1
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Kalter N, Gulati S, Rosenberg M, Ayaz Q, Nguyen J, Wang S, Schroeder B, Li CY, Hendel A. Precise measurement of CRISPR genome editing outcomes through single-cell DNA sequencing. Mol Ther Methods Clin Dev 2025; 33:101449. [PMID: 40225018 PMCID: PMC11987616 DOI: 10.1016/j.omtm.2025.101449] [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: 10/20/2024] [Accepted: 03/11/2025] [Indexed: 04/15/2025]
Abstract
Gene therapy for clinical applications necessitates a comprehensive, accurate, and precise measurement of gene-edited drug products. State-of-the-art pipelines for evaluating editing outcomes rely primarily on bulk sequencing approaches, which are limited to population-level assessment. Here, we leveraged Tapestri, a single-cell sequencing technology for an in-depth analysis of editing outcomes. Using this platform, we characterized the genotype of triple-edited cells simultaneously at more than 100 loci, including editing zygosity, structural variations, and cell clonality. Our findings revealed a unique editing pattern in nearly every edited cell, highlighting the importance of single-cell resolution measurement to ensure the highest safety standards.
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Affiliation(s)
- Nechama Kalter
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Saurabh Gulati
- Mission Bio, 400 E Jamie Ct, Suite 100, South San Francisco, CA 94080, USA
| | - Michael Rosenberg
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Qawer Ayaz
- Mission Bio, 400 E Jamie Ct, Suite 100, South San Francisco, CA 94080, USA
| | - Joanne Nguyen
- Mission Bio, 400 E Jamie Ct, Suite 100, South San Francisco, CA 94080, USA
| | - Shu Wang
- Mission Bio, 400 E Jamie Ct, Suite 100, South San Francisco, CA 94080, USA
| | - Benjamin Schroeder
- Mission Bio, 400 E Jamie Ct, Suite 100, South San Francisco, CA 94080, USA
| | - Chieh-Yuan Li
- Mission Bio, 400 E Jamie Ct, Suite 100, South San Francisco, CA 94080, USA
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
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2
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Osborn MJ, Panda S, Reineke TM, Tolar J, Nyström A. Progress in skin gene therapy: From the inside and out. Mol Ther 2025; 33:2065-2081. [PMID: 40077969 DOI: 10.1016/j.ymthe.2025.03.017] [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: 01/31/2025] [Revised: 03/04/2025] [Accepted: 03/07/2025] [Indexed: 03/14/2025] Open
Abstract
The skin is the largest organ of the body and forms and serves as the barrier for preventing external material from accessing and damaging internal organs. As the outward interface to the environment, it is accessible for the application of therapeutic agents and cellular and gene therapy represent attractive and promising options to treat severe genetic conditions for which palliation has long been the main stay. However, because of its barrier function, transit across and to the subdermal compartment can be challenging. This commentary examines the current approaches of cell and gene therapies for genetic skin disorders. We write this from a local and systemic "outside and inside." perspective. Delivery from the outside encompasses topical, intradermal, and transdermal strategies for cell and vector delivery and ex vivo cell expansion and grafting. The inside approach details systemic delivery via infusion of cells or agents toward providing benefit to the skin. We use recessive dystrophic epidermolysis bullosa (RDEB) as a representative and paradigmatic disease to showcase these approaches as a means to highlight potential broader applicability to other conditions.
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Affiliation(s)
- Mark J Osborn
- Medical School, Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular and Gene Therapy, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Sidharth Panda
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jakub Tolar
- Medical School, Department of Pediatrics, Division of Blood and Marrow Transplant and Cellular and Gene Therapy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alexander Nyström
- Department of Dermatology, Medical Faculty, Medical Center, University of Freiburg, 79106 Freiburg, Germany.
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3
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Ramos-Hernández I, Fuster-García C, Aguilar-González A, Lozano-Vinagre M, Guenechea-Amurrio G, Sanchez-Luque F, Gonçalves MFV, Cathomen T, Muñoz P, Molina-Estévez F, Martín F. Donor insertion into CX3CR1 allows epigenetic modulation of a constitutive promoter on hematopoietic stem cells and its activation upon myeloid differentiation. Nucleic Acids Res 2025; 53:gkaf344. [PMID: 40298109 PMCID: PMC12038399 DOI: 10.1093/nar/gkaf344] [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: 08/12/2024] [Revised: 04/03/2025] [Accepted: 04/24/2025] [Indexed: 04/30/2025] Open
Abstract
To improve ex vivo gene therapy strategies involving hematopoietic stem and progenitor cells (HSPCs), we propose a novel knock-in strategy (named KI-Ep) aiming to achieve transgene regulation of the inserted cassette through the acquisition of naturally occurring epigenetic marks. Based on this hypothesis, we selected CX3CR1 (a myeloid-specific gene presenting a poised histone signature on primitive HSPCs) as safe harbor to generate KI-Ep HSPCs. We demonstrated that, unlike the expression pattern achieved with lentiviral vectors (LVs), the insertion of a constitutive expression cassette into the intron 1 of the CX3CR1 locus (CX3CR1-I) in HSPCs resulted in very low expression levels in the more primitive HSPCs but, crucially, strong expression in HSPC-differentiated populations (especially myeloid cells), both in vitro and in vivo. Furthermore, we showed that the promoter of the expression cassette inserted into CX3CR1-I acquired epigenetic marks associated with poised genes during the HSPC stage. These marks transitioned to activated histone states upon KI-Ep HSPCs differentiation. In summary, here, we introduce the KI-Ep concept which enables the epigenetic modulation of the inserted transgene during the HSPCs stem cell stages and its subsequent activation upon differentiation.
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Affiliation(s)
- Iris Ramos-Hernández
- GENYO, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research, Andalusian Regional Government. PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
- Fundación Pública Andaluza para la Investigación Biosanitaria en Andalucía Oriental Alejandro Otero (FIBAO), Avenida de Madrid, 15, Beiro, 18012 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, 18012 Granada, Spain
| | - Carla Fuster-García
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Araceli Aguilar-González
- GENYO, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research, Andalusian Regional Government. PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, 18012 Granada, Spain
- Department of Medicinal and Organic Chemistry and Excellence Research Unit of Chemistry Applied to Biomedicine and the Environment, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071 Granada, Spain
| | - María L Lozano-Vinagre
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Guillermo Guenechea-Amurrio
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine ‘López-Neyra’ (Spanish National Research Council), Avda. del Conocimiento 17 (PTS Granada), 18016 Armilla (Granada), Spain
| | - Manuel A F V Gonçalves
- Leiden University Medical Center, Department of Cell and Chemical Biology, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg,79110 Freiburg, Germany
| | - Pilar Muñoz
- Fundación Pública Andaluza para la Investigación Biosanitaria en Andalucía Oriental Alejandro Otero (FIBAO), Avenida de Madrid, 15, Beiro, 18012 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, 18012 Granada, Spain
- Departmento de Biología Celular, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Francisco J Molina-Estévez
- Fundación Pública Andaluza para la Investigación Biosanitaria en Andalucía Oriental Alejandro Otero (FIBAO), Avenida de Madrid, 15, Beiro, 18012 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, 18012 Granada, Spain
- Departmento de Biología Celular, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, 18071 Granada, Spain
| | - Francisco Martín
- Fundación Pública Andaluza para la Investigación Biosanitaria en Andalucía Oriental Alejandro Otero (FIBAO), Avenida de Madrid, 15, Beiro, 18012 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, 18012 Granada, Spain
- Departamento de Bioquímica y Biología Molecular 3 e Inmunología, Facultad de Medicina, Universidad de Granada, Avda. de la Investigación 11, 18071 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016, 34 Granada, Spain
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4
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Baatz F, Ghosh A, Herbst J, Polten S, Meyer J, Rhiel M, Maetzig T, Geffers R, Rothe M, Bastone AL, John-Neek P, Frühauf J, Eiz-Vesper B, Bonifacius A, Falk CS, Kaisenberg CV, Cathomen T, Schambach A, van den Brink MRM, Hust M, Sauer MG. Targeting BCL11B in CAR-engineered lymphoid progenitors drives NK-like cell development with prolonged anti-leukemic activity. Mol Ther 2025; 33:1584-1607. [PMID: 39955618 PMCID: PMC11997514 DOI: 10.1016/j.ymthe.2025.02.024] [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: 04/26/2024] [Revised: 09/26/2024] [Accepted: 02/12/2025] [Indexed: 02/17/2025] Open
Abstract
Chimeric antigen receptor (CAR)-induced suppression of the transcription factor B cell CLL/lymphoma 11B (BCL11B) propagates CAR-induced killer (CARiK) cell development from lymphoid progenitors. Here, we show that CRISPR-Cas9-mediated Bcl11b knockout in human and murine early lymphoid progenitors distinctively modulates this process either alone or in combination with a CAR. Upon adoptive transfer into hematopoietic stem cell recipients, Bcl11b-edited progenitors mediated innate-like antigen-independent anti-leukemic immune responses. With CAR expression allowing for additional antigen-specific responses, the progeny of double-edited lymphoid progenitors acquired prolonged anti-leukemic activity in vivo. These findings give important insights into how Bcl11b targeting can be used to tailor anti-leukemia functionality of CAR-engineered lymphoid progenitor cells.
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Affiliation(s)
- Franziska Baatz
- Department of Pediatric Hematology, Department of Oncology and Blood Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnab Ghosh
- Adult BMT Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Herbst
- Department of Pediatric Hematology, Department of Oncology and Blood Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Saskia Polten
- Department of Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Johann Meyer
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
| | - Tobias Maetzig
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Philipp John-Neek
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Jörg Frühauf
- Clinic for Radiation Therapy and special Oncology, Hannover Medical School, Hannover, Germany
| | - Britta Eiz-Vesper
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Agnes Bonifacius
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Christine S Falk
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Constantin V Kaisenberg
- Department of Obstetrics, Clinic of Gynecology and Reproductive Medicine, and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Michael Hust
- Department of Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Martin G Sauer
- Department of Pediatric Hematology, Department of Oncology and Blood Stem Cell Transplantation, Hannover Medical School, Hannover, Germany.
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5
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Tremblay F, Xiong Q, Shah SS, Ko CW, Kelly K, Morrison MS, Giancarlo C, Ramirez RN, Hildebrand EM, Voytek SB, El Sebae GK, Wright SH, Lofgren L, Clarkson S, Waters C, Linder SJ, Liu S, Eom T, Parikh S, Weber Y, Martinez S, Malyala P, Abubucker S, Friedland AE, Maeder ML, Lombardo A, Myer VE, Jaffe AB. A potent epigenetic editor targeting human PCSK9 for durable reduction of low-density lipoprotein cholesterol levels. Nat Med 2025; 31:1329-1338. [PMID: 39930141 PMCID: PMC12003160 DOI: 10.1038/s41591-025-03508-x] [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: 09/13/2024] [Accepted: 01/13/2025] [Indexed: 02/27/2025]
Abstract
Epigenetic editing holds the promise of durable therapeutic effects by silencing disease-causing genes without changing the underlying DNA sequence. In this study, we designed an epigenetic editor to target human PCSK9 and thereby induce DNA methylation at this locus. A single administration of lipid nanoparticles encapsulating mRNA encoding this epigenetic editor was sufficient to drive near-complete silencing of human PCSK9 in transgenic mice. Silencing was durable for at least 1 year and was fully maintained after partial hepatectomy-induced liver regeneration. In addition, we showed reversibility of epigenetic editing in mice with previously silenced PCSK9 upon treatment with a targeted epigenetic activator designed to demethylate the PCSK9 locus. Notably, in cynomolgus monkeys, a single administration of the epigenetic editor potently and durably decreased circulating PCSK9 protein levels by approximately 90% with concomitant reduction in low-density lipoprotein cholesterol levels by approximately 70%. These findings demonstrate the therapeutic potential of durable and reversible epigenetic editing in vivo and support the development of epigenetic editor-based treatment for hypercholesterolemia.
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Affiliation(s)
| | - Qiang Xiong
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | - Shrijal S Shah
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | - Chih-Wei Ko
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | | | | | | | | | | | - Sarah B Voytek
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | | | - Shane H Wright
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | | | | | | | | | - Songlei Liu
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | - Taesun Eom
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | - Shefal Parikh
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | - Yuki Weber
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | | | - Padma Malyala
- Chroma Medicine, Boston, MA, USA
- nChromaBio, Boston, MA, USA
| | | | | | | | - Angelo Lombardo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | | | - Aron B Jaffe
- Chroma Medicine, Boston, MA, USA
- Curie.Bio, Cambridge, MA, USA
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6
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Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol 2025; 43:593-607. [PMID: 38773305 PMCID: PMC11579250 DOI: 10.1038/s41587-024-02240-0] [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: 05/06/2022] [Accepted: 04/10/2024] [Indexed: 05/23/2024]
Abstract
Base editors (BEs) enable efficient, programmable installation of point mutations while avoiding the use of double-strand breaks. Simultaneous application of two or more different BEs, such as an adenine BE (which converts A·T base pairs to G·C) and a cytosine BE (which converts C·G base pairs to T·A), is not feasible because guide RNA crosstalk results in non-orthogonal editing, with all BEs modifying all target loci. Here we engineer both adenine BEs and cytosine BEs that can be orthogonally multiplexed by using RNA aptamer-coat protein systems to recruit the DNA-modifying enzymes directly to the guide RNAs. We generate four multiplexed orthogonal BE systems that enable rates of precise co-occurring edits of up to 7.1% in the same DNA strand without enrichment or selection strategies. The addition of a fluorescent enrichment strategy increases co-occurring edit rates up to 24.8% in human cells. These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 variants, function well in multiple cell types, have equivalent or reduced off-target propensities compared with their parental systems and can model disease-relevant point mutation combinations.
