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Koodamvetty A, Thangavel S. Advancing Precision Medicine: Recent Innovations in Gene Editing Technologies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2410237. [PMID: 40025867 PMCID: PMC11984848 DOI: 10.1002/advs.202410237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 12/13/2024] [Indexed: 03/04/2025]
Abstract
The advent of gene editing has significantly advanced the field of medicine, opening new frontiers in the treatment of genetic disorders, cancer, and infectious diseases. Gene editing technology remains a dynamic and promising area of research and development. Recent advancements in protein and RNA engineering within this field have addressed critical issues such as imprecise edits, poor editing efficiency, and off-target effects. Advancements in delivery methods have allowed the achievement of therapeutic or even selection-free gene editing efficiency with reduced toxicity in primary cells, thereby enhancing the safety and efficacy of gene manipulation. This progress paves the way for transformative changes in molecular biology, medicine, and other fields. This review provides a comprehensive overview of the advancements in gene editing techniques, focusing on prime editor proteins and their engineered variants. It also explores alternative systems that expand the toolkit for precise genomic modifications and highlights the potential of these innovations in treating hematological disorders, while also discussing the limitations and challenges that remain.
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Affiliation(s)
- Abhijith Koodamvetty
- Centre for Stem Cell Research (CSCR)A unit of InStem BengaluruChristian Medical College campusVelloreTamil Nadu632002India
- Manipal Academy of Higher EducationManipalKarnataka576104India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (CSCR)A unit of InStem BengaluruChristian Medical College campusVelloreTamil Nadu632002India
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Purdy R, John M, Bray A, Clare AJ, Copland DA, Chan YK, Henderson RH, Nerinckx F, Leroy BP, Yang P, Pennesi ME, MacLaren RE, Fischer MD, Dick AD, Xue K. Gene Therapy-Associated Uveitis (GTAU): Understanding and mitigating the adverse immune response in retinal gene therapy. Prog Retin Eye Res 2025; 106:101354. [PMID: 40090458 DOI: 10.1016/j.preteyeres.2025.101354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Revised: 03/04/2025] [Accepted: 03/14/2025] [Indexed: 03/18/2025]
Abstract
Retinal gene therapy using adeno-associated viral (AAV) vectors has been a groundbreaking step-change in the treatment of inherited retinal diseases (IRDs) and could also be used to treat more common retinal diseases such as age-related macular degeneration and diabetic retinopathy. The delivery and expression of therapeutic transgenes in the eye is limited by innate and adaptive immune responses against components of the vector product, which has been termed gene therapy-associated uveitis (GTAU). This is clinically important as intraocular inflammation could lead to irreversible loss of retinal cells, deterioration of visual function and reduced durability of treatment effect associated with a costly one-off treatment. For retinal gene therapy to achieve an improved efficacy and safety profile for treating additional IRDs and more common diseases, the risk of GTAU must be minimised. We have collated insights from pre-clinical research, clinical trials, and the real-world implementation of AAV-mediated retinal gene therapy to help understand the risk factors for GTAU. We draw attention to an emerging framework, which includes patient demographics, vector construct, vector dose, route of administration, and choice of immunosuppression regime. Importantly, we consider efforts to date and potential future strategies to mitigate the adverse immune response across each of these domains. We advocate for more targeted immunomodulatory approaches to the prevention and treatment of GTAU based on better understanding of the underlying immune response.
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Affiliation(s)
- Ryan Purdy
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Molly John
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Alison J Clare
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, UK; University College London (UCL) Institute of Ophthalmology, London, UK; NIHR Biomedical Research Centre of Ophthalmology, Moorfields Eye Hospital, London, UK
| | - David A Copland
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, UK; University College London (UCL) Institute of Ophthalmology, London, UK; NIHR Biomedical Research Centre of Ophthalmology, Moorfields Eye Hospital, London, UK
| | - Ying Kai Chan
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, UK; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Cirrus Therapeutics, Cambridge, MA, USA
| | - Robert H Henderson
- University College London (UCL) Great Ormond Street Institute of Child Health, London, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Fanny Nerinckx
- Chirec Delta Hospital, Brussels, Belgium; Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium; Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium; Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Paul Yang
- Casey Eye Institute, Oregon Health & Science University, Portland, USA
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, USA; Retina Foundation of the Southwest, Dallas, TX, USA
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M Dominik Fischer
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Andrew D Dick
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, UK; University College London (UCL) Institute of Ophthalmology, London, UK; NIHR Biomedical Research Centre of Ophthalmology, Moorfields Eye Hospital, London, UK
| | - Kanmin Xue
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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Garg P, Singhal G, Pareek S, Kulkarni P, Horne D, Nath A, Salgia R, Singhal SS. Unveiling the potential of gene editing techniques in revolutionizing Cancer treatment: A comprehensive overview. Biochim Biophys Acta Rev Cancer 2025; 1880:189233. [PMID: 39638158 DOI: 10.1016/j.bbcan.2024.189233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 11/27/2024] [Accepted: 11/28/2024] [Indexed: 12/07/2024]
Abstract
Gene editing techniques have emerged as powerful tools in biomedical research, offering precise manipulation of genetic material with the potential to revolutionize cancer treatment strategies. This review provides a comprehensive overview of the current landscape of gene editing technologies, including CRISPR-Cas systems, base editing, prime editing, and synthetic gene circuits, highlighting their applications and potential in cancer therapy. It discusses the mechanisms, advantages, and limitations of each gene editing approach, emphasizing their transformative impact on targeting oncogenes, tumor suppressor genes, and drug resistance mechanisms in various cancer types. The review delves into population-level interventions and precision prevention strategies enabled by gene editing technologies, including gene drives, synthetic gene circuits, and precision prevention tools, for controlling cancer-causing genes, targeting pre-cancerous lesions, and implementing personalized preventive measures. Ethical considerations, regulatory challenges, and future directions in gene editing research for cancer treatment are also addressed. This review highlights how gene editing could revolutionize precision medicine by enhancing patient care and advancing cancer treatments with targeted, personalized methods. For these benefits to be fully realized, collaboration among researchers, doctors, regulators, and patient advocates is crucial in fighting cancer and meeting clinical needs.
