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Chen D, Zhao C, Zhang J, Knol CWJ, Osipyan A, Majerníková N, Chen T, Xiao Z, Adriana J, Griffith AJ, Gamez AS, van der Wouden PE, Coppes RP, Dolga AM, Haisma HJ, Dekker FJ. Small Molecule MIF Modulation Enhances Ferroptosis by Impairing DNA Repair Mechanisms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403963. [PMID: 38924362 DOI: 10.1002/advs.202403963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Ferroptosis is a form of regulated cell death that can be modulated by small molecules and has the potential for the development of therapeutics for oncology. Although excessive lipid peroxidation is the defining hallmark of ferroptosis, DNA damage may also play a significant role. In this study, a potential mechanistic role for MIF in homologous recombination (HR) DNA repair is identified. The inhibition or genetic depletion of MIF or other HR proteins, such as breast cancer type 1 susceptibility protein (BRCA1), is demonstrated to significantly enhance the sensitivity of cells to ferroptosis. The interference with HR results in the translocation of the tumor suppressor protein p53 to the mitochondria, which in turn stimulates the production of reactive oxygen species. Taken together, the findings demonstrate that MIF-directed small molecules enhance ferroptosis via a putative MIF-BRCA1-RAD51 axis in HR, which causes resistance to ferroptosis. This suggests a potential novel druggable route to enhance ferroptosis by targeted anticancer therapeutics in the future.
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Affiliation(s)
- Deng Chen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Chunlong Zhao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Jianqiu Zhang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Catharina W J Knol
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Angelina Osipyan
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Nad'a Majerníková
- Research School of Behavioural and Cognitive Neuroscience, University of Groningen, Groningen, 9713 AV, The Netherlands
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, 9713 GZ, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Tingting Chen
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Zhangping Xiao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Jeaunice Adriana
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Andrew J Griffith
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Abel Soto Gamez
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, 9712 CP, The Netherlands
- Department of Radiation Oncology, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
| | - Petra E van der Wouden
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Robert P Coppes
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, 9712 CP, The Netherlands
- Department of Radiation Oncology, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
| | - Amalia M Dolga
- Research School of Behavioural and Cognitive Neuroscience, University of Groningen, Groningen, 9713 AV, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Hidde J Haisma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
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2
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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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3
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Seclen E, Jang JC, Lawal AO, Pulicani S, Boyne A, Tkach D, Juillerat A, Duchateau P, Valton J. TALEN-mediated intron editing of HSPCs enables transgene expression restricted to the myeloid lineage. Mol Ther 2024; 32:1643-1657. [PMID: 38582963 PMCID: PMC11184328 DOI: 10.1016/j.ymthe.2024.04.001] [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: 09/26/2023] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
Gene therapy in hematopoietic stem and progenitor cells (HSPCs) shows great potential for the treatment of inborn metabolic diseases. Typical HSPC gene therapy approaches rely on constitutive promoters to express a therapeutic transgene, which is associated with multiple disadvantages. Here, we propose a novel promoterless intronic gene editing approach that triggers transgene expression only after cellular differentiation into the myeloid lineage. We integrated a splicing-competent eGFP cassette into the first intron of CD11b and observed expression of eGFP in the myeloid lineage but minimal to no expression in HSPCs or differentiated non-myeloid lineages. In vivo, edited HSPCs successfully engrafted in immunodeficient mice and displayed transgene expression in the myeloid compartment of multiple tissues. Using the same approach, we expressed alpha-L-iduronidase (IDUA), the defective enzyme in Mucopolysaccharidosis type I, and observed a 10-fold supraendogenous IDUA expression exclusively after myeloid differentiation. Edited cells efficiently populated bone marrow, blood, and spleen of immunodeficient mice, and retained the capacity to secrete IDUA ex vivo. Importantly, cells edited with the eGFP and IDUA transgenes were also found in the brain. This approach may unlock new therapeutic strategies for inborn metabolic and neurological diseases that require the delivery of therapeutics in brain.
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Shi H, Li L, Mu S, Gou S, Liu X, Chen F, Chen M, Jin Q, Lai L, Wang K. Exonuclease editor promotes precision of gene editing in mammalian cells. BMC Biol 2024; 22:119. [PMID: 38769511 PMCID: PMC11107001 DOI: 10.1186/s12915-024-01918-w] [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: 04/28/2023] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Many efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing byproducts, which proved to be challenging. RESULTS Here, we have developed a human exonuclease 1-based genome-editing tool, referred to as exonuclease editor. When compared to Cas9, the exonuclease editor gave rise to increased HDR efficiency, reduced NHEJ repair frequency, and significantly elevated HDR/indel ratio. Robust gene editing precision of exonuclease editor was even superior to the fusion of Cas9 with E1B or DN1S, two previously reported precision-enhancing domains. Notably, exonuclease editor inhibited NHEJ at double strand breaks locally rather than globally, reducing indel frequency without compromising genome integrity. The replacement of Cas9 with single-strand DNA break-creating Cas9 nickase further increased the HDR/indel ratio by 453-fold than the original Cas9. In addition, exonuclease editor resulted in high microhomology-mediated end joining efficiency, allowing accurate and flexible deletion of targeted sequences with extended lengths with the aid of paired sgRNAs. Exonuclease editor was further used for correction of DMD patient-derived induced pluripotent stem cells, where 30.0% of colonies were repaired by HDR versus 11.1% in the control. CONCLUSIONS Therefore, the exonuclease editor system provides a versatile and safe genome editing tool with high precision and holds promise for therapeutic gene correction.
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Affiliation(s)
- Hui Shi
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Lei Li
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangshuang Mu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shixue Gou
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Xiaoyi Liu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Menglong Chen
- Department of Neurology and Stroke Centre, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qin Jin
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
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5
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Selvaraj S, Feist WN, Viel S, Vaidyanathan S, Dudek AM, Gastou M, Rockwood SJ, Ekman FK, Oseghale AR, Xu L, Pavel-Dinu M, Luna SE, Cromer MK, Sayana R, Gomez-Ospina N, Porteus MH. High-efficiency transgene integration by homology-directed repair in human primary cells using DNA-PKcs inhibition. Nat Biotechnol 2024; 42:731-744. [PMID: 37537500 DOI: 10.1038/s41587-023-01888-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Therapeutic applications of nuclease-based genome editing would benefit from improved methods for transgene integration via homology-directed repair (HDR). To improve HDR efficiency, we screened six small-molecule inhibitors of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key protein in the alternative repair pathway of non-homologous end joining (NHEJ), which generates genomic insertions/deletions (INDELs). From this screen, we identified AZD7648 as the most potent compound. The use of AZD7648 significantly increased HDR (up to 50-fold) and concomitantly decreased INDELs across different genomic loci in various therapeutically relevant primary human cell types. In all cases, the ratio of HDR to INDELs markedly increased, and, in certain situations, INDEL-free high-frequency (>50%) targeted integration was achieved. This approach has the potential to improve the therapeutic efficacy of cell-based therapies and broaden the use of targeted integration as a research tool.
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Affiliation(s)
- Sridhar Selvaraj
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - William N Feist
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sebastien Viel
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Immunology Department, Lyon Sud University Hospital, Pierre-Bénite, France
- International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Sriram Vaidyanathan
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Marc Gastou
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sarah J Rockwood
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Freja K Ekman
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Aluya R Oseghale
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Liwen Xu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ruhi Sayana
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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6
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Pavel-Dinu M, Gardner CL, Nakauchi Y, Kawai T, Delmonte OM, Palterer B, Bosticardo M, Pala F, Viel S, Malech HL, Ghanim HY, Bode NM, Kurgan GL, Detweiler AM, Vakulskas CA, Neff NF, Sheikali A, Menezes ST, Chrobok J, Hernández González EM, Majeti R, Notarangelo LD, Porteus MH. Genetically corrected RAG2-SCID human hematopoietic stem cells restore V(D)J-recombinase and rescue lymphoid deficiency. Blood Adv 2024; 8:1820-1833. [PMID: 38096800 PMCID: PMC11006817 DOI: 10.1182/bloodadvances.2023011766] [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: 09/24/2023] [Accepted: 10/23/2023] [Indexed: 04/10/2024] Open
Abstract
ABSTRACT Recombination-activating genes (RAG1 and RAG2) are critical for lymphoid cell development and function by initiating the variable (V), diversity (D), and joining (J) (V(D)J)-recombination process to generate polyclonal lymphocytes with broad antigen specificity. The clinical manifestations of defective RAG1/2 genes range from immune dysregulation to severe combined immunodeficiencies (SCIDs), causing life-threatening infections and death early in life without hematopoietic cell transplantation (HCT). Despite improvements, haploidentical HCT without myeloablative conditioning carries a high risk of graft failure and incomplete immune reconstitution. The RAG complex is only expressed during the G0-G1 phase of the cell cycle in the early stages of T- and B-cell development, underscoring that a direct gene correction might capture the precise temporal expression of the endogenous gene. Here, we report a feasibility study using the CRISPR/Cas9-based "universal gene-correction" approach for the RAG2 locus in human hematopoietic stem/progenitor cells (HSPCs) from healthy donors and RAG2-SCID patient. V(D)J-recombinase activity was restored after gene correction of RAG2-SCID-derived HSPCs, resulting in the development of T-cell receptor (TCR) αβ and γδ CD3+ cells and single-positive CD4+ and CD8+ lymphocytes. TCR repertoire analysis indicated a normal distribution of CDR3 length and preserved usage of the distal TRAV genes. We confirmed the in vivo rescue of B-cell development with normal immunoglobulin M surface expression and a significant decrease in CD56bright natural killer cells. Together, we provide specificity, toxicity, and efficacy data supporting the development of a gene-correction therapy to benefit RAG2-deficient patients.
