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Klapwijk JC, Del Rio Espinola A, Libertini S, Collin P, Fellows MD, Jobling S, Lynch AM, Martus H, Vickers C, Zeller A, Biasco L, Brugman MH, Bushmann FD, Cathomen T, Ertl HCJ, Gabriel R, Gao G, Jadlowsky JK, Kimber I, Lanz TA, Levine BL, Micklethwaite KP, Onodera M, Pizzurro DM, Reed S, Rothe M, Sabatino DE, Salk JJ, Schambach A, Themis M, Yuan J. Improving the Assessment of Risk Factors Relevant to Potential Carcinogenicity of Gene Therapies: A Consensus Article. Hum Gene Ther 2024; 35:527-542. [PMID: 39049734 DOI: 10.1089/hum.2024.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024] Open
Abstract
Regulators and industry are actively seeking improvements and alternatives to current models and approaches to evaluate potential carcinogenicity of gene therapies (GTs). A meeting of invited experts was organized by NC3Rs/UKEMS (London, March 2023) to discuss this topic. This article describes the consensus reached among delegates on the definition of vector genotoxicity, sources of uncertainty, suitable toxicological endpoints for genotoxic assessment of GTs, and future research needs. The collected recommendations should inform the further development of regulatory guidelines for the nonclinical toxicological assessment of GT products.
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Affiliation(s)
| | | | | | - Philippe Collin
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Mick D Fellows
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Susan Jobling
- TestaVec Ltd, Maidenhead, United Kingdom
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | | | - Catherine Vickers
- National Centre for the Replacement Refinement and Reduction of Animals in Research, London, United Kingdom
| | - Andreas Zeller
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Luca Biasco
- UCL Zayed Centre for Research (ZCR), London, United Kingdom
| | - Martijn H Brugman
- Cell and Gene Therapy, GSK Medicine Research Centre, Stevenage, United Kingdom
| | - Frederic D Bushmann
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, Pennsylvania, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center- University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hildegrund C J Ertl
- Ertl Laboratory, Vaccine & Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | - Guangping Gao
- Horae Gene Therapy Center, UMass Chan Medical School, University of Massachusetts, Worcester, Massachusetts, USA
| | - Julie K Jadlowsky
- Center for Cellular Immunotherapies and Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian Kimber
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Thomas A Lanz
- Drug Safety Research & Development, Pfizer, Inc., Groton, Connecticut, USA
| | - Bruce L Levine
- Center for Cellular Immunotherapies and Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kenneth P Micklethwaite
- Department of Haematology, Blood Transplant and Cell Therapies Program, Westmead Hospital, Sydney, Australia
- NSW Health Pathology Blood Transplant and Cell Therapies Laboratory - ICPMR Westmead, Sydney, Australia
- Westmead Institute for Medical Research, Sydney, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Masafumi Onodera
- Gene & Cell Therapy Promotion Center, National Center for Child Health and Development, Tokyo, Japan
| | | | - Simon Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Denise E Sabatino
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jesse J Salk
- Department of Medicine, Divisions of Hematology and Medical Oncology, University of Washington School of Medicine, Seattle, Washington, USA
- TwinStrand Biosciences Inc., Seattle, Washington, USA
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Themis
- TestaVec Ltd, Maidenhead, United Kingdom
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Jing Yuan
- Kymera Therapeutics, Watertown, Massachusetts, USA
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Moradi V, Khodabandehloo E, Alidadi M, Omidkhoda A, Ahmadbeigi N. Progress and pitfalls of gene editing technology in CAR-T cell therapy: a state-of-the-art review. Front Oncol 2024; 14:1388475. [PMID: 38912057 PMCID: PMC11190338 DOI: 10.3389/fonc.2024.1388475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024] Open
Abstract
CAR-T cell therapy has shown remarkable promise in treating B-cell malignancies, which has sparked optimism about its potential to treat other types of cancer as well. Nevertheless, the Expectations of CAR-T cell therapy in solid tumors and non-B cell hematologic malignancies have not been met. Furthermore, safety concerns regarding the use of viral vectors and the current personalized production process are other bottlenecks that limit its widespread use. In recent years the use of gene editing technology in CAR-T cell therapy has opened a new way to unleash the latent potentials of CAR-T cell therapy and lessen its associated challenges. Moreover, gene editing tools have paved the way to manufacturing CAR-T cells in a fully non-viral approach as well as providing a universal, off-the-shelf product. Despite all the advantages of gene editing strategies, the off-target activity of classical gene editing tools (ZFNs, TALENs, and CRISPR/Cas9) remains a major concern. Accordingly, several efforts have been made in recent years to reduce their off-target activity and genotoxicity, leading to the introduction of advanced gene editing tools with an improved safety profile. In this review, we begin by examining advanced gene editing tools, providing an overview of how these technologies are currently being applied in clinical trials of CAR-T cell therapies. Following this, we explore various gene editing strategies aimed at enhancing the safety and efficacy of CAR-T cell therapy.