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Affiliation(s)
- Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Tatum S Simonson
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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7
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Georgiadis C, Preece R, Qasim W. Clinical development of allogeneic chimeric antigen receptor αβ-T cells. Mol Ther 2025:S1525-0016(25)00214-X. [PMID: 40156192 DOI: 10.1016/j.ymthe.2025.03.040] [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: 01/03/2025] [Revised: 03/10/2025] [Accepted: 03/24/2025] [Indexed: 04/01/2025] Open
Abstract
Ready-made banks of allogeneic chimeric antigen receptor (CAR) T cells, produced to be available at the time of need, offer the prospect of accessible and cost-effective cellular therapies. Various strategies have been developed to overcome allogeneic barriers, drawing on cell engineering platforms including RNA interference, protein-based restriction, and genome editing, including RNA-guided CRISPR-Cas and base editing tools. Alloreactivity and the risk of graft-versus-host disease from non-matched donor cells have been mitigated by disruption of αβ-T cell receptor expression on the surface of T cells and stringent removal of any residual αβ-T cell populations. In addition, host-mediated rejection has been tackled through a combination of augmented lymphodepletion and cell engineering strategies that have allowed infused cells to evade immune recognition or conferred resistance to lymphodepleting agents to promote persistence and expansion of effector populations. Early-phase studies using off-the-shelf universal donor CAR T cells have been undertaken mainly in the context of blood malignancies, where emerging data of clinical responses have supported wider adoption and further applications. These developments offer the prospect of alternatives to current autologous approaches through the emerging application of genome engineering solutions to improve safety, persistence, and function of universal donor products.
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Affiliation(s)
- Christos Georgiadis
- University College London Great Ormond Street Institute of Child Health, Zayed Centre for Research, 20 Guilford Street, London WC1N 1DZ, UK
| | - Roland Preece
- University College London Great Ormond Street Institute of Child Health, Zayed Centre for Research, 20 Guilford Street, London WC1N 1DZ, UK
| | - Waseem Qasim
- University College London Great Ormond Street Institute of Child Health, Zayed Centre for Research, 20 Guilford Street, London WC1N 1DZ, UK.
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8
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Liu D, Cao D, Han R. Recent advances in therapeutic gene-editing technologies. Mol Ther 2025:S1525-0016(25)00200-X. [PMID: 40119516 DOI: 10.1016/j.ymthe.2025.03.026] [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: 12/13/2024] [Revised: 02/26/2025] [Accepted: 03/17/2025] [Indexed: 03/24/2025] Open
Abstract
The advent of gene-editing technologies, particularly CRISPR-based systems, has revolutionized the landscape of biomedical research and gene therapy. Ongoing research in gene editing has led to the rapid iteration of CRISPR technologies, such as base and prime editors, enabling precise nucleotide changes without the need for generating harmful double-strand breaks (DSBs). Furthermore, innovations such as CRISPR fusion systems with DNA recombinases, DNA polymerases, and DNA ligases have expanded the size limitations for edited sequences, opening new avenues for therapeutic development. Beyond the CRISPR system, mobile genetic elements (MGEs) and epigenetic editors are emerging as efficient alternatives for precise large insertions or stable gene manipulation in mammalian cells. These advances collectively set the stage for next-generation gene therapy development. This review highlights recent developments of genetic and epigenetic editing tools and explores preclinical innovations poised to advance the field.
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Affiliation(s)
- Dongqi Liu
- Department of Pediatrics, Department of Molecular and Medical Genetics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Di Cao
- Department of Pediatrics, Department of Molecular and Medical Genetics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Renzhi Han
- Department of Pediatrics, Department of Molecular and Medical Genetics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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9
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Hunt JM, du Rand A, Verdon D, Clemance L, Loef E, Malhi C, Buttle B, Knapp DJ, Michaels YS, Garlick J, Dunbar PR, Purvis D, Feisst V, Sheppard H. Enhanced HDR-mediated correction of heterozygous COL7A1 mutations for recessive dystrophic epidermolysis bullosa. MOLECULAR THERAPY. NUCLEIC ACIDS 2025; 36:102472. [PMID: 40027886 PMCID: PMC11872078 DOI: 10.1016/j.omtn.2025.102472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 01/28/2025] [Indexed: 03/05/2025]
Abstract
Gene editing facilitated by homology-directed repair (HDR) holds great potential for treating monogenetic disorders such as recessive dystrophic epidermolysis bullosa (RDEB). However, low efficiency and variability between loci must be overcome for its widespread adoption into personalized therapies. To address these challenges, we developed a highly efficient and versatile gene editing strategy for RDEB that incorporates the small molecule inhibitor M3814 to enhance HDR. We focused on three RDEB causative COL7A1 mutations not previously targeted by existing gene therapies. Editing was achieved using Cas9-nuclease ribonucleoproteins with short single-stranded DNA donor templates, and outcomes were assessed with an Oxford Nanopore Technology sequencing analysis pipeline. We demonstrate precise genomic HDR rates of up to 75% of alleles in primary RDEB keratinocytes and 32% in fibroblasts. This approach restored collagen VII expression in up to 80% of keratinocytes within a bulk-edited population and resulted in correct collagen VII deposition in a 3D skin model. Additionally, at one locus we show that a dual Cas9-nickase strategy is less effective than Cas9-nuclease and prone to large on-target deletions. Our results demonstrate a significant advancement in the efficiency and consistency of HDR editing, potentially paving the way for more effective personalized gene therapies.
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Affiliation(s)
- John M.T. Hunt
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Maurice Wilkins Center, New Zealand
| | - Alex du Rand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Daniel Verdon
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Leah Clemance
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Evert Loef
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Chloe Malhi
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Ben Buttle
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - David J.H.F. Knapp
- Institut de recherche en immunologie et en cancérologie (IRIC) and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yale S. Michaels
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, MB R2H 2A6, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Jonathan Garlick
- School of Dental Medicine, Tufts University, Boston, MA 02111, USA
| | - P. Rod Dunbar
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Maurice Wilkins Center, New Zealand
| | - Diana Purvis
- Te Whatu Ora Health New Zealand, Te Toka Tumai, Auckland 1023, New Zealand
| | - Vaughan Feisst
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Hilary Sheppard
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Maurice Wilkins Center, New Zealand
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10
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Lu C, Li Y, Cummings JR, Banskota S. Delivery of genome editors with engineered virus-like particles. Methods Enzymol 2025; 712:475-516. [PMID: 40121085 DOI: 10.1016/bs.mie.2025.01.007] [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: 03/25/2025]
Abstract
Genome editing technologies have revolutionized biomedical sciences and biotechnology. However, their delivery in vivo remains one of the major obstacles for clinical translation. Here, we introduce various emerging genome editing systems and review different delivery systems have been developed to realize the promise of in vivo gene editing therapies. In particular, we focus on virus-like particles (VLPs), an emerging delivery platform and provide in depth analysis on recent advancements to improve VLPs delivery potential and highlight opportunities for future improvements. To this end, we also provide detail workflows for engineered VLP (eVLP) selection, production, and purification, along with methods for characterization and validation.
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Affiliation(s)
- Christopher Lu
- Department of Biomedical Engineering, Boston University, Boston, MA, United States; Biological Design Center, Boston University, Boston, MA, United States
| | - Yuanhang Li
- Biological Design Center, Boston University, Boston, MA, United States; Department of Mechanical Engineering, Boston University, Boston, MA, United States
| | - Jacob Ryan Cummings
- Department of Biomedical Engineering, Boston University, Boston, MA, United States; Biological Design Center, Boston University, Boston, MA, United States
| | - Samagya Banskota
- Department of Biomedical Engineering, Boston University, Boston, MA, United States; Biological Design Center, Boston University, Boston, MA, United States.
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11
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Du W, Noyan F, McCallion O, Drosdek V, Kath J, Glaser V, Fuster-Garcia C, Yang M, Stein M, Franke C, Pu Y, Weber O, Polansky JK, Cathomen T, Jaeckel E, Hester J, Issa F, Volk HD, Schmueck-Henneresse M, Reinke P, Wagner DL. Gene editing of CD3 epsilon to redirect regulatory T cells for adoptive T cell transfer. Mol Ther 2025; 33:997-1013. [PMID: 39905729 PMCID: PMC11897813 DOI: 10.1016/j.ymthe.2025.01.045] [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: 06/02/2024] [Revised: 12/20/2024] [Accepted: 01/30/2025] [Indexed: 02/06/2025] Open
Abstract
Adoptive transfer of antigen-specific regulatory T cells (Tregs) is a promising strategy to combat immunopathologies in transplantation and autoimmune diseases. However, their low frequency in peripheral blood poses challenges for both manufacturing and clinical application. Chimeric antigen receptors have been used to redirect the specificity of Tregs, using retroviral vectors. However, retroviral gene transfer is costly, time consuming, and raises safety issues. Here, we explored non-viral CRISPR-Cas12a gene editing to redirect Tregs, using human leukocyte antigen (HLA)-A2-specific constructs for proof-of-concept studies in transplantation models. Knock-in of an antigen-binding domain into the N terminus of CD3 epsilon (CD3ε) gene generates Tregs expressing a chimeric CD3ε-T cell receptor fusion construct (TRuC) protein that integrates into the endogenous TCR/CD3 complex. These CD3ε-TRuC Tregs exhibit potent antigen-dependent activation while maintaining responsiveness to TCR/CD3 stimulation. This enables preferential enrichment of TRuC-redirected Tregs over CD3ε knockout Tregs via repetitive CD3/CD28 stimulation in a good manufacturing practice-compatible expansion system. CD3ε-TRuC Tregs retained their phenotypic, epigenetic, and functional identity. In a humanized mouse model, HLA-A2-specific CD3ε-TRuC Tregs demonstrate superior protection of allogeneic HLA-A2+ skin grafts from rejection compared with polyclonal Tregs. This approach provides a pathway for developing clinical-grade CD3ε-TRuC-based Treg cell products for transplantation immunotherapy and other immunopathologies.
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Affiliation(s)
- Weijie Du
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Fatih Noyan
- Department of Gastroenterology, Infectious Diseases and Hepatology & Endocrinology, Hannover Medical School, Hannover, Germany
| | - Oliver McCallion
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Science, University of Oxford, Oxford OX3 9DU, UK
| | - Vanessa Drosdek
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Jonas Kath
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Viktor Glaser
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Carla Fuster-Garcia
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Mingxing Yang
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Maik Stein
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Clemens Franke
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Yaolin Pu
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Olaf Weber
- Institute of Molecular Medicine and Experimental Immunology (IMMEI), University of Bonn, Biomedical Center II, Venusberg Campus 1, 53127 Bonn, Germany
| | - Julia K Polansky
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany; German Rheumatism Research Centre, Deutsches Rheuma-Forschungszentrum, ein Leibniz Institut, Berlin, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Elmar Jaeckel
- Department of Gastroenterology, Infectious Diseases and Hepatology & Endocrinology, Hannover Medical School, Hannover, Germany; Department of Liver Transplantation, Multi Organ Transplant Program, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Joanna Hester
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Science, University of Oxford, Oxford OX3 9DU, UK
| | - Fadi Issa
- Transplantation Research and Immunology Group, Nuffield Department of Surgical Science, University of Oxford, Oxford OX3 9DU, UK
| | - Hans-Dieter Volk
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany; Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Petra Reinke
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dimitrios L Wagner
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 13353 Berlin, Germany; BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany; Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Transfusion Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany; Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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12
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Peña-Gutiérrez I, Olalla-Sastre B, Río P, Rodríguez-Madoz JR. Beyond precision: evaluation of off-target clustered regularly interspaced short palindromic repeats/Cas9-mediated genome editing. Cytotherapy 2025; 27:279-286. [PMID: 39652018 DOI: 10.1016/j.jcyt.2024.10.010] [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: 08/08/2024] [Revised: 10/21/2024] [Accepted: 10/21/2024] [Indexed: 12/16/2024]
Abstract
The gene editing field has advanced rapidly since the development of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system because of its applicability in precisely modifying the genome. Among its multiple applications, the correction of genetic diseases has emerged as a potential curative treatment for many disorders that have eluded a cure to date. Despite its efficiency in achieving therapeutic levels of correction, the unexpected adverse effects of editing due to CRISPR/Cas9 nuclease activity are a major concern when translating these new strategies to the clinic. Multiple in silico tools and empirical methods have been developed to evaluate these off-target edits as well as other adverse alterations of the genome, including rearrangements, not only in ex vivo experiments but also in in vivo experiments. In this review, we summarize the available methods for the assessment of off-target effects of CRISPR/Cas9 systems, highlighting their advantages and limitations. Special attention will be paid to their application in pre-clinical studies and clinical trials, both in the manufacturing product and in the long-term follow-up of patients.
