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Mog BJ, Marcou N, DiNapoli SR, Pearlman AH, Nichakawade TD, Hwang MS, Douglass J, Hsiue EHC, Glavaris S, Wright KM, Konig MF, Paul S, Wyhs N, Ge J, Miller MS, Azurmendi P, Watson E, Pardoll DM, Gabelli SB, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S. Preclinical studies show that Co-STARs combine the advantages of chimeric antigen and T cell receptors for the treatment of tumors with low antigen densities. Sci Transl Med 2024; 16:eadg7123. [PMID: 38985855 DOI: 10.1126/scitranslmed.adg7123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/01/2024] [Accepted: 06/13/2024] [Indexed: 07/12/2024]
Abstract
Two types of engineered T cells have been successfully used to treat patients with cancer, one with an antigen recognition domain derived from antibodies [chimeric antigen receptors (CARs)] and the other derived from T cell receptors (TCRs). CARs use high-affinity antigen-binding domains and costimulatory domains to induce T cell activation but can only react against target cells with relatively high amounts of antigen. TCRs have a much lower affinity for their antigens but can react against target cells displaying only a few antigen molecules. Here, we describe a new type of receptor, called a Co-STAR (for costimulatory synthetic TCR and antigen receptor), that combines aspects of both CARs and TCRs. In Co-STARs, the antigen-recognizing components of TCRs are replaced by high-affinity antibody fragments, and costimulation is provided by two modules that drive NF-κB signaling (MyD88 and CD40). Using a TCR-mimic antibody fragment that targets a recurrent p53 neoantigen presented in a common human leukocyte antigen (HLA) allele, we demonstrate that T cells equipped with Co-STARs can kill cancer cells bearing low densities of antigen better than T cells engineered with conventional CARs and patient-derived TCRs in vitro. In mouse models, we show that Co-STARs mediate more robust T cell expansion and more durable tumor regressions than TCRs similarly modified with MyD88 and CD40 costimulation. Our data suggest that Co-STARs may have utility for other peptide-HLA antigens in cancer and other targets where antigen density may limit the efficacy of engineered T cells.
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Affiliation(s)
- Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nikita Marcou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tushar D Nichakawade
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephanie Glavaris
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Katharine M Wright
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nicolas Wyhs
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jiaxin Ge
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michelle S Miller
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - P Azurmendi
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Evangeline Watson
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
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2
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Hew BE, Gupta S, Sato R, Waller DF, Stoytchev I, Short JE, Sharek L, Tran CT, Badran AH, Owens JB. Directed evolution of hyperactive integrases for site specific insertion of transgenes. Nucleic Acids Res 2024:gkae534. [PMID: 38953167 DOI: 10.1093/nar/gkae534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/16/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Abstract
The ability to deliver large transgenes to a single genomic sequence with high efficiency would accelerate biomedical interventions. Current methods suffer from low insertion efficiency and most rely on undesired double-strand DNA breaks. Serine integrases catalyze the insertion of large DNA cargos at attachment (att) sites. By targeting att sites to the genome using technologies such as prime editing, integrases can target safe loci while avoiding double-strand breaks. We developed a method of phage-assisted continuous evolution we call IntePACE, that we used to rapidly perform hundreds of rounds of mutagenesis to systematically improve activity of PhiC31 and Bxb1 serine integrases. Novel hyperactive mutants were generated by combining synergistic mutations resulting in integration of a multi-gene cargo at rates as high as 80% of target chromosomes. Hyperactive integrases inserted a 15.7 kb therapeutic DNA cargo containing von Willebrand Factor. This technology could accelerate gene delivery therapeutics and our directed evolution strategy can easily be adapted to improve novel integrases from nature.
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Affiliation(s)
- Brian E Hew
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - Sabranth Gupta
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - Ryuei Sato
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - David F Waller
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - Ilko Stoytchev
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - James E Short
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - Lisa Sharek
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - Christopher T Tran
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
| | - Ahmed H Badran
- Department of Chemistry, Department of Integrative Structural and Computational Biology, Beckman Center for Chemical Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jesse B Owens
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96814, USA
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3
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Hall AE, Klompstra D, Nance J. C. elegans Afadin is required for epidermal morphogenesis and functionally interfaces with the cadherin-catenin complex and RhoGAP PAC-1/ARHGAP21. Dev Biol 2024; 511:12-25. [PMID: 38556137 PMCID: PMC11088504 DOI: 10.1016/j.ydbio.2024.03.007] [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: 07/28/2023] [Revised: 03/07/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
During epithelial morphogenesis, the apical junctions connecting cells must remodel as cells change shape and make new connections with their neighbors. In the C. elegans embryo, new apical junctions form when epidermal cells migrate and seal with one another to encase the embryo in skin ('ventral enclosure'), and junctions remodel when epidermal cells change shape to squeeze the embryo into a worm shape ('elongation'). The junctional cadherin-catenin complex (CCC), which links epithelial cells to each other and to cortical actomyosin, is essential for C. elegans epidermal morphogenesis. RNAi genetic enhancement screens have identified several genes encoding proteins that interact with the CCC to promote epidermal morphogenesis, including the scaffolding protein Afadin (AFD-1), whose depletion alone results in only minor morphogenesis defects. Here, by creating a null mutation in afd-1, we show that afd-1 provides a significant contribution to ventral enclosure and elongation on its own. Unexpectedly, we find that afd-1 mutant phenotypes are strongly modified by diet, revealing a previously unappreciated parental nutritional input to morphogenesis. We identify functional interactions between AFD-1 and the CCC by demonstrating that E-cadherin is required for the polarized distribution of AFD-1 to cell contact sites in early embryos. Finally, we show that afd-1 promotes the enrichment of polarity regulator, and CCC-interacting protein, PAC-1/ARHGAP21 to cell contact sites, and we identify genetic interactions suggesting that afd-1 and pac-1 regulate epidermal morphogenesis at least in part through parallel mechanisms. Our findings reveal that C. elegans AFD-1 makes a significant contribution to epidermal morphogenesis and functionally interfaces with core and associated CCC proteins.
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Affiliation(s)
- Allison E Hall
- Department of Cell Biology, NYU School of Medicine, New York, NY, 10016, USA; Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, 10016, USA; Regis University, Biology Department, Denver, CO, 80221, USA.
| | - Diana Klompstra
- Department of Cell Biology, NYU School of Medicine, New York, NY, 10016, USA; Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, 10016, USA
| | - Jeremy Nance
- Department of Cell Biology, NYU School of Medicine, New York, NY, 10016, USA; Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, 10016, USA; University of Wisconsin - Madison, Department of Cell and Regenerative Biology and Center for Quantitative Cell Imaging, Madison, WI, 53706, USA.
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4
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Peng D, Vangipuram M, Wong J, Leonetti MD. protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in. Nucleic Acids Res 2024:gkae553. [PMID: 38922690 DOI: 10.1093/nar/gkae553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
CRISPR/Cas-mediated knock-in of DNA sequences enables precise genome engineering for research and therapeutic applications. However, designing effective guide RNAs (gRNAs) and homology-directed repair (HDR) donors remains a bottleneck. Here, we present protoSpaceJAM, an open-source algorithm to automate and optimize gRNA and HDR donor design for CRISPR/Cas insertional knock-in experiments, currently supporting SpCas9, SpCas9-VQR and enAsCas12a Cas enzymes. protoSpaceJAM utilizes biological rules to rank gRNAs based on specificity, distance to insertion site, and position relative to regulatory regions. protoSpaceJAM can introduce 'recoding' mutations (silent mutations and mutations in non-coding sequences) in HDR donors to prevent re-cutting and increase knock-in efficiency. Users can customize parameters and design double-stranded or single-stranded donors. We validated protoSpaceJAM's design rules by demonstrating increased knock-in efficiency with recoding mutations and optimal strand selection for single-stranded donors. An additional module enables the design of genotyping primers for deep sequencing of edited alleles. Overall, protoSpaceJAM streamlines and optimizes CRISPR knock-in experimental design in a flexible and modular manner to benefit diverse research and therapeutic applications. protoSpaceJAM is available open-source as an interactive web tool at protospacejam.czbiohub.org or as a standalone Python package at github.com/czbiohub-sf/protoSpaceJAM.
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Affiliation(s)
- Duo Peng
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Hew BE, Gupta S, Sato R, Waller DF, Stoytchev I, Short JE, Sharek L, Tran CT, Badran AH, Owens JB. Directed evolution of hyperactive integrases for site specific insertion of transgenes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598370. [PMID: 38915697 PMCID: PMC11195097 DOI: 10.1101/2024.06.10.598370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The ability to deliver large transgenes to a single genomic sequence with high efficiency would accelerate biomedical interventions. Current methods suffer from low insertion efficiency and most rely on undesired double-strand DNA breaks. Serine integrases catalyze the insertion of large DNA cargos at attachment (att) sites. By targeting att sites to the genome using technologies such as prime editing, integrases can target safe loci while avoiding double-strand breaks. We developed a method of phage-assisted continuous evolution we call IntePACE, that we used to rapidly perform hundreds of rounds of mutagenesis to systematically improve activity of PhiC31 and Bxb1 serine integrases. Novel hyperactive mutants were generated by combining synergistic mutations resulting in integration of a multi-gene cargo at rates as high as 80% of target chromosomes. Hyperactive integrases inserted a 15.7 kb therapeutic DNA cargo containing Von Willebrand Factor. This technology could accelerate gene delivery therapeutics and our directed evolution strategy can easily be adapted to improve novel integrases from nature.
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Affiliation(s)
- Brian E. Hew
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - Sabranth Gupta
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - Ryuei Sato
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - David F. Waller
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - Ilko Stoytchev
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - James E. Short
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - Lisa Sharek
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - Christopher T. Tran
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
| | - Ahmed H. Badran
- Department of Chemistry, Department of Integrative Structural and Computational Biology, Beckman Center for Chemical Sciences, The Scripps Research Institute, La Jolla, California, 92037 USA
| | - Jesse B. Owens
- Department of Cell and Molecular Biology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, 96814 USA
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Chung E, Deacon P, Hu YC, Lim HW, Park JS. Hedgehog signaling is required for the maintenance of mesenchymal nephron progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.12.553098. [PMID: 37645929 PMCID: PMC10461989 DOI: 10.1101/2023.08.12.553098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mesenchymal nephron progenitors (mNPs) give rise to all nephron tubules in the mammalian kidney. Since premature depletion of these cells leads to low nephron numbers, high blood pressure, and various renal diseases, it is critical that we understand how mNPs are maintained. While Fgf, Bmp, and Wnt signaling pathways are known to be required for the maintenance of these cells, it is unclear if any other signaling pathways also play roles. In this report, we explored the role of Hedgehog signaling in mNPs. We found that loss of either Shh in the collecting duct or Smo from the nephron lineage resulted in premature depletion of mNPs. Transcriptional profiling of mNPs with different Smo dosages suggested that Hedgehog signaling inhibited Notch signaling and upregulated the expression of Fox transcription factors such as Foxc1 and Foxp4. Consistent with these observations, we found that ectopic expression of Jag1 caused the premature depletion of mNPs as seen in the Smo mutant kidney. We also found that Foxc1 was capable of binding to mitotic condensed chromatin, a feature of a mitotic bookmarking factor. Our study demonstrates a previously unappreciated role of Hedgehog signaling in preventing premature depletion of mNPs by repressing Notch signaling and likely by activating the expression of Fox factors.