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Affiliation(s)
- Vahid Moradi
- Hematology and Blood Transfusion Science Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Elnaz Khodabandehloo
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehdi Alidadi
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Omidkhoda
- Hematology and Blood Transfusion Science Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Naser Ahmadbeigi
- Gene Therapy Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Lemmens M, Dorsheimer L, Zeller A, Dietz-Baum Y. Non-clinical safety assessment of novel drug modalities: Genome safety perspectives on viral-, nuclease- and nucleotide-based gene therapies. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503767. [PMID: 38821669 DOI: 10.1016/j.mrgentox.2024.503767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
Gene therapies have emerged as promising treatments for various conditions including inherited diseases as well as cancer. Ensuring their safe clinical application requires the development of appropriate safety testing strategies. Several guidelines have been provided by health authorities to address these concerns. These guidelines state that non-clinical testing should be carried out on a case-by-case basis depending on the modality. This review focuses on the genome safety assessment of frequently used gene therapy modalities, namely Adeno Associated Viruses (AAVs), Lentiviruses, designer nucleases and mRNAs. Important safety considerations for these modalities, amongst others, are vector integrations into the patient genome (insertional mutagenesis) and off-target editing. Taking into account the constraints of in vivo studies, health authorities endorse the development of novel approach methodologies (NAMs), which are innovative in vitro strategies for genotoxicity testing. This review provides an overview of NAMs applied to viral and CRISPR/Cas9 safety, including next generation sequencing-based methods for integration site analysis and off-target editing. Additionally, NAMs to evaluate the oncogenicity risk arising from unwanted genomic modifications are discussed. Thus, a range of promising techniques are available to support the safe development of gene therapies. Thorough validation, comparisons and correlations with clinical outcomes are essential to identify the most reliable safety testing strategies. By providing a comprehensive overview of these NAMs, this review aims to contribute to a better understanding of the genome safety perspectives of gene therapies.
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Affiliation(s)
| | - Lena Dorsheimer
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany.
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel 4070, Switzerland
| | - Yasmin Dietz-Baum
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany
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Liu Z, Krstic A, Neve A, Casalou C, Rauch N, Wynne K, Cassidy H, McCann A, Kavanagh E, McCann B, Blanco A, Rauch J, Kolch W. Kinase Suppressor of RAS 1 (KSR1) Maintains the Transformed Phenotype of BRAFV600E Mutant Human Melanoma Cells. Int J Mol Sci 2023; 24:11821. [PMID: 37511580 PMCID: PMC10380721 DOI: 10.3390/ijms241411821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Kinase Suppressor of RAS 1 (KSR1) is a scaffolding protein for the RAS-RAF-MEK-ERK pathway, which is one of the most frequently altered pathways in human cancers. Previous results have shown that KSR1 has a critical role in mutant RAS-mediated transformation. Here, we examined the role of KSR1 in mutant BRAF transformation. We used CRISPR/Cas9 to knock out KSR1 in a BRAFV600E-transformed melanoma cell line. KSR1 loss produced a complex phenotype characterised by impaired proliferation, cell cycle defects, decreased transformation, decreased invasive migration, increased cellular senescence, and increased apoptosis. To decipher this phenotype, we used a combination of proteomic ERK substrate profiling, global protein expression profiling, and biochemical validation assays. The results suggest that KSR1 directs ERK to phosphorylate substrates that have a critical role in ensuring cell survival. The results further indicate that KSR1 loss induces the activation of p38 Mitogen-Activated Protein Kinase (MAPK) and subsequent cell cycle aberrations and senescence. In summary, KSR1 function plays a key role in oncogenic BRAF transformation.