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Affiliation(s)
- Irene Peña-Gutiérrez
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; Instituto de Investigaciones Sanitarias, Fundación Jiménez Díaz, Madrid, Spain
| | - Beatriz Olalla-Sastre
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; Instituto de Investigaciones Sanitarias, Fundación Jiménez Díaz, Madrid, Spain
| | - Paula Río
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; Instituto de Investigaciones Sanitarias, Fundación Jiménez Díaz, Madrid, Spain.
| | - Juan R Rodríguez-Madoz
- Hemato-Oncology Program, Instituto de Investigación Sanitaria de Navarra, Cima Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain.
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13
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Mentani A, Maresca M, Shiriaeva A. Prime Editing: Mechanistic Insights and DNA Repair Modulation. Cells 2025; 14:277. [PMID: 39996750 PMCID: PMC11853414 DOI: 10.3390/cells14040277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 01/15/2025] [Accepted: 01/24/2025] [Indexed: 02/26/2025] Open
Abstract
Prime editing is a genome editing technique that allows precise modifications of cellular DNA without relying on donor DNA templates. Recently, several different prime editor proteins have been published in the literature, relying on single- or double-strand breaks. When prime editing occurs, the DNA undergoes one of several DNA repair pathways, and these processes can be modulated with the use of inhibitors. Firstly, this review provides an overview of several DNA repair mechanisms and their modulation by known inhibitors. In addition, we summarize different published prime editors and provide a comprehensive overview of associated DNA repair mechanisms. Finally, we discuss the delivery and safety aspects of prime editing.
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Affiliation(s)
- Astrid Mentani
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Marcello Maresca
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Anna Shiriaeva
- Genome Engineering, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
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14
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Cavazza A, Santilli G. The future of ex vivo hematopoietic stem cell gene editing: what's next. Regen Med 2025; 20:73-76. [PMID: 40137438 PMCID: PMC11951688 DOI: 10.1080/17460751.2025.2480003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 03/12/2025] [Indexed: 03/27/2025] Open
Affiliation(s)
- Alessia Cavazza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia School of Medicine, Modena, Italy
- Molecular and Cellular Immunology Section, Department of Infection, Immunity & Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Giorgia Santilli
- Molecular and Cellular Immunology Section, Department of Infection, Immunity & Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
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15
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Hwang GH, Lee SH, Oh M, Kim S, Habib O, Jang HK, Kim HS, Kim Y, Kim CH, Kim S, Bae S. Large DNA deletions occur during DNA repair at 20-fold lower frequency for base editors and prime editors than for Cas9 nucleases. Nat Biomed Eng 2025; 9:79-92. [PMID: 39496933 PMCID: PMC11754094 DOI: 10.1038/s41551-024-01277-5] [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: 01/09/2024] [Accepted: 10/01/2024] [Indexed: 11/06/2024]
Abstract
When used to edit genomes, Cas9 nucleases produce targeted double-strand breaks in DNA. Subsequent DNA-repair pathways can induce large genomic deletions (larger than 100 bp), which constrains the applicability of genome editing. Here we show that Cas9-mediated double-strand breaks induce large deletions at varying frequencies in cancer cell lines, human embryonic stem cells and human primary T cells, and that most deletions are produced by two repair pathways: end resection and DNA-polymerase theta-mediated end joining. These findings required the optimization of long-range amplicon sequencing, the development of a k-mer alignment algorithm for the simultaneous analysis of large DNA deletions and small DNA alterations, and the use of CRISPR-interference screening. Despite leveraging mutated Cas9 nickases that produce single-strand breaks, base editors and prime editors also generated large deletions, yet at approximately 20-fold lower frequency than Cas9. We provide strategies for the mitigation of such deletions.
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Affiliation(s)
- Gue-Ho Hwang
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seok-Hoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Minsik Oh
- School of Software Convergence, Myongji University, Seoul, Republic of Korea
| | - Segi Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | | | - Hyeon-Ki Jang
- Division of Chemical Engineering and Bioengineering, College of Art Culture and Engineering, Kangwon National University, Chuncheon-si, Gangwon-do, Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon-si, Gangwon-do, Republic of Korea
| | - Heon Seok Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Youngkuk Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Chan Hyuk Kim
- School of Transdisciplinary Innovations, Seoul National University, Seoul, Republic of Korea
- Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Sangsu Bae
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
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16
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Gehrke L, Gonçalves VDR, Andrae D, Rasko T, Ho P, Einsele H, Hudecek M, Friedel SR. Current Non-Viral-Based Strategies to Manufacture CAR-T Cells. Int J Mol Sci 2024; 25:13685. [PMID: 39769449 PMCID: PMC11728233 DOI: 10.3390/ijms252413685] [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: 11/19/2024] [Revised: 12/12/2024] [Accepted: 12/14/2024] [Indexed: 01/16/2025] Open
Abstract
The successful application of CAR-T cells in the treatment of hematologic malignancies has fundamentally changed cancer therapy. With increasing numbers of registered CAR-T cell clinical trials, efforts are being made to streamline and reduce the costs of CAR-T cell manufacturing while improving their safety. To date, all approved CAR-T cell products have relied on viral-based gene delivery and genomic integration methods. While viral vectors offer high transfection efficiencies, concerns regarding potential malignant transformation coupled with costly and time-consuming vector manufacturing are constant drivers in the search for cheaper, easier-to-use, safer, and more efficient alternatives. In this review, we examine different non-viral gene transfer methods as alternatives for CAR-T cell production, their advantages and disadvantages, and examples of their applications. Transposon-based gene transfer methods lead to stable but non-targeted gene integration, are easy to handle, and achieve high gene transfer rates. Programmable endonucleases allow targeted integration, reducing the potential risk of integration-mediated malignant transformation of CAR-T cells. Non-integrating CAR-encoding vectors avoid this risk completely and achieve only transient CAR expression. With these promising alternative techniques for gene transfer, all avenues are open to fully exploiting the potential of next-generation CAR-T cell therapy and applying it in a wide range of applications.
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Affiliation(s)
- Leon Gehrke
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Vasco Dos Reis Gonçalves
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Dominik Andrae
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Tamas Rasko
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Patrick Ho
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Michael Hudecek
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
- Fraunhofer-Institut für Zelltherapie und Immunologie, Außenstelle Zelluläre Immuntherapie, 97070 Würzburg, Germany
| | - Sabrina R. Friedel
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
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17
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Ursch LT, Müschen JS, Ritter J, Klermund J, Bernard BE, Kolb S, Warmuth L, Andrieux G, Miller G, Jiménez-Muñoz M, Theis FJ, Boerries M, Busch DH, Cathomen T, Schumann K. Modulation of TCR stimulation and pifithrin-α improve the genomic safety profile of CRISPR-engineered human T cells. Cell Rep Med 2024; 5:101846. [PMID: 39637860 PMCID: PMC11722128 DOI: 10.1016/j.xcrm.2024.101846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/24/2024] [Accepted: 11/11/2024] [Indexed: 12/07/2024]
Abstract
CRISPR-engineered chimeric antigen receptor (CAR) T cells are at the forefront of novel cancer treatments. However, several reports describe the occurrence of CRISPR-induced chromosomal aberrations. So far, measures to increase the genomic safety of T cell products focused mainly on the components of the CRISPR-Cas9 system and less on T cell-intrinsic features, such as their massive expansion after T cell receptor (TCR) stimulation. Here, we describe driving forces of indel formation in primary human T cells. Increased T cell activation and proliferation speed correlate with larger deletions. Editing of non-activated T cells reduces the risk of large deletions with the downside of reduced knockout efficiencies. Alternatively, the addition of the small-molecule pifithrin-α limits large deletions, chromosomal translocations, and aneuploidy in a p53-independent manner while maintaining the functionality of CRISPR-engineered T cells, including CAR T cells. Controlling T cell activation and pifithrin-α treatment are easily implementable strategies to improve the genomic integrity of CRISPR-engineered T cells.
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Affiliation(s)
- Laurenz T Ursch
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany
| | - Jule S Müschen
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany
| | - Julia Ritter
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Bettina E Bernard
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany
| | - Saskia Kolb
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany
| | - Linda Warmuth
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Gregor Miller
- Core Facility Statistical Consulting, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Marina Jiménez-Muñoz
- Core Facility Statistical Consulting, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; School of Computing, Information and Technology, Technical University of Munich, 85748 Garching, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Dirk H Busch
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany; German Center for Infection Research, Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Kathrin Schumann
- Technical University of Munich (TUM), School of Medicine and Health, Department of Preclinical Medicine, Institute for Medical Microbiology, Immunology and Hygiene, 81675 Munich, Germany; TUM, Institute for Advanced Study, 85748 Garching, Germany.
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18
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Frati G, Brusson M, Sartre G, Mlayah B, Felix T, Chalumeau A, Antoniou P, Hardouin G, Concordet JP, Romano O, Turchiano G, Miccio A. Safety and efficacy studies of CRISPR-Cas9 treatment of sickle cell disease highlights disease-specific responses. Mol Ther 2024; 32:4337-4352. [PMID: 39044427 PMCID: PMC11638826 DOI: 10.1016/j.ymthe.2024.07.015] [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: 01/26/2024] [Revised: 05/15/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024] Open
Abstract
Fetal hemoglobin (HbF) reactivation expression through CRISPR-Cas9 is a promising strategy for the treatment of sickle cell disease (SCD). Here, we describe a genome editing strategy leading to reactivation of HbF expression by targeting the binding sites (BSs) for the lymphoma-related factor (LRF) repressor in the γ-globin promoters. CRISPR-Cas9 treatment in healthy donor (HD) and patient-derived HSPCs resulted in a high frequency of LRF BS disruption and potent HbF synthesis in their erythroid progeny. LRF BS disruption did not impair HSPC engraftment and differentiation but was more efficient in SCD than in HD cells. However, SCD HSPCs showed a reduced engraftment and a myeloid bias compared with HD cells. We detected off-target activity and chromosomal rearrangements, particularly in SCD samples (likely because of the higher overall editing efficiency) but did not impact the target gene expression and HSPC engraftment and differentiation. Transcriptomic analyses showed that the editing procedure results in the up-regulation of genes involved in DNA damage and inflammatory responses, which was more evident in SCD HSPCs. This study provides evidence of efficacy and safety for an editing strategy based on HbF reactivation and highlights the need of performing safety studies in clinically relevant conditions, i.e., in patient-derived HSPCs.
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Affiliation(s)
- Giacomo Frati
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Megane Brusson
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Gilles Sartre
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Bochra Mlayah
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Tristan Felix
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Anne Chalumeau
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Panagiotis Antoniou
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Giulia Hardouin
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris, France
| | - Oriana Romano
- University of Padova, Department of Molecular Medicine, Padova, Italy
| | | | - Annarita Miccio
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France.
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19
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Wu WY, Adiego-Pérez B, van der Oost J. Biology and applications of CRISPR-Cas12 and transposon-associated homologs. Nat Biotechnol 2024; 42:1807-1821. [PMID: 39633151 DOI: 10.1038/s41587-024-02485-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 10/24/2024] [Indexed: 12/07/2024]
Abstract
CRISPR-associated Cas12 proteins are a highly variable collection of nucleic acid-targeting proteins. All Cas12 variants use RNA guides and a single nuclease domain to target complementary DNA or, in rare cases, RNA. The high variability of Cas12 effectors can be explained by a series of independent evolution events from different transposon-associated TnpB-like ancestors. Despite basic structural and functional similarities, this has resulted in unprecedented variation of the Cas12 effector proteins in terms of size, domain composition, guide structure, target identity and interference strategy. In this Review, we compare the unique molecular features of natural and engineered Cas12 and TnpB variants. Furthermore, we provide an overview of established genome editing and diagnostic applications and discuss potential future directions.
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Affiliation(s)
- Wen Y Wu
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, the Netherlands.
| | - Belén Adiego-Pérez
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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20
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Gilioli G, Lankester AC, de Kivit S, Staal FJT, Ott de Bruin LM. Gene therapy strategies for RAG1 deficiency: Challenges and breakthroughs. Immunol Lett 2024; 270:106931. [PMID: 39303994 DOI: 10.1016/j.imlet.2024.106931] [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: 07/23/2024] [Revised: 09/14/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
Mutations in the recombination activating genes (RAG) cause various forms of immune deficiency. Hematopoietic stem cell transplantation (HSCT) is the only cure for patients with severe manifestations of RAG deficiency; however, outcomes are suboptimal with mismatched donors. Gene therapy aims to correct autologous hematopoietic stem and progenitor cells (HSPC) and is emerging as an alternative to allogeneic HSCT. Gene therapy based on viral gene addition exploits viral vectors to add a correct copy of a mutated gene into the genome of HSPCs. Only recently, after a prolonged phase of development, viral gene addition has been approved for clinical testing in RAG1-SCID patients. In the meantime, a new technology, CRISPR/Cas9, has made its debut to compete with viral gene addition. Gene editing based on CRISPR/Cas9 allows to perform targeted genomic integrations of a correct copy of a mutated gene, circumventing the risk of virus-mediated insertional mutagenesis. In this review, we present the biology of the RAG genes, the challenges faced during the development of viral gene addition for RAG1-SCID, and the current status of gene therapy for RAG1 deficiency. In particular, we highlight the latest advances and challenges in CRISPR/Cas9 gene editing and their potential for the future of gene therapy.