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Affiliation(s)
- Mara Pavel-Dinu
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Cameron L. Gardner
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Yusuke Nakauchi
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Tomoki Kawai
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ottavia M. Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Boaz Palterer
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Marita Bosticardo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Francesca Pala
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sebastien Viel
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
- Service d’immunologie biologique, Hospices Civils de Lyon, Centre International de Recherche en Infectivologie, Centre International de Recheerche in Infectivalogie, INSERM U1111, Université Claude Bernard Lyon 1, Centre National de la Recherge Scientifique, UMR5308, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Harry L. Malech
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hana Y. Ghanim
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | | | | | | | | | | | - Adam Sheikali
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Sherah T. Menezes
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Jade Chrobok
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Elaine M. Hernández González
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Luigi D. Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Matthew H. Porteus
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
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7
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Lee BC, Gin A, Wu C, Singh K, Grice M, Mortlock R, Abraham D, Fan X, Zhou Y, AlJanahi A, Choi U, DeRavin SS, Shin T, Hong S, Dunbar CE. Impact of CRISPR/HDR editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques. Cell Stem Cell 2024; 31:455-466.e4. [PMID: 38508195 PMCID: PMC10997443 DOI: 10.1016/j.stem.2024.02.010] [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: 12/18/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) is required. The impact of HDR on true LT-HSC clonal dynamics in a relevant large animal model has not been studied. To track the output and clonality of HDR-edited cells and to provide a comparison to lentivirally transduced HSCs in vivo, we developed a competitive rhesus macaque (RM) autologous transplantation model, co-infusing HSCs transduced with a barcoded GFP-expressing lentiviral vector (LV) and HDR edited at the CD33 locus. CRISPR/HDR-edited cells showed a two-log decrease by 2 months following transplantation, with little improvement via p53 inhibition, in comparison to minimal loss of LV-transduced cells long term. HDR long-term clonality was oligoclonal in contrast to highly polyclonal LV-transduced HSCs. These results suggest marked clinically relevant differences in the impact of current genetic modification approaches on HSCs.
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Affiliation(s)
- Byung-Chul Lee
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Biological Sciences, Sookmyung Women's University, Seoul, Korea; Research Institute of Women's Health, Sookmyung Women's University, Seoul, Korea.
| | - Ashley Gin
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Komudi Singh
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Max Grice
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryland Mortlock
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diana Abraham
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Aisha AlJanahi
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Uimook Choi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Suk See DeRavin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Taehoon Shin
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Korea
| | - Sogun Hong
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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8
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Liang CT, Roscow O, Zhang W. Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade. Cold Spring Harb Protoc 2024; 2024:107784. [PMID: 36997275 DOI: 10.1101/pdb.over107784] [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: 06/19/2023]
Abstract
The ubiquitin signaling cascade plays a crucial role in human cells. Consistent with this, malfunction of ubiquitination and deubiquitination is implicated in the initiation and progression of numerous human diseases, including cancer. Therefore, the development of potent and specific modulators of ubiquitin signal transduction has been at the forefront of drug development. In the past decade, a structure-based combinatorial protein-engineering approach has been used to generate ubiquitin variants (UbVs) as protein-based modulators of multiple components in the ubiquitin-proteasome system. Here, we review the design and generation of phage-displayed UbV libraries, including the processes of binder selection and library improvement. We also provide a comprehensive overview of the general in vitro and cellular methodologies involved in characterizing UbV binders. Finally, we describe two recent applications of UbVs for developing molecules with therapeutic potential.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Ontario M5G1M1, Canada
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9
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Perez-Bermejo JA, Efagene O, Matern WM, Holden JK, Kabir S, Chew GM, Andreoletti G, Catton E, Ennis CL, Garcia A, Gerstenberg TL, Hill KA, Jain A, Krassovsky K, Lalisan CD, Lord D, Quejarro BJ, Sales-Lee J, Shah M, Silva BJ, Skowronski J, Strukov YG, Thomas J, Veraz M, Vijay T, Wallace KA, Yuan Y, Grogan JL, Wienert B, Lahiri P, Treusch S, Dever DP, Soros VB, Partridge JR, Seim KL. Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair. Nat Commun 2024; 15:2625. [PMID: 38521763 PMCID: PMC10960832 DOI: 10.1038/s41467-024-46816-5] [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: 08/07/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meet Shah
- Graphite Bio, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Yue Yuan
- Graphite Bio, South San Francisco, CA, USA
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10
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Singh S, Pugliano CM, Honaker Y, Laird A, DeGottardi MQ, Lopez E, Lachkar S, Stoffers C, Sommer K, Khan IF, Rawlings DJ. Efficient and sustained FOXP3 locus editing in hematopoietic stem cells as a therapeutic approach for IPEX syndrome. Mol Ther Methods Clin Dev 2024; 32:101183. [PMID: 38282895 PMCID: PMC10818254 DOI: 10.1016/j.omtm.2023.101183] [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: 06/14/2022] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a monogenic disorder caused by mutations in the FOXP3 gene, required for generation of regulatory T (Treg) cells. Loss of Treg cells leads to immune dysregulation characterized by multi-organ autoimmunity and early mortality. Hematopoietic stem cell (HSC) transplantation can be curative, but success is limited by autoimmune complications, donor availability and/or graft-vs.-host disease. Correction of FOXP3 in autologous HSC utilizing a homology-directed repair (HDR)-based platform may provide a safer alternative therapy. Here, we demonstrate efficient editing of FOXP3 utilizing co-delivery of Cas9 ribonucleoprotein complexes and adeno-associated viral vectors to achieve HDR rates of >40% in vitro using mobilized CD34+ cells from multiple donors. Using this approach to deliver either a GFP or a FOXP3 cDNA donor cassette, we demonstrate sustained bone marrow engraftment of approximately 10% of HDR-edited cells in immune-deficient recipient mice at 16 weeks post-transplant. Further, we show targeted integration of FOXP3 cDNA in CD34+ cells from an IPEX patient and expression of the introduced FOXP3 transcript in gene-edited primary T cells from both healthy individuals and IPEX patients. Our combined findings suggest that refinement of this approach is likely to provide future clinical benefit in IPEX.
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Affiliation(s)
- Swati Singh
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - 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
| | - Yuchi Honaker
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, 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
| | - 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
| | - Ezra Lopez
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Stefan Lachkar
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Claire Stoffers
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Karen Sommer
- 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
| | - 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 98101, USA
- Department of Immunology, University of Washington, Seattle, WA 98101, USA
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11
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De Saeger J, Coulembier Vandelannoote E, Lee H, Park J, Blomme J. Genome editing in macroalgae: advances and challenges. Front Genome Ed 2024; 6:1380682. [PMID: 38516199 PMCID: PMC10955705 DOI: 10.3389/fgeed.2024.1380682] [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: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
This minireview examines the current state and challenges of genome editing in macroalgae. Despite the ecological and economic significance of this group of organisms, genome editing has seen limited applications. While CRISPR functionality has been established in two brown (Ectocarpus species 7 and Saccharina japonica) and one green seaweed (Ulva prolifera), these studies are limited to proof-of-concept demonstrations. All studies also (co)-targeted ADENINE PHOSPHORIBOSYL TRANSFERASE to enrich for mutants, due to the relatively low editing efficiencies. To advance the field, there should be a focus on advancing auxiliary technologies, particularly stable transformation, so that novel editing reagents can be screened for their efficiency. More work is also needed on understanding DNA repair in these organisms, as this is tightly linked with the editing outcomes. Developing efficient genome editing tools for macroalgae will unlock the ability to characterize their genes, which is largely uncharted terrain. Moreover, given their economic importance, genome editing will also impact breeding campaigns to develop strains that have better yields, produce more commercially valuable compounds, and show improved resilience to the impacts of global change.
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Affiliation(s)
- Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Emma Coulembier Vandelannoote
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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12
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [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: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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13
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Li S, Wang Y, van der Stoel M, Zhou X, Madhusudan S, Kanerva K, Nguyen VD, Eskici N, Olkkonen VM, Zhou Y, Raivio T, Ikonen E. HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells. Genome Biol 2024; 25:58. [PMID: 38409044 PMCID: PMC10895734 DOI: 10.1186/s13059-024-03187-w] [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: 05/30/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of proteolysis. However, generation of human AID cell lines is challenging, especially in human embryonic stem cells (hESCs). Here, we develop HiHo-AID2, a streamlined procedure for rapid, one-step generation of human cancer and hESC lines with high homozygous degron-tagging efficiency based on an optimized AID2 system and homology-directed repair enhancers. We demonstrate its application for rapid and inducible functional inactivation of twelve endogenous target proteins in five cell lines, including targets with diverse expression levels and functions in hESCs and cells differentiated from hESCs.