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Affiliation(s)
- Pankaj Garg
- Department of Chemistry, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Gargi Singhal
- Undergraduate Medical Sciences, S.N. Medical College Agra, Uttar Pradesh 282002, India
| | - Siddhika Pareek
- Department of Medical Oncology & Therapeutics Research, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- Department of Medical Oncology & Therapeutics Research, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Aritro Nath
- Department of Medical Oncology & Therapeutics Research, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sharad S Singhal
- Department of Medical Oncology & Therapeutics Research, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA.
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Pechnikova NA, Poimenidou M, Iliadis I, Zafeiriou-Chatziefraimidou M, Iaremenko AV, Yaremenko TV, Domvri K, Yaremenko AV. Pre-Clinical and Clinical Advances in Gene Therapy of X-Linked Retinitis Pigmentosa: Hope on the Horizon. J Clin Med 2025; 14:898. [PMID: 39941570 PMCID: PMC11818521 DOI: 10.3390/jcm14030898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 01/13/2025] [Accepted: 01/21/2025] [Indexed: 02/16/2025] Open
Abstract
X-linked retinitis pigmentosa (XLRP) is a severe inherited retinal degenerative disease characterized by progressive loss of photoreceptors and retinal pigment epithelium, leading to blindness. Predominantly affecting males due to mutations in the RPGR gene, XLRP currently lacks effective treatments beyond supportive care. Gene therapy has emerged as a promising approach to restore photoreceptor function by delivering functional copies of the RPGR gene. Recent clinical trials using AAV vectors, such as AAV5-RPGR and AGTC-501, have demonstrated encouraging results, including improvements in retinal sensitivity and visual function. While early successes like LUXTURNA have set the precedent for gene therapy in retinal diseases, adapting these strategies to XLRP presents unique challenges due to the complexity of RPGR mutations and the need for efficient photoreceptor targeting. Advances in vector design, including the use of optimized AAV serotypes with enhanced tropism for photoreceptors and specific promoters, have significantly improved gene delivery. Despite setbacks in some studies, ongoing research and clinical trials continue to refine these therapies, offering hope for patients affected by XLRP. This review explores the etiology and pathophysiology of XLRP, evaluates current treatment challenges, highlights recent clinical advances in gene therapy, and discusses future perspectives for bringing these therapies into clinical practice.
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Affiliation(s)
- Nadezhda A. Pechnikova
- Department of Biochemistry and Biotechnology, University of Thessaly, 38446 Volos, Greece;
- Laboratory of Chemical Engineering A’, Department of Chemical Engineering, Faculty of Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
- Saint Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Malamati Poimenidou
- School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (M.P.); (I.I.); (M.Z.-C.); (K.D.)
| | - Ioannis Iliadis
- School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (M.P.); (I.I.); (M.Z.-C.); (K.D.)
| | | | - Aleksandra V. Iaremenko
- Faculty of Pediatrics, Pirogov Russian National Research Medical University, Moscow 117513, Russia;
| | | | - Kalliopi Domvri
- School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (M.P.); (I.I.); (M.Z.-C.); (K.D.)
| | - Alexey V. Yaremenko
- School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (M.P.); (I.I.); (M.Z.-C.); (K.D.)
- Harvard Medical School, Brigham and Women’s Hospital, Boston, MA 02115, USA
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Seitz IP, Wozar F, Ochakovski GA, Reichel FF, Korte S, Korbmacher B, Wilhelm B, Süsskind D, Bartz-Schmidt KU, Fischer MD, Peters T. Ocular Safety and Toxicology of Subretinal Gene Therapy With rAAV.hPDE6A in Nonhuman Primates. Transl Vis Sci Technol 2025; 14:29. [PMID: 39878701 PMCID: PMC11781330 DOI: 10.1167/tvst.14.1.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 07/10/2024] [Indexed: 01/31/2025] Open
Abstract
Purpose Reports of gene therapy-associated retinal atrophies and inflammation have highlighted the importance of preclinical safety assessments of adeno-associated virus (AAV) vector systems. We evaluated in nonhuman primates (NHPs) the ocular safety and toxicology of a novel AAV gene therapy targeting retinitis pigmentosa caused by mutations in PDE6A, which has since been used in a phase I/II clinical trial (NCT04611503). Methods A total of 34 healthy cynomolgus animals (Macaca fascicularis) were treated with subretinal injections of rAAV.hPDE6A and followed over 13 weeks. Three dose levels (low: 1 × 1011, intermediate: 5 × 1011, and high: 1 × 1012 vector genomes [vg]) were compared to sham-injected controls. Safety and toxicity were determined using ophthalmic examinations, electroretinography, ocular histology, and retinal imaging. Results At the low and intermediate doses, inflammation was mild, electroretinography response was unimpeded, and histology results were in line with surgically induced changes. In contrast, three high-dose animals displayed atrophic changes of the retina and abnormalities in electroretinography, which were considered test article related and adverse. Conclusions A single subretinal injection of up to 5 × 1011 vg was well tolerated, and a 10-fold lower dose of 5 × 1010 vg was chosen as the starting dose for the ongoing phase I/II clinical trial. Atrophic retinal changes and abnormalities in electroretinography emerged as dose-limiting findings in the high-dose cohort. Translational Relevance This study demonstrates that treatment candidate rAAV.PDE6A was well tolerated in NHPs. Occurrence of retinal atrophy as a dose-limiting finding highlights the importance of further study into the mechanisms of atrophy induction after retinal gene therapy.