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Affiliation(s)
- Giorgio Gilioli
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arjan C Lankester
- Department of Pediatrics, Pediatric Stem Cell Transplantation Program and Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, the Netherlands
| | - Sander de Kivit
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Lisa M Ott de Bruin
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands; Department of Pediatrics, Pediatric Stem Cell Transplantation Program and Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, the Netherlands
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21
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Zhang D, Zheng R, Chen Z, Wang L, Chen X, Yang L, Huo Y, Yin S, Zhang D, Huang J, Cui X, Li D, Geng H. Lipid nanoparticle-mediated base-editing of the Hao1 gene achieves sustainable primary hyperoxaluria type 1 therapy in rats. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2575-2586. [PMID: 39425833 DOI: 10.1007/s11427-024-2697-3] [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: 03/20/2024] [Accepted: 07/28/2024] [Indexed: 10/21/2024]
Abstract
Primary hyperoxaluria type 1 (PH1) is a severe hereditary disease, leading to the accumulation of oxalate in multiple organs, particularly the kidney. Hydroxyacid oxidase 1 (HAO1), a pivotal gene involved in oxalate production, is an approved target for the treatment of PH1. In this study, we demonstrated the discovery of several novel therapeutic sites of the Hao1 gene and the efficient editing of Hao1 c.290-2 A in vivo with lipid nanoparticles (LNP) delivered adenine base editing (ABE) mRNA. A single infusion of LNP-ABE resulted in a near-complete knockout of Hao1 in the liver, leading to the sustainable normalization of urinary oxalate (for at least 6 months) and complete rescue of the patho-physiology in PH1 rats. Additionally, a significant correlation between Hao1 editing efficiency and urinary oxalate levels was observed and over 60% Hao1 editing efficiency was required to achieve the normalization of urinary oxalate in PH1 rats. These findings suggest that the LNP-mediated base-editing of Hao1 c.290-2 A is an efficient and safe approach to PH1 therapy, highlighting its potential utility in clinical settings.
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Affiliation(s)
- Dexin Zhang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Rui Zheng
- Department of Urology, Children's Hospital of Fudan University, Shanghai, 201100, China
| | - Zhoutong Chen
- Department of Urology, Children's Hospital of Fudan University, Shanghai, 201100, China
| | - Liren Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xi Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lei Yang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yanan Huo
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Shuming Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dan Zhang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiaxin Huang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Hongquan Geng
- Department of Urology, Children's Hospital of Fudan University, Shanghai, 201100, China.
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22
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Cullot G, Aird EJ, Schlapansky MF, Yeh CD, van de Venn L, Vykhlyantseva I, Kreutzer S, Mailänder D, Lewków B, Klermund J, Montellese C, Biserni M, Aeschimann F, Vonarburg C, Gehart H, Cathomen T, Corn JE. Genome editing with the HDR-enhancing DNA-PKcs inhibitor AZD7648 causes large-scale genomic alterations. Nat Biotechnol 2024:10.1038/s41587-024-02488-6. [PMID: 39604565 DOI: 10.1038/s41587-024-02488-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 10/24/2024] [Indexed: 11/29/2024]
Abstract
The DNA-PKcs inhibitor AZD7648 enhances CRISPR-Cas9-directed homology-directed repair efficiencies, with potential for clinical utility, but its possible on-target consequences are unknown. We found that genome editing with AZD7648 causes frequent kilobase-scale and megabase-scale deletions, chromosome arm loss and translocations. These large-scale chromosomal alterations evade detection through typical genome editing assays, prompting caution in deploying AZD7648 and reinforcing the need to investigate multiple types of potential editing outcomes.
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Affiliation(s)
- Grégoire Cullot
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
| | - Eric J Aird
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Moritz F Schlapansky
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Charles D Yeh
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lilly van de Venn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Iryna Vykhlyantseva
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Susanne Kreutzer
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Dominic Mailänder
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Bohdan Lewków
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christian Montellese
- CSL Behring Research, Bern, Switzerland
- Swiss Institute for Translational Medicine sitem-insel, Bern, Switzerland
| | - Martina Biserni
- CSL Behring Research, Bern, Switzerland
- Swiss Institute for Translational Medicine sitem-insel, Bern, Switzerland
| | - Florian Aeschimann
- CSL Behring Research, Bern, Switzerland
- Swiss Institute for Translational Medicine sitem-insel, Bern, Switzerland
| | - Cédric Vonarburg
- CSL Behring Research, Bern, Switzerland
- Swiss Institute for Translational Medicine sitem-insel, Bern, Switzerland
| | - Helmuth Gehart
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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23
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Chen Y, van Til NP, Bosma PJ. Gene Therapy for Inherited Liver Disease: To Add or to Edit. Int J Mol Sci 2024; 25:12514. [PMID: 39684224 DOI: 10.3390/ijms252312514] [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: 08/23/2024] [Revised: 11/06/2024] [Accepted: 11/12/2024] [Indexed: 12/18/2024] Open
Abstract
Patients suffering from an inherited severe liver disorder require lifelong treatment to prevent premature death. Until recently, the only curative treatment option was liver transplantation, which requires lifelong immune suppression. Now, liver-directed gene therapy, which is a much less invasive procedure, has become a market-approved treatment for hemophilia A and B. This may pave the way for it to become the treatment of choice for many other recessive inherited liver disorders with loss-of-function mutations. Inherited liver disease with toxic-gain-of-function or intrinsic hepatocyte damage may require alternative applications, such as integrating vectors or genome editing technologies, that can provide permanent or specific modification of the genome. We present an overview of currently available gene therapy strategies, i.e., gene supplementation, gene editing, and gene repair investigated in preclinical and clinical studies to treat inherited severe liver disorders. The advantages and limitations of these gene therapy applications are discussed in relation to the underlying disease mechanism.
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Affiliation(s)
- Yue Chen
- Amsterdam University Medical Center, Tytgat Institute for Liver and Intestinal Research, AG&M, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Niek P van Til
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam Neuroscience, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Piter J Bosma
- Amsterdam University Medical Center, Tytgat Institute for Liver and Intestinal Research, AG&M, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
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24
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Raimondi F, Siow KM, Wrona D, Fuster-García C, Pastukhov O, Schmitz M, Bargsten K, Kissling L, Swarts DC, Andrieux G, Cathomen T, Modlich U, Jinek M, Siler U, Reichenbach J. Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements. Commun Biol 2024; 7:1291. [PMID: 39384978 PMCID: PMC11464842 DOI: 10.1038/s42003-024-06959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 09/24/2024] [Indexed: 10/11/2024] Open
Abstract
CRISPR-based genome editing of pseudogene-associated disorders, such as p47phox-deficient chronic granulomatous disease (p47 CGD), is challenged by chromosomal rearrangements due to presence of multiple targets. We report that interactions between highly homologous sequences that are localized on the same chromosome contribute substantially to post-editing chromosomal rearrangements. We successfully employed editing approaches at the NCF1 gene and its pseudogenes, NCF1B and NCF1C, in a human cell line model of p47 CGD and in patient-derived human hematopoietic stem and progenitor cells. Upon genetic engineering, a droplet digital PCR-based method identified cells with altered copy numbers, spanning megabases from the edited loci. We attributed the high aberration frequency to the interaction between repetitive sequences and their predisposition to recombination events. Our findings emphasize the need for careful evaluation of the target-specific genomic context, such as the presence of homologous regions, whose instability can constitute a risk factor for chromosomal rearrangements upon genome editing.
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Affiliation(s)
- Federica Raimondi
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich (Schlieren Campus), Schlieren, Switzerland
| | - Kah Mun Siow
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich (Schlieren Campus), Schlieren, Switzerland
| | - Dominik Wrona
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich (Schlieren Campus), Schlieren, Switzerland
| | - Carla Fuster-García
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
| | - Oleksandr Pastukhov
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich (Schlieren Campus), Schlieren, Switzerland
| | - Michael Schmitz
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lucas Kissling
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daan C Swarts
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Geoffroy Andrieux
- Institute for Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ute Modlich
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich (Schlieren Campus), Schlieren, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ulrich Siler
- School of Life Sciences, Institute for Pharma Technology, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Janine Reichenbach
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich (Schlieren Campus), Schlieren, Switzerland.
- Department of Somatic Gene Therapy, University Children's Hospital Zurich, Zurich, Switzerland.
- The Competence Center for Applied Biotechnology and Molecular Medicine, University of Zurich, Zurich, Switzerland.
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25
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Golikova EA, Alshevskaya AA, Alrhmoun S, Sivitskaya NA, Sennikov SV. TCR-T cell therapy: current development approaches, preclinical evaluation, and perspectives on regulatory challenges. J Transl Med 2024; 22:897. [PMID: 39367419 PMCID: PMC11451006 DOI: 10.1186/s12967-024-05703-9] [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: 06/21/2024] [Accepted: 09/24/2024] [Indexed: 10/06/2024] Open
Abstract
TCR-T cell therapy represents a promising advancement in adoptive immunotherapy for cancer treatment. Despite its potential, the development and preclinical testing of TCR-T cells face significant challenges. This review provides a structured overview of the key stages in preclinical testing, including in silico, in vitro, and in vivo methods, within the context of the sequential development of novel therapies. This review aimed to systematically outline the processes for evaluating TCR-T cells at each stage: from in silico approaches used to predict target antigens, assess cross-reactivity, and minimize off-target effects, to in vitro assays designed to measure cell functionality, cytotoxicity, and activation. Additionally, the review discusses the limitations of in vivo testing in animal models, particularly in accurately reflecting the human tumor microenvironment and immune responses. Performed analysis emphasizes the importance of these preclinical stages in the safe and effective development of TCR-T cell therapies. While current models provide valuable insights, we identify critical gaps, particularly in in vivo biodistribution and toxicity assessments, and propose the need for enhanced standardization and the development of more representative models. This structured approach aims to improve the predictability and safety of TCR-T cell therapy as it advances towards clinical application.
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Affiliation(s)
- Elena A Golikova
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
| | - Alina A Alshevskaya
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia.
| | - Saleh Alrhmoun
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
- Federal State Budgetary Scientific Institution, "Research Institute of Fundamental and Clinical Immunology" (RIFCI), 630099, Novosibirsk, Russia
| | - Natalia A Sivitskaya
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
| | - Sergey V Sennikov
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435, Moscow, Russia
- Federal State Budgetary Scientific Institution, "Research Institute of Fundamental and Clinical Immunology" (RIFCI), 630099, Novosibirsk, Russia
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26
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Ritter MU, Nasri M, Dannenmann B, Mir P, Secker B, Amend D, Klimiankou M, Welte K, Skokowa J. Comparison of Gene-Editing Approaches for Severe Congenital Neutropenia-Causing Mutations in the ELANE Gene. CRISPR J 2024; 7:258-271. [PMID: 39436283 DOI: 10.1089/crispr.2024.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2024] Open
Abstract
Safety considerations for gene therapies of inherited preleukemia syndromes, including severe congenital neutropenia (CN), are paramount. We compared several strategies for CRISPR/Cas9 gene editing of autosomal-dominant ELANE mutations in CD34+ cells from two CN patients head-to-head. We tested universal and allele-specific ELANE knockout, ELANE mutation correction by homology-directed repair (HDR) with AAV6, and allele-specific HDR with ssODN. All strategies were not toxic, had at least 30% editing, and rescued granulopoiesis in vitro. In contrast to published data, allele-specific indels in the last exon of ELANE also restored granulopoiesis. Moreover, by implementing patient-derived induced pluripotent stem cells for GUIDE-Seq off-target analysis, we established a clinically relevant "personalized" assessment of off-target activity of gene editing on the background of the patient's genome. We found that allele-specific approaches had the most favorable off-target profiles. Taken together, a well-defined head-to-head comparison pipeline for selecting the appropriate gene therapy is essential for diseases, with several gene editing strategies available.
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Affiliation(s)
- Malte Ulrich Ritter
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Masoud Nasri
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Benjamin Dannenmann
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Perihan Mir
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Benjamin Secker
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Diana Amend
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Maksim Klimiankou
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Karl Welte
- Department of Pediatric Hematology, Oncology and Bone Marrow Transplantation, University Hospital Tübingen, Tübingen, Germany
| | - Julia Skokowa
- Department of Hematology, Oncology, Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
- Gene and RNA Therapy Center, Tübingen University, Tübingen, Germany
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27
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Bexte T, Albinger N, Al Ajami A, Wendel P, Buchinger L, Gessner A, Alzubi J, Särchen V, Vogler M, Rasheed HM, Jung BA, Wolf S, Bhayadia R, Oellerich T, Klusmann JH, Penack O, Möker N, Cathomen T, Rieger MA, Imkeller K, Ullrich E. CRISPR/Cas9 editing of NKG2A improves the efficacy of primary CD33-directed chimeric antigen receptor natural killer cells. Nat Commun 2024; 15:8439. [PMID: 39349459 PMCID: PMC11442982 DOI: 10.1038/s41467-024-52388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 08/30/2024] [Indexed: 10/02/2024] Open
Abstract
Chimeric antigen receptor (CAR)-modified natural killer (NK) cells show antileukemic activity against acute myeloid leukemia (AML) in vivo. However, NK cell-mediated tumor killing is often impaired by the interaction between human leukocyte antigen (HLA)-E and the inhibitory receptor, NKG2A. Here, we describe a strategy that overcomes CAR-NK cell inhibition mediated by the HLA-E-NKG2A immune checkpoint. We generate CD33-specific, AML-targeted CAR-NK cells (CAR33) combined with CRISPR/Cas9-based gene disruption of the NKG2A-encoding KLRC1 gene. Using single-cell multi-omics analyses, we identified transcriptional features of activation and maturation in CAR33-KLRC1ko-NK cells, which are preserved following exposure to AML cells. Moreover, CAR33-KLRC1ko-NK cells demonstrate potent antileukemic killing activity against AML cell lines and primary blasts in vitro and in vivo. We thus conclude that NKG2A-deficient CAR-NK cells have the potential to bypass immune suppression in AML.