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Affiliation(s)
- Shiqian Li
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
| | - Yafei Wang
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Miesje van der Stoel
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Xin Zhou
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Shrinidhi Madhusudan
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Kristiina Kanerva
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Van Dien Nguyen
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Nazli Eskici
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Vesa M Olkkonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - You Zhou
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Taneli Raivio
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00290, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
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14
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Leal AF, Herreno-Pachón AM, Benincore-Flórez E, Karunathilaka A, Tomatsu S. Current Strategies for Increasing Knock-In Efficiency in CRISPR/Cas9-Based Approaches. Int J Mol Sci 2024; 25:2456. [PMID: 38473704 PMCID: PMC10931195 DOI: 10.3390/ijms25052456] [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: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a promising panorama for developing novel and highly precise genome editing-based gene therapy (GT) alternatives, leading to overcoming the challenges associated with classical GT. Classical GT aims to deliver transgenes to the cells via their random integration in the genome or episomal persistence into the nucleus through lentivirus (LV) or adeno-associated virus (AAV), respectively. Although high transgene expression efficiency is achieved by using either LV or AAV, their nature can result in severe side effects in humans. For instance, an LV (NCT03852498)- and AAV9 (NCT05514249)-based GT clinical trials for treating X-linked adrenoleukodystrophy and Duchenne Muscular Dystrophy showed the development of myelodysplastic syndrome and patient's death, respectively. In contrast with classical GT, the CRISPR/Cas9-based genome editing requires the homologous direct repair (HDR) machinery of the cells for inserting the transgene in specific regions of the genome. This sophisticated and well-regulated process is limited in the cell cycle of mammalian cells, and in turn, the nonhomologous end-joining (NHEJ) predominates. Consequently, seeking approaches to increase HDR efficiency over NHEJ is crucial. This manuscript comprehensively reviews the current alternatives for improving the HDR for CRISPR/Cas9-based GTs.
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Affiliation(s)
- Andrés Felipe Leal
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Angelica María Herreno-Pachón
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Eliana Benincore-Flórez
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
| | - Amali Karunathilaka
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shunji Tomatsu
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19144, USA
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15
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Lu M, Billerbeck S. Improving homology-directed repair by small molecule agents for genetic engineering in unconventional yeast?-Learning from the engineering of mammalian systems. Microb Biotechnol 2024; 17:e14398. [PMID: 38376092 PMCID: PMC10878012 DOI: 10.1111/1751-7915.14398] [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: 08/30/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024] Open
Abstract
The ability to precisely edit genomes by deleting or adding genetic information enables the study of biological functions and the building of efficient cell factories. In many unconventional yeasts, such as those promising new hosts for cell factory design but also human pathogenic yeasts and food spoilers, this progress has been limited by the fact that most yeasts favour non-homologous end joining (NHEJ) over homologous recombination (HR) as a DNA repair mechanism, impairing genetic access to these hosts. In mammalian cells, small molecules that either inhibit proteins involved in NHEJ, enhance protein function in HR, or arrest the cell cycle in HR-dominant phases are regarded as promising agents for the simple and transient increase of HR-mediated genome editing without the need for a priori host engineering. Only a few of these chemicals have been applied to the engineering of yeast, although the targeted proteins are mostly conserved, making chemical agents a yet-underexplored area for enhancing yeast engineering. Here, we consolidate knowledge of the available small molecules that have been used to improve HR efficiency in mammalian cells and the few ones that have been used in yeast. We include available high-throughput-compatible NHEJ/HR quantification assays that could be used to screen for and isolate yeast-specific inhibitors.
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Affiliation(s)
- Min Lu
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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16
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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] [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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17
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Lee BC, Gin A, Wu C, Singh K, Grice M, Mortlock R, Abraham D, Fan X, Zhou Y, AlJanahi A, Choi U, de Ravin SS, Shin T, Hong S, Dunbar CE. Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571396. [PMID: 38168153 PMCID: PMC10760194 DOI: 10.1101/2023.12.13.571396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34 + cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34 + cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively. CD33 knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction in CD33 KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP + cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.
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18
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Yang ZX, Fu YW, Zhao JJ, Zhang F, Li SA, Zhao M, Wen W, Zhang L, Cheng T, Zhang JP, Zhang XB. Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1206-1220. [PMID: 36549468 PMCID: PMC11082263 DOI: 10.1016/j.gpb.2022.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 11/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
A series of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) systems have been engineered for genome editing. The most widely used Cas9 is SpCas9 from Streptococcus pyogenes and SaCas9 from Staphylococcus aureus. However, a comparison of their detailed gene editing outcomes is still lacking. By characterizing the editing outcomes of 11 sites in human induced pluripotent stem cells (iPSCs) and K562 cells, we found that SaCas9 could edit the genome with greater efficiencies than SpCas9. We also compared the effects of spacer lengths of single-guide RNAs (sgRNAs; 18-21 nt for SpCas9 and 19-23 nt for SaCas9) and found that the optimal spacer lengths were 20 nt and 21 nt for SpCas9 and SaCas9, respectively. However, the optimal spacer length for a particular sgRNA was 18-21 nt for SpCas9 and 21-22 nt for SaCas9. Furthermore, SpCas9 exhibited a more substantial bias than SaCas9 for nonhomologous end-joining (NHEJ) +1 insertion at the fourth nucleotide upstream of the protospacer adjacent motif (PAM), indicating a characteristic of a staggered cut. Accordingly, editing with SaCas9 led to higher efficiencies of NHEJ-mediated double-stranded oligodeoxynucleotide (dsODN) insertion or homology-directed repair (HDR)-mediated adeno-associated virus serotype 6 (AAV6) donor knock-in. Finally, GUIDE-seq analysis revealed that SaCas9 exhibited significantly reduced off-target effects compared with SpCas9. Our work indicates the superior performance of SaCas9 to SpCas9 in transgene integration-based therapeutic gene editing and the necessity to identify the optimal spacer length to achieve desired editing results.
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Affiliation(s)
- Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Ya-Wen Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Juan-Juan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
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19
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Zhang R, Pan S, Zheng S, Liao Q, Jiang Z, Wang D, Li X, Hu A, Li X, Zhu Y, Shen X, Lei J, Zhong S, Zhang X, Huang L, Wang X, Huang L, Shen L, Song BL, Zhao JW, Wang Z, Yang B, Guo X. Lipid-anchored proteasomes control membrane protein homeostasis. SCIENCE ADVANCES 2023; 9:eadj4605. [PMID: 38019907 PMCID: PMC10686573 DOI: 10.1126/sciadv.adj4605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Protein degradation in eukaryotic cells is mainly carried out by the 26S proteasome, a macromolecular complex not only present in the cytosol and nucleus but also associated with various membranes. How proteasomes are anchored to the membrane and the biological meaning thereof have been largely unknown in higher organisms. Here, we show that N-myristoylation of the Rpt2 subunit is a general mechanism for proteasome-membrane interaction. Loss of this modification in the Rpt2-G2A mutant cells leads to profound changes in the membrane-associated proteome, perturbs the endomembrane system, and undermines critical cellular processes such as cell adhesion, endoplasmic reticulum-associated degradation and membrane protein trafficking. Rpt2G2A/G2A homozygous mutation is embryonic lethal in mice and is sufficient to abolish tumor growth in a nude mice xenograft model. These findings have defined an evolutionarily conserved mechanism for maintaining membrane protein homeostasis and underscored the significance of compartmentalized protein degradation by myristoyl-anchored proteasomes in health and disease.
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Affiliation(s)
- Ruizhu Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuxian Pan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Suya Zheng
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qingqing Liao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhaodi Jiang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Dixian Wang
- Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Cryo-Electron Microscopy Center, Zhejiang University, Hangzhou 310058, China
| | - Xuemei Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ao Hu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Wuhan University, Wuhan 430072, China
| | - Xinran Li
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Yezhang Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaoqi Shen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jing Lei
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
- The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Siming Zhong
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining 314400, China
- Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Xiaomei Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Lingyun Huang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA 92697, USA
| | - Li Shen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Bao-Liang Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Wuhan University, Wuhan 430072, China
| | - Jing-Wei Zhao
- Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Cryo-Electron Microscopy Center, Zhejiang University, Hangzhou 310058, China
| | - Zhiping Wang
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
- The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xing Guo
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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20
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Allen D, Knop O, Itkowitz B, Kalter N, Rosenberg M, Iancu O, Beider K, Lee YN, Nagler A, Somech R, Hendel A. CRISPR-Cas9 engineering of the RAG2 locus via complete coding sequence replacement for therapeutic applications. Nat Commun 2023; 14:6771. [PMID: 37891182 PMCID: PMC10611791 DOI: 10.1038/s41467-023-42036-5] [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: 02/08/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
RAG2-SCID is a primary immunodeficiency caused by mutations in Recombination-activating gene 2 (RAG2), a gene intimately involved in the process of lymphocyte maturation and function. ex-vivo manipulation of a patient's own hematopoietic stem and progenitor cells (HSPCs) using CRISPR-Cas9/rAAV6 gene editing could provide a therapeutic alternative to the only current treatment, allogeneic hematopoietic stem cell transplantation (HSCT). Here we show an innovative RAG2 correction strategy that replaces the entire endogenous coding sequence (CDS) for the purpose of preserving the critical endogenous spatiotemporal gene regulation and locus architecture. Expression of the corrective transgene leads to successful development into CD3+TCRαβ+ and CD3+TCRγδ+ T cells and promotes the establishment of highly diverse TRB and TRG repertoires in an in-vitro T-cell differentiation platform. Thus, our proof-of-concept study holds promise for safer gene therapy techniques of tightly regulated genes.