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Affiliation(s)
- Immanuel P. Seitz
- University Eye Hospital Tuebingen, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Fabian Wozar
- University Eye Hospital Tuebingen, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | | | - Felix F. Reichel
- University Eye Hospital Tuebingen, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Sven Korte
- Labcorp Early Development Services GmbH, Muenster, Germany
- Virscio, Inc., New Haven, CT, USA
| | | | - Barbara Wilhelm
- STZ eyetrialat the Centre for Ophthalmology, Tuebingen, Germany
| | - Daniela Süsskind
- University Eye Hospital Tuebingen, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Karl-Ulrich Bartz-Schmidt
- University Eye Hospital Tuebingen, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - M. Dominik Fischer
- University Eye Hospital Tuebingen, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Tobias Peters
- STZ eyetrialat the Centre for Ophthalmology, Tuebingen, Germany
| | - for the RD Cure Consortium
- University Eye Hospital Tuebingen, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
- University Eye Hospital Munich, Munich, Germany
- Labcorp Early Development Services GmbH, Muenster, Germany
- Virscio, Inc., New Haven, CT, USA
- STZ eyetrialat the Centre for Ophthalmology, Tuebingen, Germany
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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Gila F, Alamdari-Palangi V, Rafiee M, Jokar A, Ehtiaty S, Dianatinasab A, Khatami SH, Taheri-Anganeh M, Movahedpour A, Fallahi J. Gene-edited cells: novel allogeneic gene/cell therapy for epidermolysis bullosa. J Appl Genet 2024; 65:705-726. [PMID: 38459407 DOI: 10.1007/s13353-024-00839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 03/10/2024]
Abstract
Epidermolysis bullosa (EB) is a group of rare genetic skin fragility disorders, which are hereditary. These disorders are associated with mutations in at least 16 genes that encode components of the epidermal adhesion complex. Currently, there are no effective treatments for this disorder. All current treatment approaches focus on topical treatments to prevent complications and infections. In recent years, significant progress has been achieved in the treatment of the severe genetic skin blistering condition known as EB through preclinical and clinical advancements. Promising developments have emerged in the areas of protein and cell therapies, such as allogeneic stem cell transplantation; in addition, RNA-based therapies and gene therapy approaches have also become a reality. Stem cells obtained from embryonic or adult tissues, including the skin, are undifferentiated cells with the ability to generate, maintain, and replace fully developed cells and tissues. Recent advancements in preclinical and clinical research have significantly enhanced stem cell therapy, presenting a promising treatment option for various diseases that are not effectively addressed by current medical treatments. Different types of stem cells such as primarily hematopoietic and mesenchymal, obtained from the patient or from a donor, have been utilized to treat severe forms of diseases, each with some beneficial effects. In addition, extensive research has shown that gene transfer methods targeting allogeneic and autologous epidermal stem cells to replace or correct the defective gene are promising. These methods can regenerate and restore the adhesion of primary keratinocytes in EB patients. The long-term treatment of skin lesions in a small number of patients has shown promising results through the transplantation of skin grafts produced from gene-corrected autologous epidermal stem cells. This article attempts to summarize the current situation, potential development prospects, and some of the challenges related to the cell therapy approach for EB treatment.
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Affiliation(s)
- Fatemeh Gila
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Vahab Alamdari-Palangi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maedeh Rafiee
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Arezoo Jokar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sajad Ehtiaty
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aria Dianatinasab
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | | | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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Ross M, Sade K, Obolensky A, Averbukh E, Desrosiers M, Rosov A, Dvir H, Gootwine E, Banin E, Dalkara D, Ofri R. Characterization of anti-AAV2 neutralizing antibody levels in sheep prior to and following intravitreal AAV2.7m8 injection. Gene Ther 2024; 31:580-586. [PMID: 39472677 DOI: 10.1038/s41434-024-00495-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 11/21/2024]
Abstract
Gene augmentation therapy is a promising treatment for incurable, blinding inherited retinal diseases, and intravitreal delivery is being studied as a safe alternative to subretinal injections. Adeno-Associated Viruses (AAV) are commonly-used vectors for ocular gene augmentation therapy. Naturally occurring pre-operative exposure and infection with AAV could result in presence of neutralizing antibodies (NAB's) in patients' serum, and may affect the safety and efficacy of treatment. Our aim was to characterize the humoral response against AAV pre- and post-intravitreal delivery of AAV2.7m8 vectors in a naturally-occurring sheep model of CNGA3 achromatopsia. Serial serum neutralization assays were performed to screen sheep for pre-exiting anti-AAV2 NAB's, and to assess the effect of intravitreal AAV2.7m8 injection on post-operative NAB titers and intraocular inflammation in sheep. The effect of viral dose and transgene type were also assessed. Serological screening revealed pre-operative seropositivity in 21.4% of animals, with age being a risk factor for the presence of anti-AAV2 NAB's. NAB titers increased following intravitreal AAV administration in the majority of sheep. There was no significant difference in the degree of post-operative serum neutralization between pre-operatively seronegative sheep and those with pre-existing antibodies. However, only sheep with pre-existing antibodies presented with signs of post-operative inflammation. We conclude that pre-existing anti-AAV2 NAB's do not affect the level of post-operative NAB titers; however, they increase the risk of post-operative ocular inflammation. Our results could have implications for the management of AAV-mediated ocular gene therapies, a technology being increasingly studied and used in patients.
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Affiliation(s)
- Maya Ross
- Department of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Kareen Sade
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot, Israel
| | - Alexey Obolensky
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edward Averbukh
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Melissa Desrosiers
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Alexander Rosov
- Department of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Hay Dvir
- Department of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Elisha Gootwine
- Department of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France
| | - Ron Ofri
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot, Israel.