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MESH Headings
- Humans
- CRISPR-Cas Systems
- NK Cell Lectin-Like Receptor Subfamily C/genetics
- NK Cell Lectin-Like Receptor Subfamily C/metabolism
- NK Cell Lectin-Like Receptor Subfamily C/immunology
- Killer Cells, Natural/immunology
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/genetics
- Gene Editing/methods
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/genetics
- Cell Line, Tumor
- Animals
- Sialic Acid Binding Ig-like Lectin 3/genetics
- Sialic Acid Binding Ig-like Lectin 3/immunology
- Mice
- Immunotherapy, Adoptive/methods
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Affiliation(s)
- Tobias Bexte
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany
- Goethe University Frankfurt, Department of Pediatrics, Frankfurt am Main, Germany
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- German Red Cross Blood Service Baden-Württemberg - Hessen, Institute for Transfusion Medicine and Immunohematology, Frankfurt am Main, Germany
| | - Nawid Albinger
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany
- Goethe University Frankfurt, Department of Pediatrics, Frankfurt am Main, Germany
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
| | - Ahmad Al Ajami
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- University Cancer Center (UCT), Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Neurological Institute / Edinger Institute, Frankfurt am Main, Germany
| | - Philipp Wendel
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany
- Goethe University Frankfurt, Department of Pediatrics, Frankfurt am Main, Germany
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leon Buchinger
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany
- Goethe University Frankfurt, Department of Pediatrics, Frankfurt am Main, Germany
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
| | - Alec Gessner
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Department of Medicine II - Hematology and Oncology, Frankfurt am Main, Germany
| | - Jamal Alzubi
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vinzenz Särchen
- Goethe University Frankfurt, Institute for Experimental Pediatric Hematology and Oncology, Frankfurt am Main, Germany
| | - Meike Vogler
- Goethe University Frankfurt, Institute for Experimental Pediatric Hematology and Oncology, Frankfurt am Main, Germany
| | - Hadeer Mohamed Rasheed
- Charité, University Berlin and Humboldt-University Berlin, Department of Hematology, Oncology and Tumor Immunology, Berlin, Germany
- Clinical Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Beate Anahita Jung
- Charité, University Berlin and Humboldt-University Berlin, Department of Hematology, Oncology and Tumor Immunology, Berlin, Germany
| | - Sebastian Wolf
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Department of Medicine II - Hematology and Oncology, Frankfurt am Main, Germany
| | - Raj Bhayadia
- Goethe University Frankfurt, Department of Pediatrics, Frankfurt am Main, Germany
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
| | - Thomas Oellerich
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Department of Medicine II - Hematology and Oncology, Frankfurt am Main, Germany
| | - Jan-Henning Klusmann
- Goethe University Frankfurt, Department of Pediatrics, Frankfurt am Main, Germany
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
| | - Olaf Penack
- Charité, University Berlin and Humboldt-University Berlin, Department of Hematology, Oncology and Tumor Immunology, Berlin, Germany
- German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany
| | - Nina Möker
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg, Freiburg, Germany
| | - Michael A Rieger
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Department of Medicine II - Hematology and Oncology, Frankfurt am Main, Germany
- Cardio-Pulmonary-Institute, Frankfurt am Main, Germany
| | - Katharina Imkeller
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- University Cancer Center (UCT), Frankfurt am Main, Germany
- Goethe University Frankfurt, University Hospital, Neurological Institute / Edinger Institute, Frankfurt am Main, Germany
| | - Evelyn Ullrich
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany.
- Goethe University Frankfurt, Department of Pediatrics, Frankfurt am Main, Germany.
- Goethe University Frankfurt, Frankfurt Cancer Institute, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt am Main, Germany.
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28
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Pugliano CM, Berger M, Ray RM, Sapkos K, Wu B, Laird A, Ye Y, Thomson D, DeGottardi MQ, Khan IF, Tatiossian K, Miles BA, Aeschimann F, Pasquier J, Kim MM, Rawlings DJ. DNA-PK inhibition enhances gene editing efficiency in HSPCs for CRISPR-based treatment of X-linked hyper IgM syndrome. Mol Ther Methods Clin Dev 2024; 32:101297. [PMID: 40012884 PMCID: PMC11863497 DOI: 10.1016/j.omtm.2024.101297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 02/28/2025]
Abstract
Targeted gene editing to restore CD40L expression via homology-directed repair (HDR) in CD34+ hematopoietic stem and progenitor cells (HSPCs) represents a potential long-term therapy for X-linked hyper IgM syndrome. However, clinical translation of HSPC editing is limited by inefficient long-term engraftment of HDR-edited HSPCs. Here, we ameliorate this issue by employing a small-molecule inhibitor of DNA-PKcs, AZD7648, to bias DNA repair mechanisms to facilitate HDR upon CRISPR SpCas9-based gene editing. Using AZD7648 treatment and a clinically relevant HSPC source, mobilized peripheral blood CD34+ cells, we achieve ∼60% HDR efficiency at the CD40LG locus and enhanced engraftment of HDR-edited HSPCs in primary and secondary xenotransplants. Specifically, we observed a 1.6-fold increase of HDR-edited long-term HSPCs in primary transplant recipients without disturbing chimerism levels or differentiation capacity. As CD40L is primarily expressed in T cells, we demonstrate T cell differentiation from HDR-edited HSPCs in vivo and in artificial thymic organoid cultures, and endogenously regulated CD40L expression following activation of in-vivo-derived CD4+ T cells. Our combined findings demonstrate HDR editing at the CD40LG locus at potentially clinically beneficial levels. More broadly, these data support using DNA-PKcs inhibition with AZD7648 as a simple and efficacious addition to HSPC editing platforms.
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Affiliation(s)
- Cole M. Pugliano
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Mason Berger
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Roslyn M. Ray
- Gene Therapy Research, CSL Behring, Pasadena, CA 91101, USA
| | - Kai Sapkos
- Gene Therapy Research, CSL Behring, Pasadena, CA 91101, USA
| | - Betty Wu
- Gene Therapy Research, CSL Behring, Pasadena, CA 91101, USA
| | - Aidan Laird
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yidian Ye
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Daniel Thomson
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - M. Quinn DeGottardi
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Iram F. Khan
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | | | | | - Florian Aeschimann
- CSL Behring, Research Bern, 3000 Bern, Switzerland
- Swiss Institute for Translational Medicine, Sitem-insel, 3010 Bern, Switzerland
| | - Jerome Pasquier
- CSL Behring, Research Bern, 3000 Bern, Switzerland
- Swiss Institute for Translational Medicine, Sitem-insel, 3010 Bern, Switzerland
| | - Mihee M. Kim
- Gene Therapy Research, CSL Behring, Pasadena, CA 91101, USA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
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29
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Simoni C, Barbon E, Muro AF, Cantore A. In vivo liver targeted genome editing as therapeutic approach: progresses and challenges. Front Genome Ed 2024; 6:1458037. [PMID: 39246827 PMCID: PMC11378722 DOI: 10.3389/fgeed.2024.1458037] [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: 07/01/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024] Open
Abstract
The liver is an essential organ of the body that performs several vital functions, including the metabolism of biomolecules, foreign substances, and toxins, and the production of plasma proteins, such as coagulation factors. There are hundreds of genetic disorders affecting liver functions and, for many of them, the only curative option is orthotopic liver transplantation, which nevertheless entails many risks and long-term complications. Some peculiar features of the liver, such as its large blood flow supply and the tolerogenic immune environment, make it an attractive target for in vivo gene therapy approaches. In recent years, several genome-editing tools mainly based on the clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) system have been successfully exploited in the context of liver-directed preclinical or clinical therapeutic applications. These include gene knock-out, knock-in, activation, interference, or base and prime editing approaches. Despite many achievements, important challenges still need to be addressed to broaden clinical applications, such as the optimization of the delivery methods, the improvement of the editing efficiency, and the risk of on-target or off-target unwanted effects and chromosomal rearrangements. In this review, we highlight the latest progress in the development of in vivo liver-targeted genome editing approaches for the treatment of genetic disorders. We describe the technological advancements that are currently under investigation, the challenges to overcome for clinical applicability, and the future perspectives of this technology.
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Affiliation(s)
- Chiara Simoni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Barbon
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrés F Muro
- International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alessio Cantore
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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30
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Feng Q, Li Q, Zhou H, Wang Z, Lin C, Jiang Z, Liu T, Wang D. CRISPR technology in human diseases. MedComm (Beijing) 2024; 5:e672. [PMID: 39081515 PMCID: PMC11286548 DOI: 10.1002/mco2.672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Gene editing is a growing gene engineering technique that allows accurate editing of a broad spectrum of gene-regulated diseases to achieve curative treatment and also has the potential to be used as an adjunct to the conventional treatment of diseases. Gene editing technology, mainly based on clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein systems, which is capable of generating genetic modifications in somatic cells, provides a promising new strategy for gene therapy for a wide range of human diseases. Currently, gene editing technology shows great application prospects in a variety of human diseases, not only in therapeutic potential but also in the construction of animal models of human diseases. This paper describes the application of gene editing technology in hematological diseases, solid tumors, immune disorders, ophthalmological diseases, and metabolic diseases; focuses on the therapeutic strategies of gene editing technology in sickle cell disease; provides an overview of the role of gene editing technology in the construction of animal models of human diseases; and discusses the limitations of gene editing technology in the treatment of diseases, which is intended to provide an important reference for the applications of gene editing technology in the human disease.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Qirong Li
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Hengzong Zhou
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Zhan Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Chao Lin
- School of Grain Science and TechnologyJilin Business and Technology CollegeChangchunChina
| | - Ziping Jiang
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
| | - Tianjia Liu
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Dongxu Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
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31
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Pardi N, Ivics Z. An LNP-CRISPR gene editing drug demonstrates efficacy and safety in patients with hereditary angioedema following in vivo administration. J Allergy Clin Immunol 2024; 154:272-274. [PMID: 38925443 DOI: 10.1016/j.jaci.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Zoltán Ivics
- Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.
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32
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Esposito F, Dell'Aquila F, Rhiel M, Auricchio S, Chmielewski KO, Andrieux G, Ferla R, Horrach PS, Padmanabhan A, Di Cunto R, Notaro S, Santeularia ML, Boerries M, Dell'Anno M, Nusco E, Padula A, Nutarelli S, Cornu TI, Sorrentino NC, Piccolo P, Trapani I, Cathomen T, Auricchio A. Safe and effective liver-directed AAV-mediated homology-independent targeted integration in mouse models of inherited diseases. Cell Rep Med 2024; 5:101619. [PMID: 38897206 PMCID: PMC11293346 DOI: 10.1016/j.xcrm.2024.101619] [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: 10/04/2023] [Revised: 02/13/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
Liver-directed adeno-associated viral (AAV) vector-mediated homology-independent targeted integration (AAV-HITI) by CRISPR-Cas9 at the highly transcribed albumin locus is under investigation to provide sustained transgene expression following neonatal treatment. We show that targeting the 3' end of the albumin locus results in productive integration in about 15% of mouse hepatocytes achieving therapeutic levels of systemic proteins in two mouse models of inherited diseases. We demonstrate that full-length HITI donor DNA is preferentially integrated upon nuclease cleavage and that, despite partial AAV genome integrations in the target locus, no gross chromosomal rearrangements or insertions/deletions at off-target sites are found. In line with this, no evidence of hepatocellular carcinoma is observed within the 1-year follow-up. Finally, AAV-HITI is effective at vector doses considered safe if directly translated to humans providing therapeutic efficacy in the adult liver in addition to newborn. Overall, our data support the development of this liver-directed AAV-based knockin strategy.
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Affiliation(s)
- Federica Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Fabio Dell'Aquila
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Medical Genetics, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefano Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Kay Ole Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany; PhD Program, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rita Ferla
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Arjun Padmanabhan
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Roberto Di Cunto
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Simone Notaro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Agnese Padula
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Sofia Nutarelli
- Department of Life Science and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nicolina Cristina Sorrentino
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Pasquale Piccolo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Ivana Trapani
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Medical Genetics, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), Partner site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Freiburg, Germany
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Gene Therapy Joint lab, Dept. of Advanced Biomedical Sciences and Dept. of Translational Medicine, University of Naples "Federico II", Naples, Italy.
