1
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Hammad R, Alzubi J, Rhiel M, Chmielewski KO, Mosti L, Rositzka J, Heugel M, Lawrenz J, Pennucci V, Gläser B, Fischer J, Schambach A, Moritz T, Lachmann N, Cornu TI, Mussolino C, Schäfer R, Cathomen T. CRISPR-Cas12a for Highly Efficient and Marker-Free Targeted Integration in Human Pluripotent Stem Cells. Int J Mol Sci 2024; 25:985. [PMID: 38256061 PMCID: PMC10816062 DOI: 10.3390/ijms25020985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The CRISPR-Cas12a platform has attracted interest in the genome editing community because the prototypical Acidaminococcus Cas12a generates a staggered DNA double-strand break upon binding to an AT-rich protospacer-adjacent motif (PAM, 5'-TTTV). The broad application of the platform in primary human cells was enabled by the development of an engineered version of the natural Cas12a protein, called Cas12a Ultra. In this study, we confirmed that CRISPR-Cas12a Ultra ribonucleoprotein complexes enabled allelic gene disruption frequencies of over 90% at multiple target sites in human T cells, hematopoietic stem and progenitor cells (HSPCs), and induced pluripotent stem cells (iPSCs). In addition, we demonstrated, for the first time, the efficient knock-in potential of the platform in human iPSCs and achieved targeted integration of a GFP marker gene into the AAVS1 safe harbor site and a CSF2RA super-exon into CSF2RA in up to 90% of alleles without selection. Clonal analysis revealed bi-allelic integration in >50% of the screened iPSC clones without compromising their pluripotency and genomic integrity. Thus, in combination with the adeno-associated virus vector system, CRISPR-Cas12a Ultra provides a highly efficient genome editing platform for performing targeted knock-ins in human iPSCs.
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Affiliation(s)
- Ruba Hammad
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Freiburg iPS Core Facility, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- PhD Program, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jamal Alzubi
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- 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; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Kay O. Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- PhD Program, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Laura Mosti
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Julia Rositzka
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Marcel Heugel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Jan Lawrenz
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Valentina Pennucci
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Birgitta Gläser
- Institute of Human Genetics, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (B.G.); (J.F.)
| | - Judith Fischer
- Institute of Human Genetics, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (B.G.); (J.F.)
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Axel Schambach
- Institute for Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (A.S.); (T.M.)
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
| | - Thomas Moritz
- Institute for Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (A.S.); (T.M.)
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
| | - Nico Lachmann
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
- Department of Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 30625 Hannover, Germany
| | - Tatjana I. Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Richard Schäfer
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Freiburg iPS Core Facility, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
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2
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Baik R, Cromer MK, Glenn SE, Vakulskas CA, Chmielewski KO, Dudek AM, Feist WN, Klermund J, Shipp S, Cathomen T, Dever DP, Porteus MH. Transient inhibition of 53BP1 increases the frequency of targeted integration in human hematopoietic stem and progenitor cells. Nat Commun 2024; 15:111. [PMID: 38169468 PMCID: PMC10762240 DOI: 10.1038/s41467-023-43413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named "i53") as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.
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Affiliation(s)
- Ron Baik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steve E Glenn
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Amanda M Dudek
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - William N Feist
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Suzette Shipp
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel P Dever
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Torella L, Klermund J, Bilbao-Arribas M, Tamayo I, Andrieux G, Chmielewski KO, Vales A, Olagüe C, Moreno-Luqui D, Raimondi I, Abad A, Torrens-Baile J, Salido E, Huarte M, Hernaez M, Boerries M, Cathomen T, Zabaleta N, Gonzalez-Aseguinolaza G. Efficient and safe therapeutic use of paired Cas9-nickases for primary hyperoxaluria type 1. EMBO Mol Med 2024; 16:112-131. [PMID: 38182795 PMCID: PMC10897483 DOI: 10.1038/s44321-023-00008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/07/2024] Open
Abstract
The therapeutic use of adeno-associated viral vector (AAV)-mediated gene disruption using CRISPR-Cas9 is limited by potential off-target modifications and the risk of uncontrolled integration of vector genomes into CRISPR-mediated double-strand breaks. To address these concerns, we explored the use of AAV-delivered paired Staphylococcus aureus nickases (D10ASaCas9) to target the Hao1 gene for the treatment of primary hyperoxaluria type 1 (PH1). Our study demonstrated effective Hao1 gene disruption, a significant decrease in glycolate oxidase expression, and a therapeutic effect in PH1 mice. The assessment of undesired genetic modifications through CIRCLE-seq and CAST-Seq analyses revealed neither off-target activity nor chromosomal translocations. Importantly, the use of paired-D10ASaCas9 resulted in a significant reduction in AAV integration at the target site compared to SaCas9 nuclease. In addition, our study highlights the limitations of current analytical tools in characterizing modifications introduced by paired D10ASaCas9, necessitating the development of a custom pipeline for more accurate characterization. These results describe a positive advance towards a safe and effective potential long-term treatment for PH1 patients.