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Cheng L, Zhu Y, Ma J, Aggarwal A, Toh WH, Shin C, Sangpachatanaruk W, Weng G, Kumar R, Mao HQ. Machine Learning Elucidates Design Features of Plasmid Deoxyribonucleic Acid Lipid Nanoparticles for Cell Type-Preferential Transfection. ACS NANO 2024; 18:28735-28747. [PMID: 39375194 PMCID: PMC11512640 DOI: 10.1021/acsnano.4c07615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
Abstract
To broaden the accessibility of cell and gene therapies, it is essential to develop and optimize nonviral, cell type-preferential gene carriers such as lipid nanoparticles (LNPs). While high-throughput screening (HTS) approaches have proven effective in accelerating LNP discovery, they are often costly, labor-intensive, and do not consistently yield actionable design rules that direct screening efforts toward the most relevant chemical and formulation parameters. In this study, we employed a machine learning (ML) workflow, utilizing well-curated plasmid DNA LNP transfection data sets across six cell types, to extract compositional and chemical insights from HTS studies. Our approach achieved prediction errors averaging between 5 and 10%, depending on the cell type. By applying SHapley Additive exPlanations to our ML models, we uncovered key composition-function relationships that govern cell type-preferential LNP transfection efficiency. Notably, we identified consistent LNP composition parameters that enhance in vitro transfection efficiency across diverse cell types, including a helper lipid molar percentage of charged lipids between 9 and 50% and the inclusion of cationic/zwitterionic helper lipids. Additionally, several parameters were found to modulate cell type-preferentiality, such as the total molar percentage of ionizable and helper lipids, N/P ratio, PEGylated lipid molar percentage of uncharged lipids, and hydrophobicity of the helper lipid. This study leverages HTS of compositionally diverse LNP libraries combined with ML analysis to elucidate the interactions between lipid components in LNP formulations, providing insights that contribute to the design of LNP compositions tailored for cell type-preferential transfection.
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Affiliation(s)
- Leonardo Cheng
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Yining Zhu
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Jingyao Ma
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
- Department of Materials Science and Engineering, Whiting School of Engineering. Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ataes Aggarwal
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Wu Han Toh
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Charles Shin
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
| | - Will Sangpachatanaruk
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gene Weng
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ramya Kumar
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Hai-Quan Mao
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, United States
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
- Department of Materials Science and Engineering, Whiting School of Engineering. Johns Hopkins University, Baltimore, Maryland 21218, United States
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Alsalloum A, Gornostal E, Mingaleva N, Pavlov R, Kuznetsova E, Antonova E, Nadzhafova A, Kolotova D, Kadyshev V, Mityaeva O, Volchkov P. A Comparative Analysis of Models for AAV-Mediated Gene Therapy for Inherited Retinal Diseases. Cells 2024; 13:1706. [PMID: 39451224 PMCID: PMC11506034 DOI: 10.3390/cells13201706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/13/2024] [Accepted: 10/14/2024] [Indexed: 10/26/2024] Open
Abstract
Inherited retinal diseases (IRDs) represent a diverse group of genetic disorders leading to progressive degeneration of the retina due to mutations in over 280 genes. This review focuses on the various methodologies for the preclinical characterization and evaluation of adeno-associated virus (AAV)-mediated gene therapy as a potential treatment option for IRDs, particularly focusing on gene therapies targeting mutations, such as those in the RPE65 and FAM161A genes. AAV vectors, such as AAV2 and AAV5, have been utilized to deliver therapeutic genes, showing promise in preserving vision and enhancing photoreceptor function in animal models. Despite their advantages-including high production efficiency, low pathogenicity, and minimal immunogenicity-AAV-mediated therapies face limitations such as immune responses beyond the retina, vector size constraints, and challenges in large-scale manufacturing. This review systematically compares different experimental models used to investigate AAV-mediated therapies, such as mouse models, human retinal explants (HREs), and induced pluripotent stem cell (iPSC)-derived retinal organoids. Mouse models are advantageous for genetic manipulation and detailed investigations of disease mechanisms; however, anatomical differences between mice and humans may limit the translational applicability of results. HREs offer valuable insights into human retinal pathophysiology but face challenges such as tissue degradation and lack of systemic physiological effects. Retinal organoids, on the other hand, provide a robust platform that closely mimics human retinal development, thereby enabling more comprehensive studies on disease mechanisms and therapeutic strategies, including AAV-based interventions. Specific outcomes targeted in these studies include vision preservation and functional improvements of retinas damaged by genetic mutations. This review highlights the strengths and weaknesses of each experimental model and advocates for their combined use in developing targeted gene therapies for IRDs. As research advances, optimizing AAV vector design and delivery methods will be critical for enhancing therapeutic efficacy and improving clinical outcomes for patients with IRDs.
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Affiliation(s)
- Almaqdad Alsalloum
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia (P.V.)
| | | | - Natalia Mingaleva
- Moscow Center for Advanced Studies, Kulakova Str. 20, 123592 Moscow, Russia
| | - Roman Pavlov
- Moscow Center for Advanced Studies, Kulakova Str. 20, 123592 Moscow, Russia
| | | | - Ekaterina Antonova
- Moscow Center for Advanced Studies, Kulakova Str. 20, 123592 Moscow, Russia
| | - Aygun Nadzhafova
- Moscow Center for Advanced Studies, Kulakova Str. 20, 123592 Moscow, Russia
| | - Daria Kolotova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia
| | | | - Olga Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Pavel Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- Moscow Clinical Scientific Center N.A. A.S. Loginov, 111123 Moscow, Russia
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10
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Khaparde A, Mathias GP, Poornachandra B, Thirumalesh MB, Shetty R, Ghosh A. Gene therapy for retinal diseases: From genetics to treatment. Indian J Ophthalmol 2024; 72:1091-1101. [PMID: 39078952 PMCID: PMC11451791 DOI: 10.4103/ijo.ijo_2902_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/31/2024] [Accepted: 04/19/2024] [Indexed: 10/06/2024] Open
Abstract
The gene therapy approach for retinal disorders has been considered largely over the last decade owing to the favorable outcomes of the US Food and Drug Administration-approved commercial gene therapy, Luxturna. Technological advances in recent years, such as next-generation sequencing, research in molecular pathogenesis of retinal disorders, and precise correlations with their clinical phenotypes, have contributed to the progress of gene therapies for various diseases worldwide, and more recently in India as well. Thus, considerable research is being conducted for the right choice of vectors, transgene engineering, and accessible and cost-effective large-scale vector production. Many retinal disease-specific clinical trials are presently being conducted, thereby necessitating the collation of such information as a ready reference for the scientific and clinical community. In this article, we present an overview of existing gene therapy research, which is derived from an extensive search across PubMed, Google Scholar, and clinicaltrials.gov sources. This contributes to prime the understanding of basic aspects of this cutting-edge technology and information regarding current clinical trials across many different conditions. This information will provide a comprehensive evaluation of therapies in existing use/research for personalized treatment approaches in retinal disorders.