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Affiliation(s)
- Daniel Allen
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Orli Knop
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Bryan Itkowitz
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Nechama Kalter
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Ortal Iancu
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Katia Beider
- The Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, 5266202, Israel
| | - Yu Nee Lee
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, 5266202, Israel
| | - Arnon Nagler
- The Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, 5266202, Israel
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, 5266202, Israel
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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21
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Shell DJ, Foley CA, Wang Q, Smith CM, Guduru SKR, Zeng H, Dong A, Norris-Drouin JL, Axtman M, Hardy PB, Gupta G, Halabelian L, Frye SV, James LI, Pearce KH. Discovery of a 53BP1 Small Molecule Antagonist Using a Focused DNA-Encoded Library Screen. J Med Chem 2023; 66:14133-14149. [PMID: 37782247 PMCID: PMC10630848 DOI: 10.1021/acs.jmedchem.3c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Methyl-lysine reader p53 binding protein 1 (53BP1) is a central mediator of DNA break repair and is associated with various human diseases, including cancer. Thus, high-quality 53BP1 chemical probes can aid in further understanding the role of 53BP1 in genome repair pathways. Herein, we utilized focused DNA-encoded library screening to identify the novel hit compound UNC8531, which binds the 53BP1 tandem Tudor domain (TTD) with an IC50 of 0.47 ± 0.09 μM in a TR-FRET assay and Kd values of 0.85 ± 0.17 and 0.79 ± 0.52 μM in ITC and SPR, respectively. UNC8531 was cocrystallized with the 53BP1 TTD to guide further optimization efforts, leading to UNC9512. NanoBRET and 53BP1-dependent foci formation experiments confirmed cellular target engagement. These results show that UNC9512 is a best-in-class small molecule 53BP1 antagonist that can aid further studies investigating the role of 53BP1 in DNA repair, gene editing, and oncogenesis.
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Affiliation(s)
- Devan J Shell
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Caroline A Foley
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Qinhong Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Chelsea M Smith
- Lineberger Comprehensive Cancer Center, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shiva K R Guduru
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Ontario M5S 1A1, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Ontario M5S 1A1, Canada
| | - Jacqueline L Norris-Drouin
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew Axtman
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - P Brian Hardy
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Gaorav Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Ontario M5S 1A1, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Ontario M5S 1A1, Canada
| | - Stephen V Frye
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lindsey I James
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kenneth H Pearce
- UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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22
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Ghasemi HI, Bacal J, Yoon AC, Tavasoli KU, Cruz C, Vu JT, Gardner BM, Richardson CD. Interstrand crosslinking of homologous repair template DNA enhances gene editing in human cells. Nat Biotechnol 2023; 41:1398-1404. [PMID: 36849829 PMCID: PMC10460463 DOI: 10.1038/s41587-022-01654-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/22/2022] [Indexed: 03/01/2023]
Abstract
We describe a strategy to boost the efficiency of gene editing via homology-directed repair (HDR) by covalently modifying the template DNA with interstrand crosslinks. Crosslinked templates (xHDRTs) increase Cas9-mediated editing efficiencies by up to fivefold in K562, HEK293T, U2OS, iPS and primary T cells. Increased editing from xHDRTs is driven by events on the template molecule and requires ataxia telangiectasia and Rad3-related (ATR) kinase and components of the Fanconi anemia pathway.
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Affiliation(s)
- Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Julien Bacal
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Amanda C Yoon
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Katherine U Tavasoli
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Carmen Cruz
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Jonathan T Vu
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
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23
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Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. Nat Commun 2023; 14:6091. [PMID: 37773238 PMCID: PMC10541411 DOI: 10.1038/s41467-023-41821-6] [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: 03/20/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1-autoinhibited for chromatin binding-that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.
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Affiliation(s)
- Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Pascal Drané
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Benoît Bragantini
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - David J Schuller
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, USA
| | | | - Michael T Perfetti
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Department of Cancer Biology, Mayo Clinic, Rochester, MN, USA.
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24
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Xu L, Lahiri P, Skowronski J, Bhatia N, Lattanzi A, Porteus MH. Molecular dynamics of genome editing with CRISPR-Cas9 and rAAV6 virus in human HSPCs to treat sickle cell disease. Mol Ther Methods Clin Dev 2023; 30:317-331. [PMID: 37637384 PMCID: PMC10447934 DOI: 10.1016/j.omtm.2023.07.009] [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: 01/08/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Ex vivo gene correction with CRISPR-Cas9 and a recombinant adeno-associated virus serotype 6 (rAAV6) in autologous hematopoietic stem/progenitor cells (HSPCs) to treat sickle cell disease (SCD) has now entered early-phase clinical investigation. To facilitate the progress of CRISPR-Cas9/rAAV6 genome editing technology, we analyzed the molecular changes in key reagents and cellular responses during and after the genome editing procedure in human HSPCs. We demonstrated the high stability of rAAV6 to serve as the donor DNA template. We assessed the benefit of longer HSPC pre-stimulation in terms of increased numbers of edited cells. We observed that the p53 pathway was transiently activated, peaking at 6 h, and resolved over time. Notably, we revealed a strong correlation between p21 mRNA level and rAAV6 genome number in cells and beneficial effects of transient inhibition of p53 with siRNA on genome editing, cell proliferation, and cell survival. In terms of potential immunogenicity, we found that rAAV6 capsid protein was not detectable, while a trace amount of residual Cas9 protein was still detected at 48 h post-genome editing. We believe this information will provide important insights for future improvements of gene correction protocols in HSPCs.
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Affiliation(s)
- Liwen Xu
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Premanjali Lahiri
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Jason Skowronski
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Neehar Bhatia
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Annalisa Lattanzi
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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25
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Kawakami N, Sato H, Terasaka N, Matsumoto K, Suga H. MET-Activating Ubiquitin Multimers. Angew Chem Int Ed Engl 2023; 62:e202307157. [PMID: 37450419 DOI: 10.1002/anie.202307157] [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: 05/22/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Receptor tyrosine kinases (RTKs) are generally activated through their dimerization and/or oligomerization induced by their cognate ligands, and one such RTK hepatocyte growth factor (HGF) receptor, known as MET, plays an important role in tissue regeneration. Here we show the development of ubiquitin (Ub)-based protein ligand multimers, referred to as U-bodies, which act as surrogate agonists for MET and are derived from MET-binding macrocyclic peptides. Monomeric Ub constructs (U-body) were first generated by genetic implantation of a macrocyclic peptide pharmacophore into a structural loop of Ub (lasso-grafting) and subsequent optimization of its flanking spacer sequences via mRNA display. Such U-body constructs exhibit potent binding affinity to MET, thermal stability, and proteolytic stability. The U-body constructs also partially/fully inhibited or enhanced HGF-induced MET-phosphorylation. Their multimerization to dimeric, tetrameric, and octameric U-bodies linked by an appropriate peptide linker yielded potent MET activation activity and downstream cell proliferation-promoting activity. This work suggests that lasso-grafting of macrocycles to Ub is an effective approach to devising protein-based artificial RTK agonists and it can be useful in the development of a new class of biologics for various therapeutic applications.
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Affiliation(s)
- Naoya Kawakami
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki Sato
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
- WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University Kakuma-machi, Kanazawa City, Ishikawa, 920-1192, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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26
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Tang JQ, Marchand MM, Veggiani G. Ubiquitin Engineering for Interrogating the Ubiquitin-Proteasome System and Novel Therapeutic Strategies. Cells 2023; 12:2117. [PMID: 37626927 PMCID: PMC10453149 DOI: 10.3390/cells12162117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Protein turnover, a highly regulated process governed by the ubiquitin-proteasome system (UPS), is essential for maintaining cellular homeostasis. Dysregulation of the UPS has been implicated in various diseases, including viral infections and cancer, making the proteins in the UPS attractive targets for therapeutic intervention. However, the functional and structural redundancies of UPS enzymes present challenges in identifying precise drug targets and achieving target selectivity. Consequently, only 26S proteasome inhibitors have successfully advanced to clinical use thus far. To overcome these obstacles, engineered peptides and proteins, particularly engineered ubiquitin, have emerged as promising alternatives. In this review, we examine the impact of engineered ubiquitin on UPS and non-UPS proteins, as well as on viral enzymes. Furthermore, we explore their potential to guide the development of small molecules targeting novel surfaces, thereby expanding the range of druggable targets.
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Affiliation(s)
- Jason Q. Tang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Mary M. Marchand
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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27
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Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.534960. [PMID: 37131705 PMCID: PMC10153216 DOI: 10.1101/2023.04.20.534960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1 - autoinhibited for chromatin binding - that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.
