons. Expression of the OAS2 gene was increased >150-fold, a result that was validated by quantitative PCR. Gene ontology analysis of the 318 genes with altered expression following correction for multiple comparisons indicated that upregulated genes were significantly enriched for genes involved in immune response, and downregulated genes were significantly enriched for genes involved in chromatin remodeling. These data indicate multiple transcriptional and translational functions of MSNP1AS that impact ASD-relevant biological processes. Chromatin remodeling and immune response are biological processes implicated by genes with rare mutations associated with ASD. Our data suggest that the functional elements implicated by association of common genetic variants impact the same biological processes, suggesting a possible shared common molecular pathway of ASD.
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Affiliation(s)
- Jessica J DeWitt
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Abstract
Cells communicate with one another to create microenvironments and share resources. One avenue by which cells communicate is through the action of exosomes. Exosomes are extracellular vesicles that are released by one cell and taken up by neighbouring cells. But how exosomes instigate communication between cells has remained largely unknown. We present evidence here that particular long non-coding RNA molecules are preferentially packaged into exosomes. We also find that a specific class of these exosome associated non-coding RNAs functionally modulate cell viability by direct interactions with l-lactate dehydrogenase B (LDHB), high-mobility group protein 17 (HMG-17), and CSF2RB, proteins involved in metabolism, nucleosomal architecture and cell signalling respectively. Knowledge of this endogenous cell to cell pathway, those proteins interacting with exosome associated non-coding transcripts and their interacting domains, could lead to a better understanding of not only cell to cell interactions but also the development of exosome targeted approaches in patient specific cell-based therapies.
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Affiliation(s)
- Chris Hewson
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052 Australia
| | - David Capraro
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052 Australia
| | - Jon Burdach
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052 Australia
| | - Noel Whitaker
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052 Australia
| | - Kevin V Morris
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052 Australia; Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States, 92037; City of Hope - Beckman Research Institute, Center for Gene Therapy, Duarte, CA, 91010, United States
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Abstract
Amplification or overexpression of neuronal MYC (MYCN) is associated with poor prognosis of human neuroblastoma. Three isoforms of the MYCN protein have been described as well as a protein encoded by an antisense transcript (MYCNOS) that originates from the opposite strand at the MYCN locus. Recent findings suggest that some antisense long non-coding RNAs (lncRNAs) can play a role in epigenetically regulating gene expression. Here we report that MYCNOS transcripts function as a modulator of the MYCN locus, affecting MYCN promoter usage and recruiting various proteins, including the Ras GTPase-activating protein-binding protein G3BP1, to the upstream MYCN promoter. Overexpression of MYCNOS results in a reduction of upstream MYCN promoter usage and increased MYCN expression, suggesting that the protein-coding MYCNOS also functions as a regulator of MYCN ultimately controlling MYCN transcriptional variants. The observations presented here demonstrate that protein-coding transcripts can regulate gene transcription and can tether regulatory proteins to target loci.
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Affiliation(s)
- Nadia Vadie
- a Molecular and Experimental Medicine ; The Scripps Research Institute ; La Jolla , CA USA
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Lopez-Lemus UA, Ackley A, Saayman S, Embree H, Dropulic B, Akkina R, Charlins P, Weinberg MS, Morris KV. 532. Stable Transcriptional Repression, Gene Excision, and Parastism of HIV by Conditionally Replicating Lentiviral Vectors. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)33341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Abstract
Natural selective processes have been known to drive phenotypic plasticity, which is the emergence of different phenotypes from one genome following environmental stimulation. Long non-coding RNAs (lncRNAs) have been observed to modulate transcriptional and epigenetic states of genes in human cells. We surmised that lncRNAs are governors of phenotypic plasticity and drive natural selective processes through epigenetic modulation of gene expression. Using heat shocked human cells as a model we find several differentially expressed transcripts with the top candidates being lncRNAs derived from retro-elements. One particular retro-element derived transcripts, Retro-EIF2S2, was found to be abundantly over-expressed in heat shocked cells. Over-expression of Retro-EIF2S2 significantly enhanced cell viability and modulated a predisposition for an adherent cellular phenotype upon heat shock. Mechanistically, we find that this retro-element derived transcript interacts directly with a network of proteins including 40S ribosomal protein S30 (FAU), Eukaryotic translation initiation factor 5A (EIF5A), and Ubiquitin-60S ribosomal protein L40 (UBA52) to affect protein modulated cell adhesion pathways. We find one motif in Retro-EIF2S2 that exhibits binding to FAU and modulates phenotypic cell transitions from adherent to suspension states. The observations presented here suggest that retroviral derived transcripts actively modulate phenotypic plasticity in human cells in response to environmental selective pressures and suggest that natural selection may play out through the action of retro-elements in human cells.