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Affiliation(s)
- Ashish Khaparde
- GROW Research Laboratory, Narayana Nethralaya Foundation, Manipal, Karnataka, India
| | - Grace P Mathias
- GROW Research Laboratory, Narayana Nethralaya Foundation, Manipal, Karnataka, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - B Poornachandra
- Department of Vitreo Retina Services, Narayana Nethralaya, Manipal, Karnataka, India
| | - M B Thirumalesh
- Department of Vitreo Retina Services, Narayana Nethralaya, Manipal, Karnataka, India
| | - Rohit Shetty
- Department of Cornea and Refractive Surgery, Narayana Nethralaya, Bengaluru, Karnataka, India
| | - Arkasubhra Ghosh
- GROW Research Laboratory, Narayana Nethralaya Foundation, Manipal, Karnataka, India
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11
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Sun L, Rao S, Kerim K, Lu J, Li H, Zhao S, Shen P, Sun W. A chemically adjustable BMP6-IL6 axis in mesenchymal stem cells drives acute myeloid leukemia cell differentiation. Biochem Pharmacol 2024; 225:116262. [PMID: 38705535 DOI: 10.1016/j.bcp.2024.116262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Chemotherapy alone or in combination with allogeneic stem cell transplantation has been the standard of care for acute myeloid leukemia (AML) for decades. Leukemia relapse with limited treatment options remains the main cause of treatment failure. Therefore, an effective and safe approach to improve treatment outcomes is urgently needed for most AML patients. Mesenchymal stem cells (MSCs) have been reported to efficiently induce apoptosis and shape the fate of acute myeloid leukemia cells. Here, we identified LG190155 as a potent compound that enhances the antileukemia efficiency of MSCs. Pretreatment of MSCs with LG190155 significantly provoked differentiation in both AML patient-derived primary leukemia cells and AML cell lines and reduced the tumor burden in the AML mouse model. Using the quantitative proteomic technique, we discovered a pivotal mechanism that mediates AML cell differentiation, in which autocrine bone morphogenetic protein 6 (BMP6) in MSCs boosted IL-6 secretion and further acted on leukemic cells to trigger differentiation. Furthermore, the activity of the BMP6-IL6 axis was dramatically enhanced by activating vitamin D receptor (VDR) in MSCs. Our data illustrated an effective preactivated approach to reinforcing the antileukemia effect of MSCs, which could serve as an effective therapeutic strategy for AML.
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Affiliation(s)
- Luchen Sun
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Shangrui Rao
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Kamran Kerim
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jianhua Lu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Hongzheng Li
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Shengsheng Zhao
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Pingping Shen
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Shenzhen Research Institute of NanJing University, Shenzhen 518000, China.
| | - Weijian Sun
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, China.
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12
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Neumann EN, Bertozzi TM, Wu E, Serack F, Harvey JW, Brauer PP, Pirtle CP, Coffey A, Howard M, Kamath N, Lenz K, Guzman K, Raymond MH, Khalil AS, Deverman BE, Minikel EV, Vallabh SM, Weissman JS. Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor. Science 2024; 384:ado7082. [PMID: 38935715 PMCID: PMC11875203 DOI: 10.1126/science.ado7082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/02/2024] [Indexed: 06/29/2024]
Abstract
Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid-onset dementia and death. However, elimination of endogenous PrP halts prion disease progression. In this study, we describe Coupled Histone tail for Autoinhibition Release of Methyltransferase (CHARM), a compact, enzyme-free epigenetic editor capable of silencing transcription through programmable DNA methylation. Using a histone H3 tail-Dnmt3l fusion, CHARM recruits and activates endogenous DNA methyltransferases, thereby reducing transgene size and cytotoxicity. When delivered to the mouse brain by systemic injection of adeno-associated virus (AAV), Prnp-targeted CHARM ablates PrP expression across the brain. Furthermore, we have temporally limited editor expression by implementing a kinetically tuned self-silencing approach. CHARM potentially represents a broadly applicable strategy to suppress pathogenic proteins, including those implicated in other neurodegenerative diseases.
