1
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Woo HJ, Kim J, Kim SM, Kim D, Moon JY, Park D, Lee JS. Context-dependent genomic locus effects on antibody production in recombinant Chinese hamster ovary cells generated through random integration. Comput Struct Biotechnol J 2024; 23:1654-1665. [PMID: 38680870 PMCID: PMC11046053 DOI: 10.1016/j.csbj.2024.04.023] [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: 12/06/2023] [Revised: 03/30/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
High-yield production of therapeutic protein using Chinese hamster ovary (CHO) cells requires stable cell line development (CLD). CLD typically uses random integration of transgenes; however, this results in clonal variation and subsequent laborious clone screening. Therefore, site-specific integration of a protein expression cassette into a desired chromosomal locus showing high transcriptional activity and stability, referred to as a hot spot, is emerging. Although positional effects are important for therapeutic protein expression, the sequence-specific mechanisms by which hotspots work are not well understood. In this study, we performed whole-genome sequencing (WGS) to locate randomly inserted vectors in the genome of recombinant CHO cells expressing high levels of monoclonal antibodies (mAbs) and experimentally validated these locations and vector compositions. The integration site was characterized by active histone marks and potential enhancer activities, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated indel mutations in the region upstream of the integration site led to a significant reduction in specific antibody productivity by up to 30%. Notably, the integration site and its core region did not function equivalently outside the native genomic context, showing a minimal effect on the increase in exogenous protein expression in the host cell line. We also observed a superior production capacity of the mAb expressing cell line compared to that of the host cell line. Collectively, this study demonstrates that developing recombinant CHO cell lines to produce therapeutic proteins at high levels requires a balance of factors including transgene configuration, genomic locus landscape, and host cell properties.
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Affiliation(s)
- Hyun Jee Woo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jaehoon Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Molecular Science and Technology Research Center, Ajou University, Suwon 16499, Republic of Korea
| | - Seul Mi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Dongwoo Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Yun Moon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Daechan Park
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Biological Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
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2
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Li B, Sun C, Li J, Gao C. Targeted genome-modification tools and their advanced applications in crop breeding. Nat Rev Genet 2024; 25:603-622. [PMID: 38658741 DOI: 10.1038/s41576-024-00720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2024] [Indexed: 04/26/2024]
Abstract
Crop improvement by genome editing involves the targeted alteration of genes to improve plant traits, such as stress tolerance, disease resistance or nutritional content. Techniques for the targeted modification of genomes have evolved from generating random mutations to precise base substitutions, followed by insertions, substitutions and deletions of small DNA fragments, and are finally starting to achieve precision manipulation of large DNA segments. Recent developments in base editing, prime editing and other CRISPR-associated systems have laid a solid technological foundation to enable plant basic research and precise molecular breeding. In this Review, we systematically outline the technological principles underlying precise and targeted genome-modification methods. We also review methods for the delivery of genome-editing reagents in plants and outline emerging crop-breeding strategies based on targeted genome modification. Finally, we consider potential future developments in precise genome-editing technologies, delivery methods and crop-breeding approaches, as well as regulatory policies for genome-editing products.
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Affiliation(s)
- Boshu Li
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao Sun
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiayang Li
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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3
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Liu S, Maruzuru Y, Takeshima K, Koyanagi N, Kato A, Kawaguchi Y. Impact of the interaction between herpes simplex virus 1 ICP22 and FACT on viral gene expression and pathogenesis. J Virol 2024; 98:e0073724. [PMID: 39016551 PMCID: PMC11338292 DOI: 10.1128/jvi.00737-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
Facilitates chromatin transcription (FACT) interacts with nucleosomes to promote gene transcription by regulating the dissociation and reassembly of nucleosomes downstream and upstream of RNA polymerase II (Pol II). A previous study reported that herpes simplex virus 1 (HSV-1) regulatory protein ICP22 interacted with FACT and was required for its recruitment to the viral DNA genome in HSV-1-infected cells. However, the biological importance of interactions between ICP22 and FACT in relation to HSV-1 infection is unclear. Here, we mapped the minimal domain of ICP22 required for its efficient interaction with FACT to a cluster of five basic amino acids in ICP22. A recombinant virus harboring alanine substitutions in this identified cluster led to the decreased accumulation of viral mRNAs from UL54, UL38, and UL44 genes, reduced Pol II occupancy of these genes in MRC-5 cells, and impaired HSV-1 virulence in mice following ocular or intracranial infection. Furthermore, the treatment of mice infected with wild-type HSV-1 with CBL0137, a FACT inhibitor currently being investigated in clinical trials, significantly improved the survival rate of mice. These results suggested that the interaction between ICP22 and FACT was required for efficient HSV-1 gene expression and pathogenicity. Therefore, FACT might be a potential therapeutic target for HSV-1 infection.IMPORTANCEICP22 is a well-known regulatory factor of HSV-1 gene expression, but its mechanism(s) are poorly understood. Although the interaction of FACT with ICP22 was reported previously, its significance in HSV-1 infection is unknown. Given that FACT is involved in gene transcription, it is of interest to investigate this interaction as it relates to HSV-1 gene expression. To determine a direct link between the interaction and HSV-1 infection, we mapped a minimal domain of ICP22 required for its efficient interaction with FACT and generated a recombinant virus carrying mutations in the identified domain. Using the recombinant virus, we obtained evidence suggesting that the interaction between ICP22 and FACT promoted Pol II transcription from HSV-1 genes and viral virulence in mice. In addition, CBL0137, an inhibitor of FACT, effectively protected mice from lethal HSV-1 infection, suggesting FACT might be a potential target for the development of novel anti-HSV drugs.