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Affiliation(s)
- Laura Torella
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - 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
| | - Martin Bilbao-Arribas
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
- IdISNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Ibon Tamayo
- IdISNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
- Bioinformatics Core, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, 79110, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Kay O 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
| | - Africa Vales
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Cristina Olagüe
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Daniel Moreno-Luqui
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Ivan Raimondi
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Amaya Abad
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Julen Torrens-Baile
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Universidad La Laguna, CIBERER, 38320, Tenerife, Spain
| | - Maite Huarte
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Mikel Hernaez
- IdISNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
- Bioinformatics Core, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, 79110, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106, Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, 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.
| | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Harvard Medical School, 02114, Boston, MA, USA.
| | - Gloria Gonzalez-Aseguinolaza
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain.
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4
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Carusillo A, Haider S, Schäfer R, Rhiel M, Türk D, Chmielewski KO, Klermund J, Mosti L, Andrieux G, Schäfer R, Cornu TI, Cathomen T, Mussolino C. A novel Cas9 fusion protein promotes targeted genome editing with reduced mutational burden in primary human cells. Nucleic Acids Res 2023; 51:4660-4673. [PMID: 37070192 DOI: 10.1093/nar/gkad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
Precise genome editing requires the resolution of nuclease-induced DNA double strand breaks (DSBs) via the homology-directed repair (HDR) pathway. In mammals, this is typically outcompeted by non-homologous end-joining (NHEJ) that can generate potentially genotoxic insertion/deletion mutations at DSB sites. Because of higher efficacy, clinical genome editing has been restricted to imperfect but efficient NHEJ-based approaches. Hence, strategies that promote DSB resolution via HDR are essential to facilitate clinical transition of HDR-based editing strategies and increase safety. Here we describe a novel platform that consists of a Cas9 fused to DNA repair factors to synergistically inhibit NHEJ and favor HDR for precise repairing of Cas-induced DSBs. Compared to canonical CRISPR/Cas9, the increase in error-free editing ranges from 1.5-fold to 7-fold in multiple cell lines and in primary human cells. This novel CRISPR/Cas9 platform accepts clinically relevant repair templates, such as oligodeoxynucleotides (ODNs) and adeno-associated virus (AAV)-based vectors, and has a lower propensity to induce chromosomal translocations as compared to benchmark CRISPR/Cas9. The observed reduced mutational burden, resulting from diminished indel formation at on- and off-target sites, provides a remarkable gain in safety and advocates this novel CRISPR system as an attractive tool for therapeutic applications depending on precision genome editing.