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Affiliation(s)
- Edwin N. Neumann
- Whitehead Institute for Biomedical Research; Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Tessa M. Bertozzi
- Whitehead Institute for Biomedical Research; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Elaine Wu
- Whitehead Institute for Biomedical Research; Cambridge, MA 02142, USA
| | - Fiona Serack
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
| | - John W. Harvey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
| | - Pamela P. Brauer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
| | - Catherine P. Pirtle
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
| | - Alissa Coffey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
| | - Michael Howard
- Comparative Medicine, Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Nikita Kamath
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
| | - Kenney Lenz
- Comparative Medicine, Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Kenia Guzman
- Comparative Medicine, Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Michael H. Raymond
- Biological Design Center, Boston University; Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University; Boston, MA 02215, USA
| | - Ahmad S. Khalil
- Biological Design Center, Boston University; Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University; Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University; Boston, MA 02115. USA
| | - Benjamin E. Deverman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
| | - Eric Vallabh Minikel
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital; Boston, MA 02114, USA
| | - Sonia M. Vallabh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital; Boston, MA 02114, USA
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
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13
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Corradetti G, Verma A, Tojjar J, Almidani L, Oncel D, Emamverdi M, Bradley A, Lindenberg S, Nittala MG, Sadda SR. Retinal Imaging Findings in Inherited Retinal Diseases. J Clin Med 2024; 13:2079. [PMID: 38610844 PMCID: PMC11012835 DOI: 10.3390/jcm13072079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Inherited retinal diseases (IRDs) represent one of the major causes of progressive and irreversible vision loss in the working-age population. Over the last few decades, advances in retinal imaging have allowed for an improvement in the phenotypic characterization of this group of diseases and have facilitated phenotype-to-genotype correlation studies. As a result, the number of clinical trials targeting IRDs has steadily increased, and commensurate to this, the need for novel reproducible outcome measures and endpoints has grown. This review aims to summarize and describe the clinical presentation, characteristic imaging findings, and imaging endpoint measures that are being used in clinical research on IRDs. For the purpose of this review, IRDs have been divided into four categories: (1) panretinal pigmentary retinopathies affecting rods or cones; (2) macular dystrophies; (3) stationary conditions; (4) hereditary vitreoretinopathies.
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Affiliation(s)
- Giulia Corradetti
- Doheny Eye Institute, Pasadena, CA 91103, USA (J.T.); (L.A.)
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Aditya Verma
- Doheny Eye Institute, Pasadena, CA 91103, USA (J.T.); (L.A.)
- Department of Ophthalmology and Visual Sciences, University of Louisville, Louisville, KY 40202, USA
| | - Jasaman Tojjar
- Doheny Eye Institute, Pasadena, CA 91103, USA (J.T.); (L.A.)
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Louay Almidani
- Doheny Eye Institute, Pasadena, CA 91103, USA (J.T.); (L.A.)
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Deniz Oncel
- Doheny Eye Institute, Pasadena, CA 91103, USA (J.T.); (L.A.)
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60153, USA
| | - Mehdi Emamverdi
- Doheny Eye Institute, Pasadena, CA 91103, USA (J.T.); (L.A.)
| | - Alec Bradley
- Department of Ophthalmology and Visual Sciences, University of Louisville, Louisville, KY 40202, USA
| | | | | | - SriniVas R. Sadda
- Doheny Eye Institute, Pasadena, CA 91103, USA (J.T.); (L.A.)
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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14
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McCall MA. Pig Models in Retinal Research and Retinal Disease. Cold Spring Harb Perspect Med 2024; 14:a041296. [PMID: 37553210 PMCID: PMC10982707 DOI: 10.1101/cshperspect.a041296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The pig has been used as a large animal model in biomedical research for many years and its use continues to increase because induced mutations phenocopy several inherited human diseases. In addition, they are continuous breeders, can be propagated by artificial insemination, have large litter sizes (on the order of mice), and can be genetically manipulated using all of the techniques that are currently available in mice. The pioneering work of Petters and colleagues set the stage for the use of the pig as a model of inherited retinal disease. In the last 10 years, the pig has become a model of choice where specific disease-causing mutations that are not phenocopied in rodents need to be studied and therapeutic approaches explored. The pig is not only used for retinal eye disease but also for the study of the cornea and lens. This review attempts to show how broad the use of the pig has become and how it has contributed to the assessment of treatments for eye disease. In the last 10 years, there have been several reviews that included the use of the pig in biomedical research (see body of the review) that included information about retinal disease. None directly discuss the use of the pig as an animal model for retinal diseases, including inherited diseases, where a single genetic mutation has been identified or for multifactorial diseases such as glaucoma and diabetic retinopathy. Although the pig is used to explore diseases of the cornea and lens, this review focuses on how and why the pig, as a large animal model, is useful for research in neural retinal disease and its treatment.
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Affiliation(s)
- Maureen A McCall
- Departments of Ophthalmology & Visual Sciences and Anatomical Sciences & Neurobiology, University of Louisville, Louisville, Kentucky 40202, USA
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15
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Appell MB, Pejavar J, Pasupathy A, Rompicharla SVK, Abbasi S, Malmberg K, Kolodziejski P, Ensign LM. Next generation therapeutics for retinal neurodegenerative diseases. J Control Release 2024; 367:708-736. [PMID: 38295996 PMCID: PMC10960710 DOI: 10.1016/j.jconrel.2024.01.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/05/2024] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
Neurodegenerative diseases affecting the visual system encompass glaucoma, macular degeneration, retinopathies, and inherited genetic disorders such as retinitis pigmentosa. These ocular pathologies pose a serious burden of visual impairment and blindness worldwide. Current treatment modalities include small molecule drugs, biologics, or gene therapies, most of which are administered topically as eye drops or as injectables. However, the topical route of administration faces challenges in effectively reaching the posterior segment and achieving desired concentrations at the target site, while injections and implants risk severe complications, such as retinal detachment and endophthalmitis. This necessitates the development of innovative therapeutic strategies that can prolong drug release, deliver effective concentrations to the back of the eye with minimal systemic exposure, and improve patient compliance and safety. In this review, we introduce retinal degenerative diseases, followed by a discussion of the existing clinical standard of care. We then delve into detail about drug and gene delivery systems currently in preclinical and clinical development, including formulation and delivery advantages/drawbacks, with a special emphasis on potential for clinical translation.