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33
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Neumayer G, Torkelson JL, Li S, McCarthy K, Zhen HH, Vangipuram M, Mader MM, Gebeyehu G, Jaouni TM, Jacków-Malinowska J, Rami A, Hansen C, Guo Z, Gaddam S, Tate KM, Pappalardo A, Li L, Chow GM, Roy KR, Nguyen TM, Tanabe K, McGrath PS, Cramer A, Bruckner A, Bilousova G, Roop D, Tang JY, Christiano A, Steinmetz LM, Wernig M, Oro AE. A scalable and cGMP-compatible autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa. Nat Commun 2024; 15:5834. [PMID: 38992003 PMCID: PMC11239819 DOI: 10.1038/s41467-024-49400-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/25/2024] [Indexed: 07/13/2024] Open
Abstract
We present Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a scalable platform producing autologous organotypic iPS cell-derived induced skin composite (iSC) grafts for definitive treatment. Clinical-grade manufacturing integrates CRISPR-mediated genetic correction with reprogramming into one step, accelerating derivation of COL7A1-edited iPS cells from patients. Differentiation into epidermal, dermal and melanocyte progenitors is followed by CD49f-enrichment, minimizing maturation heterogeneity. Mouse xenografting of iSCs from four patients with different mutations demonstrates disease modifying activity at 1 month. Next-generation sequencing, biodistribution and tumorigenicity assays establish a favorable safety profile at 1-9 months. Single cell transcriptomics reveals that iSCs are composed of the major skin cell lineages and include prominent holoclone stem cell-like signatures of keratinocytes, and the recently described Gibbin-dependent signature of fibroblasts. The latter correlates with enhanced graftability of iSCs. In conclusion, DEBCT overcomes manufacturing and safety roadblocks and establishes a reproducible, safe, and cGMP-compatible therapeutic approach to heal lesions of DEB patients.
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Affiliation(s)
- Gernot Neumayer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jessica L Torkelson
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Shengdi Li
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Kelly McCarthy
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Hanson H Zhen
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Madhuri Vangipuram
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Marius M Mader
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gulilat Gebeyehu
- Thermo Fisher Scientific, Life Sciences Solutions Group, Cell Biology, Research and Development, Frederick, MD, USA
| | - Taysir M Jaouni
- Thermo Fisher Scientific, Life Sciences Solutions Group, Cell Biology, Research and Development, Frederick, MD, USA
| | - Joanna Jacków-Malinowska
- Department of Dermatology, Columbia University, New York, NY, USA
- St. John's Institute of Dermatology, King's College London, London, UK
| | - Avina Rami
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Corey Hansen
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Zongyou Guo
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Sadhana Gaddam
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Keri M Tate
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Lingjie Li
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Grace M Chow
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Kevin R Roy
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Thuylinh Michelle Nguyen
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Patrick S McGrath
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Amber Cramer
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Anna Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Dennis Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Jean Y Tang
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA.
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA, USA.
| | - Anthony E Oro
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
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34
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Bahal S, Zinicola M, Moula SE, Whittaker TE, Schejtman A, Naseem A, Blanco E, Vetharoy W, Hu YT, Rai R, Gomez-Castaneda E, Cunha-Santos C, Burns SO, Morris EC, Booth C, Turchiano G, Cavazza A, Thrasher AJ, Santilli G. Hematopoietic stem cell gene editing rescues B-cell development in X-linked agammaglobulinemia. J Allergy Clin Immunol 2024; 154:195-208.e8. [PMID: 38479630 PMCID: PMC11752842 DOI: 10.1016/j.jaci.2024.03.003] [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: 12/01/2023] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND X-linked agammaglobulinemia (XLA) is an inborn error of immunity that renders boys susceptible to life-threatening infections due to loss of mature B cells and circulating immunoglobulins. It is caused by defects in the gene encoding the Bruton tyrosine kinase (BTK) that mediates the maturation of B cells in the bone marrow and their activation in the periphery. This paper reports on a gene editing protocol to achieve "knock-in" of a therapeutic BTK cassette in hematopoietic stem and progenitor cells (HSPCs) as a treatment for XLA. METHODS To rescue BTK expression, this study employed a clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 system that creates a DNA double-strand break in an early exon of the BTK locus and an adeno-associated virus 6 virus that carries the donor template for homology-directed repair. The investigators evaluated the efficacy of the gene editing approach in HSPCs from patients with XLA that were cultured in vitro under B-cell differentiation conditions or that were transplanted in immunodeficient mice to study B-cell output in vivo. RESULTS A (feeder-free) B-cell differentiation protocol was successfully applied to blood-mobilized HSPCs to reproduce in vitro the defects in B-cell maturation observed in patients with XLA. Using this system, the investigators could show the rescue of B-cell maturation by gene editing. Transplantation of edited XLA HSPCs into immunodeficient mice led to restoration of the human B-cell lineage compartment in the bone marrow and immunoglobulin production in the periphery. CONCLUSIONS Gene editing efficiencies above 30% could be consistently achieved in human HSPCs. Given the potential selective advantage of corrected cells, as suggested by skewed X-linked inactivation in carrier females and by competitive repopulating experiments in mouse models, this work demonstrates the potential of this strategy as a future definitive therapy for XLA.
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Affiliation(s)
- Sameer Bahal
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Marta Zinicola
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Shefta E Moula
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Thomas E Whittaker
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Andrea Schejtman
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Asma Naseem
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Elena Blanco
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Winston Vetharoy
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Yi-Ting Hu
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Rajeev Rai
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Eduardo Gomez-Castaneda
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Catarina Cunha-Santos
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Siobhan O Burns
- University College London Institute of Immunity and Transplantation, London, United Kingdom; Department of Immunology, Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | - Emma C Morris
- University College London Institute of Immunity and Transplantation, London, United Kingdom; Department of Immunology, Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | - Claire Booth
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Great Ormond Street Hospital, National Health Service Foundation Trust, London, United Kingdom
| | - Giandomenico Turchiano
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Alessia Cavazza
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Great Ormond Street Hospital, National Health Service Foundation Trust, London, United Kingdom
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Research and Teaching Department, University College London Great Ormond Street Institute of Child Health, London, United Kingdom.
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Kath J, Franke C, Drosdek V, Du W, Glaser V, Fuster-Garcia C, Stein M, Zittel T, Schulenberg S, Porter CE, Andersch L, Künkele A, Alcaniz J, Hoffmann J, Abken H, Abou-el-Enein M, Pruß A, Suzuki M, Cathomen T, Stripecke R, Volk HD, Reinke P, Schmueck-Henneresse M, Wagner DL. Integration of ζ-deficient CARs into the CD3ζ gene conveys potent cytotoxicity in T and NK cells. Blood 2024; 143:2599-2611. [PMID: 38493479 PMCID: PMC11196866 DOI: 10.1182/blood.2023020973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
ABSTRACT Chimeric antigen receptor (CAR)-redirected immune cells hold significant therapeutic potential for oncology, autoimmune diseases, transplant medicine, and infections. All approved CAR-T therapies rely on personalized manufacturing using undirected viral gene transfer, which results in nonphysiological regulation of CAR-signaling and limits their accessibility due to logistical challenges, high costs and biosafety requirements. Random gene transfer modalities pose a risk of malignant transformation by insertional mutagenesis. Here, we propose a novel approach utilizing CRISPR-Cas gene editing to redirect T cells and natural killer (NK) cells with CARs. By transferring shorter, truncated CAR-transgenes lacking a main activation domain into the human CD3ζ (CD247) gene, functional CAR fusion-genes are generated that exploit the endogenous CD3ζ gene as the CAR's activation domain. Repurposing this T/NK-cell lineage gene facilitated physiological regulation of CAR expression and redirection of various immune cell types, including conventional T cells, TCRγ/δ T cells, regulatory T cells, and NK cells. In T cells, CD3ζ in-frame fusion eliminated TCR surface expression, reducing the risk of graft-versus-host disease in allogeneic off-the-shelf settings. CD3ζ-CD19-CAR-T cells exhibited comparable leukemia control to TCRα chain constant (TRAC)-replaced and lentivirus-transduced CAR-T cells in vivo. Tuning of CD3ζ-CAR-expression levels significantly improved the in vivo efficacy. Notably, CD3ζ gene editing enabled redirection of NK cells without impairing their canonical functions. Thus, CD3ζ gene editing is a promising platform for the development of allogeneic off-the-shelf cell therapies using redirected killer lymphocytes.
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Affiliation(s)
- Jonas Kath
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Clemens Franke
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Vanessa Drosdek
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Weijie Du
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Viktor Glaser
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Carla Fuster-Garcia
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maik Stein
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Tatiana Zittel
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sarah Schulenberg
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Caroline E. Porter
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | - Lena Andersch
- Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium, Partner Site Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium, Partner Site Berlin, Berlin, Germany
| | - Joshua Alcaniz
- Experimental Pharmacology & Oncology Berlin Buch GmbH, Berlin, Germany
| | - Jens Hoffmann
- Experimental Pharmacology & Oncology Berlin Buch GmbH, Berlin, Germany
| | - Hinrich Abken
- Division of Genetic Immunotherapy, Leibniz Institute for Immunotherapy, Regensburg, Germany
- Chair Genetic Immunotherapy, University of Regensburg, Regensburg, Germany
| | - Mohamed Abou-el-Enein
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
- USC/CHLA Cell Therapy Program, University of Southern California, and Children's Hospital Los Angeles, Los Angeles, CA
| | - Axel Pruß
- Institute of Transfusion Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Masataka Suzuki
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Renata Stripecke
- Clinic of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, University of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Center for Molecular Medicine Cologne, Cologne, Germany
- Institute for Translational Immune-Oncology, Cancer Research Center Cologne-Essen, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Hans-Dieter Volk
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Reinke
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Schmueck-Henneresse
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Dimitrios L. Wagner
- Berlin Center for Advanced Therapies, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Institute of Transfusion Medicine, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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36
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Naiisseh B, Papasavva PL, Papaioannou NY, Tomazou M, Koniali L, Felekis X, Constantinou CG, Sitarou M, Christou S, Kleanthous M, Lederer CW, Patsali P. Context base editing for splice correction of IVSI-110 β-thalassemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102183. [PMID: 38706633 PMCID: PMC11068610 DOI: 10.1016/j.omtn.2024.102183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/28/2024] [Indexed: 05/07/2024]
Abstract
β-Thalassemia is brought about by defective β-globin (HBB [hemoglobin subunit β]) formation and, in severe cases, requires regular blood transfusion and iron chelation for survival. Genome editing of hematopoietic stem cells allows correction of underlying mutations as curative therapy. As potentially safer alternatives to double-strand-break-based editors, base editors (BEs) catalyze base transitions for precision editing of DNA target sites, prompting us to reclone and evaluate two recently published adenine BEs (ABEs; SpRY and SpG) with relaxed protospacer adjacent motif requirements for their ability to correct the common HBBIVSI-110(G>A) splice mutation. Nucleofection of ABE components as RNA into patient-derived CD34+ cells achieved up to 90% editing of upstream sequence elements critical for aberrant splicing, allowing full characterization of the on-target base-editing profile of each ABE and the detection of differences in on-target insertions and deletions. In addition, this study identifies opposing effects on splice correction for two neighboring context bases, establishes the frequency distribution of multiple BE editing events in the editing window, and shows high-efficiency functional correction of HBBIVSI-110(G>A) for our ABEs, including at the levels of RNA, protein, and erythroid differentiation.
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Affiliation(s)
- Basma Naiisseh
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Panayiota L. Papasavva
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Nikoletta Y. Papaioannou
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, Agios Dometios, Nicosia 2371, Cyprus
| | - Lola Koniali
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Xenia Felekis
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Constantina G. Constantinou
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, State Health Services Organization, Larnaca 6301, Cyprus
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, State Health Services Organization, Strovolos, Nicosia 2012, Cyprus
| | - Marina Kleanthous
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Carsten W. Lederer
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
| | - Petros Patsali
- Molecular Genetics of Thalassemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Agios Dometios, Nicosia 2371, Cyprus
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37
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Moiani A, Letort G, Lizot S, Chalumeau A, Foray C, Felix T, Le Clerre D, Temburni-Blake S, Hong P, Leduc S, Pinard N, Marechal A, Seclen E, Boyne A, Mayer L, Hong R, Pulicani S, Galetto R, Gouble A, Cavazzana M, Juillerat A, Miccio A, Duclert A, Duchateau P, Valton J. Non-viral DNA delivery and TALEN editing correct the sickle cell mutation in hematopoietic stem cells. Nat Commun 2024; 15:4965. [PMID: 38862518 PMCID: PMC11166989 DOI: 10.1038/s41467-024-49353-3] [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: 08/08/2023] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
Sickle cell disease is a devastating blood disorder that originates from a single point mutation in the HBB gene coding for hemoglobin. Here, we develop a GMP-compatible TALEN-mediated gene editing process enabling efficient HBB correction via a DNA repair template while minimizing risks associated with HBB inactivation. Comparing viral versus non-viral DNA repair template delivery in hematopoietic stem and progenitor cells in vitro, both strategies achieve comparable HBB correction and result in over 50% expression of normal adult hemoglobin in red blood cells without inducing β-thalassemic phenotype. In an immunodeficient female mouse model, transplanted cells edited with the non-viral strategy exhibit higher engraftment and gene correction levels compared to those edited with the viral strategy. Transcriptomic analysis reveals that non-viral DNA repair template delivery mitigates P53-mediated toxicity and preserves high levels of long-term hematopoietic stem cells. This work paves the way for TALEN-based autologous gene therapy for sickle cell disease.
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Affiliation(s)
| | - Gil Letort
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Sabrina Lizot
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Anne Chalumeau
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | - Chloe Foray
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Tristan Felix
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | | | | | - Patrick Hong
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Sophie Leduc
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Noemie Pinard
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Alan Marechal
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | | | - Alex Boyne
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Louisa Mayer
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | - Robert Hong
- Cellectis Inc., 430 East 29th Street, New York, NY, USA
| | | | - Roman Galetto
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Agnès Gouble
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France
| | - Marina Cavazzana
- Biotherapy Clinical Investigation Center, Necker Children's Hospital, Assistance Publique Hopitaux de Paris, Paris, France
- Human Lymphohematopoiesis Laboratory, Imagine Institute, INSERM UMR1163, Paris Cité University, Paris, France
- Biotherapy Department, Necker Children's Hospital, Assistance Publique Hopitaux de Paris, Paris, France
| | | | - Annarita Miccio
- Université Paris Cité, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France
| | | | | | - Julien Valton
- Cellectis S.A., 8 Rue de la Croix Jarry, Paris, France.