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Affiliation(s)
- Laura Trakman
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
| | - Chris Hewson
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
| | - Jon Burdach
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
| | - Kevin V. Morris
- The University of New South Wales, Biotechnology and Biomedical Sciences, Sydney NSW 2052, Australia
- City of Hope – Beckman Research Institute, Center for Gene Therapy, Duarte, California, 91010, United States of America
- * E-mail:
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Abstract
It has been over a decade since the first observation that small non-coding RNAs can functionally modulate epigenetic states in human cells to achieve functional transcriptional gene silencing (TGS). TGS is mechanistically distinct from the RNA interference (RNAi) gene-silencing pathway. TGS can result in long-term stable epigenetic modifications to gene expression that can be passed on to daughter cells during cell division, whereas RNAi does not. Early studies of TGS have been largely overlooked, overshadowed by subsequent discoveries of small RNA-directed post-TGS and RNAi. A reappraisal of early work has been brought about by recent findings in human cells where endogenous long non-coding RNAs function to regulate the epigenome. There are distinct and common overlaps between the proteins involved in small and long non-coding RNA transcriptional regulatory mechanisms, suggesting that the early studies using small non-coding RNAs to modulate transcription were making use of a previously unrecognized endogenous mechanism of RNA-directed gene regulation. Here we review how non-coding RNA plays a role in regulation of transcription and epigenetic gene silencing in human cells by revisiting these earlier studies and the mechanistic insights gained to date. We also provide a list of mammalian genes that have been shown to be transcriptionally regulated by non-coding RNAs. Lastly, we explore how TGS may serve as the basis for development of future therapeutic agents.
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Affiliation(s)
- Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS 2050, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA Center for Gene Therapy, City of Hope - BeckmanResearch Institute; Duarte, CA 91010, USA School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, 2033 Australia
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Milligan MJ, Harvey E, Yu A, Morgan AL, Smith DL, Zhang E, Berengut J, Sivananthan J, Subramaniam R, Skoric A, Collins S, Damski C, Morris KV, Lipovich L. Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome. Front Genet 2016; 7:26. [PMID: 27047535 PMCID: PMC4805607 DOI: 10.3389/fgene.2016.00026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/08/2016] [Indexed: 12/19/2022] Open
Abstract
Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA) transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72); Retroposed Pseudogenes V5 (processed only), and Yale Pseudo60 (processed and unprocessed, Ensembl 60); two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation.
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Affiliation(s)
- Michael J Milligan
- Center for Molecular Medicine and Genetics, Wayne State University Detroit, MI, USA
| | - Erin Harvey
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Albert Yu
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Ashleigh L Morgan
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Daniela L Smith
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Eden Zhang
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Jonathan Berengut
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Jothini Sivananthan
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Radhini Subramaniam
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Aleksandra Skoric
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Scott Collins
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Caio Damski
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Kevin V Morris
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University Detroit, MI, USA
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Saayman SM, Lazar DC, Scott TA, Hart JR, Takahashi M, Burnett JC, Planelles V, Morris KV, Weinberg MS. Potent and Targeted Activation of Latent HIV-1 Using the CRISPR/dCas9 Activator Complex. Mol Ther 2016; 24:488-98. [PMID: 26581162 PMCID: PMC4786915 DOI: 10.1038/mt.2015.202] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/23/2015] [Indexed: 02/08/2023] Open
Abstract
HIV-1 provirus integration results in a persistent latently infected reservoir that is recalcitrant to combined antiretroviral therapy (cART) with lifelong treatment being the only option. The "shock and kill" strategy aims to eradicate latent HIV by reactivating proviral gene expression in the context of cART treatment. Gene-specific transcriptional activation can be achieved using the RNA-guided CRISPR-Cas9 system comprising single guide RNAs (sgRNAs) with a nuclease-deficient Cas9 mutant (dCas9) fused to the VP64 transactivation domain (dCas9-VP64). We engineered this system to target 23 sites within the long terminal repeat promoter of HIV-1 and identified a "hotspot" for activation within the viral enhancer sequence. Activating sgRNAs transcriptionally modulated the latent proviral genome across multiple different in vitro latency cell models including T cells comprising a clonally integrated mCherry-IRES-Tat (LChIT) latency system. We detected consistent and effective activation of latent virus mediated by activator sgRNAs, whereas latency reversal agents produced variable activation responses. Transcriptomic analysis revealed dCas9-VP64/sgRNAs to be highly specific, while the well-characterized chemical activator TNFα induced widespread gene dysregulation. CRISPR-mediated gene activation represents a novel system which provides enhanced efficiency and specificity in a targeted latency reactivation strategy and represents a promising approach to a "functional cure" of HIV/AIDS.