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Affiliation(s)
- Matthew B Appell
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Jahnavi Pejavar
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Ashwin Pasupathy
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Sri Vishnu Kiran Rompicharla
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Saed Abbasi
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Kiersten Malmberg
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Patricia Kolodziejski
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Laura M Ensign
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Departments of Gynecology and Obstetrics, Biomedical Engineering, Oncology, and Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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16
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Antas P, Carvalho C, Cabral-Teixeira J, de Lemos L, Seabra MC. Toward low-cost gene therapy: mRNA-based therapeutics for treatment of inherited retinal diseases. Trends Mol Med 2024; 30:136-146. [PMID: 38044158 DOI: 10.1016/j.molmed.2023.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023]
Abstract
Inherited retinal diseases (IRDs) stem from genetic mutations that result in vision impairment. Gene therapy shows promising therapeutic potential, exemplified by the encouraging initial results with voretigene neparvovec. Nevertheless, the associated costs impede widespread access, particularly in low-to-middle income countries. The primary challenge remains: how can we make these therapies globally affordable? Leveraging advancements in mRNA therapies might offer a more economically viable alternative. Furthermore, transitioning to nonviral delivery systems could provide a dual benefit of reduced costs and increased scalability. Relevant stakeholders must collaboratively devise and implement a research agenda to realize the potential of mRNA strategies in equitable access to treatments to prevent vision loss.
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Affiliation(s)
- Pedro Antas
- Champalimaud Research, Champalimaud Foundation, 1400-038 Lisbon, Portugal; iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal.
| | - Cláudia Carvalho
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
| | | | - Luísa de Lemos
- Champalimaud Research, Champalimaud Foundation, 1400-038 Lisbon, Portugal
| | - Miguel C Seabra
- Champalimaud Research, Champalimaud Foundation, 1400-038 Lisbon, Portugal; iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal.
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17
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Cheng L, Zhu Y, Ma J, Aggarwal A, Toh WH, Shin C, Sangpachatanaruk W, Weng G, Kumar R, Mao HQ. Machine Learning Elucidates Design Features of Plasmid DNA Lipid Nanoparticles for Cell Type-Preferential Transfection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570602. [PMID: 38106206 PMCID: PMC10723465 DOI: 10.1101/2023.12.07.570602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
For cell and gene therapies to become more broadly accessible, it is critical to develop and optimize non-viral cell type-preferential gene carriers such as lipid nanoparticles (LNPs). Despite the effectiveness of high throughput screening (HTS) approaches in expediting LNP discovery, they are often costly, labor-intensive, and often do not provide actionable LNP design rules that focus screening efforts on the most relevant chemical and formulation parameters. Here we employed a machine learning (ML) workflow using well-curated plasmid DNA LNP transfection datasets across six cell types to maximize chemical insights from HTS studies and has achieved predictions with 5-9% error on average depending on cell type. By applying Shapley additive explanations to our ML models, we unveiled composition-function relationships dictating cell type-preferential LNP transfection efficiency. Notably, we identified consistent LNP composition parameters that enhance in vitro transfection efficiency across diverse cell types, such as ionizable to helper lipid ratios near 1:1 or 10:1 and the incorporation of cationic/zwitterionic helper lipids. In addition, several parameters were found to modulate cell type-preferentiality, including the ionizable and helper lipid total molar percentage, N/P ratio, cholesterol to PEGylated lipid ratio, and the chemical identity of the helper lipid. This study leverages HTS of compositionally diverse LNP libraries and ML analysis to understand the interactions between lipid components in LNP formulations; and offers fundamental insights that contribute to the establishment of unique sets of LNP compositions tailored for cell type-preferential transfection.
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18
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Fischer A, Ehrlich A, Plotkin Y, Ouyang Y, Asulin K, Konstantinos I, Fan C, Nahmias Y, Willner I. Stimuli-Responsive Hydrogel Microcapsules Harnessing the COVID-19 Immune Response for Cancer Therapeutics. Angew Chem Int Ed Engl 2023; 62:e202311590. [PMID: 37675854 DOI: 10.1002/anie.202311590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
The combination of gene therapy and immunotherapy concepts, along recent advances in DNA nanotechnology, have the potential to provide important tools for cancer therapies. We present the development of stimuli-responsive microcapsules, loaded with a viral immunogenetic agent, harnessing the immune response against the Coronavirus Disease 2019, COVID-19, to selectively attack liver cancer cells (hepatoma) or recognize breast cancer or hepatoma, by expression of green fluorescence protein, GFP. The pH-responsive microcapsules, modified with DNA-tetrahedra nanostructures, increased hepatoma permeation by 50 %. Incorporation of a GFP-encoding lentivirus vector inside the tumor-targeting pH-stimulated miRNA-triggered and Alpha-fetoprotein-dictated microcapsules enables the demonstration of neoplasm selectivity, with approximately 5,000-, 8,000- and 50,000-fold more expression in the cancerous cells, respectively. The incorporation of the SARS-CoV-2 spike protein in the gene vector promotes specific recognition of the immune-evading hepatoma by the COVID-19-analogous immune response, which leads to cytotoxic and inflammatory activity, mediated by serum components taken from vaccinated or recovered COVID-19 patients, resulting in effective elimination of the hepatoma (>85 % yield).
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Affiliation(s)
- Amit Fischer
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Avner Ehrlich
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yevgeni Plotkin
- The Department of Anesthesiology, Critical Care and Pain Medicine, Hadassah University Hospital, Jerusalem, 9112001, Israel
- Faculty of Medicine, Hebrew University of Jerusalem Jerusalem, 9112001, (Israel)
| | - Yu Ouyang
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Klil Asulin
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ioannidis Konstantinos
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yaakov Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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Nasrullah M, Meenakshi Sundaram DN, Claerhout J, Ha K, Demirkaya E, Uludag H. Nanoparticles and cytokine response. Front Bioeng Biotechnol 2023; 11:1243651. [PMID: 37701495 PMCID: PMC10493271 DOI: 10.3389/fbioe.2023.1243651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Synthetic nanoparticles (NPs) are non-viral equivalents of viral gene delivery systems that are actively explored to deliver a spectrum of nucleic acids for diverse range of therapies. The success of the nanoparticulate delivery systems, in the form of efficacy and safety, depends on various factors related to the physicochemical features of the NPs, as well as their ability to remain "stealth" in the host environment. The initial cytokine response upon exposure to nucleic acid bearing NPs is a critical component of the host response and, unless desired, should be minimized to prevent the unintended consequences of NP administration. In this review article, we will summarize the most recent literature on cytokine responses to nanoparticulate delivery systems and identify the main factors affecting this response. The NP features responsible for eliciting the cytokine response are articulated along with other factors related to the mode of therapeutic administration. For diseases arising from altered cytokine pathophysiology, attempts to silence the individual components of cytokine response are summarized in the context of different diseases, and the roles of NP features on this respect are presented. We finish with the authors' perspective on the possibility of engineering NP systems with controlled cytokine responses. This review is intended to sensitize the reader with important issues related to cytokine elicitation of non-viral NPs and the means of controlling them to design improved interventions in the clinical setting.