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Affiliation(s)
- Eunah Chung
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
- Division of Pediatric Urology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Patrick Deacon
- Division of Pediatric Urology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Joo-Seop Park
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
- Division of Pediatric Urology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
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7
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Sollazzo G, Nikolouli K, Gouvi G, Aumann RA, Schetelig MF, Bourtzis K. Deep orange gene editing triggers temperature-sensitive lethal phenotypes in Ceratitis capitata. BMC Biotechnol 2024; 24:7. [PMID: 38302991 PMCID: PMC10835909 DOI: 10.1186/s12896-024-00832-x] [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: 10/06/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND The Mediterranean fruit fly, Ceratitis capitata, is a significant agricultural pest managed through area-wide integrated pest management (AW-IPM) including a sterile insect technique (SIT) component. Male-only releases increase the efficiency and cost-effectiveness of SIT programs, which can be achieved through the development of genetic sexing strains (GSS). The most successful GSS developed to date is the C. capitata VIENNA 8 GSS, constructed using classical genetic approaches and an irradiation-induced translocation with two selectable markers: the white pupae (wp) and temperature-sensitive lethal (tsl) genes. However, currently used methods for selecting suitable markers and inducing translocations are stochastic and non-specific, resulting in a laborious and time-consuming process. Recent efforts have focused on identifying the gene(s) and the causal mutation(s) for suitable phenotypes, such as wp and tsl, which could be used as selectable markers for developing a generic approach for constructing GSS. The wp gene was recently identified, and efforts have been initiated to identify the tsl gene. This study investigates Ceratitis capitata deep orange (Ccdor) as a tsl candidate gene and its potential to induce tsl phenotypes. RESULTS An integrated approach based on cytogenetics, genomics, bioinformatics, and gene editing was used to characterize the Ccdor. Its location was confirmed on the right arm of chromosome 5 in the putative tsl genomic region. Knock-out of Ccdor using CRISPR/Cas9-NHEJ and targeting the fourth exon resulted in lethality at mid- and late-pupal stage, while the successful application of CRISPR HDR introducing a point mutation on the sixth exon resulted in the establishment of the desired strain and two additional strains (dor 12del and dor 51dup), all of them expressing tsl phenotypes and presenting no (or minimal) fitness cost when reared at 25 °C. One of the strains exhibited complete lethality when embryos were exposed at 36 °C. CONCLUSIONS Gene editing of the deep orange gene in Ceratitis capitata resulted in the establishment of temperature-sensitive lethal mutant strains. The induced mutations did not significantly affect the rearing efficiency of the strains. As deep orange is a highly conserved gene, these data suggest that it can be considered a target for the development of tsl mutations which could potentially be used to develop novel genetic sexing strains in insect pests and disease vectors.
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Affiliation(s)
- Germano Sollazzo
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria
- Institute for Insect Biotechnology, Department of Insect Biotechnology in Plant Protection, Justus-Liebig-University Gießen, Winchesterstr. 2, Gießen, 35394, Germany
- Present address: Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, Imperial College Road, London, SW7 2AZ, UK
| | - Katerina Nikolouli
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria
| | - Georgia Gouvi
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, 2 G. Seferi St., Agrinio, 30100, Greece
- Present address: Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, Imperial College Road, London, SW7 2AZ, UK
| | - Roswitha A Aumann
- Institute for Insect Biotechnology, Department of Insect Biotechnology in Plant Protection, Justus-Liebig-University Gießen, Winchesterstr. 2, Gießen, 35394, Germany
| | - Marc F Schetelig
- Institute for Insect Biotechnology, Department of Insect Biotechnology in Plant Protection, Justus-Liebig-University Gießen, Winchesterstr. 2, Gießen, 35394, Germany.
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria.
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8
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Kuhns S, Juhl AD, Anvarian Z, Wüstner D, Pedersen LB, Andersen JS. Endogenous Tagging of Ciliary Genes in Human RPE1 Cells for Live-Cell Imaging. Methods Mol Biol 2024; 2725:147-166. [PMID: 37856023 DOI: 10.1007/978-1-0716-3507-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
CRISPR-mediated endogenous tagging of genes provides unique possibilities to explore the function and dynamic subcellular localization of proteins in living cells. Here, we describe experimental strategies for endogenous PCR-tagging of ciliary genes in human RPE1 cells and how image acquisition and analysis of the expressed fluorescently tagged proteins can be utilized to study the dynamic ciliary processes of intraflagellar transport and vesicular trafficking.
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Affiliation(s)
- Stefanie Kuhns
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Zeinab Anvarian
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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9
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Becker HJ, Yamazaki S. Understanding genetic heterogeneity in gene-edited hematopoietic stem cell products. Exp Hematol 2024; 129:104133. [PMID: 38036097 DOI: 10.1016/j.exphem.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
CRISPR/Cas gene editing has transformed genetic research and is poised to drive the next generation of gene therapies targeting hematopoietic stem cells (HSCs). However, the installation of the "desired" edit is most often only achieved in a minor subset of alleles. The array of cellular pathways triggered by gene editing tools produces a broad spectrum of "undesired" editing outcomes, including short insertions and deletions (indels) and chromosome rearrangements, leading to considerable genetic heterogeneity in gene-edited HSC populations. This heterogeneity may undermine the effect of the genetic intervention since only a subset of cells will carry the intended modification. Also, undesired mutations represent a potential safety concern as gene editing advances toward broader clinical use. Here, we will review the different sources of "undesired" edits and will discuss strategies for their mitigation and control.
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Affiliation(s)
- Hans Jiro Becker
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamazaki
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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10
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Liu L, Wei J, Chen C, Liang Q, Wang B, Wu W, Li G, Zheng X. Electroporation-based Easi-CRISPR yields biallelic insertions of EGFP-HiBiT cassette in immortalized chicken oviduct epithelial cells. Poult Sci 2023; 102:103112. [PMID: 37806084 PMCID: PMC10568294 DOI: 10.1016/j.psj.2023.103112] [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: 05/25/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Laying hens are an excellent experimental oviduct model for studying reproduction biology. Because chicken oviduct epithelial cells (cOECs) have a crucial role in synthesizing and secreting ovalbumin, laying hens have been regarded an ideal bioreactor for producing pharmaceuticals in egg white through transgene or gene editing of the ovalbumin (OVA) gene. However, related studies in cOECs are largely limited because of the lack of immortalized model cells. In addition, the editing efficiency of conventional CRISPR-HDR knock-in in chicken cells is suboptimal (ranging from 1 to 10%) and remains elevated. Here, primary cOECs were isolated from young laying hens, then infected with a retrovirus vector of human telomerase reverse transcriptase (hTERT), and immortalized cOECs were established. Subsequently, an electroporation-based Easi-CRISPR (Efficient additions with ssDNA inserts-CRISPR) method was adopted to integrate an EGFP-HiBiT cassette into the chicken OVA locus (immediately upstream of the stop codon). The immortalized cOECs reflected the self-renewal capability and phenotype of oviduct epithelial cells. This is because these cells not only maintained stable proliferation and normal karyotype and had no potential for malignant transformation, but also expressed oviduct markers and an epithelial marker and had a morphology similar to that of primary cOECs. EGFP expression was detected in the edited cells through microscopy, flow cytometry, and HiBiT/Western blotting. The EGFP-HiBiT knock-in efficiency reached 27.9% after a single round of electroporation, which was determined through genotyping and DNA sequencing. Two single cell clones contained biallelic insertions of EGFP-HiBiT donor cassettes. In conclusion, our established immortalized cOECs could act as an in vitro cell model for gene editing in chicken, and this electroporation-based Easi-CRISPR strategy will contribute to the generation of avian bioreactors and other gene-edited (GE) birds.
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Affiliation(s)
- Lingkang Liu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China
| | - Jinyu Wei
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Buffalo Research Institute, Chinese Academy of Agricultural Sciences and Guangxi Zhuang Nationality Autonomous Region, Nanning 530004, China
| | - Chen Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Qianxue Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Boyong Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wende Wu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China
| | - Gonghe Li
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China
| | - Xibang Zheng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Reproduction, Breeding and Disease Control, Nanning 530004, China.
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11
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Wang J, Saul J, Nikonorova IA, Cruz CN, Power KM, Nguyen KC, Hall DH, Barr MM. Ciliary intrinsic mechanisms regulate dynamic ciliary extracellular vesicle release from sensory neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565151. [PMID: 37961114 PMCID: PMC10635059 DOI: 10.1101/2023.11.01.565151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cilia-derived extracellular vesicles (EVs) contain signaling proteins and act in intercellular communication. Polycystin-2 (PKD-2), a transient receptor potential channel, is a conserved ciliary EVs cargo. Caenorhabditis elegans serves as a model for studying ciliary EV biogenesis and function. C. elegans males release EVs in a mechanically-induced manner and deposit PKD-2-labeled EVs onto the hermaphrodite vulva during mating, suggesting an active release process. Here, we study the dynamics of ciliary EV release using time-lapse imaging and find that cilia can sustain the release of PKD-2-labeled EVs for a two-hour duration. Intriguingly, this extended release doesn't require neuronal synaptic transmission. Instead, ciliary intrinsic mechanisms regulate PKD-2 ciliary membrane replenishment and dynamic EV release. The ciliary kinesin-3 motor KLP-6 is necessary for both initial and extended ciliary EV release, while the transition zone protein NPHP-4 is required only for sustained EV release. The dihydroceramide desaturase DEGS1/2 ortholog TTM-5 is highly expressed in the EV-releasing sensory neurons, localizes to cilia, and is required for sustained but not initial ciliary EV release, implicating ceramide in ciliary ectocytosis. The study offers a comprehensive portrait of real-time ciliary EV release, and mechanisms supporting cilia as proficient EV release platforms.