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38
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Nasri M, Ritter MU, Mir P, Dannenmann B, Kaufmann MM, Arreba-Tutusaus P, Xu Y, Borbaran-Bravo N, Klimiankou M, Lengerke C, Zeidler C, Cathomen T, Welte K, Skokowa J. CRISPR-Cas9n-mediated ELANE promoter editing for gene therapy of severe congenital neutropenia. Mol Ther 2024; 32:1628-1642. [PMID: 38556793 PMCID: PMC11184331 DOI: 10.1016/j.ymthe.2024.03.037] [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: 06/29/2023] [Revised: 12/07/2023] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Severe congenital neutropenia (CN) is an inherited pre-leukemia bone marrow failure syndrome commonly caused by autosomal-dominant ELANE mutations (ELANE-CN). ELANE-CN patients are treated with daily injections of recombinant human granulocyte colony-stimulating factor (rhG-CSF). However, some patients do not respond to rhG-CSF, and approximately 15% of ELANE-CN patients develop myelodysplasia or acute myeloid leukemia. Here, we report the development of a curative therapy for ELANE-CN through inhibition of ELANE mRNA expression by introducing two single-strand DNA breaks at the opposing DNA strands of the ELANE promoter TATA box using CRISPR-Cas9D10A nickases-termed MILESTONE. This editing effectively restored defective neutrophil differentiation of ELANE-CN CD34+ hematopoietic stem and progenitor cells (HSPCs) in vitro and in vivo, without affecting the functions of the edited neutrophils. CRISPResso analysis of the edited ELANE-CN CD34+ HSPCs revealed on-target efficiencies of over 90%. Simultaneously, GUIDE-seq, CAST-Seq, and rhAmpSeq indicated a safe off-target profile with no off-target sites or chromosomal translocations. Taken together, ex vivo gene editing of ELANE-CN HSPCs using MILESTONE in the setting of autologous stem cell transplantation could be a universal, safe, and efficient gene therapy approach for ELANE-CN patients.
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Affiliation(s)
- Masoud Nasri
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany.
| | - Malte U Ritter
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany.
| | - Perihan Mir
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Benjamin Dannenmann
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Masako M Kaufmann
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Patricia Arreba-Tutusaus
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Yun Xu
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Natalia Borbaran-Bravo
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Maksim Klimiankou
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Claudia Lengerke
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Cornelia Zeidler
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Karl Welte
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; Department of Pediatric Hematology, Oncology and Bone Marrow Transplantation, Children`s Hospital, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Julia Skokowa
- Department of Oncology, Hematology, Clinical Immunology, and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; Gene and RNA Therapy Center (GRTC), University Hospital Tübingen, 72076 Tübingen, Germany
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39
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Garaudé S, Marone R, Lepore R, Devaux A, Beerlage A, Seyres D, Dell' Aglio A, Juskevicius D, Zuin J, Burgold T, Wang S, Katta V, Manquen G, Li Y, Larrue C, Camus A, Durzynska I, Wellinger LC, Kirby I, Van Berkel PH, Kunz C, Tamburini J, Bertoni F, Widmer CC, Tsai SQ, Simonetta F, Urlinger S, Jeker LT. Selective haematological cancer eradication with preserved haematopoiesis. Nature 2024; 630:728-735. [PMID: 38778101 PMCID: PMC11186773 DOI: 10.1038/s41586-024-07456-3] [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: 08/07/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Haematopoietic stem cell (HSC) transplantation (HSCT) is the only curative treatment for a broad range of haematological malignancies, but the standard of care relies on untargeted chemotherapies and limited possibilities to treat malignant cells after HSCT without affecting the transplanted healthy cells1. Antigen-specific cell-depleting therapies hold the promise of much more targeted elimination of diseased cells, as witnessed in the past decade by the revolution of clinical practice for B cell malignancies2. However, target selection is complex and limited to antigens expressed on subsets of haematopoietic cells, resulting in a fragmented therapy landscape with high development costs2-5. Here we demonstrate that an antibody-drug conjugate (ADC) targeting the pan-haematopoietic marker CD45 enables the antigen-specific depletion of the entire haematopoietic system, including HSCs. Pairing this ADC with the transplantation of human HSCs engineered to be shielded from the CD45-targeting ADC enables the selective eradication of leukaemic cells with preserved haematopoiesis. The combination of CD45-targeting ADCs and engineered HSCs creates an almost universal strategy to replace a diseased haematopoietic system, irrespective of disease aetiology or originating cell type. We propose that this approach could have broad implications beyond haematological malignancies.
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Affiliation(s)
- Simon Garaudé
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Rosalba Lepore
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
- Cimeio Therapeutics, Basel, Switzerland
| | - Anna Devaux
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Astrid Beerlage
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
- Department of Hematology, Basel University Hospital, Basel, Switzerland
| | - Denis Seyres
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Alessandro Dell' Aglio
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Darius Juskevicius
- Department of Laboratory Medicine, Diagnostic Hematology, Basel University Hospital, Basel, Switzerland
| | - Jessica Zuin
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Thomas Burgold
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland
| | - Sisi Wang
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Varun Katta
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Garret Manquen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Clément Larrue
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
| | | | | | | | | | | | | | - Jérôme Tamburini
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Corinne C Widmer
- Department of Hematology, Basel University Hospital, Basel, Switzerland
- Department of Laboratory Medicine, Diagnostic Hematology, Basel University Hospital, Basel, Switzerland
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Federico Simonetta
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland.
- Transplantation Immunology & Nephrology, Basel University Hospital, Basel, Switzerland.
- Innovation Focus Cell Therapy, Basel University Hospital, Basel, Switzerland.
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Fiumara M, Ferrari S, Omer-Javed A, Beretta S, Albano L, Canarutto D, Varesi A, Gaddoni C, Brombin C, Cugnata F, Zonari E, Naldini MM, Barcella M, Gentner B, Merelli I, Naldini L. Genotoxic effects of base and prime editing in human hematopoietic stem cells. Nat Biotechnol 2024; 42:877-891. [PMID: 37679541 PMCID: PMC11180610 DOI: 10.1038/s41587-023-01915-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/26/2023] [Indexed: 09/09/2023]
Abstract
Base and prime editors (BEs and PEs) may provide more precise genetic engineering than nuclease-based approaches because they bypass the dependence on DNA double-strand breaks. However, little is known about their cellular responses and genotoxicity. Here, we compared state-of-the-art BEs and PEs and Cas9 in human hematopoietic stem and progenitor cells with respect to editing efficiency, cytotoxicity, transcriptomic changes and on-target and genome-wide genotoxicity. BEs and PEs induced detrimental transcriptional responses that reduced editing efficiency and hematopoietic repopulation in xenotransplants and also generated DNA double-strand breaks and genotoxic byproducts, including deletions and translocations, at a lower frequency than Cas9. These effects were strongest for cytidine BEs due to suboptimal inhibition of base excision repair and were mitigated by tailoring delivery timing and editor expression through optimized mRNA design. However, BEs altered the mutational landscape of hematopoietic stem and progenitor cells across the genome by increasing the load and relative proportions of nucleotide variants. These findings raise concerns about the genotoxicity of BEs and PEs and warrant further investigation in view of their clinical application.
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Affiliation(s)
- Martina Fiumara
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
| | - Attya Omer-Javed
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luisa Albano
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Canarutto
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelica Varesi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Gaddoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Brombin
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Cugnata
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Erika Zonari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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Berthault C, Gaucher S, Gouin O, Schmitt A, Chen M, Woodley D, Titeux M, Hovnanian A, Izmiryan A. Highly Efficient Ex Vivo Correction of COL7A1 through Ribonucleoprotein-Based CRISPR/Cas9 and Homology-Directed Repair to Treat Recessive Dystrophic Epidermolysis Bullosa. J Invest Dermatol 2024; 144:1322-1333.e13. [PMID: 38043638 DOI: 10.1016/j.jid.2023.10.035] [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: 03/23/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare and severe genetic skin disease responsible for blistering of the skin and mucosa after minor trauma. RDEB is caused by a wide variety of variants in COL7A1 encoding type VII Collagen, the major component of anchoring fibrils that form key attachment structures for dermal-epidermal adherence. In this study, we achieved highly efficient COL7A1 editing in primary RDEB keratinocytes and fibroblasts from 2 patients homozygous for the c.6508C>T (p.Gln2170∗) variant through CRISPR/Cas9-mediated homology-directed repair. Three guide RNAs targeting the c.6508C>T variant or harboring sequences were delivered together with high-fidelity Cas9 as a ribonucleoprotein complex. Among them, one achieved 73% cleavage activity in primary RDEB keratinocytes and RDEB fibroblasts. Then, we treated RDEB keratinocytes and RDEB fibroblasts with this specific ribonucleoprotein complex and the corresponding donor template delivered as single-stranded oligodeoxynucleotide and achieved up to 58% of genetic correction as well as type VII Collagen rescue. Finally, grafting of corrected 3-dimensional skin onto nude mice induced re-expression and normal localization of type VII Collagen as well as anchoring fibril formation at the dermal-epidermal junction 5 and 10 weeks after grafting. With this promising nonviral approach, we achieved therapeutically relevant specific gene editing that could be applicable to all variants in exon 80 of COL7A1 in primary RDEB cells.
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Affiliation(s)
- Camille Berthault
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Sonia Gaucher
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Olivier Gouin
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Alain Schmitt
- Electronic Microscopy Facility, INSERM UMR 1016, Cochin Institute, Paris, France
| | - Mei Chen
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - David Woodley
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Matthias Titeux
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France
| | - Alain Hovnanian
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France; Department of Genomic Medicine for Rare Diseases, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Araksya Izmiryan
- INSERM UMR 1163, Laboratory of Genetic skin diseases, Imagine Institute, Paris, France; Paris Cité University, Paris, France.
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Palaz F, Ozsoz M, Zarrinpar A, Sahin I. CRISPR in Targeted Therapy and Adoptive T Cell Immunotherapy for Hepatocellular Carcinoma. J Hepatocell Carcinoma 2024; 11:975-995. [PMID: 38832119 PMCID: PMC11146628 DOI: 10.2147/jhc.s456683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Despite recent therapeutic advancements, outcomes for advanced hepatocellular carcinoma (HCC) remain unsatisfactory, highlighting the need for novel treatments. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology offers innovative treatment approaches, involving genetic manipulation of either cancer cells or adoptive T cells to combat HCC. This review comprehensively assesses the applications of CRISPR systems in HCC treatment, focusing on in vivo targeting of cancer cells and the development of chimeric antigen receptor (CAR) T cells and T cell receptor (TCR)-engineered T cells. We explore potential synergies between CRISPR-based cancer therapeutics and existing treatment options, discussing ongoing clinical trials and the role of CRISPR technology in improving HCC treatment outcomes with advanced safety measures. In summary, this review provides insights into the promising prospects and current challenges of using CRISPR technology in HCC treatment, with the ultimate goal of improving patient outcomes and revolutionizing the landscape of HCC therapeutics.
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Affiliation(s)
- Fahreddin Palaz
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Mehmet Ozsoz
- Department of Biomedical Engineering, Near East University, Nicosia, Turkey
| | - Ali Zarrinpar
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Ilyas Sahin
- University of Florida Health Cancer Center, Gainesville, FL, USA
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, FL, USA
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Pavlovic K, Carmona-Luque MD, Corsi GI, Maldonado-Pérez N, Molina-Estevez FJ, Peralbo-Santaella E, Cortijo-Gutiérrez M, Justicia-Lirio P, Tristán-Manzano M, Ronco-Díaz V, Ballesteros-Ribelles A, Millán-López A, Heredia-Velázquez P, Fuster-García C, Cathomen T, Seemann SE, Gorodkin J, Martin F, Herrera C, Benabdellah K. Generating universal anti-CD19 CAR T cells with a defined memory phenotype by CRISPR/Cas9 editing and safety evaluation of the transcriptome. Front Immunol 2024; 15:1401683. [PMID: 38868778 PMCID: PMC11167079 DOI: 10.3389/fimmu.2024.1401683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024] Open
Abstract
Introduction Chimeric antigen receptor-expressing T cells (CAR T cells) have revolutionized cancer treatment, particularly in B cell malignancies. However, the use of autologous T cells for CAR T therapy presents several limitations, including high costs, variable efficacy, and adverse effects linked to cell phenotype. Methods To overcome these challenges, we developed a strategy to generate universal and safe anti-CD19 CAR T cells with a defined memory phenotype. Our approach utilizes CRISPR/Cas9 technology to target and eliminate the B2M and TRAC genes, reducing graft-versus-host and host-versus-graft responses. Additionally, we selected less differentiated T cells to improve the stability and persistence of the universal CAR T cells. The safety of this method was assessed using our CRISPRroots transcriptome analysis pipeline, which ensures successful gene knockout and the absence of unintended off-target effects on gene expression or transcriptome sequence. Results In vitro experiments demonstrated the successful generation of functional universal CAR T cells. These cells exhibited potent lytic activity against tumor cells and a reduced cytokine secretion profile. The CRISPRroots analysis confirmed effective gene knockout and no unintended off-target effects, validating it as a pioneering tool for on/off-target and transcriptome analysis in genome editing experiments. Discussion Our findings establish a robust pipeline for manufacturing safe, universal CAR T cells with a favorable memory phenotype. This approach has the potential to address the current limitations of autologous CAR T cell therapy, offering a more stable and persistent treatment option with reduced adverse effects. The use of CRISPRroots enhances the reliability and safety of gene editing in the development of CAR T cell therapies. Conclusion We have developed a potent and reliable method for producing universal CAR T cells with a defined memory phenotype, demonstrating both efficacy and safety in vitro. This innovative approach could significantly improve the therapeutic landscape for patients with B cell malignancies.