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Affiliation(s)
- Mohammad Nasrullah
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Jillian Claerhout
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khanh Ha
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Erkan Demirkaya
- Department of Paediatrics, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Hasan Uludag
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB, Canada
- Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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20
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Lee DY, Amirthalingam S, Lee C, Rajendran AK, Ahn YH, Hwang NS. Strategies for targeted gene delivery using lipid nanoparticles and cell-derived nanovesicles. NANOSCALE ADVANCES 2023; 5:3834-3856. [PMID: 37496613 PMCID: PMC10368001 DOI: 10.1039/d3na00198a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/10/2023] [Indexed: 07/28/2023]
Abstract
Gene therapy is a promising approach for the treatment of many diseases. However, the effective delivery of the cargo without degradation in vivo is one of the major hurdles. With the advent of lipid nanoparticles (LNPs) and cell-derived nanovesicles (CDNs), gene delivery holds a very promising future. The targeting of these nanosystems is a prerequisite for effective transfection with minimal side-effects. In this review, we highlight the emerging strategies utilized for the effective targeting of LNPs and CDNs, and we summarize the preparation methodologies for LNPs and CDNs. We have also highlighted the non-ligand targeting of LNPs toward certain organs based on their composition. It is highly expected that continuing the developments in the targeting approaches of LNPs and CDNs for the delivery system will further promote them in clinical translation.
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Affiliation(s)
- Dong-Yup Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
| | - Sivashanmugam Amirthalingam
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
- Institute of Engineering Research, Seoul National University Seoul 08826 Republic of Korea
| | - Changyub Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
| | - Arun Kumar Rajendran
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
| | - Young-Hyun Ahn
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
- Bio-MAX/N-Bio Institute, Institute of Bio-Engineering, Seoul National University Seoul 08826 Republic of Korea
| | - Nathaniel S Hwang
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University Seoul 08826 Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University Seoul 08826 Republic of Korea
- Bio-MAX/N-Bio Institute, Institute of Bio-Engineering, Seoul National University Seoul 08826 Republic of Korea
- Institute of Engineering Research, Seoul National University Seoul 08826 Republic of Korea
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21
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Qiu C, Xia F, Zhang J, Shi Q, Meng Y, Wang C, Pang H, Gu L, Xu C, Guo Q, Wang J. Advanced Strategies for Overcoming Endosomal/Lysosomal Barrier in Nanodrug Delivery. RESEARCH (WASHINGTON, D.C.) 2023; 6:0148. [PMID: 37250954 PMCID: PMC10208951 DOI: 10.34133/research.0148] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023]
Abstract
Nanocarriers have therapeutic potential to facilitate drug delivery, including biological agents, small-molecule drugs, and nucleic acids. However, their efficiency is limited by several factors; among which, endosomal/lysosomal degradation after endocytosis is the most important. This review summarizes advanced strategies for overcoming endosomal/lysosomal barriers to efficient nanodrug delivery based on the perspective of cellular uptake and intracellular transport mechanisms. These strategies include promoting endosomal/lysosomal escape, using non-endocytic methods of delivery to directly cross the cell membrane to evade endosomes/lysosomes and making a detour pathway to evade endosomes/lysosomes. On the basis of the findings of this review, we proposed several promising strategies for overcoming endosomal/lysosomal barriers through the smarter and more efficient design of nanodrug delivery systems for future clinical applications.
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Affiliation(s)
- Chong Qiu
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fei Xia
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Junzhe Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiaoli Shi
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yuqing Meng
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chen Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Huanhuan Pang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Liwei Gu
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chengchao Xu
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiuyan Guo
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica,
China Academy of Chinese Medical Sciences, Beijing 100700, China
- Department of Nephrology, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, The First Affiliated Hospital,
Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
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22
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Ewaisha R, Anderson KS. Immunogenicity of CRISPR therapeutics-Critical considerations for clinical translation. Front Bioeng Biotechnol 2023; 11:1138596. [PMID: 36873375 PMCID: PMC9978118 DOI: 10.3389/fbioe.2023.1138596] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
CRISPR offers new hope for many patients and promises to transform the way we think of future therapies. Ensuring safety of CRISPR therapeutics is a top priority for clinical translation and specific recommendations have been recently released by the FDA. Rapid progress in the preclinical and clinical development of CRISPR therapeutics leverages years of experience with gene therapy successes and failures. Adverse events due to immunogenicity have been a major setback that has impacted the field of gene therapy. As several in vivo CRISPR clinical trials make progress, the challenge of immunogenicity remains a significant roadblock to the clinical availability and utility of CRISPR therapeutics. In this review, we examine what is currently known about the immunogenicity of CRISPR therapeutics and discuss several considerations to mitigate immunogenicity for the design of safe and clinically translatable CRISPR therapeutics.
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Affiliation(s)
- Radwa Ewaisha
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Department of Microbiology and Immunology, School of Pharmacy, Newgiza University, Newgiza, Egypt
| | - Karen S. Anderson
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
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