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Affiliation(s)
- Juan Wang
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Josh Saul
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Inna A. Nikonorova
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Carlos Nava Cruz
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Kaiden M. Power
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Ken C. Nguyen
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - David H. Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Maureen M. Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
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12
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Shu R, Hammett M, Evtimov V, Pupovac A, Nguyen N, Islam R, Zhuang J, Lee S, Kang T, Lee K, Nisbet I, Hudson P, Lee JY, Boyd R, Trounson A. Engineering T cell receptor fusion proteins using nonviral CRISPR/Cas9 genome editing for cancer immunotherapy. Bioeng Transl Med 2023; 8:e10571. [PMID: 38023726 PMCID: PMC10658519 DOI: 10.1002/btm2.10571] [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: 01/09/2023] [Revised: 06/04/2023] [Accepted: 06/25/2023] [Indexed: 12/01/2023] Open
Abstract
Manufacture of chimeric antigen receptor (CAR)-T cells usually involves the use of viral delivery systems to achieve high transgene expression. However, it can be costly and may result in random integration of the CAR into the genome, creating several disadvantages including variation in transgene expression, functional gene silencing and potential oncogenic transformation. Here, we optimized the method of nonviral, CRISPR/Cas9 genome editing using large donor DNA delivery, knocked-in an anti-tumor single chain variable fragment (scFv) into the N-terminus of CD3ε and efficiently generated fusion protein (FP) T cells. These cells displayed FP integration within the TCR/CD3 complex, lower variability in gene expression compared to CAR-T cells and good cell expansion after transfection. CD3ε FP T cells were predominantly CD8+ effector memory T cells, and exhibited anti-tumor activity in vitro and in vivo. Dual targeting FP T cells were also generated through the incorporation of scFvs into other CD3 subunits and CD28. Compared to viral-based methods, this method serves as an alternative and versatile way of generating T cells with tumor-targeting receptors for cancer immunotherapy.
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Affiliation(s)
- Runzhe Shu
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Maree Hammett
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Vera Evtimov
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Aleta Pupovac
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Nhu‐Y Nguyen
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Rasa Islam
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Junli Zhuang
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | | | | | | | - Ian Nisbet
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Peter Hudson
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | | | - Richard Boyd
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
| | - Alan Trounson
- Cartherics Pty Ltd.Notting HillAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonAustralia
- Department of Obstetrics and GynaecologyMonash UniversityClaytonAustralia
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13
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Daniels DE, Ferrer-Vicens I, Hawksworth J, Andrienko TN, Finnie EM, Bretherton NS, Ferguson DCJ, Oliveira ASF, Szeto JYA, Wilson MC, Brewin JN, Frayne J. Human cellular model systems of β-thalassemia enable in-depth analysis of disease phenotype. Nat Commun 2023; 14:6260. [PMID: 37803026 PMCID: PMC10558456 DOI: 10.1038/s41467-023-41961-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/26/2023] [Indexed: 10/08/2023] Open
Abstract
β-thalassemia is a prevalent genetic disorder causing severe anemia due to defective erythropoiesis, with few treatment options. Studying the underlying molecular defects is impeded by paucity of suitable patient material. In this study we create human disease cellular model systems for β-thalassemia by gene editing the erythroid line BEL-A, which accurately recapitulate the phenotype of patient erythroid cells. We also develop a high throughput compatible fluorometric-based assay for evaluating severity of disease phenotype and utilize the assay to demonstrate that the lines respond appropriately to verified reagents. We next use the lines to perform extensive analysis of the altered molecular mechanisms in β-thalassemia erythroid cells, revealing upregulation of a wide range of biological pathways and processes along with potential novel targets for therapeutic investigation. Overall, the lines provide a sustainable supply of disease cells as research tools for identifying therapeutic targets and as screening platforms for new drugs and reagents.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jenn-Yeu A Szeto
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | | | - John N Brewin
- Haematology Department, King's college Hospital NHS Foundation, London, SE5 9RS, UK
- Red Cell Biology Group, Kings College London, London, SE5 9NU, UK
| | - Jan Frayne
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
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14
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Willet AH, Chen JS, Ren L, Gould KL. Membrane binding of endocytic myosin-1s is inhibited by a class of ankyrin repeat proteins. Mol Biol Cell 2023; 34:br17. [PMID: 37531259 PMCID: PMC10559312 DOI: 10.1091/mbc.e23-06-0233] [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: 06/15/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
Myosin-1s are monomeric actin-based motors that function at membranes. Myo1 is the single myosin-1 isoform in Schizosaccharomyces pombe that works redundantly with Wsp1-Vrp1 to activate the Arp2/3 complex for endocytosis. Here, we identified Ank1 as an uncharacterized cytoplasmic Myo1 binding partner. We found that in ank1Δ cells, Myo1 dramatically redistributed from endocytic patches to decorate the entire plasma membrane and endocytosis was defective. Biochemical analysis and structural predictions suggested that the Ank1 ankyrin repeats bind the Myo1 lever arm and the Ank1 acidic tail binds the Myo1 TH1 domain to prevent TH1-dependent Myo1 membrane binding. Indeed, Ank1 overexpression precluded Myo1 membrane localization and recombinant Ank1 reduced purified Myo1 liposome binding in vitro. Based on biochemical and cell biological analyses, we propose budding yeast Ank1 and human OSTF1 are functional Ank1 orthologs and that cytoplasmic sequestration by small ankyrin repeat proteins is a conserved mechanism regulating myosin-1s in endocytosis.
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Affiliation(s)
- Alaina H. Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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15
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Eroglu M, Yu B, Derry WB. Efficient CRISPR/Cas9 mediated large insertions using long single-stranded oligonucleotide donors in C. elegans. FEBS J 2023; 290:4429-4439. [PMID: 37254814 DOI: 10.1111/febs.16876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/05/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Highly efficient generation of deletions, substitutions, and small insertions (up to ~ 150 bp) into the Caenorhabditis elegans genome by CRISPR/Cas9 has been facilitated by the use of single-stranded oligonucleotide donors as repair templates. However, insertion of larger sequences such as fluorescent markers and other functional domains remains challenging due to uncertainty of optimal performance between single-stranded or double-stranded repair templates and labor-intensive as well as inefficient protocols for their preparations. Here, we simplify the generation of long ssDNA as donors in CRISPR/Cas9. High yields of ssDNA can be rapidly generated using a standard PCR followed by a single enzymatic digest with lambda exonuclease. Comparison of long ssDNA donors obtained using this method to dsDNA demonstrates orders of magnitude increased insertion frequency for ssDNA donors. This can be leveraged to simultaneously generate multiple large insertions as well as successful edits without the use of selection or co-conversion (co-CRISPR) markers when necessary. Our approach complements the CRISPR/Cas9 toolkit for C. elegans to enable highly efficient insertion of longer sequences with a simple, standardized, and labor-minimal protocol.
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Affiliation(s)
- Matthew Eroglu
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Canada
| | - Bin Yu
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
| | - W Brent Derry
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Canada
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16
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González-Romero E, Martínez-Valiente C, García-García G, Rosal-Vela A, Millán JM, Sanz MÁ, Sanz G, Liquori A, Cervera JV, Vázquez-Manrique RP. PCR-Based Strategy for Introducing CRISPR/Cas9 Machinery into Hematopoietic Cell Lines. Cancers (Basel) 2023; 15:4263. [PMID: 37686539 PMCID: PMC10487029 DOI: 10.3390/cancers15174263] [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: 07/10/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Acute myeloid leukemia is a complex heterogeneous disease characterized by the clonal expansion of undifferentiated myeloid precursors. Due to the difficulty in the transfection of blood cells, several hematological models have recently been developed with CRISPR/Cas9, using viral vectors. In this study, we developed an alternative strategy in order to generate CRISPR constructs by fusion PCR, which any lab equipped with basic equipment can implement. Our PCR-generated constructs were easily introduced into hard-to-transfect leukemic cells, and their function was dually validated with the addition of MYBL2 and IDH2 genes into HEK293 cells. We then successfully modified the MYBL2 gene and introduced the R172 mutation into the IDH2 gene within NB4 and HL60 cells that constitutively expressed the Cas9 nuclease. The efficiency of mutation introduction with our methodology was similar to that of ribonucleoprotein strategies, and no off-target events were detected. Overall, our strategy represents a valid and intuitive alternative for introducing desired mutations into hard-to-transfect leukemic cells without viral transduction.
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Affiliation(s)
- Elisa González-Romero
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
| | - Cristina Martínez-Valiente
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
| | - Gema García-García
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Antonio Rosal-Vela
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- Biomedicine, Biotechnology and Public Health Department, Cádiz University, 11002 Cádiz, Spain
- Institute of Research and Innovation in Biomedical Sciences of Cadiz (INIBICA), 11009 Cádiz, Spain
| | - José María Millán
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
| | - Miguel Ángel Sanz
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
| | - Guillermo Sanz
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
- Hematology Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
| | - Alessandro Liquori
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
| | - José Vicente Cervera
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (E.G.-R.); (C.M.-V.); (A.R.-V.); (M.Á.S.); (G.S.); (A.L.)
- CIBERONC, 28029 Madrid, Spain
- Hematology Department, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain
| | - Rafael P. Vázquez-Manrique
- Laboratory of Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain (J.M.M.)
- CIBERER, 46010 Valencia, Spain
- Joint Unit for Rare Diseases IIS La Fe-CIPF, 46012 Valencia, Spain
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17
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Zhou Z, Ma X, Lin Y, Cheng D, Bavi N, Secker GA, Li JV, Janbandhu V, Sutton DL, Scott HS, Yao M, Harvey RP, Harvey NL, Corry B, Zhang Y, Cox CD. MyoD-family inhibitor proteins act as auxiliary subunits of Piezo channels. Science 2023; 381:799-804. [PMID: 37590348 DOI: 10.1126/science.adh8190] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Piezo channels are critical cellular sensors of mechanical forces. Despite their large size, ubiquitous expression, and irreplaceable roles in an ever-growing list of physiological processes, few Piezo channel-binding proteins have emerged. In this work, we found that MyoD (myoblast determination)-family inhibitor proteins (MDFIC and MDFI) are PIEZO1/2 interacting partners. These transcriptional regulators bind to PIEZO1/2 channels, regulating channel inactivation. Using single-particle cryogenic electron microscopy, we mapped the interaction site in MDFIC to a lipidated, C-terminal helix that inserts laterally into the PIEZO1 pore module. These Piezo-interacting proteins fit all the criteria for auxiliary subunits, contribute to explaining the vastly different gating kinetics of endogenous Piezo channels observed in many cell types, and elucidate mechanisms potentially involved in human lymphatic vascular disease.