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Affiliation(s)
- Kristina Pavlovic
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
- Cell Therapy Group, Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cordoba, Spain
| | - MDolores Carmona-Luque
- Cell Therapy Group, Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cordoba, Spain
| | - Giulia I. Corsi
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Thorvaldsensvej, Denmark
| | - Noelia Maldonado-Pérez
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Francisco J. Molina-Estevez
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Esther Peralbo-Santaella
- Flow Cytometry Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, Spain
| | - Marina Cortijo-Gutiérrez
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Pedro Justicia-Lirio
- LentiStem Biotech, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - María Tristán-Manzano
- LentiStem Biotech, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Víctor Ronco-Díaz
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | | | - Alejandro Millán-López
- Cell Therapy Group, Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cordoba, Spain
| | - Paula Heredia-Velázquez
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Carla Fuster-García
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefan E. Seemann
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Thorvaldsensvej, Denmark
| | - Jan Gorodkin
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Thorvaldsensvej, Denmark
| | - Francisco Martin
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Granada, Spain
- Biosanitary Research Institute of Granada (ibs.GRANADA), University of Granada, Granada, Spain
| | - Concha Herrera
- Cell Therapy Group, Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), Cordoba, Spain
- Department of Hematology, Reina Sofia University Hospital, Cordoba, Spain
- Department of Medical and Surgical Sciences, School of Medicine, University of Cordoba, Cordoba, Spain
| | - Karim Benabdellah
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain
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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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Piñón Hofbauer J, Guttmann-Gruber C, Wally V, Sharma A, Gratz IK, Koller U. Challenges and progress related to gene editing in rare skin diseases. Adv Drug Deliv Rev 2024; 208:115294. [PMID: 38527624 DOI: 10.1016/j.addr.2024.115294] [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: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Genodermatoses represent a large group of inherited skin disorders encompassing clinically-heterogeneous conditions that manifest in the skin and other organs. Depending on disease variant, associated clinical manifestations and secondary complications can severely impact patients' quality of life and currently available treatments are transient and not curative. Multiple emerging approaches using CRISPR-based technologies offer promising prospects for therapy. Here, we explore current advances and challenges related to gene editing in rare skin diseases, including different strategies tailored to mutation type and structural organization of the affected gene, considerations for in vivo and ex vivo applications, the critical issue of delivery into the skin, and immune aspects of therapy. Against the backdrop of a landmark FDA approval for the first re-dosable gene replacement therapy for a rare genetic skin disorder, gene editing approaches are inching closer to the clinics and the possibility of a local permanent cure for patients affected by these disorders.
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Affiliation(s)
- Josefina Piñón Hofbauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Christina Guttmann-Gruber
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Anshu Sharma
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Iris K Gratz
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; Center for Tumor Biology and Immunology, University of Salzburg, 5020 Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria.
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Klermund J, Rhiel M, Kocher T, Chmielewski KO, Bischof J, Andrieux G, El Gaz M, Hainzl S, Boerries M, Cornu TI, Koller U, Cathomen T. On- and off-target effects of paired CRISPR-Cas nickase in primary human cells. Mol Ther 2024; 32:1298-1310. [PMID: 38459694 PMCID: PMC11081867 DOI: 10.1016/j.ymthe.2024.03.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/28/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
Undesired on- and off-target effects of CRISPR-Cas nucleases remain a challenge in genome editing. While the use of Cas9 nickases has been shown to minimize off-target mutagenesis, their use in therapeutic genome editing has been hampered by a lack of efficacy. To overcome this limitation, we and others have developed double-nickase-based strategies to generate staggered DNA double-strand breaks to mediate gene disruption or gene correction with high efficiency. However, the impact of paired single-strand nicks on genome integrity has remained largely unexplored. Here, we developed a novel CAST-seq pipeline, dual CAST, to characterize chromosomal aberrations induced by paired CRISPR-Cas9 nickases at three different loci in primary keratinocytes derived from patients with epidermolysis bullosa. While targeting COL7A1, COL17A1, or LAMA3 with Cas9 nucleases caused previously undescribed chromosomal rearrangements, no chromosomal translocations were detected following paired-nickase editing. While the double-nicking strategy induced large deletions/inversions within a 10 kb region surrounding the target sites at all three loci, similar to the nucleases, the chromosomal on-target aberrations were qualitatively different and included a high proportion of insertions. Taken together, our data indicate that double-nickase approaches combine efficient editing with greatly reduced off-target effects but still leave substantial chromosomal aberrations at on-target sites.
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Affiliation(s)
- Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Thomas Kocher
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Kay Ole Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany; PhD Program, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Melina El Gaz
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Stefan Hainzl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, 79110 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79106 Freiburg, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany.
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47
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Lo Presti V, Meringa A, Dunnebach E, van Velzen A, Moreira AV, Stam RW, Kotecha RS, Krippner-Heidenreich A, Heidenreich OT, Plantinga M, Cornel A, Sebestyen Z, Kuball J, van Til NP, Nierkens S. Combining CRISPR-Cas9 and TCR exchange to generate a safe and efficient cord blood-derived T cell product for pediatric relapsed AML. J Immunother Cancer 2024; 12:e008174. [PMID: 38580329 PMCID: PMC11002379 DOI: 10.1136/jitc-2023-008174] [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] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Hematopoietic cell transplantation (HCT) is an effective treatment for pediatric patients with high-risk, refractory, or relapsed acute myeloid leukemia (AML). However, a large proportion of transplanted patients eventually die due to relapse. To improve overall survival, we propose a combined strategy based on cord blood (CB)-HCT with the application of AML-specific T cell receptor (TCR)-engineered T cell therapy derived from the same CB graft. METHODS We produced CB-CD8+ T cells expressing a recombinant TCR (rTCR) against Wilms tumor 1 (WT1) while lacking endogenous TCR (eTCR) expression to avoid mispairing and competition. CRISPR-Cas9 multiplexing was used to target the constant region of the endogenous TCRα (TRAC) and TCRβ (TRBC) chains. Next, an optimized method for lentiviral transduction was used to introduce recombinant WT1-TCR. The cytotoxic and migration capacity of the product was evaluated in coculture assays for both cell lines and primary pediatric AML blasts. RESULTS The gene editing and transduction procedures achieved high efficiency, with up to 95% of cells lacking eTCR and over 70% of T cells expressing rWT1-TCR. WT1-TCR-engineered T cells lacking the expression of their eTCR (eTCR-/- WT1-TCR) showed increased cell surface expression of the rTCR and production of cytotoxic cytokines, such as granzyme A and B, perforin, interferon-γ (IFNγ), and tumor necrosis factor-α (TNFα), on antigen recognition when compared with WT1-TCR-engineered T cells still expressing their eTCR (eTCR+/+ WT1-TCR). CRISPR-Cas9 editing did not affect immunophenotypic characteristics or T cell activation and did not induce increased expression of inhibitory molecules. eTCR-/- WT1-TCR CD8+ CB-T cells showed effective migratory and killing capacity in cocultures with neoplastic cell lines and primary AML blasts, but did not show toxicity toward healthy cells. CONCLUSIONS In summary, we show the feasibility of developing a potent CB-derived CD8+ T cell product targeting WT1, providing an option for post-transplant allogeneic immune cell therapy or as an off-the-shelf product, to prevent relapse and improve the clinical outcome of children with AML.
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Affiliation(s)
- Vania Lo Presti
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Angelo Meringa
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ester Dunnebach
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Alice van Velzen
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Ronald W Stam
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Rishi S Kotecha
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, Western Australia, Australia
- University of Western Australia, Perth, Western Australia, Australia
| | | | | | - Maud Plantinga
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Annelisa Cornel
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Zsolt Sebestyen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jurgen Kuball
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Niek P van Til
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - S Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
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48
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Vaidyanathan S, Kerschner JL, Paranjapye A, Sinha V, Lin B, Bedrosian TA, Thrasher AJ, Turchiano G, Harris A, Porteus MH. Investigating adverse genomic and regulatory changes caused by replacement of the full-length CFTR cDNA using Cas9 and AAV. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102134. [PMID: 38384445 PMCID: PMC10879780 DOI: 10.1016/j.omtn.2024.102134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
A "universal strategy" replacing the full-length CFTR cDNA may treat >99% of people with cystic fibrosis (pwCF), regardless of their specific mutations. Cas9-based gene editing was used to insert the CFTR cDNA and a truncated CD19 (tCD19) enrichment tag at the CFTR locus in airway basal stem cells. This strategy restores CFTR function to non-CF levels. Here, we investigate the safety of this approach by assessing genomic and regulatory changes after CFTR cDNA insertion. Safety was first assessed by quantifying genetic rearrangements using CAST-seq. After validating restored CFTR function in edited and enriched airway cells, the CFTR locus open chromatin profile was characterized using ATAC-seq. The regenerative potential and differential gene expression in edited cells was assessed using scRNA-seq. CAST-seq revealed a translocation in ∼0.01% of alleles primarily occurring at a nononcogenic off-target site and large indels in 1% of alleles. The open chromatin profile of differentiated airway epithelial cells showed no appreciable changes, except in the region corresponding to the CFTR cDNA and tCD19 cassette, indicating no detectable changes in gene regulation. Edited stem cells produced the same types of airway cells as controls with minimal alternations in gene expression. Overall, the universal strategy showed minor undesirable genomic changes.
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Affiliation(s)
- Sriram Vaidyanathan
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny L. Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vrishti Sinha
- Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Brian Lin
- Department of Developmental, Molecular, and Chemical Biology, Tufts University, Boston, MA 02111, USA
| | - Tracy A. Bedrosian
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Adrian J. Thrasher
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Giandomenico Turchiano
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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49
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Waldo JJ, Halmai JANM, Fink KD. Epigenetic editing for autosomal dominant neurological disorders. Front Genome Ed 2024; 6:1304110. [PMID: 38510848 PMCID: PMC10950933 DOI: 10.3389/fgeed.2024.1304110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
Epigenetics refers to the molecules and mechanisms that modify gene expression states without changing the nucleotide context. These modifications are what encode the cell state during differentiation or epigenetic memory in mitosis. Epigenetic modifications can alter gene expression by changing the chromatin architecture by altering the affinity for DNA to wrap around histone octamers, forming nucleosomes. The higher affinity the DNA has for the histones, the tighter it will wrap and therefore induce a heterochromatin state, silencing gene expression. Several groups have shown the ability to harness the cell's natural epigenetic modification pathways to engineer proteins that can induce changes in epigenetics and consequently regulate gene expression. Therefore, epigenetic modification can be used to target and treat disorders through the modification of endogenous gene expression. The use of epigenetic modifications may prove an effective path towards regulating gene expression to potentially correct or cure genetic disorders.
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Affiliation(s)
| | | | - Kyle D. Fink
- Neurology Department, Stem Cell Program and Gene Therapy Center, MIND Institute, UC Davis Health System, Sacramento, CA, United States
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50
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Cappelluti MA, Mollica Poeta V, Valsoni S, Quarato P, Merlin S, Merelli I, Lombardo A. Durable and efficient gene silencing in vivo by hit-and-run epigenome editing. Nature 2024; 627:416-423. [PMID: 38418872 PMCID: PMC10937395 DOI: 10.1038/s41586-024-07087-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
Permanent epigenetic silencing using programmable editors equipped with transcriptional repressors holds great promise for the treatment of human diseases1-3. However, to unlock its full therapeutic potential, an experimental confirmation of durable epigenetic silencing after the delivery of transient delivery of editors in vivo is needed. To this end, here we targeted Pcsk9, a gene expressed in hepatocytes that is involved in cholesterol homeostasis. In vitro screening of different editor designs indicated that zinc-finger proteins were the best-performing DNA-binding platform for efficient silencing of mouse Pcsk9. A single administration of lipid nanoparticles loaded with the editors' mRNAs almost halved the circulating levels of PCSK9 for nearly one year in mice. Notably, Pcsk9 silencing and accompanying epigenetic repressive marks also persisted after forced liver regeneration, further corroborating the heritability of the newly installed epigenetic state. Improvements in construct design resulted in the development of an all-in-one configuration that we term evolved engineered transcriptional repressor (EvoETR). This design, which is characterized by a high specificity profile, further reduced the circulating levels of PCSK9 in mice with an efficiency comparable with that obtained through conventional gene editing, but without causing DNA breaks. Our study lays the foundation for the development of in vivo therapeutics that are based on epigenetic silencing.
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Affiliation(s)
| | - Valeria Mollica Poeta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Valsoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Piergiuseppe Quarato
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simone Merlin
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - Angelo Lombardo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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