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Affiliation(s)
- Sheena M Saayman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
- HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel C Lazar
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Tristan A Scott
- HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan R Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Mayumi Takahashi
- Division of Molecular Biology, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - John C Burnett
- Division of Molecular Biology, Beckman Research Institute at the City of Hope, Duarte, California, USA
| | - Vicente Planelles
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
- HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Wits/SA MRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
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Morris KV. In the first post-genomic decade, the ENCODE and FANTOM consortia have revolutionized. Introduction. Curr Top Microbiol Immunol 2016; 394:v. [PMID: 27336089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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Abstract
Using RNA-seq (RNA sequencing) of ribosome-depleted RNA, we have identified 1,273 lncRNAs (long non-coding RNAs) in P493-6 human B-cells. Of these, 534 are either up- or downregulated in response to MYC overexpression. An increase in MYC occupancy near their TSS (transcription start sites) was observed for MYC-responsive lncRNAs suggesting these are direct MYC targets. MYC binds to the same TSS across several cell lines, but the number of TSS bound depends on cellular MYC levels and increases with higher MYC concentrations. Despite this concordance in promoter binding, a majority of expressed lncRNAs are specific for one cell line, suggesting a determinant role of additional, possibly differentiation-specific factors in the activity of MYC-bound lncRNA promoters. A significant fraction of the lncRNA transcripts lack polyadenylation. The RNA-seq data were confirmed on eight selected lncRNAs by NRO (nuclear run-on) and RT-qPCR (quantitative reverse transcription PCR).
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Affiliation(s)
- Jonathan R Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas C Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, WITS, South Africa
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA. School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW, Australia
| | - Peter K Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
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Abstract
Viral infections induce strong modifications in the cell transcriptome. Among the RNAs whose expression is altered by infection are long noncoding RNAs (lncRNAs). LncRNAs are transcripts with potential to function as RNA molecules. Infected cells may express viral lncRNAs, cellular lncRNAs and chimeric lncRNAs formed by viral and cellular sequences. Some viruses express viral lncRNAs whose function is essential for viral viability. They are transcribed by polymerase II or III and some of them can be processed by unique maturation steps performed by host cell machineries. Some viral lncRNAs control transcription, stability or translation of cellular and viral genes. Surprisingly, similar functions can be exerted by cellular lncRNAs induced by infection. Expression of cellular lncRNAs may be altered in response to viral replication or viral protein expression. However, many cellular lncRNAs respond to the antiviral pathways induced by infection. In fact, many lncRNAs function as positive or negative regulators of the innate antiviral response. Our current knowledge about the identity and function of lncRNAs in infected cells is very limited. However, research into this field has already helped in the identification of novel cellular pathways and may help in the development of therapeutic tools for the treatment of viral infections, autoimmune diseases, neurological disorders and cancer.
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Affiliation(s)
- Puri Fortes
- Center for Applied Medical Research (CIMA) and Navarra Institute for Health Research (IdiSNA), Department of Gene Therapy and Hepatology, University of Navarra, Pamplona, Spain.
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia
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