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28
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Fichter KM, Setayesh T, Malik P. Strategies for precise gene edits in mammalian cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:536-552. [PMID: 37215153 PMCID: PMC10192336 DOI: 10.1016/j.omtn.2023.04.012] [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] [Indexed: 05/24/2023]
Abstract
CRISPR-Cas technologies have the potential to revolutionize genetic medicine. However, work is still needed to make this technology clinically efficient for gene correction. A barrier to making precise genetic edits in the human genome is controlling how CRISPR-Cas-induced DNA breaks are repaired by the cell. Since error-prone non-homologous end-joining is often the preferred cellular repair pathway, CRISPR-Cas-induced breaks often result in gene disruption. Homology-directed repair (HDR) makes precise genetic changes and is the clinically desired pathway, but this repair pathway requires a homology donor template and cycling cells. Newer editing strategies, such as base and prime editing, can affect precise repair for relatively small edits without requiring HDR and circumvent cell cycle dependence. However, these technologies have limitations in the extent of genetic editing and require the delivery of bulky cargo. Here, we discuss the pros and cons of precise gene correction using CRISPR-Cas-induced HDR, as well as base and prime editing for repairing small mutations. Finally, we consider emerging new technologies, such as recombination and transposases, which can circumvent both cell cycle and cellular DNA repair dependence for editing the genome.
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Affiliation(s)
- Katye M. Fichter
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tahereh Setayesh
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Hematology, Cancer and Blood Disease Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
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29
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Chae K, Overcash JM, Dawson C, Valentin C, Tsujimoto H, Myles KM, Adelman ZN. CRISPR-based gene editing of non-homologous end joining factors biases DNA repair pathway choice toward single-strand annealing in Aedes aegypti. CURRENT RESEARCH IN BIOTECHNOLOGY 2023; 5:100133. [PMID: 37475832 PMCID: PMC10357993 DOI: 10.1016/j.crbiot.2023.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
To maintain genome stability, eukaryotic cells orchestrate DNA repair pathways to process DNA double-strand breaks (DSBs) that result from diverse developmental or environmental stimuli. Bias in the selection of DSB repair pathways, either non-homologous end joining (NHEJ) or homology-directed repair (HDR), is also critical for efficient gene editing and for homing-based gene drive approaches developed for the control of disease-transmitting vector mosquitoes. However, little is understood about DNA repair homeostasis in the mosquito genome. Here, we utilized CRISPR/Cas9 to generate indel mutant strains for core NHEJ factors ku80, DNA ligase IV (lig4), and DNA-PKcs in the mosquito Aedes aegypti and evaluated the corresponding effects on DNA repair. In a plasmid-based assay, disruption of ku80 or lig4, but not DNA-PKcs, reduced both NHEJ and SSA. However, a transgenic reporter strain-based test revealed that those mutations significantly biased DNA repair events toward SSA. Interestingly, ku80 mutation also significantly increased the end joining rate by a yet-characterized mechanism in males. Our study provides evidence that the core NHEJ factors have an antagonistic effect on SSA-based DSB repair of the Ae. aegypti genome. Down-modulating the NHEJ pathway can enhance the efficiency of nuclease-based genetic control approaches, as most of those operate by homology-based repair processes along with extensive DNA end resection that is antagonized by NHEJ.
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Affiliation(s)
- Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Justin M. Overcash
- U.S. Department of Agriculture-Animal and Plant Health Inspection Service (USDA-APHIS), Biotechnology Regulatory Services, Riverdale, MD 20737, United States
| | - Chanell Dawson
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Collin Valentin
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Hitoshi Tsujimoto
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Kevin M. Myles
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
| | - Zach N. Adelman
- Department of Entomology, Texas A&M University, College Station, TX 77843, United States
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30
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Ferrari S, Valeri E, Conti A, Scala S, Aprile A, Di Micco R, Kajaste-Rudnitski A, Montini E, Ferrari G, Aiuti A, Naldini L. Genetic engineering meets hematopoietic stem cell biology for next-generation gene therapy. Cell Stem Cell 2023; 30:549-570. [PMID: 37146580 DOI: 10.1016/j.stem.2023.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
The growing clinical success of hematopoietic stem/progenitor cell (HSPC) gene therapy (GT) relies on the development of viral vectors as portable "Trojan horses" for safe and efficient gene transfer. The recent advent of novel technologies enabling site-specific gene editing is broadening the scope and means of GT, paving the way to more precise genetic engineering and expanding the spectrum of diseases amenable to HSPC-GT. Here, we provide an overview of state-of-the-art and prospective developments of the HSPC-GT field, highlighting how advances in biological characterization and manipulation of HSPCs will enable the design of the next generation of these transforming therapeutics.
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Affiliation(s)
- Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Erika Valeri
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Anastasia Conti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Annamaria Aprile
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Anna Kajaste-Rudnitski
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Giuliana Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy.
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31
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Allen D, Kalter N, Rosenberg M, Hendel A. Homology-Directed-Repair-Based Genome Editing in HSPCs for the Treatment of Inborn Errors of Immunity and Blood Disorders. Pharmaceutics 2023; 15:pharmaceutics15051329. [PMID: 37242571 DOI: 10.3390/pharmaceutics15051329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Genome engineering via targeted nucleases, specifically CRISPR-Cas9, has revolutionized the field of gene therapy research, providing a potential treatment for diseases of the blood and immune system. While numerous genome editing techniques have been used, CRISPR-Cas9 homology-directed repair (HDR)-mediated editing represents a promising method for the site-specific insertion of large transgenes for gene knock-in or gene correction. Alternative methods, such as lentiviral/gammaretroviral gene addition, gene knock-out via non-homologous end joining (NHEJ)-mediated editing, and base or prime editing, have shown great promise for clinical applications, yet all possess significant drawbacks when applied in the treatment of patients suffering from inborn errors of immunity or blood system disorders. This review aims to highlight the transformational benefits of HDR-mediated gene therapy and possible solutions for the existing problems holding the methodology back. Together, we aim to help bring HDR-based gene therapy in CD34+ hematopoietic stem progenitor cells (HSPCs) from the lab bench to the bedside.
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Affiliation(s)
- Daniel Allen
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Nechama Kalter
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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32
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Anuchina AA, Zaynitdinova MI, Demchenko AG, Evtushenko NA, Lavrov AV, Smirnikhina SA. Bridging Gaps in HDR Improvement: The Role of MAD2L2, SCAI, and SCR7. Int J Mol Sci 2023; 24:ijms24076704. [PMID: 37047677 PMCID: PMC10095018 DOI: 10.3390/ijms24076704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/07/2023] Open
Abstract
This study aimed to enhance homology-directed repair (HDR) efficiency in CRISPR/Cas-mediated genome editing by targeting three key factors regulating the balance between HDR and non-homologous end joining (NHEJ): MAD2L2, SCAI, and Ligase IV. In order to achieve this, a cellular model using mutated eGFP was designed to monitor HDR events. Results showed that MAD2L2 knockdown and SCR7 treatment significantly improved HDR efficiency during Cas9-mediated HDR repair of the mutated eGFP gene in the HEK293T cell line. Fusion protein Cas9-SCAI did not improve HDR. This study is the first to demonstrate that MAD2L2 knockdown during CRISPR-mediated gene editing in HEK293T cells can increase precise correction by up to 10.2 times. The study also confirmed a moderate but consistent effect of SCR7, an inhibitor of Ligase IV, which increased HDR by 1.7 times. These findings provide valuable insights into improving HDR-based genome editing efficiency.
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Affiliation(s)
- Arina A. Anuchina
- Research Centre for Medical Genetics, Moskvorechie 1, 115522 Moscow, Russia
| | | | - Anna G. Demchenko
- Research Centre for Medical Genetics, Moskvorechie 1, 115522 Moscow, Russia
| | - Nadezhda A. Evtushenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
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33
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Chauhan VP, Sharp PA, Langer R. Altered DNA repair pathway engagement by engineered CRISPR-Cas9 nucleases. Proc Natl Acad Sci U S A 2023; 120:e2300605120. [PMID: 36881621 PMCID: PMC10242711 DOI: 10.1073/pnas.2300605120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/10/2023] [Indexed: 03/08/2023] Open
Abstract
CRISPR-Cas9 introduces targeted DNA breaks that engage competing DNA repair pathways, producing a spectrum of imprecise insertion/deletion mutations (indels) and precise templated mutations (precise edits). The relative frequencies of these pathways are thought to primarily depend on genomic sequence and cell state contexts, limiting control over mutational outcomes. Here, we report that engineered Cas9 nucleases that create different DNA break structures engage competing repair pathways at dramatically altered frequencies. We accordingly designed a Cas9 variant (vCas9) that produces breaks which suppress otherwise dominant nonhomologous end-joining (NHEJ) repair. Instead, breaks created by vCas9 are predominantly repaired by pathways utilizing homologous sequences, specifically microhomology-mediated end-joining (MMEJ) and homology-directed repair (HDR). Consequently, vCas9 enables efficient precise editing through HDR or MMEJ while suppressing indels caused by NHEJ in dividing and nondividing cells. These findings establish a paradigm of targeted nucleases custom-designed for specific mutational applications.