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Grants
- 20H05692 MEXT | Japan Society for the Promotion of Science (JSPS)
- 22H04803 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H05584 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JPMJPR22R5 MEXT | Japan Science and Technology Agency (JST)
- JP20wm0125002, JP22fk0108640, JP223fa627001, JP23wm0225031, JP23wm0225035 Japan Agency for Medical Research and Development (AMED)
- JP22gm1610008 Japan Agency for Medical Research and Development (AMED)
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Affiliation(s)
- Shaocong Liu
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuhei Maruzuru
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kosuke Takeshima
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoto Koyanagi
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akihisa Kato
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Kawaguchi
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo, Japan
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4
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Lau CH, Liang QL, Zhu H. Next-generation CRISPR technology for genome, epigenome and mitochondrial editing. Transgenic Res 2024:10.1007/s11248-024-00404-x. [PMID: 39158822 DOI: 10.1007/s11248-024-00404-x] [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: 06/04/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024]
Abstract
The application of rapidly growing CRISPR toolboxes and methods has great potential to transform biomedical research. Here, we provide a snapshot of up-to-date CRISPR toolboxes, then critically discuss the promises and hurdles associated with CRISPR-based nuclear genome editing, epigenome editing, and mitochondrial editing. The technical challenges and key solutions to realize epigenome editing in vivo, in vivo base editing and prime editing, mitochondrial editing in complex tissues and animals, and CRISPR-associated transposases and integrases in targeted genomic integration of very large DNA payloads are discussed. Lastly, we discuss the latest situation of the CRISPR/Cas9 clinical trials and provide perspectives on CRISPR-based gene therapy. Apart from technical shortcomings, ethical and societal considerations for CRISPR applications in human therapeutics and research are extensively highlighted.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biology, College of Science, Shantou University, Shantou, 515063, Guangdong, China
| | - Qing-Le Liang
- Department of Clinical Laboratory Medicine, Chongqing University Jiangjin Hospital, Chongqing, China
| | - Haibao Zhu
- Department of Biology, College of Science, Shantou University, Shantou, 515063, Guangdong, China.
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5
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Wang Y, Liu M, Lin X, Wang H, Dong N, Liu H, Shao H, Zhang W. Genome Editing of Mammalian Cells Through RNA Transcript-Mediated Homologous Recombination Repair. Hum Gene Ther 2024; 35:555-563. [PMID: 39046112 DOI: 10.1089/hum.2024.025] [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: 07/25/2024] Open
Abstract
Double-stranded break (DSB) repair of eukaryotic DNA is mainly accomplished by nonhomologous end joining and homologous recombination (HR). Providing exogenous templates during HR repair can result in the editing of target genes, which is the central mechanism of the well-established clustered regularly interspaced short palindromic repeats (CRISPR) gene editing system. Currently, exogenous templates are mainly DNA molecules, which can provoke a cellular immune response within the cell. In order to verify the feasibility of RNA molecules as repair templates for HR in mammalian cell genome editing, we fused RNA template molecules to the 3'-end of single guide RNA (sgRNA), so that the sgRNA and the homologous template RNA form a single RNA molecule. The results show this construct can be used as a repair template to achieve target gene editing in mammalian cells. In addition, the factors influencing HR mediated by RNA template molecules were investigated, and it was found that increasing the length of homologous arms and inducing an R-loop near the DSBcan effectively promote HR repair. Furthermore, intracellular homologous chromosomes may compete with exogenous RNA templates. The findings in this article provide a reference for the utilization of RNA template molecules to mediate target gene editing in eukaryotic cells, as well as a basis for the study of the mechanism by which RNA molecules mediate the repair of DSBs.
