1
|
Kulhankova K, Traore S, Cheng X, Benk-Fortin H, Hallée S, Harvey M, Roberge J, Couture F, Kohli S, Gross TJ, Meyerholz DK, Rettig GR, Thommandru B, Kurgan G, Wohlford-Lenane C, Hartigan-O'Connor DJ, Yates BP, Newby GA, Liu DR, Tarantal AF, Guay D, McCray PB. Shuttle peptide delivers base editor RNPs to rhesus monkey airway epithelial cells in vivo. Nat Commun 2023; 14:8051. [PMID: 38052872 PMCID: PMC10698009 DOI: 10.1038/s41467-023-43904-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: 02/01/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Gene editing strategies for cystic fibrosis are challenged by the complex barrier properties of airway epithelia. We previously reported that the amphiphilic S10 shuttle peptide non-covalently combined with CRISPR-associated (Cas) ribonucleoprotein (RNP) enabled editing of human and mouse airway epithelial cells. Here, we derive the S315 peptide as an improvement over S10 in delivering base editor RNP. Following intratracheal aerosol delivery of Cy5-labeled peptide in rhesus macaques, we confirm delivery throughout the respiratory tract. Subsequently, we target CCR5 with co-administration of ABE8e-Cas9 RNP and S315. We achieve editing efficiencies of up-to 5.3% in rhesus airway epithelia. Moreover, we document persistence of edited epithelia for up to 12 months in mice. Finally, delivery of ABE8e-Cas9 targeting the CFTR R553X mutation restores anion channel function in cultured human airway epithelia. These results demonstrate the therapeutic potential of base editor delivery with S315 to functionally correct the CFTR R553X mutation in respiratory epithelia.
Collapse
Affiliation(s)
| | - Soumba Traore
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | | | | | | | | | | | | | - Sajeev Kohli
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Thomas J Gross
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | | | | | | | - Gavin Kurgan
- Integrated DNA Technologies, Coralville, IA, USA
| | | | - Dennis J Hartigan-O'Connor
- Department of Medical Microbiology and Immunology, School of Medicine, UC Davis, Davis, CA, USA
- California National Primate Research Center, UC Davis, Davis, CA, USA
| | - Bradley P Yates
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Alice F Tarantal
- California National Primate Research Center, UC Davis, Davis, CA, USA
- Department of Pediatrics, School of Medicine, UC Davis, Davis, CA, USA
- Department of Cell Biology and Human Anatomy, School of Medicine, UC Davis, Davis, CA, USA
| | | | - Paul B McCray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
2
|
Wu X, Srinivasan P, Basu M, Zhang P, Saruwatari M, Thommandru B, Jacobi A, Behlke M, Sandler A. Tumor Apolipoprotein E is a key checkpoint blocking anti-tumor immunity in mouse melanoma. Front Immunol 2022; 13:991790. [PMID: 36341364 PMCID: PMC9626815 DOI: 10.3389/fimmu.2022.991790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Immunotherapy is a key modality in the treatment of cancer, but many tumors remain immune resistant. The classic mouse model of B16-F10 melanoma is immune resistant even in the face of checkpoint inhibition. Apolipoprotein E (apoE), a known immune suppressant is strikingly elevated in many human tumors, but its role in cancer immunology is not defined. We investigated the role of apoE in the immune micro-environment using a mouse melanoma model. We demonstrate that ApoE is -highly expressed in wild-type B16-F10 melanoma and serum levels progressively increase as tumors grow. The conditioned media from wild type ApoE secreting melanoma cells suppress T-cell activation in vitro while this suppressive effect is absent in conditioned media from ApoE knock out tumor cells. Mechanistically, apoE induces IL-10 secreting dendritic cells and stimulates T-cell apoptosis and arrest partially via the lrp8 receptor. Ablating ApoE in mice inoculated with tumor cells enabled tumor cell rejection and was associated with induction of immune pathway activation and immune cell infiltration. Tumor secreted apoE appears to be a potent immune cell checkpoint and targeting apoE is associated with enhanced tumor immunity in the mouse melanoma model.