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Affiliation(s)
- Vikash P. Chauhan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Phillip A. Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Robert Langer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
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34
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Schimmel J, Muñoz-Subirana N, Kool H, van Schendel R, van der Vlies S, Kamp JA, de Vrij FMS, Kushner SA, Smith GCM, Boulton SJ, Tijsterman M. Modulating mutational outcomes and improving precise gene editing at CRISPR-Cas9-induced breaks by chemical inhibition of end-joining pathways. Cell Rep 2023; 42:112019. [PMID: 36701230 DOI: 10.1016/j.celrep.2023.112019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/18/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Gene editing through repair of CRISPR-Cas9-induced chromosomal breaks offers a means to correct a wide range of genetic defects. Directing repair to produce desirable outcomes by modulating DNA repair pathways holds considerable promise to increase the efficiency of genome engineering. Here, we show that inhibition of non-homologous end joining (NHEJ) or polymerase theta-mediated end joining (TMEJ) can be exploited to alter the mutational outcomes of CRISPR-Cas9. We show robust inhibition of TMEJ activity at CRISPR-Cas9-induced double-strand breaks (DSBs) using ART558, a potent polymerase theta (Polϴ) inhibitor. Using targeted sequencing, we show that ART558 suppresses the formation of microhomology-driven deletions in favor of NHEJ-specific outcomes. Conversely, NHEJ deficiency triggers the formation of large kb-sized deletions, which we show are the products of mutagenic TMEJ. Finally, we show that combined chemical inhibition of TMEJ and NHEJ increases the efficiency of homology-driven repair (HDR)-mediated precise gene editing. Our work reports a robust strategy to improve the fidelity and safety of genome engineering.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Núria Muñoz-Subirana
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sven van der Vlies
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Juliette A Kamp
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Femke M S de Vrij
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Simon J Boulton
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK; The Francis Crick Institute, London, UK
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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35
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Li X, Zhang G, Huang S, Liu Y, Tang J, Zhong M, Wang X, Sun W, Yao Y, Ji Q, Wang X, Liu J, Zhu S, Huang X. Development of a versatile nuclease prime editor with upgraded precision. Nat Commun 2023; 14:305. [PMID: 36658146 PMCID: PMC9852468 DOI: 10.1038/s41467-023-35870-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
The applicability of nuclease-based form of prime editor (PEn) has been hindered by its complexed editing outcomes. A chemical inhibitor against DNA-PK, which mediates the nonhomologous end joining (NHEJ) pathway, was recently shown to promote precise insertions by PEn. Nevertheless, the intrinsic issues of specificity and toxicity for such a chemical approach necessitate development of alternative strategies. Here, we find that co-introduction of PEn and a NHEJ-restraining, 53BP1-inhibitory ubiquitin variant potently drives precise edits via mitigation of unintended edits, framing a high-activity editing platform (uPEn) apparently complementing the canonical PE. Further developments involve exploring the effective configuration of a homologous region-containing pegRNA (HR-pegRNA). Overall, uPEn can empower high-efficiency installation of insertions (38%), deletions (43%) and replacements (52%) in HEK293T cells. When compared with PE3/5max, uPEn demonstrates superior activities for typically refractory base substitutions, and for small-block edits. Collectively, this work establishes a highly efficient PE platform with broad application potential.
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Affiliation(s)
- Xiangyang Li
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China.,Zhejiang Lab, Hangzhou, Zhejiang, 311121, China
| | - Guiquan Zhang
- Zhejiang Lab, Hangzhou, Zhejiang, 311121, China.,State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center at Medical School of Nanjing University, 210061, Nanjing, China
| | | | - Yao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Jin Tang
- Zhejiang Lab, Hangzhou, Zhejiang, 311121, China
| | - Mingtian Zhong
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Xin Wang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Wenjun Sun
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Yuan Yao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China.,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Jianghuai Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center at Medical School of Nanjing University, 210061, Nanjing, China.
| | - Shiqiang Zhu
- Zhejiang Lab, Hangzhou, Zhejiang, 311121, China.
| | - Xingxu Huang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China. .,Zhejiang Lab, Hangzhou, Zhejiang, 311121, China.
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Parkinson J, Hard R, Ainsworth R, Wang W. Engineering human JMJD2A tudor domains for an improved understanding of histone peptide recognition. Proteins 2023; 91:32-46. [PMID: 35927178 PMCID: PMC9771871 DOI: 10.1002/prot.26408] [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: 04/08/2022] [Revised: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022]
Abstract
JMJD2A is a histone lysine demethylase which recognizes and demethylates H3K9me3 and H3K36me3 residues and is overexpressed in various cancers. It utilizes a tandem tudor domain to facilitate its own recruitment to histone sites, recognizing various di- and tri-methyl lysine residues with moderate affinity. In this study, we successfully engineered the tudor domain of JMJD2A to specifically bind to H4K20me3 with a 20-fold increase of affinity and improved selectivity. To reveal the molecular basis, we performed molecular dynamics and free energy decomposition analysis on the human JMJD2A tandem tudor domains bound to H4K20me2, H4K20me3, and H3K23me3 peptides to uncover the residues and conformational changes important for the enhanced binding affinity and selectivity toward H4K20me2/3. These analyses revealed new insights into understanding chromatin reader domains recognizing histone modifications and improving binding affinity and selectivity of these domains. Furthermore, we showed that the tight binding of JMJD2A to H4K20me2/3 is not sufficient to improve the efficiency of CRISPR-CAS9 mediated homology directed repair (HDR), suggesting a complicated relationship between JMJD2A and the DNA damage response beyond binding affinity toward the H4K20me2/3 mark.
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Affiliation(s)
- Jonathan Parkinson
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California, USA
| | - Ryan Hard
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California, USA
| | - Richard Ainsworth
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California, USA
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Singh S, Chaudhary R, Deshmukh R, Tiwari S. Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals. PLANT MOLECULAR BIOLOGY 2023; 111:1-20. [PMID: 36315306 DOI: 10.1007/s11103-022-01321-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
We summarise recent advancements to achieve higher homologous recombination based gene targeting efficiency in different animals and plants. The genome editing has revolutionized the agriculture and human therapeutic sectors by its ability to create precise, stable and predictable mutations in the genome. It depends upon targeted double-strand breaks induction by the engineered endonucleases, which then gets repaired by highly conserved endogenous DNA repair mechanisms. The repairing could be done either through non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways. The HDR-based editing can be applied for precise gene targeting such as insertion of a new gene, gene replacement and altering of the regulatory sequence of a gene to control the existing protein expression. However, HDR-mediated editing is considered challenging because of lower efficiency in higher eukaryotes, thus, preventing its widespread application. This article reviews the recent progress of HDR-mediated editing and discusses novel strategies such as cell cycle synchronization, modulation of DNA damage repair factors, engineering of Cas protein favoring HDR and CRISPR-Cas reagents delivery methods to improve efficiency for generating knock-in events in both plants and animals. Further, multiplexing of described methods may be promising towards achieving higher donor template-assisted homologous recombination efficiency at the target locus.
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Affiliation(s)
- Surender Singh
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Roni Chaudhary
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | | | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India.
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38
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Iancu O, Allen D, Knop O, Zehavi Y, Breier D, Arbiv A, Lev A, Lee YN, Beider K, Nagler A, Somech R, Hendel A. Multiplex HDR for disease and correction modeling of SCID by CRISPR genome editing in human HSPCs. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:105-121. [PMID: 36618262 PMCID: PMC9813580 DOI: 10.1016/j.omtn.2022.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Severe combined immunodeficiency (SCID) is a group of disorders caused by mutations in genes involved in the process of lymphocyte maturation and function. CRISPR-Cas9 gene editing of the patient's own hematopoietic stem and progenitor cells (HSPCs) ex vivo could provide a therapeutic alternative to allogeneic hematopoietic stem cell transplantation, the current gold standard for treatment of SCID. To eliminate the need for scarce patient samples, we engineered genotypes in healthy donor (HD)-derived CD34+ HSPCs using CRISPR-Cas9/rAAV6 gene-editing, to model both SCID and the therapeutic outcomes of gene-editing therapies for SCID via multiplexed homology-directed repair (HDR). First, we developed a SCID disease model via biallelic knockout of genes critical to the development of lymphocytes; and second, we established a knockin/knockout strategy to develop a proof-of-concept single-allelic gene correction. Based on these results, we performed gene correction of RAG2-SCID patient-derived CD34+ HSPCs that successfully developed into CD3+ T cells with diverse TCR repertoires in an in vitro T cell differentiation platform. In summary, we present a strategy to determine the optimal configuration for CRISPR-Cas9 gene correction of SCID using HD-derived CD34+ HSPCs, and the feasibility of translating this gene correction approach in patient-derived CD34+ HSPCs.