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Affiliation(s)
- Yangmin Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Meilin Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Xinjian Lin
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Haozheng Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Na Dong
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hengshen Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hongwei Shao
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Wenfeng Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
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6
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Gao J, Gunasekar S, Xia ZJ, Shalin K, Jiang C, Chen H, Lee D, Lee S, Pisal ND, Luo JN, Griciuc A, Karp JM, Tanzi R, Joshi N. Gene therapy for CNS disorders: modalities, delivery and translational challenges. Nat Rev Neurosci 2024; 25:553-572. [PMID: 38898231 DOI: 10.1038/s41583-024-00829-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Gene therapy is emerging as a powerful tool to modulate abnormal gene expression, a hallmark of most CNS disorders. The transformative potentials of recently approved gene therapies for the treatment of spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and active cerebral adrenoleukodystrophy are encouraging further development of this approach. However, most attempts to translate gene therapy to the clinic have failed to make it to market. There is an urgent need not only to tailor the genes that are targeted to the pathology of interest but to also address delivery challenges and thereby maximize the utility of genetic tools. In this Review, we provide an overview of gene therapy modalities for CNS diseases, emphasizing the interconnectedness of different delivery strategies and routes of administration. Important gaps in understanding that could accelerate the clinical translatability of CNS genetic interventions are addressed, and we present lessons learned from failed clinical trials that may guide the future development of gene therapies for the treatment and management of CNS disorders.
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Affiliation(s)
- Jingjing Gao
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA.
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA.
| | - Swetharajan Gunasekar
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziting Judy Xia
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kiruba Shalin
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - Christopher Jiang
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hao Chen
- Marine College, Shandong University, Weihai, China
| | - Dongtak Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sohyung Lee
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nishkal D Pisal
- Department of Biomedical Engineering, University of Massachusetts, Amherst, MA, USA
| | - James N Luo
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Ana Griciuc
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Jeffrey M Karp
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Rudolph Tanzi
- Harvard Medical School, Boston, MA, USA.
- Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
| | - Nitin Joshi
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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7
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Choi W, Cha S, Kim K. Navigating the CRISPR/Cas Landscape for Enhanced Diagnosis and Treatment of Wilson's Disease. Cells 2024; 13:1214. [PMID: 39056796 PMCID: PMC11274827 DOI: 10.3390/cells13141214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system continues to evolve, thereby enabling more precise detection and repair of mutagenesis. The development of CRISPR/Cas-based diagnosis holds promise for high-throughput, cost-effective, and portable nucleic acid screening and genetic disease diagnosis. In addition, advancements in transportation strategies such as adeno-associated virus (AAV), lentiviral vectors, nanoparticles, and virus-like vectors (VLPs) offer synergistic insights for gene therapeutics in vivo. Wilson's disease (WD), a copper metabolism disorder, is primarily caused by mutations in the ATPase copper transporting beta (ATP7B) gene. The condition is associated with the accumulation of copper in the body, leading to irreversible damage to various organs, including the liver, nervous system, kidneys, and eyes. However, the heterogeneous nature and individualized presentation of physical and neurological symptoms in WD patients pose significant challenges to accurate diagnosis. Furthermore, patients must consume copper-chelating medication throughout their lifetime. Herein, we provide a detailed description of WD and review the application of novel CRISPR-based strategies for its diagnosis and treatment, along with the challenges that need to be overcome.