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Affiliation(s)
- Zijing Zhou
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Xiaonuo Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiechang Lin
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Delfine Cheng
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Navid Bavi
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637, USA
| | - Genevieve A Secker
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia
| | - Jinyuan Vero Li
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Drew L Sutton
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005 Australia
| | - Hamish S Scott
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005 Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA 5000, Australia
| | - Mingxi Yao
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, Kensington, NSW 2052, Australia
| | - Natasha L Harvey
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005 Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Yixiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Charles D Cox
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales Sydney, Kensington, NSW 2052, Australia
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18
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Bekaert B, Boel A, De Witte L, Vandenberghe W, Popovic M, Stamatiadis P, Cosemans G, Tordeurs L, De Loore AM, Chuva de Sousa Lopes SM, De Sutter P, Stoop D, Coucke P, Menten B, Heindryckx B. Retained chromosomal integrity following CRISPR-Cas9-based mutational correction in human embryos. Mol Ther 2023; 31:2326-2341. [PMID: 37376733 PMCID: PMC10422011 DOI: 10.1016/j.ymthe.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/11/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Human germline gene correction by targeted nucleases holds great promise for reducing mutation transmission. However, recent studies have reported concerning observations in CRISPR-Cas9-targeted human embryos, including mosaicism and loss of heterozygosity (LOH). The latter has been associated with either gene conversion or (partial) chromosome loss events. In this study, we aimed to correct a heterozygous basepair substitution in PLCZ1, related to infertility. In 36% of the targeted embryos that originated from mutant sperm, only wild-type alleles were observed. By performing genome-wide double-digest restriction site-associated DNA sequencing, integrity of the targeted chromosome (i.e., no deletions larger than 3 Mb or chromosome loss) was confirmed in all seven targeted GENType-analyzed embryos (mutant editing and absence of mutation), while short-range LOH events (shorter than 10 Mb) were clearly observed by single-nucleotide polymorphism assessment in two of these embryos. These results fuel the currently ongoing discussion on double-strand break repair in early human embryos, making a case for the occurrence of gene conversion events or partial template-based homology-directed repair.
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Affiliation(s)
- Bieke Bekaert
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Annekatrien Boel
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Lisa De Witte
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Winter Vandenberghe
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Mina Popovic
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Panagiotis Stamatiadis
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Gwenny Cosemans
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Lise Tordeurs
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Athina-Maria De Loore
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Susana Marina Chuva de Sousa Lopes
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium; Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Petra De Sutter
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Dominic Stoop
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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Hall AE, Klompstra D, Nance J. C. elegans Afadin is required for epidermal morphogenesis and functionally interfaces with the cadherin-catenin complex and RhoGAP PAC-1/ARHGAP21. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551013. [PMID: 37546884 PMCID: PMC10402129 DOI: 10.1101/2023.07.28.551013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
During epithelial morphogenesis, the apical junctions connecting cells must remodel as cells change shape and make new connections with their neighbors. In the C. elegans embryo, new apical junctions form when epidermal cells migrate and seal with one another to encase the embryo in skin ('ventral enclosure'), and junctions remodel when epidermal cells change shape to squeeze the embryo into a worm shape ('elongation'). The junctional cadherin-catenin complex (CCC), which links epithelial cells to each other and to cortical actomyosin, is essential for C. elegans epidermal morphogenesis. RNAi genetic enhancement screens have identified several proteins that interact with the CCC to promote epidermal morphogenesis, including the scaffolding protein Afadin (AFD-1), whose depletion alone results in only minor morphogenesis defects. Here, by creating a null mutation in afd-1 , we show that afd-1 provides a significant contribution to ventral enclosure and elongation on its own. Unexpectedly, we find that afd-1 mutant phenotypes are strongly modified by diet, revealing a previously unappreciated maternal nutritional input to morphogenesis. We identify functional interactions between AFD-1 and the CCC by demonstrating that E-cadherin is required for the polarized distribution of AFD-1 to cell contact sites in early embryos. Finally, we show that afd-1 promotes the enrichment of polarity regulator and CCC-interacting protein PAC-1/ARHGAP21 to cell contact sites, and identify genetic interactions suggesting that afd-1 and pac-1 regulate epidermal morphogenesis at least in part through parallel mechanisms. Our findings reveal that C. elegans AFD-1 makes a significant contribution to epidermal morphogenesis and functionally interfaces with core and associated CCC proteins.
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20
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Wang C, Fang S, Chen Y, Tang N, Jiao G, Hu Y, Li J, Shan Q, Wang X, Feng G, Zhou Q, Li W. High-efficiency targeted transgene integration via primed micro-homologues. Cell Discov 2023; 9:69. [PMID: 37402729 DOI: 10.1038/s41421-023-00552-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/03/2023] [Indexed: 07/06/2023] Open
Abstract
Due to the difficulties in precisely manipulating DNA repair pathways, high-fidelity targeted integration of large transgenes triggered by double-strand breaks is inherently inefficient. Here, we exploit prime editors to devise a robust knock-in (KI) strategy named primed micro-homologues-assisted integration (PAINT), which utilizes reverse-transcribed single-stranded micro-homologues to boost targeted KIs in different types of cells. The improved version of PAINT, designated PAINT 3.0, maximizes editing efficiency and minimizes off-target integration, especially in dealing with scarless in-frame KIs. Using PAINT 3.0, we target a reporter transgene into housekeeping genes with editing efficiencies up to 80%, more than 10-fold higher than the traditional homology-directed repair method. Moreover, the use of PAINT 3.0 to insert a 2.5-kb transgene achieves up to 85% KI frequency at several therapeutically relevant genomic loci, suggesting its potential for clinical applications. Finally, PAINT 3.0 enables high-efficiency non-viral genome targeting in primary T cells and produces functional CAR-T cells with specific tumor-killing ability. Thus, we establish that the PAINT method is a powerful gene editing tool for large transgene integrations and may open new avenues for cell and gene therapies and genome writing technologies.
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Affiliation(s)
- Chenxin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Sen Fang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Na Tang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guanyi Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
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21
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Liu Y, Cottle WT, Ha T. Mapping cellular responses to DNA double-strand breaks using CRISPR technologies. Trends Genet 2023; 39:560-574. [PMID: 36967246 PMCID: PMC11062594 DOI: 10.1016/j.tig.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/15/2023]
Abstract
DNA double-strand breaks (DSBs) are one of the most genotoxic DNA lesions, driving a range of pathological defects from cancers to immunodeficiencies. To combat genomic instability caused by DSBs, evolution has outfitted cells with an intricate protein network dedicated to the rapid and accurate repair of these lesions. Pioneering studies have identified and characterized many crucial repair factors in this network, while the advent of genome manipulation tools like clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has reinvigorated interest in DSB repair mechanisms. This review surveys the latest methodological advances and biological insights gained by utilizing Cas9 as a precise 'damage inducer' for the study of DSB repair. We highlight rapidly inducible Cas9 systems that enable synchronized and efficient break induction. When combined with sequencing and genome-specific imaging approaches, inducible Cas9 systems greatly expand our capability to spatiotemporally characterize cellular responses to DSB at specific genomic coordinates, providing mechanistic insights that were previously unobtainable.
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Affiliation(s)
- Yang Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - W Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.
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22
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Han W, Li Z, Guo Y, He K, Li W, Xu C, Ge L, He M, Yin X, Zhou J, Li C, Yao D, Bao J, Liang H. Efficient precise integration of large DNA sequences with 3'-overhang dsDNA donors using CRISPR/Cas9. Proc Natl Acad Sci U S A 2023; 120:e2221127120. [PMID: 37216515 PMCID: PMC10235934 DOI: 10.1073/pnas.2221127120] [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: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
CRISPR/Cas9 genome-editing tools have tremendously boosted our capability of manipulating the eukaryotic genomes in biomedical research and innovative biotechnologies. However, the current approaches that allow precise integration of gene-sized large DNA fragments generally suffer from low efficiency and high cost. Herein, we developed a versatile and efficient approach, termed LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in), by utilizing specially designed 3'-overhang double-stranded DNA (odsDNA) donors harboring 50-nt homology arm. The length of the 3'-overhangs of odsDNA is specified by the five consecutive phosphorothioate modifications. Compared with existing methods, LOCK allows highly efficient targeted insertion of kilobase-sized DNA fragments into the mammalian genomes with low cost and low off-target effects, yielding >fivefold higher knock-in frequencies than conventional homologous recombination-based approaches. This newly designed LOCK approach based on homology-directed repair is a powerful tool suitable for gene-sized fragment integration that is urgently needed for genetic engineering, gene therapies, and synthetic biology.
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Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Yijun Guo
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Kaining He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Wenqing Li
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Caoling Xu
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Lishuang Ge
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Chengxu Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Jianqiang Bao
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
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23
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Mabuchi A, Hata S, Genova M, Tei C, Ito KK, Hirota M, Komori T, Fukuyama M, Chinen T, Toyoda A, Kitagawa D. ssDNA is not superior to dsDNA as long HDR donors for CRISPR-mediated endogenous gene tagging in human diploid RPE1 and HCT116 cells. BMC Genomics 2023; 24:289. [PMID: 37248464 DOI: 10.1186/s12864-023-09377-3] [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: 11/15/2022] [Accepted: 05/14/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Recent advances in CRISPR technology have enabled us to perform gene knock-in in various species and cell lines. CRISPR-mediated knock-in requires donor DNA which serves as a template for homology-directed repair (HDR). For knock-in of short sequences or base substitutions, ssDNA donors are frequently used among various other forms of HDR donors, such as linear dsDNA. However, partly due to the complexity of long ssDNA preparation, it remains unclear whether ssDNA is the optimal type of HDR donors for insertion of long transgenes such as fluorescent reporters in human cells. RESULTS In this study, we established a nuclease-based simple method for the preparation of long ssDNA with high yield and purity, and comprehensively compared the performance of ssDNA and dsDNA donors with 90 bases of homology arms for endogenous gene tagging with long transgenes in human diploid RPE1 and HCT116 cells. Quantification using flow cytometry revealed lower efficiency of endogenous fluorescent tagging with ssDNA donors than with dsDNA. By analyzing knock-in outcomes using long-read amplicon sequencing and a classification framework, a variety of mis-integration events were detected regardless of the donor type. Importantly, the ratio of precise insertion was lower with ssDNA donors than with dsDNA. Moreover, in off-target integration analyses using donors without homology arms, ssDNA and dsDNA were comparably prone to non-homologous integration. CONCLUSIONS These results indicate that ssDNA is not superior to dsDNA as long HDR donors with relatively short homology arms for gene knock-in in human RPE1 and HCT116 cells.
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Affiliation(s)
- Akira Mabuchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shoji Hata
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO) Program, Japan Science and Technology Agency, Honcho Kawaguchi, Saitama, Japan.
| | - Mariya Genova
- Zentrum Für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Chiharu Tei
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kei K Ito
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masayasu Hirota
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takuma Komori
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masamitsu Fukuyama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Takumi Chinen
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory and Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan.