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Affiliation(s)
- Ortal Iancu
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Daniel Allen
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Orli Knop
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yonathan Zehavi
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dor Breier
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Adaya Arbiv
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Atar Lev
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel,Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-HaShomer, Ramat Gan 5266202, Israel
| | - Yu Nee Lee
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-HaShomer, Ramat Gan 5266202, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Katia Beider
- The Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-HaShomer, Ramat Gan 5266202, Israel
| | - Arnon Nagler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel,The Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-HaShomer, Ramat Gan 5266202, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-HaShomer, Ramat Gan 5266202, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ayal Hendel
- The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel,Corresponding author Ayal Hendel, The Institute for Advanced Materials and Nanotechnology, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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Liu SC, Feng YL, Sun XN, Chen RD, Liu Q, Xiao JJ, Zhang JN, Huang ZC, Xiang JF, Chen GQ, Yang Y, Lou C, Li HD, Cai Z, Xu SM, Lin H, Xie AY. Target residence of Cas9-sgRNA influences DNA double-strand break repair pathway choices in CRISPR/Cas9 genome editing. Genome Biol 2022; 23:165. [PMID: 35915475 PMCID: PMC9341079 DOI: 10.1186/s13059-022-02736-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 07/22/2022] [Indexed: 12/05/2022] Open
Abstract
Background Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target interaction of Cas9-sgRNA determines its target binding affinity and modulates its post-cleavage target residence duration and exposure of Cas9-induced DSBs. This exposure, via different mechanisms, may initiate variable DNA damage responses, influencing DSB repair pathway choices and contributing to mutational heterogeneity in genome editing. However, this regulation of DSB repair pathway choices is poorly understood. Results In repair of Cas9-induced DSBs, repair pathway choices vary widely at different target sites and classical nonhomologous end joining (c-NHEJ) is not even engaged at some sites. In mouse embryonic stem cells, weakening the target interaction of Cas9-sgRNA promotes bias towards c-NHEJ and increases target dissociation and reduces target residence of Cas9-sgRNAs in vitro. As an important strategy for enhancing homology-directed repair, inactivation of c-NHEJ aggravates off-target activities of Cas9-sgRNA due to its weak interaction with off-target sites. By dislodging Cas9-sgRNA from its cleaved targets, DNA replication alters DSB end configurations and suppresses c-NHEJ in favor of other repair pathways, whereas transcription has little effect on c-NHEJ engagement. Dissociation of Cas9-sgRNA from its cleaved target by DNA replication may generate three-ended DSBs, resulting in palindromic fusion of sister chromatids, a potential source for CRISPR/Cas9-induced on-target chromosomal rearrangements. Conclusions Target residence of Cas9-sgRNA modulates DSB repair pathway choices likely through varying dissociation of Cas9-sgRNA from cleaved DNA, thus widening on-target and off-target mutational spectra in CRISPR/Cas9 genome editing. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02736-5.
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Fischer A. Gene therapy for inborn errors of immunity: past, present and future. Nat Rev Immunol 2022:10.1038/s41577-022-00800-6. [DOI: 10.1038/s41577-022-00800-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/27/2022]
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Çerçi B, Uzay IA, Kara MK, Dinçer P. Clinical trials and promising preclinical applications of CRISPR/Cas gene editing. Life Sci 2022; 312:121204. [PMID: 36403643 DOI: 10.1016/j.lfs.2022.121204] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/03/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Treatment of genetic disorders by genomic manipulation has been the unreachable goal of researchers for many decades. Although our understanding of the genetic basis of genetic diseases has advanced tremendously in the last few decades, the tools developed for genomic editing were not efficient and practical for their use in the clinical setting until now. The recent advancements in the research of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems offered an easy and efficient way to edit the genome and accelerated the research on their potential use in the treatment of genetic disorders. In this review, we summarize the clinical trials that evaluate the CRISPR/Cas systems for treating different genetic diseases and highlight promising preclinical research on CRISPR/Cas mediated treatment of a great diversity of genetic disorders. Ultimately, we discuss the future of CRISPR/Cas mediated genome editing in genetic diseases.
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Affiliation(s)
- Barış Çerçi
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey.
| | - Ihsan Alp Uzay
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | | | - Pervin Dinçer
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
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42
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Wienert B, Cromer MK. CRISPR nuclease off-target activity and mitigation strategies. Front Genome Ed 2022; 4:1050507. [PMID: 36439866 PMCID: PMC9685173 DOI: 10.3389/fgeed.2022.1050507] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
The discovery of CRISPR has allowed site-specific genomic modification to become a reality and this technology is now being applied in a number of human clinical trials. While this technology has demonstrated impressive efficacy in the clinic to date, there remains the potential for unintended on- and off-target effects of CRISPR nuclease activity. A variety of in silico-based prediction tools and empirically derived experimental methods have been developed to identify the most common unintended effect-small insertions and deletions at genomic sites with homology to the guide RNA. However, large-scale aberrations have recently been reported such as translocations, inversions, deletions, and even chromothripsis. These are more difficult to detect using current workflows indicating a major unmet need in the field. In this review we summarize potential sequencing-based solutions that may be able to detect these large-scale effects even at low frequencies of occurrence. In addition, many of the current clinical trials using CRISPR involve ex vivo isolation of a patient's own stem cells, modification, and re-transplantation. However, there is growing interest in direct, in vivo delivery of genome editing tools. While this strategy has the potential to address disease in cell types that are not amenable to ex vivo manipulation, in vivo editing has only one desired outcome-on-target editing in the cell type of interest. CRISPR activity in unintended cell types (both on- and off-target) is therefore a major safety as well as ethical concern in tissues that could enable germline transmission. In this review, we have summarized the strengths and weaknesses of current editing and delivery tools and potential improvements to off-target and off-tissue CRISPR activity detection. We have also outlined potential mitigation strategies that will ensure that the safety of CRISPR keeps pace with efficacy, a necessary requirement if this technology is to realize its full translational potential.
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Affiliation(s)
- Beeke Wienert
- Graphite Bio, Inc., South San Francisco, CA, United States
| | - M. Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States,Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA, United States,*Correspondence: M. Kyle Cromer,
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43
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Maguire JA, Gadue P, French DL. Highly Efficient CRISPR/Cas9-Mediated Genome Editing in Human Pluripotent Stem Cells. Curr Protoc 2022; 2:e590. [PMID: 36426905 PMCID: PMC9708095 DOI: 10.1002/cpz1.590] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Human pluripotent stem cells hold tremendous potential for both basic biology and cell-based therapies for a wide variety of diseases. The ability to manipulate the genome of these cells using the CRISPR/Cas9 technology has expanded this potential by providing a valuable tool to engineer or correct disease-associated mutations. Because of the high efficiency with which CRISPR/Cas9 creates targeted double-strand breaks, a major challenge has been the introduction of precise genetic modifications on one allele without indel formation on the non-targeted allele. To overcome this obstacle, we describe use of two oligonucleotide repair templates: one expressing the sequence change and the other maintaining the normal sequence. In addition, we have streamlined both the transfection and screening methodologies to make the protocols efficient, with small numbers of cells and a limited amount of labor-intensive clone passaging. This article provides a technically simple approach for generating valuable tools to model human disease in stem cells. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Application and optimization of CRISPR-based genome editing in human pluripotent stem cells Basic Protocol 2: Genetic modification of human pluripotent stem cells using a double-oligonucleotide CRISPR/Cas9 recombination system.
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Affiliation(s)
- Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania
| | - Deborah L. French
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania
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44
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Marker-free co-selection for successive rounds of prime editing in human cells. Nat Commun 2022; 13:5909. [PMID: 36207338 PMCID: PMC9546848 DOI: 10.1038/s41467-022-33669-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies. Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. Here the authors develop a co-selection strategy to facilitate prime editing in human cells and provide design principles to prevent the formation of undesired editing byproducts at the target site.
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Yan Z, Vorhies K, Feng Z, Park SY, Choi SH, Zhang Y, Winter M, Sun X, Engelhardt JF. Recombinant Adeno-Associated Virus-Mediated Editing of the G551D Cystic Fibrosis Transmembrane Conductance Regulator Mutation in Ferret Airway Basal Cells. Hum Gene Ther 2022; 33:1023-1036. [PMID: 35686451 PMCID: PMC9595624 DOI: 10.1089/hum.2022.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/03/2022] [Indexed: 12/30/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), a chronic disease that affects multiple organs, including the lung. We developed a CF ferret model of a scarless G551→D substitution in CFTR (CFTRG551D-KI), enabling approaches to correct this gating mutation in CF airways via gene editing. Homology-directed repair (HDR) was tested in Cas9-expressing CF airway basal cells (Cas9-GKI) from this model, as well as reporter basal cells (Y66S-Cas9-GKI) that express an integrated nonfluorescent Y66S-EGFP (enhanced green fluorescent protein) mutant gene to facilitate rapid assessment of HDR by the restoration of fluorescence. Recombinant adeno-associated virus (rAAV) vectors were used to deliver two DNA templates and sgRNAs for dual-gene editing at the EGFP and CFTR genes, followed by fluorescence-activated cell sorting of EGFPY66S-corrected cells. When gene-edited airway basal cells were polarized at an air-liquid interface, unsorted and EGFPY66S-corrected sorted populations gave rise to 26.0% and 70.4% CFTR-mediated Cl- transport of that observed in non-CF cultures, respectively. The consequences of gene editing at the CFTRG551D locus by HDR and nonhomologous end joining (NHEJ) were assessed by targeted gene next-generation sequencing (NGS) against a specific amplicon. NGS revealed HDR corrections of 3.1% of G551 sequences in the unsorted population of rAAV-infected cells, and 18.4% in the EGFPY66S-corrected cells. However, the largest proportion of sequences had indels surrounding the CRISPR (clustered regularly interspaced short palindromic repeats) cut site, demonstrating that NHEJ was the dominant repair pathway. This approach to simultaneously coedit at two genomic loci using rAAV may have utility as a model system for optimizing gene-editing efficiencies in proliferating airway basal cells through the modulation of DNA repair pathways in favor of HDR.