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Affiliation(s)
- Zhi Liu
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Aleksandar Krstic
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ashish Neve
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Cristina Casalou
- Charles Institute of Dermatology, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Hilary Cassidy
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biomolecular & Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Amanda McCann
- School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Emma Kavanagh
- School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Brendan McCann
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Alfonso Blanco
- Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Jens Rauch
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biomolecular & Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland (SBI), School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
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Wang Z. Assessing Tumorigenicity in Stem Cell-Derived Therapeutic Products: A Critical Step in Safeguarding Regenerative Medicine. Bioengineering (Basel) 2023; 10:857. [PMID: 37508884 PMCID: PMC10376867 DOI: 10.3390/bioengineering10070857] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Stem cells hold promise in regenerative medicine due to their ability to proliferate and differentiate into various cell types. However, their self-renewal and multipotency also raise concerns about their tumorigenicity during and post-therapy. Indeed, multiple studies have reported the presence of stem cell-derived tumors in animal models and clinical administrations. Therefore, the assessment of tumorigenicity is crucial in evaluating the safety of stem cell-derived therapeutic products. Ideally, the assessment needs to be performed rapidly, sensitively, cost-effectively, and scalable. This article reviews various approaches for assessing tumorigenicity, including animal models, soft agar culture, PCR, flow cytometry, and microfluidics. Each method has its advantages and limitations. The selection of the assay depends on the specific needs of the study and the stage of development of the stem cell-derived therapeutic product. Combining multiple assays may provide a more comprehensive evaluation of tumorigenicity. Future developments should focus on the optimization and standardization of microfluidics-based methods, as well as the integration of multiple assays into a single platform for efficient and comprehensive evaluation of tumorigenicity.
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Affiliation(s)
- Zongjie Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
- Chan Zuckerberg Biohub Chicago, Chicago, IL 60607, USA
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Identification of marker genes to monitor residual iPSCs in iPSC-derived products. Cytotherapy 2023; 25:59-67. [PMID: 36319564 DOI: 10.1016/j.jcyt.2022.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/08/2022] [Accepted: 09/27/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Engineered tissues and cell therapies based on human induced pluripotent stem cells (iPSCs) represent a promising approach for novel medicines. However, iPSC-derived cells and tissues may contain residual undifferentiated iPSCs that could lead to teratoma formation after implantation into patients. As a consequence, highly sensitive and specific methods for detecting residual undifferentiated iPSCs are indispensable for safety evaluations of iPSC-based therapies. The present study provides an approach for identifying potential marker genes for iPSC impurities in iPSC-derived cells using RNA sequencing data from iPSCs and various differentiated cell types. METHODS Identifying iPSC marker genes for each cell type individually provided a larger and more specific set of potential marker genes than considering all cell types in the analysis. Thus, the authors focused on identifying markers for iPSC impurities in iPSC-derived cardiomyocytes (iCMs) and validated the selected genes by reverse transcription quantitative polymerase chain reaction. The sensitivity of the candidate genes was determined by spiking different amounts of iPSCs into iCMs and their performance was compared with the previously suggested marker lin-28 homolog A (LIN28A). RESULTS Embryonic stem cell-related gene (ESRG), long intergenic non-protein coding RNA 678 (LINC00678), CaM kinase-like vesicle-associated (CAMKV), indoleamine 2,3-dioxygenase 1 (IDO1), chondromodulin (CNMD), LINE1-type transposase domain containing 1 (L1DT1), LIN28A, lymphocyte-specific protein tyrosine kinase (LCK), vertebrae development-associated (VRTN) and zinc finger and SCAN domain containing 10 (ZSCAN10) detected contaminant iPSCs among iCMs with a limit of detection that ranged from 0.001% to 0.1% depending on the gene and iCM batch used. CONCLUSIONS Using the example of iCMs, the authors provide a strategy for identifying a set of highly specific and sensitive markers that can be used for quality assessment of iPSC-derived products.
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Lattanzi A, Maddalo D. The CRISPR Revolution in the Drug Discovery Workflow: An Industry Perspective. CRISPR J 2022; 5:634-641. [PMID: 35917561 DOI: 10.1089/crispr.2022.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In a relatively short time, the pharmaceutical industry has witnessed a rapid integration of the CRISPR technology in multiple areas of research, development, therapy, and diagnostics. A unique feature to this system compared with other technologies is the exceptional versatility in adapting to the broad range of needs across the drug discovery pipeline, such as target identification, cell engineering, and in vivo modeling. As a consequence, the CRISPR toolbox has been evolving to address key questions around preclinical and clinical drug development. In this review, we provide a high-level perspective of how CRISPR has impacted several aspects of the drug discovery workflow and the future ahead for this exciting technology.
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Affiliation(s)
- Annalisa Lattanzi
- Department of Molecular Biology and Genentech, Inc., South San Francisco, California, USA
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, USA
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