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24
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Kheirandish MH, Rahmani B, Zarei Jaliani H, Barkhordari F, Mazlomi MA, Davami F. Efficient site-specific integration in CHO-K1 cells using CRISPR/Cas9-modified donors. Mol Biol Rep 2023:10.1007/s11033-023-08529-8. [PMID: 37244887 DOI: 10.1007/s11033-023-08529-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Conventional methods applied to develop recombinant CHO (rCHO) cell line as a predominant host for mammalian protein expression are limited to random integration approaches, which can prolong the process of getting the desired clones for months. CRISPR/Cas9 could be an alternative by mediating site-specific integration into transcriptionally active hot spots, promoting homogenous clones, and shortening the clonal selection process. However, applying this approach for the rCHO cell line development depends on an acceptable integration rate and robust sites for the sustained expression. METHODS AND RESULTS In this study, we aimed at improving the rate of GFP reporter integration to the Chromosome 3 (Chr3) pseudo-attP site of the CHO-K1 genome via two strategies; these include the PCR-based donor linearization and increasing local concentration of donor in the vicinity of DSB site by applying the monomeric streptavidin (mSA)-biotin tethering approach. According to the results, compared to the conventional CRISPR-mediated targeting, donor linearization and tethering methods exhibited 1.6- and 2.4-fold improvement in knock-in efficiency; among on-target clones, 84% and 73% were determined to be single copy by the quantitative PCR, respectively. Finally, to evaluate the expression level of the targeted integration, the expression cassette of hrsACE2 as a secretory protein was targeted to the Chr3 pseudo-attP site by applying the established tethering method. The generated cell pool reached 2-fold productivity, as compared to the random integration cell line. CONCLUSION Our study suggested reliable strategies for enhancing the CRISPR-mediated integration, introducing Chr3 pseudo-attP site as a potential candidate for the sustained transgene expression, which might be applied to promote the rCHO cell line development.
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Affiliation(s)
- Mohammad Hassan Kheirandish
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Rahmani
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Hossein Zarei Jaliani
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Mohammad Ali Mazlomi
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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25
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Luo N, Li Z, Ling J, Zhao J, Li Y, Yang Y, Mao Z, Xie B, Li H, Jiao Y. Establishment of a CRISPR/Cas9-Mediated Efficient Knockout System of Trichoderma hamatum T21 and Pigment Synthesis PKS Gene Knockout. J Fungi (Basel) 2023; 9:jof9050595. [PMID: 37233306 DOI: 10.3390/jof9050595] [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: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
Trichoderma hamatum is a filamentous fungus that serves as a biological control agent for multiple phytopathogens and as an important resource promising for fungicides. However, the lack of adequate knockout technologies has hindered gene function and biocontrol mechanism research of this species. This study obtained a genome assembly of T. hamatum T21, with a 41.4 Mb genome sequence comprising 8170 genes. Based on genomic information, we established a CRISPR/Cas9 system with dual sgRNAs targets and dual screening markers. CRISPR/Cas9 plasmid and donor DNA recombinant plasmid were constructed for disruption of the Thpyr4 and Thpks1 genes. The result indicates the consistency between phenotypic characterization and molecular identification of the knockout strains. The knockout efficiencies of Thpyr4 and Thpks1 were 100% and 89.1%, respectively. Moreover, sequencing revealed fragment deletions between dual sgRNA target sites or GFP gene insertions presented in knockout strains. The situations were caused by different DNA repair mechanisms, nonhomologous end joining (NHEJ), and homologous recombination (HR). Overall, we have successfully constructed an efficient and convenient CRISPR/Cas9 system in T. hamatum for the first time, which has important scientific significance and application value for studies on functional genomics of Trichoderma and other filamentous fungi.
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Affiliation(s)
- Ning Luo
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zeyu Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Ling
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuhong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bingyan Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixia Li
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Yang Jiao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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26
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Eisen B, Binah O. Modeling Duchenne Muscular Dystrophy Cardiomyopathy with Patients' Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Int J Mol Sci 2023; 24:ijms24108657. [PMID: 37240001 DOI: 10.3390/ijms24108657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle degenerative disease caused by mutations in the dystrophin gene, resulting in death by the end of the third decade of life at the latest. A key aspect of the DMD clinical phenotype is dilated cardiomyopathy, affecting virtually all patients by the end of the second decade of life. Furthermore, despite respiratory complications still being the leading cause of death, with advancements in medical care in recent years, cardiac involvement has become an increasing cause of mortality. Over the years, extensive research has been conducted using different DMD animal models, including the mdx mouse. While these models present certain important similarities to human DMD patients, they also have some differences which pose a challenge to researchers. The development of somatic cell reprograming technology has enabled generation of human induced pluripotent stem cells (hiPSCs) which can be differentiated into different cell types. This technology provides a potentially endless pool of human cells for research. Furthermore, hiPSCs can be generated from patients, thus providing patient-specific cells and enabling research tailored to different mutations. DMD cardiac involvement has been shown in animal models to include changes in gene expression of different proteins, abnormal cellular Ca2+ handling, and other aberrations. To gain a better understanding of the disease mechanisms, it is imperative to validate these findings in human cells. Furthermore, with the recent advancements in gene-editing technology, hiPSCs provide a valuable platform for research and development of new therapies including the possibility of regenerative medicine. In this article, we review the DMD cardiac-related research performed so far using human hiPSCs-derived cardiomyocytes (hiPSC-CMs) carrying DMD mutations.
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Affiliation(s)
- Binyamin Eisen
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Ofer Binah
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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Willet AH, Chen JS, Ren L, Gould KL. Membrane binding of endocytic myosin-1s is inhibited by a class of ankyrin repeat proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538419. [PMID: 37163016 PMCID: PMC10168314 DOI: 10.1101/2023.04.26.538419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Myosin-1s are monomeric actin-based motors that function at membranes. Myo1 is the single myosin-1 isoform in Schizosaccharomyces pombe that works redundantly with Wsp1-Vrp1 to activate the Arp2/3 complex for endocytosis. Here, we identified Ank1 as an uncharacterized cytoplasmic Myo1 binding partner. We found that in ank1Δ cells, Myo1 dramatically redistributed from endocytic patches to decorate the entire plasma membrane and endocytosis was defective. Biochemical analysis and structural predictions suggested that the Ank1 ankyrin repeats bind the Myo1 lever arm and the Ank1 acidic tail binds the Myo1 TH1 domain to prevent TH1-dependent Myo1 membrane binding. Indeed, Ank1 over-expression precluded Myo1 membrane localization and recombinant Ank1 blocked purified Myo1 liposome binding in vitro. Based on biochemical and cell biology analyses, we propose budding yeast Ank1 and human OSTF1 are functional Ank1 orthologs and that cytoplasmic sequestration by small ankyrin repeat proteins is a conserved mechanism regulating myosin-1s in endocytosis. Summary Fission yeast long-tailed myosin-1 binds Ank1. Ank1 ankyrin repeats associate with the Myo1 lever arm and Ank1 acidic tail binds the Myo1 TH1 domain to inhibit Myo1 membrane binding. Ank1 orthologs exists in budding yeast (Ank1) and humans (OSTF1).
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Affiliation(s)
- Alaina H Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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28
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Amiri S, Adibzadeh S, Ghanbari S, Rahmani B, Kheirandish MH, Farokhi-Fard A, Dastjerdeh MS, Davami F. CRISPR-interceded CHO cell line development approaches. Biotechnol Bioeng 2023; 120:865-902. [PMID: 36597180 DOI: 10.1002/bit.28329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
For industrial production of recombinant protein biopharmaceuticals, Chinese hamster ovary (CHO) cells represent the most widely adopted host cell system, owing to their capacity to produce high-quality biologics with human-like posttranslational modifications. As opposed to random integration, targeted genome editing in genomic safe harbor sites has offered CHO cell line engineering a new perspective, ensuring production consistency in long-term culture and high biotherapeutic expression levels. Corresponding the remarkable advancements in knowledge of CRISPR-Cas systems, the use of CRISPR-Cas technology along with the donor design strategies has been pushed into increasing novel scenarios in cell line engineering, allowing scientists to modify mammalian genomes such as CHO cell line quickly, readily, and efficiently. Depending on the strategies and production requirements, the gene of interest can also be incorporated at single or multiple loci. This review will give a gist of all the most fundamental recent advancements in CHO cell line development, such as different cell line engineering approaches along with donor design strategies for targeted integration of the desired construct into genomic hot spots, which could ultimately lead to the fast-track product development process with consistent, improved product yield and quality.
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Affiliation(s)
- Shahin Amiri
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Setare Adibzadeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Samaneh Ghanbari
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Rahmani
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad H Kheirandish
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies, Tehran University of Medical Sciences, Tehran, Iran
| | - Aref Farokhi-Fard
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansoureh S Dastjerdeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Davami
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Keating SS, Bademosi AT, San Gil R, Walker AK. Aggregation-prone TDP-43 sequesters and drives pathological transitions of free nuclear TDP-43. Cell Mol Life Sci 2023; 80:95. [PMID: 36930291 PMCID: PMC10023653 DOI: 10.1007/s00018-023-04739-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023]
Abstract
Aggregation of the RNA-binding protein, TDP-43, is the unifying hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43-related neurodegeneration involves multiple changes to normal physiological TDP-43, which undergoes nuclear depletion, cytoplasmic mislocalisation, post-translational modification, and aberrant liquid-liquid phase separation, preceding inclusion formation. Along with toxic cytoplasmic aggregation, concurrent depletion and dysfunction of normal nuclear TDP-43 in cells with TDP-43 pathology is likely a key potentiator of neurodegeneration, but is not well understood. To define processes driving TDP-43 dysfunction, we used CRISPR/Cas9-mediated fluorescent tagging to investigate how disease-associated stressors and pathological TDP-43 alter abundance, localisation, self-assembly, aggregation, solubility, and mobility dynamics of normal nuclear TDP-43 over time in live cells. Oxidative stress stimulated liquid-liquid phase separation of endogenous TDP-43 into droplet-like puncta, or spherical shell-like anisosomes. Further, nuclear RNA-binding-ablated or acetylation-mimicking TDP-43 readily sequestered and depleted free normal nuclear TDP-43 into dynamic anisosomes, in which recruited endogenous TDP-43 proteins remained soluble and highly mobile. Large, phosphorylated inclusions formed by nuclear or cytoplasmic aggregation-prone TDP-43 mutants also caused sequestration, but rendered endogenous TDP-43 immobile and insoluble, indicating pathological transition. These findings suggest that RNA-binding deficiency and post-translational modifications including acetylation exacerbate TDP-43 aggregation and dysfunction by driving sequestration, mislocalisation, and depletion of normal nuclear TDP-43 in neurodegenerative diseases.
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Affiliation(s)
- Sean S Keating
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Adekunle T Bademosi
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Kmiec EB. Genome editing before CRISPR: The gnostic bible. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:525-526. [PMID: 36873110 PMCID: PMC9978322 DOI: 10.1016/j.omtn.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Eric B. Kmiec
- Gene Editing Institute, ChristianaCare, 550 S. College Avenue, Suite 208 2 Floor, Room 213, Newark, DE 19713, USA
- Corresponding author: Eric B. Kmiec, PhD Executive Director, 550 S. College Avenue, Suite 208 2 Floor, Room 213, Newark, DE 19713, USA.