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Affiliation(s)
- Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Kai Vorhies
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Zehua Feng
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Soo Yeun Park
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Soon H. Choi
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Yulong Zhang
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Michael Winter
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Xingshen Sun
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - John F. Engelhardt
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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Jiang J, Chen Y, Zhang L, Jin Q, Wang L, Xu S, Chen K, Li L, Zeng T, Fan X, Liu T, Li J, Wang J, Han C, Gao F, Yang Y, Wang Y. i-CRISPR: a personalized cancer therapy strategy through cutting cancer-specific mutations. Mol Cancer 2022; 21:164. [PMID: 35974394 PMCID: PMC9380384 DOI: 10.1186/s12943-022-01612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/26/2022] [Indexed: 11/24/2022] Open
Abstract
Developing a strategy to specifically kill cancer cells without inducing obvious damage to normal cells may be of great clinical significance for cancer treatment. In the present study, we developed a new precise personalized strategy named "i-CRISPR" for cancer treatment through adding DNA damage repair inhibitors(i) and inducing cancer cell-specific DNA double strand breaks by CRISPR. Through in vitro and in vivo experiments, we confirmed the efficacy of this strategy in multiple cancer models and revealed the mechanism of cell death. Our strategy might provide a novel concept for precise cancer therapy.
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Affiliation(s)
- Junfeng Jiang
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Yuanyuan Chen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Li Zhang
- Department of Pathology, Faculty of Medical Imaging Laboratory of Medical Imaging, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Qishu Jin
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150086, China
| | - Liujun Wang
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Sha Xu
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Kexin Chen
- Department of Plastic Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, 200433, China
| | - Li Li
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Tao Zeng
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China.,The 901th Hospital of PLA Jiont Logistic Support Force, Hefei, 230031, China
| | - Xingfei Fan
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Tingting Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China
| | - Jiaxi Li
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Jinjiang Wang
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Chaofeng Han
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China.
| | - Fu Gao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China.
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China.
| | - Yue Wang
- Histology and Embryology Department, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, People's Republic of China.
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Yao Y, Chen C, Cai Z, Liu G, Ding C, Lim D, Chao D, Feng Z. Screen identifies fasudil as a radioprotector on human fibroblasts. Toxicol Res (Camb) 2022; 11:662-672. [PMID: 36051660 PMCID: PMC9424713 DOI: 10.1093/toxres/tfac042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 07/24/2023] Open
Abstract
Background Radioprotectors safeguard biological system exposed to ionizing radiation (IR) by protecting normal cells from radiation damage during radiotherapy. Due to the toxicity and limited clinical utility of the present radioprotectors, it prompts us to identify novel radioprotectors that could alleviate IR-induced cytotoxicity of normal tissues. Aims and Methods To identify new radioprotectors, we screened a chemical molecular library comprising 253 compounds in normal human fibroblasts (HFs) or 16HBE cells upon IR by CCK-8 assays and clonogenic survival assays. Fasudil was identified as a potential effective radioprotector. Results The results indicated that Fasudil exerts radioprotective effects on HFs against IR-induced DNA double-strand breaks (DSBs) through the regulation of DSB repair. Fasudil increased homologous recombination (HR) repair by 45.24% and decreased non-homologous end-joining (NHEJ) by 63.88% compared with untreated cells, without affecting changes to cell cycle profile. We further found that fasudil significantly facilitated the expression and foci formation of HR core proteins such as Rad51 and BRCA1 upon IR, and decreased the expression of NHEJ-associated proteins such as DNA-PKcs at 24 h post-IR. Conclusion Our study identified fasudil as a novel radioprotector that exert radioprotective effects on normal cells through regulation of DSB repair by promoting HR repair.
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Affiliation(s)
- Yanling Yao
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Chen Chen
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Zuchao Cai
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Guochao Liu
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Chenxia Ding
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - David Lim
- Health services Management, School of Science and Health, Translational Health Research Institute, Western Sydney University, Campbelltown 1797, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park 5042, Australia
| | - Dong Chao
- Corresponding author: Department of Occupational Health and Occupational Medicine, The Public Health School, Cheeloo College of Medicine, Shandong University, Shandong, Jinan 250012, China. ;
| | - Zhihui Feng
- Corresponding author: Department of Occupational Health and Occupational Medicine, The Public Health School, Cheeloo College of Medicine, Shandong University, Shandong, Jinan 250012, China. ;
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Finney M, Romanowski J, Adelman ZN. Strategies to improve homology-based repair outcomes following CRISPR-based gene editing in mosquitoes: lessons in how to keep any repair disruptions local. Virol J 2022; 19:128. [PMID: 35908059 PMCID: PMC9338592 DOI: 10.1186/s12985-022-01859-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
Programmable gene editing systems such as CRISPR-Cas have made mosquito genome engineering more practical and accessible, catalyzing the development of cutting-edge genetic methods of disease vector control. This progress, however, has been limited by the low efficiency of homology-directed repair (HDR)-based sequence integration at DNA double-strand breaks (DSBs) and a lack of understanding about DSB repair in mosquitoes. Innovative efforts to optimize HDR sequence integration by inhibiting non-homologous end joining or promoting HDR have been performed in mammalian systems, however many of these approaches have not been applied to mosquitoes. Here, we review some of the most relevant steps of DNA DSB repair choice and highlight promising approaches that influence this choice to enhance HDR in the context of mosquito gene editing.
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Affiliation(s)
- Micaela Finney
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Joseph Romanowski
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA
| | - Zach N Adelman
- Department of Entomology, Texas A&M University, 329A Minnie Belle Heep Center, 370 Olsen Blvd, College Station, TX, 77843, USA.
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Matsui M, Kajita S, Tsuchiya Y, Torii W, Tamekuni S, Nishi R. USP49 is a novel deubiquitylating enzyme for γ H2AX in DNA double-strand break repair. Gene 2022; 833:146599. [PMID: 35598681 DOI: 10.1016/j.gene.2022.146599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 12/29/2022]
Abstract
DNA double-strand break (DSB) that is one of the most serious DNA lesions is mainly repaired by two mutually exclusive pathways, homologous recombination and non-homologous end-joining. Proper choice of DSB repair pathway, in which recruitment of 53BP1 to chromatin around DSB sites plays a pivotal role, is crucial for maintaining genome integrity. Ubiquitylations of histone H2A and H2AX on Lys15 are prerequisite for 53BP1 loading onto chromatin. Although ubiquitylation mechanism of H2A and H2AX had been extensively studied, mechanism regulating deubiquitylation of γH2AX that is a phosphorylated form of H2AX remains elusive. Here, we identified USP49 as a novel deubiquitylating enzyme targeting DSB-induced γH2AX ubiquitylation. Over-expressed USP49 suppressed ubiquitylation of γH2AX in an enzymatic activity-dependent manner. Catalytic dead mutant of USP49 interacted and colocalized with γH2AX. Consequently, over-expression of USP49 inhibited the DSB-induced foci formation of 53BP1 and resulted in higher cell sensitivity to DSB-inducing drug treatment. Furthermore, endogenous USP49 protein was degraded via the proteasome upon DSB induction, indicating the importance of modulating USP49 protein level for γH2AX deubiquitylation. Consistent with our cell-based data, kidney renal clear cell carcinoma patients with higher expression of USP49 showed poor survival rate in comparison to the patients with unaltered USP49 expression. In conclusion, these data suggest that fine tuning of protein level of USP49 and USP49-mediated deubiquitylation of γH2AX are important for genome integrity.
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Affiliation(s)
- Misaki Matsui
- Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan
| | - Shoki Kajita
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yuina Tsuchiya
- School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan
| | - Wakana Torii
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Shiori Tamekuni
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Ryotaro Nishi
- Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan; Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan.
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50
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Aulicino F, Pelosse M, Toelzer C, Capin J, Ilegems E, Meysami P, Rollarson R, Berggren PO, Dillingham MS, Schaffitzel C, Saleem MA, Welsh GI, Berger I. Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus. Nucleic Acids Res 2022; 50:7783-7799. [PMID: 35801912 PMCID: PMC9303279 DOI: 10.1093/nar/gkac587] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
CRISPR-based precise gene-editing requires simultaneous delivery of multiple components into living cells, rapidly exceeding the cargo capacity of traditional viral vector systems. This challenge represents a major roadblock to genome engineering applications. Here we exploit the unmatched heterologous DNA cargo capacity of baculovirus to resolve this bottleneck in human cells. By encoding Cas9, sgRNA and Donor DNAs on a single, rapidly assembled baculoviral vector, we achieve with up to 30% efficacy whole-exon replacement in the intronic β-actin (ACTB) locus, including site-specific docking of very large DNA payloads. We use our approach to rescue wild-type podocin expression in steroid-resistant nephrotic syndrome (SRNS) patient derived podocytes. We demonstrate single baculovirus vectored delivery of single and multiplexed prime-editing toolkits, achieving up to 100% cleavage-free DNA search-and-replace interventions without detectable indels. Taken together, we provide a versatile delivery platform for single base to multi-gene level genome interventions, addressing the currently unmet need for a powerful delivery system accommodating current and future CRISPR technologies without the burden of limited cargo capacity.
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Affiliation(s)
- Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Martin Pelosse
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Christine Toelzer
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Julien Capin
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Erwin Ilegems
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Parisa Meysami
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Ruth Rollarson
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Mark Simon Dillingham
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Christiane Schaffitzel
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK
| | - Moin A Saleem
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Gavin I Welsh
- Bristol Renal, Bristol Medical School, Dorothy Hodgkin Building, Whitson street, Bristol BS1 3NY, UK
| | - Imre Berger
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol BS8 1TD, UK.,Max Planck Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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