Collapse
Affiliation(s)
- Xiaofang Wu
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | - Priya Srinivasan
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | - Mousumi Basu
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | - Peng Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Michele Saruwatari
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
| | | | - Ashley Jacobi
- Integrated DNA Technologies, Inc., Coralville, IA, United States
| | - Mark Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, United States
| | - Anthony Sandler
- The Joseph E. Robert Jr. Center for Surgical Care and The Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, George Washington University, Washington, DC, United States
- *Correspondence: Anthony Sandler,
| |
Collapse
|
3
|
Kath J, Du W, Pruene A, Braun T, Thommandru B, Turk R, Sturgeon ML, Kurgan GL, Amini L, Stein M, Zittel T, Martini S, Ostendorf L, Wilhelm A, Akyüz L, Rehm A, Höpken UE, Pruß A, Künkele A, Jacobi AM, Volk HD, Schmueck-Henneresse M, Stripecke R, Reinke P, Wagner DL. Pharmacological interventions enhance virus-free generation of TRAC-replaced CAR T cells. Mol Ther Methods Clin Dev 2022; 25:311-330. [PMID: 35573047 PMCID: PMC9062427 DOI: 10.1016/j.omtm.2022.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/29/2022] [Indexed: 12/30/2022]
Abstract
Chimeric antigen receptor (CAR) redirected T cells are potent therapeutic options against hematological malignancies. The current dominant manufacturing approach for CAR T cells depends on retroviral transduction. With the advent of gene editing, insertion of a CD19-CAR into the T cell receptor (TCR) alpha constant (TRAC) locus using adeno-associated viruses for gene transfer was demonstrated, and these CD19-CAR T cells showed improved functionality over their retrovirally transduced counterparts. However, clinical-grade production of viruses is complex and associated with extensive costs. Here, we optimized a virus-free genome-editing method for efficient CAR insertion into the TRAC locus of primary human T cells via nuclease-assisted homology-directed repair (HDR) using CRISPR-Cas and double-stranded template DNA (dsDNA). We evaluated DNA-sensor inhibition and HDR enhancement as two pharmacological interventions to improve cell viability and relative CAR knockin rates, respectively. While the toxicity of transfected dsDNA was not fully prevented, the combination of both interventions significantly increased CAR knockin rates and CAR T cell yield. Resulting TRAC-replaced CD19-CAR T cells showed antigen-specific cytotoxicity and cytokine production in vitro and slowed leukemia progression in a xenograft mouse model. Amplicon sequencing did not reveal significant indel formation at potential off-target sites with or without exposure to DNA-repair-modulating small molecules. With TRAC-integrated CAR+ T cell frequencies exceeding 50%, this study opens new perspectives to exploit pharmacological interventions to improve non-viral gene editing in T cells.
Collapse
Affiliation(s)
- Jonas Kath
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 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), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Weijie Du
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 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), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Alina Pruene
- Regenerative Immune Therapies Applied, Clinics of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Region, Germany
| | - Tobias Braun
- Regenerative Immune Therapies Applied, Clinics of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Region, Germany
| | | | - Rolf Turk
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | | | - Gavin L. Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Leila Amini
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 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), Augustenburger Platz 1, 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), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tatiana Zittel
- 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), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefania Martini
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Lennard Ostendorf
- Department of Nephrology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), A Leibniz Institute, Berlin, Germany
| | | | | | - Armin Rehm
- Department of Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Uta E. Höpken
- Department of Microenvironmental Regulation in Autoimmunity and Cancer, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Axel Pruß
- 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
| | - 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 (BIH), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), 10117 Berlin, Germany
| | | | - Hans-Dieter Volk
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 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), Augustenburger Platz 1, 13353 Berlin, Germany
- Institute of Medical Immunology, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Michael Schmueck-Henneresse
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 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), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Renata Stripecke
- Regenerative Immune Therapies Applied, Clinics of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig Region, Germany
- Clinic I for Internal Medicine, Cancer Center Cologne Essen, University Hospital Cologne, Cologne, Germany
| | - Petra Reinke
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 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), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dimitrios L. Wagner
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 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), 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
- Institute of Medical Immunology, Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany
- Corresponding author Dimitrios Laurin Wagner, MD, PhD, Berlin Center for Advanced Therapies (BeCAT) BIH Center for Regenerative Therapies (BCRT) Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353 Berlin, Germany.
| |
Collapse
|
5
|
Schubert MS, Thommandru B, Woodley J, Turk R, Yan S, Kurgan G, McNeill MS, Rettig GR. Optimized design parameters for CRISPR Cas9 and Cas12a homology-directed repair. Sci Rep 2021; 11:19482. [PMID: 34593942 PMCID: PMC8484621 DOI: 10.1038/s41598-021-98965-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas proteins are RNA-guided nucleases used to introduce double-stranded breaks (DSBs) at targeted genomic loci. DSBs are repaired by endogenous cellular pathways such as non-homologous end joining (NHEJ) and homology-directed repair (HDR). Providing an exogenous DNA template during repair allows for the intentional, precise incorporation of a desired mutation via the HDR pathway. However, rates of repair by HDR are often slow compared to the more rapid but less accurate NHEJ-mediated repair. Here, we describe comprehensive design considerations and optimized methods for highly efficient HDR using single-stranded oligodeoxynucleotide (ssODN) donor templates for several CRISPR-Cas systems including S.p. Cas9, S.p. Cas9 D10A nickase, and A.s. Cas12a delivered as ribonucleoprotein (RNP) complexes. Features relating to guide RNA selection, donor strand preference, and incorporation of blocking mutations in the donor template to prevent re-cleavage were investigated and were implemented in a novel online tool for HDR donor template design. These findings allow for high frequencies of precise repair utilizing HDR in multiple mammalian cell lines. Tool availability: https://www.idtdna.com/HDR.
Collapse
Affiliation(s)
- Mollie S Schubert
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Bernice Thommandru
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Jessica Woodley
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Shuqi Yan
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gavin Kurgan
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Matthew S McNeill
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Garrett R Rettig
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
| |
Collapse
|