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Hu Y, Xu J, Gao E, Fan X, Wei J, Ye B, Xu S, Ma W. Enhanced single RNA imaging reveals dynamic gene expression in live animals. eLife 2023; 12:82178. [PMID: 36867026 PMCID: PMC10032653 DOI: 10.7554/elife.82178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/01/2023] [Indexed: 03/04/2023] Open
Abstract
Imaging endogenous mRNAs in live animals is technically challenging. Here, we describe an MS2-based signal amplification with the Suntag system that enables live-cell RNA imaging of high temporal resolution and with 8xMS2 stem-loops, which overcomes the obstacle of inserting a 1300 nt 24xMS2 into the genome for the imaging of endogenous mRNAs. Using this tool, we were able to image the activation of gene expression and the dynamics of endogenous mRNAs in the epidermis of live C. elegans.
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Affiliation(s)
- Yucen Hu
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jingxiu Xu
- International Biomedicine-X research center of the Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Erqing Gao
- International Biomedicine-X research center of the Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xueyuan Fan
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jieli Wei
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Bingcheng Ye
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Suhong Xu
- International Biomedicine-X research center of the Second Affiliated Hospital, Zhejiang University, Hangzhou, China
- Center for Stem Cell and Regenerative Medicine and Department of Burn and wound repair of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weirui Ma
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
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32
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Sake JA, Selo MA, Burtnyak L, Dähnhardt HE, Helbet C, Mairinger S, Langer O, Kelly VP, Ehrhardt C. Knockout of ABCC1 in NCI-H441 cells reveals CF to be a suboptimal substrate to study MRP1 activity in organotypic in vitro models. Eur J Pharm Sci 2023; 181:106364. [PMID: 36563915 DOI: 10.1016/j.ejps.2022.106364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/04/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Multidrug resistance-associated protein 1 (MRP1/ABCC1) is an efflux transporter responsible for the extrusion of endogenous substances as well as xenobiotics and their respective metabolites. Its high expression levels in lung tissue imply a key role in pulmonary drug disposition. Moreover, its association with inflammatory lung diseases underline MRP1's relevance in drug development and precision-medicine. With the aim to develop a tool to better understand MRP1's role in drug disposition and lung disease, we generated an ABCC1-/- clone based on the human distal lung epithelial cell line NCI-H441 via a targeted CRISPR/Cas9 approach. Successful knockout (KO) of MRP1 was confirmed by qPCR, immunoblot and Sanger sequencing. To assess potential compensatory upregulation of transporters with a similar substrate recognition pattern as MRP1, expression levels of MRP2-9 as well as OAT1-4, 6, 7 and 10 were measured. Functional transporter activity was determined via release studies with two prodrug/substrate pairs, i.e. 5(6)-carboxyfluorescein (CF; formed from its diacetate prodrug) and S-(6-(7-methylpurinyl))glutathione (MPG; formed from its prodrug 6-bromo-7-methylpurine, BMP), respectively. Lastly, transepithelial electrical resistance (TEER) of monolayers of the KO clone were compared with wildtype (WT) NCI-H441 cells. Of eight initially generated clones, the M2 titled clone showed complete absence of mRNA and protein in accordance with the designed genome edit. In transport studies using the substrate CF, however, no differences between the KO clone and WT NCI-H441 cells were observed, whilst no differences in expression of potential compensatory transporters was noted. On the other hand, when using BMP/MPG, the release of MPG was reduced to 11.5% in the KO clone. Based on these results, CF appears to be a suboptimal probe for the study of MRP1 function, particularly in organotypic in vitro and ex vivo models. Our ABCC1-/- NCI-H441 clone further retained the ability to form electrically tight barriers, making it a useful model to study MRP1 function in vitro.
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Affiliation(s)
- Johannes A Sake
- School of Pharmacy and Pharmaceutical Sciences and Trinity Biomedical Sciences Institute, Trinity College Dublin, Panoz Institute, Dublin 2, Ireland
| | - Mohammed Ali Selo
- School of Pharmacy and Pharmaceutical Sciences and Trinity Biomedical Sciences Institute, Trinity College Dublin, Panoz Institute, Dublin 2, Ireland; Faculty of Pharmacy, University of Kufa, Al-Najaf, Iraq
| | - Lyubomyr Burtnyak
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Henriette E Dähnhardt
- School of Pharmacy and Pharmaceutical Sciences and Trinity Biomedical Sciences Institute, Trinity College Dublin, Panoz Institute, Dublin 2, Ireland
| | - Camelia Helbet
- School of Pharmacy and Pharmaceutical Sciences and Trinity Biomedical Sciences Institute, Trinity College Dublin, Panoz Institute, Dublin 2, Ireland
| | - Severin Mairinger
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria; Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Oliver Langer
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria; Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Carsten Ehrhardt
- School of Pharmacy and Pharmaceutical Sciences and Trinity Biomedical Sciences Institute, Trinity College Dublin, Panoz Institute, Dublin 2, Ireland.
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Li Y, Lian D, Wang J, Zhao Y, Li Y, Liu G, Wu S, Deng S, Du X, Lian Z. MDM2 antagonists promote CRISPR/Cas9-mediated precise genome editing in sheep primary cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:309-323. [PMID: 36726409 PMCID: PMC9883270 DOI: 10.1016/j.omtn.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/31/2022] [Indexed: 01/04/2023]
Abstract
CRISPR-Cas9-mediated genome editing in sheep is of great use in both agricultural and biomedical applications. While targeted gene knockout by CRISPR-Cas9 through non-homologous end joining (NHEJ) has worked efficiently, the knockin efficiency via homology-directed repair (HDR) remains lower, which severely hampers the application of precise genome editing in sheep. Here, in sheep fetal fibroblasts (SFFs), we optimized several key parameters that affect HDR, including homology arm (HA) length and the amount of double-stranded DNA (dsDNA) repair template; we also observed synchronization of SFFs in G2/M phase could increase HDR efficiency. Besides, we identified three potent small molecules, RITA, Nutlin3, and CTX1, inhibitors of p53-MDM2 interaction, that caused activation of the p53 pathway, resulting in distinct G2/M cell-cycle arrest in response to DNA damage and improved CRISPR-Cas9-mediated HDR efficiency by 1.43- to 4.28-fold in SFFs. Furthermore, we demonstrated that genetic knockout of p53 could inhibit HDR in SFFs by suppressing the expression of several key factors involved in the HDR pathway, such as BRCA1 and RAD51. Overall, this study offers an optimized strategy for the usage of dsDNA repair template, more importantly, the application of MDM2 antagonists provides a simple and efficient strategy to promote CRISPR/Cas9-mediated precise genome editing in sheep primary cells.
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Affiliation(s)
- Yan Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing 100071, China,These authors contributed equally
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,These authors contributed equally
| | - Jiahao Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China,Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China,These authors contributed equally
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yao Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guoshi Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China,Corresponding author: Shoulong Deng, NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, 5 Panjiayuannanli, Chaoyang District, Beijing 100021, China.
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,Corresponding author: Xuguang Du, State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China,Corresponding author: Zhengxing Lian, Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2 Mingyuanxilu, Haidian District, Beijing 100193, China. .
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Lintott LG, Nutter LMJ. Genetic and Molecular Quality Control of Genetically Engineered Mice. Methods Mol Biol 2023; 2631:53-101. [PMID: 36995664 DOI: 10.1007/978-1-0716-2990-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genetically engineered mice are used as avatars to understand mammalian gene function and develop therapies for human disease. During genetic modification, unintended changes can occur, and these changes may result in misassigned gene-phenotype relationships leading to incorrect or incomplete experimental interpretations. The types of unintended changes that may occur depend on the allele type being made and the genetic engineering approach used. Here we broadly categorize allele types as deletions, insertions, base changes, and transgenes derived from engineered embryonic stem (ES) cells or edited mouse embryos. However, the methods we describe can be adapted to other allele types and engineering strategies. We describe the sources and consequ ences of common unintended changes and best practices for detecting both intended and unintended changes by screening and genetic and molecular quality control (QC) of chimeras, founders, and their progeny. Employing these practices, along with careful allele design and good colony management, will increase the chance that investigations using genetically engineered mice will produce high-quality reproducible results, to enable a robust understanding of gene function, human disease etiology, and therapeutic development.
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Affiliation(s)
- Lauri G Lintott
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada.
- The Hospital for Sick Children, Toronto, ON, Canada.
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35
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Carelli FN, Cerrato C, Dong Y, Appert A, Dernburg A, Ahringer J. Widespread transposon co-option in the Caenorhabditis germline regulatory network. SCIENCE ADVANCES 2022; 8:eabo4082. [PMID: 36525485 PMCID: PMC9757741 DOI: 10.1126/sciadv.abo4082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. We show that transposon expansions in Caenorhabditis nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one-third of Caenorhabditis elegans germline-specific promoters have been co-opted from two related miniature inverted repeat transposable elements (TEs), CERP2 and CELE2. These promoters are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. Expansion of CERP2 occurred before radiation of the Caenorhabditis genus, as did fixation of mutations in HIM-17 through positive selection, whereas CELE2 expanded only in C. elegans. Through comparative analyses in Caenorhabditis briggsae, we find not only evolutionary conservation of most CERP2 co-opted promoters but also a substantial fraction that are species-specific. Our work reveals the emergence and evolutionary conservation of a novel transcriptional network driven by TE co-option with a major impact on regulatory evolution.
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Affiliation(s)
- Francesco Nicola Carelli
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chiara Cerrato
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alex Appert
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Abby Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
- Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, Berkeley, CA 94720, USA
| | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
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Carrington B, Ramanagoudr-Bhojappa R, Bresciani E, Han TU, Sood R. A robust pipeline for efficient knock-in of point mutations and epitope tags in zebrafish using fluorescent PCR based screening. BMC Genomics 2022; 23:810. [PMID: 36476416 PMCID: PMC9730659 DOI: 10.1186/s12864-022-08971-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome editing using CRISPR/Cas9 has become a powerful tool in zebrafish to generate targeted gene knockouts models. However, its use for targeted knock-in remains challenging due to inefficient homology directed repair (HDR) pathway in zebrafish, highlighting the need for efficient and cost-effective screening methods. RESULTS: Here, we present our fluorescent PCR and capillary electrophoresis based screening approach for knock-in using a single-stranded oligodeoxynucleotide donor (ssODN) as a repair template for the targeted insertion of epitope tags, or single nucleotide changes to recapitulate pathogenic human alleles. For the insertion of epitope tags, we took advantage of the expected change in size of the PCR product. For point mutations, we combined fluorescent PCR with restriction fragment length polymorphism (RFLP) analysis to distinguish the fish with the knock-in allele. As a proof-of-principle, we present our data on the generation of fish lines with insertion of a FLAG tag at the tcnba locus, an HA tag at the gata2b locus, and a point mutation observed in Gaucher disease patients in the gba gene. Despite the low number of germline transmitting founders (1-5%), combining our screening methods with prioritization of founder fish by fin biopsies allowed us to establish stable knock-in lines by screening 12 or less fish per gene. CONCLUSIONS We have established a robust pipeline for the generation of zebrafish models with precise integration of small DNA sequences and point mutations at the desired sites in the genome. Our screening method is very efficient and easy to implement as it is PCR-based and only requires access to a capillary sequencer.