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Affiliation(s)
- Woong Choi
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
| | - Seongkwang Cha
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
- Neuroscience Research Institute, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
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8
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Stelloo S, Alejo-Vinogradova MT, van Gelder CAGH, Zijlmans DW, van Oostrom MJ, Valverde JM, Lamers LA, Rus T, Sobrevals Alcaraz P, Schäfers T, Furlan C, Jansen PWTC, Baltissen MPA, Sonnen KF, Burgering B, Altelaar MAFM, Vos HR, Vermeulen M. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics. Cell Stem Cell 2024; 31:1072-1090.e8. [PMID: 38754429 DOI: 10.1016/j.stem.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/10/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
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Affiliation(s)
- Suzan Stelloo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Maria Teresa Alejo-Vinogradova
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Charlotte A G H van Gelder
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marek J van Oostrom
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Teja Rus
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Paula Sobrevals Alcaraz
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Tilman Schäfers
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Katharina F Sonnen
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Boudewijn Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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9
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Smith DJ, Lunj S, Adamson AD, Nagarajan S, Smith TAD, Reeves KJ, Hoskin PJ, Choudhury A. CRISPR-Cas9 potential for identifying novel therapeutic targets in muscle-invasive bladder cancer. Nat Rev Urol 2024:10.1038/s41585-024-00901-y. [PMID: 38951705 DOI: 10.1038/s41585-024-00901-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 07/03/2024]
Abstract
Gene editing technologies help identify the genetic perturbations driving tumour initiation, growth, metastasis and resistance to therapeutics. This wealth of information highlights tumour complexity and is driving cancer research towards precision medicine approaches based on an individual's tumour genetics. Bladder cancer is the 11th most common cancer in the UK, with high rates of relapse and low survival rates in patients with muscle-invasive bladder cancer (MIBC). MIBC is highly heterogeneous and encompasses multiple molecular subtypes, each with different responses to therapeutics. This evidence highlights the need to identify innovative therapeutic targets to address the challenges posed by this heterogeneity. CRISPR-Cas9 technologies have been used to advance our understanding of MIBC and determine novel drug targets through the identification of drug resistance mechanisms, targetable cell-cycle regulators, and novel tumour suppressor and oncogenes. However, the use of these technologies in the clinic remains a substantial challenge and will require careful consideration of dosage, safety and ethics. CRISPR-Cas9 offers considerable potential for revolutionizing bladder cancer therapies, but substantial research is required for validation before these technologies can be used in the clinical setting.
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Affiliation(s)
- Danielle J Smith
- Division of Cancer Sciences, University of Manchester, Manchester, UK.
| | - Sapna Lunj
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Antony D Adamson
- Faculty of Biology, Medicine and Health Research and Innovation, University of Manchester, Manchester, UK
| | - Sankari Nagarajan
- Division of Molecular and Cellular Function, University of Manchester, Manchester, UK
| | - Tim A D Smith
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Nuclear Futures Institute, Bangor University, Bangor, UK
| | | | - Peter J Hoskin
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Ananya Choudhury
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
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10
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Gybeľ T, Čada Š, Klementová D, Schwalm MP, Berger BT, Šebesta M, Knapp S, Bryja V. Splice variants of CK1α and CK1α-like: Comparative analysis of subcellular localization, kinase activity, and function in the Wnt signaling pathway. J Biol Chem 2024; 300:107407. [PMID: 38796065 PMCID: PMC11255964 DOI: 10.1016/j.jbc.2024.107407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Members of the casein kinase 1 (CK1) family are important regulators of multiple signaling pathways. CK1α is a well-known negative regulator of the Wnt/β-catenin pathway, which promotes the degradation of β-catenin via its phosphorylation of Ser45. In contrast, the closest paralog of CK1α, CK1α-like, is a poorly characterized kinase of unknown function. In this study, we show that the deletion of CK1α, but not CK1α-like, resulted in a strong activation of the Wnt/β-catenin pathway. Wnt-3a treatment further enhanced the activation, which suggests there are at least two modes, a CK1α-dependent and Wnt-dependent, of β-catenin regulation. Rescue experiments showed that only two out of ten naturally occurring splice CK1α/α-like variants were able to rescue the augmented Wnt/β-catenin signaling caused by CK1α deficiency in cells. Importantly, the ability to phosphorylate β-catenin on Ser45 in the in vitro kinase assay was required but not sufficient for such rescue. Our compound CK1α and GSK3α/β KO models suggest that the additional nonredundant function of CK1α in the Wnt pathway beyond Ser45-β-catenin phosphorylation includes Axin phosphorylation. Finally, we established NanoBRET assays for the three most common CK1α splice variants as well as CK1α-like. Target engagement data revealed comparable potency of known CK1α inhibitors for all CK1α variants but not for CK1α-like. In summary, our work brings important novel insights into the biology of CK1α, including evidence for the lack of redundancy with other CK1 kinases in the negative regulation of the Wnt/β-catenin pathway at the level of β-catenin and Axin.