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Affiliation(s)
- Antonio Carusillo
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, Freiburg 79106, Germany
| | - Sibtain Haider
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, Freiburg 79106, Germany
| | - Raul Schäfer
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
| | - Daniel Türk
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
| | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, Freiburg 79106, Germany
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
| | - Laura Mosti
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Faculty of Medicine, University of Freiburg, 79106, Germany
| | - Richard Schäfer
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
- Institute for Transfusion Medicine and Immunohaematology, German Red Cross Blood Donor Service Baden-Württemberg-Hessen gGmbH, Goethe University Hospital, Frankfurt am Main, 60596, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
- Faculty of Medicine, University of Freiburg, 79106, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
- Faculty of Medicine, University of Freiburg, 79106, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg 79106, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Freiburg 79106, Germany
- Faculty of Medicine, University of Freiburg, 79106, Germany
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5
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Houghton BC, Panchal N, Haas SA, Chmielewski KO, Hildenbeutel M, Whittaker T, Mussolino C, Cathomen T, Thrasher AJ, Booth C. Genome Editing With TALEN, CRISPR-Cas9 and CRISPR-Cas12a in Combination With AAV6 Homology Donor Restores T Cell Function for XLP. Front Genome Ed 2022; 4:828489. [PMID: 35677600 PMCID: PMC9168036 DOI: 10.3389/fgeed.2022.828489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
X-linked lymphoproliferative disease is a rare inherited immune disorder, caused by mutations or deletions in the SH2D1A gene that encodes an intracellular adapter protein SAP (Slam-associated protein). SAP is essential for mediating several key immune processes and the immune system - T cells in particular - are dysregulated in its absence. Patients present with a spectrum of clinical manifestations, including haemophagocytic lymphohistiocytosis (HLH), dysgammaglobulinemia, lymphoma and autoimmunity. Treatment options are limited, and patients rarely survive to adulthood without an allogeneic haematopoietic stem cell transplant (HSCT). However, this procedure can have poor outcomes in the mismatched donor setting or in the presence of active HLH, leaving an unmet clinical need. Autologous haematopoeitic stem cell or T cell therapy may offer alternative treatment options, removing the need to find a suitable donor for HSCT and any risk of alloreactivity. SAP has a tightly controlled expression profile that a conventional lentiviral gene delivery platform may not be able to fully replicate. A gene editing approach could preserve more of the endogenous regulatory elements that govern SAP expression, potentially providing a more optimum therapy. Here, we assessed the ability of TALEN, CRISPR-Cas9 and CRISPR-Cas12a nucleases to drive targeted insertion of SAP cDNA at the first exon of the SH2D1A locus using an adeno-associated virus serotype 6 (AAV6)-based vector containing the donor template. All nuclease platforms were capable of high efficiency gene editing, which was optimised using a serum-free AAV6 transduction protocol. We show that T cells from XLP patients corrected by gene editing tools have restored physiological levels of SAP gene expression and restore SAP-dependent immune functions, indicating a new therapeutic opportunity for XLP patients.
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Affiliation(s)
- Benjamin C. Houghton
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Neelam Panchal
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Simone A. Haas
- 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
| | - Kay O. Chmielewski
- 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
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Markus Hildenbeutel
- 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
| | - Thomas Whittaker
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Claudio Mussolino
- 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
| | - 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
| | - Adrian J Thrasher
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Claire Booth
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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Mosti L, Langner LM, Chmielewski KO, Arbuthnot P, Alzubi J, Cathomen T. Targeted multi-epitope switching enables straightforward positive/negative selection of CAR T cells. Gene Ther 2021; 28:602-612. [PMID: 33526841 PMCID: PMC8455323 DOI: 10.1038/s41434-021-00220-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/11/2020] [Accepted: 01/15/2021] [Indexed: 12/27/2022]
Abstract
Chimeric antigen receptor (CAR) T cell technology has enabled successfully novel concepts to treat cancer patients, with substantial remission rates in lymphoid malignancies. This cell therapy is based on autologous T lymphocytes that are genetically modified to express a CAR that recognizes tumor-associated antigens and mediates the elimination of the respective tumor cells. Current limitations include laborious manufacturing procedures as well as severe immunological side effects upon administration of CAR T cells. To address these limitations, we integrated RQR8, a multi-epitope molecule harboring a CD34 epitope and two CD20 mimotopes, alongside a CD19-targeting CAR, into the CD52 locus. Using CRISPR-Cas9 and adeno-associated virus-based donor vectors, some 60% of genome-edited T cells were CAR+/CD20+/CD34+/CD52− without further selection. This could be increased to >95% purity after CD34 tag-based positive selection. These epitope-switched CAR T cells retained cell killing competence against CD19+ tumor cells, and were resistant to alemtuzumab (anti-CD52) but sensitive to rituximab (anti-CD20) in complement-dependent cytotoxicity assays. In conclusion, gene editing-based multiple epitope switching represents a promising development with the potential to improve both the manufacturing procedure as well as the clinical safety of CAR T cells.
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Affiliation(s)
- Laura Mosti
- 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.,Ph.D. Program, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lukas M Langner
- 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.,M.D. Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kay O 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.,Ph.D. Program, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jamal Alzubi
- 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
| | - 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.
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