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Affiliation(s)
- Blake Carrington
- Translational and Functional Genomics Branch, Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genetics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tae-Un Han
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Raman Sood
- Translational and Functional Genomics Branch, Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Pachano T, Rada-Iglesias A. Protocol to study sufficiency of cis-regulatory elements in mouse embryonic stem cells using a CRISPR-mediated knockin approach. STAR Protoc 2022; 3:101492. [PMID: 35769926 PMCID: PMC9234469 DOI: 10.1016/j.xpro.2022.101492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Tomas Pachano
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria, Albert Einstein 22, 39011 Santander, Spain.
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38
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Gao K, Zhang X, Zhang Z, Wu X, Guo Y, Fu P, Sun A, Peng J, Zheng J, Yu P, Wang T, Ye Q, Jiang J, Wang H, Lin CP, Gao G. Transcription-coupled donor DNA expression increases homologous recombination for efficient genome editing. Nucleic Acids Res 2022; 50:e109. [PMID: 35929067 DOI: 10.1093/nar/gkac676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 11/14/2022] Open
Abstract
Genomes can be edited by homologous recombination stimulated by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated peptide 9]-induced DNA double-strand breaks. However, this approach is inefficient for inserting or deleting long fragments in mammalian cells. Here, we describe a simple genome-editing method, termed transcription-coupled Cas9-mediated editing (TEd), that can achieve higher efficiencies than canonical Cas9-mediated editing (CEd) in deleting genomic fragments, inserting/replacing large DNA fragments and introducing point mutations into mammalian cell lines. We also found that the transcription on DNA templates is crucial for the promotion of homology-directed repair, and that tethering transcripts from TEd donors to targeted sites further improves editing efficiency. The superior efficiency of TEd for the insertion and deletion of long DNA fragments expands the applications of CRISPR for editing mammalian genomes.
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Affiliation(s)
- Kaixuan Gao
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xuedi Zhang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhenwu Zhang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiangyu Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Guo
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Pengchong Fu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Angyang Sun
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ju Peng
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jie Zheng
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Pengfei Yu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tengfei Wang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qinying Ye
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jingwei Jiang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haopeng Wang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chao-Po Lin
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Guanjun Gao
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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39
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Wagner A, Seiler J, Beye M. Highly efficient site-specific integration of DNA fragments into the honeybee genome using CRISPR/Cas9. G3 GENES|GENOMES|GENETICS 2022; 12:6583193. [PMID: 35536186 PMCID: PMC9157169 DOI: 10.1093/g3journal/jkac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
Abstract
Functional genetic studies in honeybees have been limited to transposon mediated transformation and site directed mutagenesis tools. However, site- and sequence-specific manipulations that insert DNA fragments or replace sequences at specific target sites are lacking. Such tools would enable the tagging of proteins, the expression of reporters and site-specific amino acid changes, which are all gold standard manipulations for physiological, organismal, and genetic studies. However, such manipulations must be very efficient in honeybees since screening and crossing procedures are laborious due to their social organization. Here, we report an accurate and remarkably efficient site-specific integration of DNA-sequences into the honeybee genome using clustered regularly interspaced short palindromic repeat/clustered regularly interspaced short palindromic repeat-associated protein 9-mediated homology-directed repair. We employed early embryonic injections and selected a highly efficient sgRNA in order to insert 294 and 729 bp long DNA sequences into a specific locus at the dsx gene. These sequences were locus-specifically integrated in 57% and 59% of injected bees. Most importantly, 21% and 25% of the individuals lacked the wildtype sequence demonstrating that we generated homozygous mutants in which all cells are affected (no mosaicism). The highly efficient, locus-specific insertions of nucleotide sequences generating homozygous mutants demonstrate that systematic molecular studies for honeybees are in hand that allow somatic mutation approaches via workers or studies in the next generation using queens with their worker progeny. The employment of early embryonic injections and screenings of highly efficient sgRNAs may offer the prospect of highly successful sequence- and locus-specific mutations also in other organisms.
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Affiliation(s)
- Anna Wagner
- Department of Biology, Institute of Evolutionary Genetics, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Jana Seiler
- Department of Biology, Institute of Evolutionary Genetics, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Martin Beye
- Department of Biology, Institute of Evolutionary Genetics, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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40
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Liang Q, Jin Y, Xu S, Zhou J, Mao J, Ma X, Wang M, Cong YS. Human UFSP1 translated from an upstream near-cognate initiation codon functions as an active UFM1-specific protease. J Biol Chem 2022; 298:102016. [PMID: 35525273 PMCID: PMC9168615 DOI: 10.1016/j.jbc.2022.102016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a recently identified ubiquitin-like posttranslational modification with important biological functions. However, the regulatory mechanisms governing UFM1 modification of target proteins (UFMylation) and the cellular processes controlled by UFMylation remain largely unknown. It has been previously shown that a UFM1-specific protease (UFSP2) mediates the maturation of the UFM1 precursor and drives the de-UFMylation reaction. Furthermore, it has long been thought that UFSP1, an ortholog of UFSP2, is inactive in many organisms, including human, because it lacks an apparent protease domain when translated from the canonical start codon (445AUG). Here, we demonstrate using the combination of site-directed mutagenesis, CRISPR/Cas9–mediated genome editing, and mass spectrometry approaches that translation of human UFSP1 initiates from an upstream near-cognate codon, 217CUG, via eukaryotic translation initiation factor eIF2A-mediated translational initiation rather than from the annotated 445AUG, revealing the presence of a catalytic protease domain containing a Cys active site. Moreover, we show that both UFSP1 and UFSP2 mediate maturation of UFM1 and de-UFMylation of target proteins. This study demonstrates that human UFSP1 functions as an active UFM1-specific protease, thus contributing to our understanding of the UFMylation/de-UFMylation process.
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Affiliation(s)
- Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yaqi Jin
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Shiwen Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xiaohe Ma
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
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41
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Validation Study to Determine the Accuracy of Widespread Promoterless EGFP Reporter at Assessing CRISPR/Cas9-Mediated Homology Directed Repair. Curr Issues Mol Biol 2022; 44:1688-1700. [PMID: 35723374 PMCID: PMC9164083 DOI: 10.3390/cimb44040116] [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: 02/04/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
An accurate visual reporter system to assess homology-directed repair (HDR) is a key prerequisite for evaluating the efficiency of Cas9-mediated precise gene editing. Herein, we tested the utility of the widespread promoterless EGFP reporter to assess the efficiency of CRISPR/Cas9-mediated homologous recombination by fluorescence expression. We firstly established a promoterless EGFP reporter donor targeting the porcine GAPDH locus to study CRISPR/Cas9-mediated homologous recombination in porcine cells. Curiously, EGFP was expressed at unexpectedly high levels from the promoterless donor in porcine cells, with or without Cas9/sgRNA. Even higher EGFP expression was detected in human cells and those of other species when the porcine donor was transfected alone. Therefore, EGFP could be expressed at certain level in various cells transfected with the promoterless EGFP reporter alone, making it a low-resolution reporter for measuring Cas9-mediated HDR events. In summary, the widespread promoterless EGFP reporter could not be an ideal measurement for HDR screening and there is an urgent need to develop a more reliable, high-resolution HDR screening system to better explore strategies of increasing the efficiency of Cas9-mediated HDR in mammalian cells.
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42
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Chen J, Li S, He Y, Li J, Xia L. An update on precision genome editing by homology-directed repair in plants. PLANT PHYSIOLOGY 2022; 188:1780-1794. [PMID: 35238390 PMCID: PMC8968426 DOI: 10.1093/plphys/kiac037] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/20/2022] [Indexed: 05/22/2023]
Abstract
Beneficial alleles derived from local landraces or related species, or even orthologs from other plant species, are often caused by differences of one or several single-nucleotide polymorphisms or indels in either the promoter region or the encoding region of a gene and often account for major differences in agriculturally important traits. Clustered regularly interspaced short palindromic repeats-associated endonuclease Cas9 system (CRISPR/Cas9)-mediated precision genome editing enables targeted allele replacement or insertion of flag or foreign genes at specific loci via homology-directed repair (HDR); however, HDR efficiency is low due to the intrinsic rare occurrence of HDR and insufficient DNA repair template in the proximity of a double-stranded break (DSB). Precise replacement of the targeted gene with elite alleles from landraces or relatives into a commercial variety through genome editing has been a holy grail in the crop genome editing field. In this update, we briefly summarize CRISPR/Cas-mediated HDR in plants. We describe diverse strategies to improve HDR efficiency by manipulating the DNA repair pathway, timing DSB induction, and donor delivery, and so on. Lastly, we outline open questions and challenges in HDR-mediated precision genome editing in both plant biological research and crop improvement.
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Affiliation(s)
| | | | - Yubing He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
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43
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Lee JH. Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases. Exp Neurobiol 2022; 31:1-16. [PMID: 35256540 PMCID: PMC8907251 DOI: 10.5607/en22003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 01/16/2023] Open
Abstract
Patients suffering from rare human diseases often go through a painful journey for finding a definite molecular diagnosis prerequisite of appropriate cures. With a novel variant isolated from a single patient, determination of its pathogenicity to end such "diagnostic odyssey" requires multi-step processes involving experts in diverse areas of interest, including clinicians, bioinformaticians and research scientists. Recent efforts in building large-scale genomic databases and in silico prediction platforms have facilitated identification of potentially pathogenic variants causative of rare human diseases of a Mendelian basis. However, the functional significance of individual variants remains elusive in many cases, thus requiring incorporation of versatile and rapid model organism (MO)-based platforms for functional analyses. In this review, the current scope of rare disease research is briefly discussed. In addition, an overview of invertebrate MOs for their key features relevant to rare neurological diseases is provided, with the characteristics of two representative invertebrate MOs, Drosophila melanogaster and Caenorhabditis elegans, as well as the challenges against them. Finally, recently developed research networks integrating these MOs in collaborative research are portraited with an array of bioinformatical analyses embedded. A comprehensive survey of MO-based research activities provided in this review will help us to design a wellstructured analysis of candidate genes or potentially pathogenic variants for their roles in rare neurological diseases in future.
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Affiliation(s)
- Ji-Hye Lee
- Department of Oral Pathology & Life Science in Dentistry, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,Dental Life Science Institute, Pusan National University, Yangsan 50612, Korea.,Periodontal Disease Signaling Network Research Center, Pusan National University, Yangsan 50612, Korea
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44
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Rezalotfi A, Fritz L, Förster R, Bošnjak B. Challenges of CRISPR-Based Gene Editing in Primary T Cells. Int J Mol Sci 2022; 23:ijms23031689. [PMID: 35163611 PMCID: PMC8835901 DOI: 10.3390/ijms23031689] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/29/2022] [Indexed: 12/30/2022] Open
Abstract
Adaptive T-cell immunotherapy holds great promise for the successful treatment of leukemia, as well as other types of cancers. More recently, it was also shown to be an effective treatment option for chronic virus infections in immunosuppressed patients. Autologous or allogeneic T cells used for immunotherapy are usually genetically modified to express novel T-cell or chimeric antigen receptors. The production of such cells was significantly simplified with the CRISPR/Cas system, allowing for the deletion or insertion of novel genes at specific locations within the genome. In this review, we describe recent methodological breakthroughs that were important for the conduction of these genetic modifications, summarize crucial points to be considered when conducting such experiments, and highlight the potential pitfalls of these approaches.
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Affiliation(s)
- Alaleh Rezalotfi
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
| | - Lea Fritz
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover, 30625 Hannover, Germany
| | - Berislav Bošnjak
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany; (A.R.); (L.F.); (R.F.)
- Correspondence: ; Tel.: +49-511-532-9731
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45
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Simone BW, Lee HB, Daby CL, Ata H, Restrepo-Castillo S, Martínez-Gálvez G, Kar B, Gendron WA, Clark KJ, Ekker SC. Chimeric RNA: DNA TracrRNA Improves Homology-Directed Repair In Vitro and In Vivo. CRISPR J 2022; 5:40-52. [PMID: 34935462 PMCID: PMC8892967 DOI: 10.1089/crispr.2021.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nearly 90% of human pathogenic mutations are caused by small genetic variations, and methods to correct these errors efficiently are critically important. One way to make small DNA changes is providing a single-stranded oligo deoxynucleotide (ssODN) containing an alteration coupled with a targeted double-strand break (DSB) at the target locus in the genome. Coupling an ssODN donor with a CRISPR-Cas9-mediated DSB is one of the most streamlined approaches to introduce small changes. However, in many systems, this approach is inefficient and introduces imprecise repair at the genetic junctions. We herein report a technology that uses spatiotemporal localization of an ssODN with CRISPR-Cas9 to improve gene alteration. We show that by fusing an ssODN template to the trans-activating RNA (tracrRNA), we recover precise genetic alterations, with increased integration and precision in vitro and in vivo. Finally, we show that this technology can be used to enhance gene conversion with other gene editing tools such as transcription activator like effector nucleases.
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Affiliation(s)
- Brandon W. Simone
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Han B. Lee
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Camden L. Daby
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Hirotaka Ata
- Department of Clinical and Translational Sciences, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Santiago Restrepo-Castillo
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Gabriel Martínez-Gálvez
- Mayo Clinic Graduate School of Biomedical Sciences, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - William A.C. Gendron
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Biomedical Engineering and Physiology Track, Mayo Clinic, Rochester, Minnesota, USA
- Address correspondence to: Stephen C. Ekker, PhD, Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA,
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46
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An oncogenic splice variant of PDGFRα in adult glioblastoma as a therapeutic target for selective CDK4/6 inhibitors. Sci Rep 2022; 12:1275. [PMID: 35075231 PMCID: PMC8786844 DOI: 10.1038/s41598-022-05391-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/06/2022] [Indexed: 12/15/2022] Open
Abstract
Understanding human genome alterations is necessary to optimize genome-based cancer therapeutics. However, some newly discovered mutations remain as variants of unknown significance (VUS). Here, the mutation c.1403A > G in exon 10 of the platelet-derived growth factor receptor-alpha (PDGFRA) gene, a VUS found in adult glioblastoma multiforme (GBM), was introduced in human embryonal kidney 293 T (HEK293T) cells using genome editing to investigate its potential oncogenic functions. Genome editing was performed using CRISPR/Cas9; the proliferation, drug sensitivity, and carcinogenic potential of genome-edited cells were investigated. We also investigated the mechanism underlying the observed phenotypes. Three GBM patients carrying the c.1403A > G mutation were studied to validate the in vitro results. The c.1403A > G mutation led to a splice variant (p.K455_N468delinsN) because of the generation of a 3’-acceptor splice site in exon 10. PDGFRA-mutated HEK293T cells exhibited a higher proliferative activity via PDGFRα and the cyclin-dependent kinase (CDK)4/CDK6-cyclin D1 signaling pathway in a ligand-independent manner. They showed higher sensitivity to multi-kinase, receptor tyrosine kinase, and CDK4/CDK6 inhibitors. Of the three GBM patients studied, two harbored the p.K455_N468delinsN splice variant. The splicing mutation c.1403A > G in PDGFRA is oncogenic in nature. Kinase inhibitors targeting PDGFRα and CDK4/CDK6 signaling should be evaluated for treating GBM patients harboring this mutation.
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47
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Sun W, Liu H, Yin W, Qiao J, Zhao X, Liu Y. Strategies for Enhancing the Homology-directed Repair Efficiency of CRISPR-Cas Systems. CRISPR J 2022; 5:7-18. [PMID: 35076280 DOI: 10.1089/crispr.2021.0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The CRISPR-Cas nuclease has emerged as a powerful genome-editing tool in recent years. The CRISPR-Cas system induces double-strand breaks that can be repaired via the non-homologous end joining or homology-directed repair (HDR) pathway. Compared to non-homologous end joining, HDR can be used for the treatment of incurable monogenetic diseases. Therefore, remarkable efforts have been dedicated to enhancing the efficacy of HDR. In this review, we summarize the currently used strategies for enhancing the HDR efficiency of CRISPR-Cas systems based on three factors: (1) regulation of the key factors in the DNA repair pathways, (2) modulation of the components in the CRISPR machinery, and (3) alteration of the intracellular environment around double-strand breaks. Representative cases and potential solutions for further improving HDR efficiency are also discussed, facilitating the development of new CRISPR technologies to achieve highly precise genetic manipulation in the future.
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Affiliation(s)
- Wenli Sun
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Hui Liu
- Department of Hematology, Renmin Hospital of Wuhan University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Wenhao Yin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Jie Qiao
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China
| | - Xueke Zhao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Henan, People's Republic of China; and Ltd., Hubei, People's Republic of China
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, People's Republic of China; Ltd., Hubei, People's Republic of China.,BravoVax Co., Ltd., Hubei, People's Republic of China
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48
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Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
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Affiliation(s)
- Tarun S. Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada,Corresponding authors: ,
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032,Lead Contact,Corresponding authors: ,
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49
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Ittiprasert W, Chatupheeraphat C, Mann VH, Li W, Miller A, Ogunbayo T, Tran K, Alrefaei YN, Mentink-Kane M, Brindley PJ. RNA-Guided AsCas12a- and SpCas9-Catalyzed Knockout and Homology Directed Repair of the Omega-1 Locus of the Human Blood Fluke, Schistosoma mansoni. Int J Mol Sci 2022; 23:631. [PMID: 35054816 PMCID: PMC8775552 DOI: 10.3390/ijms23020631] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 12/17/2022] Open
Abstract
The efficiency of the RNA-guided AsCas12a nuclease of Acidaminococcus sp. was compared with SpCas9 from Streptococcus pyogenes, for functional genomics in Schistosoma mansoni. We deployed optimized conditions for the ratio of guide RNAs to the nuclease, donor templates, and electroporation parameters, to target a key schistosome enzyme termed omega-1. Programmed cleavages catalyzed by Cas12a and Cas9 resulted in staggered- and blunt-ended strand breaks, respectively. AsCas12a was more efficient than SpCas9 for gene knockout, as determined by TIDE analysis. CRISPResso2 analysis confirmed that most mutations were deletions. Knockout efficiency of both nucleases markedly increased in the presence of single-stranded oligodeoxynucleotide (ssODN) template. With AsCas12a, ssODNs representative of both the non-CRISPR target (NT) and target (T) strands were tested, resulting in KO efficiencies of 15.67, 28.71, and 21.43% in the SpCas9 plus ssODN, AsCas12a plus NT-ssODN, and AsCas12a plus T-ssODN groups, respectively. Trans-cleavage against the ssODNs by activated AsCas12a was not apparent in vitro. SpCas9 catalyzed more precise transgene insertion, with knock-in efficiencies of 17.07% for the KI_Cas9 group, 14.58% for KI_Cas12a-NT-ssODN, and 12.37% for KI_Cas12a-T-ssODN. Although AsCas12a induced fewer mutations per genome than SpCas9, the phenotypic impact on transcription and expression of omega-1 was similar for both nucleases.
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Affiliation(s)
- Wannaporn Ittiprasert
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
| | - Chawalit Chatupheeraphat
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Victoria H. Mann
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
| | - Wenhui Li
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - André Miller
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Taiwo Ogunbayo
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Kenny Tran
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Yousef N. Alrefaei
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
- Department of Medical Laboratory Technology, College of Health Sciences, PAEET, Adailiya, Kuwait City 73101, Kuwait
| | - Margaret Mentink-Kane
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA; (A.M.); (T.O.); (K.T.); (M.M.-K.)
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA; (C.C.); (V.H.M.); (W.L.); (Y.N.A.)
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Ou T, He W, Quinlan BD, Guo Y, Tran MH, Karunadharma P, Park H, Davis-Gardner ME, Yin Y, Zhang X, Wang H, Zhong G, Farzan M. Reprogramming of the heavy-chain CDR3 regions of a human antibody repertoire. Mol Ther 2022; 30:184-197. [PMID: 34740791 PMCID: PMC8753427 DOI: 10.1016/j.ymthe.2021.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/09/2021] [Accepted: 10/27/2021] [Indexed: 01/07/2023] Open
Abstract
B cells have been engineered ex vivo to express an HIV-1 broadly neutralizing antibody (bNAb). B cell reprograming may be scientifically and therapeutically useful, but current approaches limit B cell repertoire diversity and disrupt the organization of the heavy-chain locus. A more diverse and physiologic B cell repertoire targeting a key HIV-1 epitope could facilitate evaluation of vaccines designed to elicit bNAbs, help identify more potent and bioavailable bNAb variants, or directly enhance viral control in vivo. Here we address the challenges of generating such a repertoire by replacing the heavy-chain CDR3 (HCDR3) regions of primary human B cells. To do so, we identified and utilized an uncharacterized Cas12a ortholog that recognizes PAM motifs present in human JH genes. We also optimized the design of 200 nucleotide homology-directed repair templates (HDRT) by minimizing the required 3'-5' deletion of the HDRT-complementary strand. Using these techniques, we edited primary human B cells to express a hemagglutinin epitope tag and the HCDR3 regions of the bNAbs PG9 and PG16. Those edited with bNAb HCDR3 efficiently bound trimeric HIV-1 antigens, implying they could affinity mature in vivo in response to the same antigens. This approach generates diverse B cell repertoires recognizing a key HIV-1 neutralizing epitope.
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Affiliation(s)
- Tianling Ou
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wenhui He
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Brian D Quinlan
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Yan Guo
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Mai H Tran
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Hajeung Park
- X-ray Crystallography Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Yiming Yin
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xia Zhang
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Haimin Wang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Guocai Zhong
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China; School of Biology and Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Michael Farzan
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA.
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