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Affiliation(s)
- Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Štěpán Čada
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Darja Klementová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, Heidelberg, Germany
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Marek Šebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, Heidelberg, Germany
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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11
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Chen D, Zhao C, Zhang J, Knol CWJ, Osipyan A, Majerníková N, Chen T, Xiao Z, Adriana J, Griffith AJ, Gamez AS, van der Wouden PE, Coppes RP, Dolga AM, Haisma HJ, Dekker FJ. Small Molecule MIF Modulation Enhances Ferroptosis by Impairing DNA Repair Mechanisms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403963. [PMID: 38924362 DOI: 10.1002/advs.202403963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Ferroptosis is a form of regulated cell death that can be modulated by small molecules and has the potential for the development of therapeutics for oncology. Although excessive lipid peroxidation is the defining hallmark of ferroptosis, DNA damage may also play a significant role. In this study, a potential mechanistic role for MIF in homologous recombination (HR) DNA repair is identified. The inhibition or genetic depletion of MIF or other HR proteins, such as breast cancer type 1 susceptibility protein (BRCA1), is demonstrated to significantly enhance the sensitivity of cells to ferroptosis. The interference with HR results in the translocation of the tumor suppressor protein p53 to the mitochondria, which in turn stimulates the production of reactive oxygen species. Taken together, the findings demonstrate that MIF-directed small molecules enhance ferroptosis via a putative MIF-BRCA1-RAD51 axis in HR, which causes resistance to ferroptosis. This suggests a potential novel druggable route to enhance ferroptosis by targeted anticancer therapeutics in the future.
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Affiliation(s)
- Deng Chen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Chunlong Zhao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Jianqiu Zhang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Catharina W J Knol
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Angelina Osipyan
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Nad'a Majerníková
- Research School of Behavioural and Cognitive Neuroscience, University of Groningen, Groningen, 9713 AV, The Netherlands
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, 9713 GZ, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Tingting Chen
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Zhangping Xiao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Jeaunice Adriana
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Andrew J Griffith
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Abel Soto Gamez
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, 9712 CP, The Netherlands
- Department of Radiation Oncology, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
| | - Petra E van der Wouden
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Robert P Coppes
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, 9712 CP, The Netherlands
- Department of Radiation Oncology, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
| | - Amalia M Dolga
- Research School of Behavioural and Cognitive Neuroscience, University of Groningen, Groningen, 9713 AV, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Hidde J Haisma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
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12
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Vergara X, Manjón AG, de Haas M, Morris B, Schep R, Leemans C, Friskes A, Beijersbergen RL, Sanders MA, Medema RH, van Steensel B. Widespread chromatin context-dependencies of DNA double-strand break repair proteins. Nat Commun 2024; 15:5334. [PMID: 38909016 PMCID: PMC11193718 DOI: 10.1038/s41467-024-49232-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: 02/19/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024] Open
Abstract
DNA double-strand breaks are repaired by multiple pathways, including non-homologous end-joining (NHEJ) and microhomology-mediated end-joining (MMEJ). The balance of these pathways is dependent on the local chromatin context, but the underlying mechanisms are poorly understood. By combining knockout screening with a dual MMEJ:NHEJ reporter inserted in 19 different chromatin environments, we identified dozens of DNA repair proteins that modulate pathway balance dependent on the local chromatin state. Proteins that favor NHEJ mostly synergize with euchromatin, while proteins that favor MMEJ generally synergize with distinct types of heterochromatin. Examples of the former are BRCA2 and POLL, and of the latter the FANC complex and ATM. Moreover, in a diversity of human cancer types, loss of several of these proteins alters the distribution of pathway-specific mutations between heterochromatin and euchromatin. Together, these results uncover a complex network of proteins that regulate MMEJ:NHEJ balance in a chromatin context-dependent manner.
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Affiliation(s)
- Xabier Vergara
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anna G Manjón
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Marcel de Haas
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Ben Morris
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruben Schep
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Christ Leemans
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anoek Friskes
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Roderick L Beijersbergen
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mathijs A Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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13
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Kondo K, Tanaka A, Kunieda T. Single-step generation of homozygous knockout/knock-in individuals in an extremotolerant parthenogenetic tardigrade using DIPA-CRISPR. PLoS Genet 2024; 20:e1011298. [PMID: 38870088 PMCID: PMC11175437 DOI: 10.1371/journal.pgen.1011298] [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: 01/06/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Tardigrades are small aquatic invertebrates known for their remarkable tolerance to diverse extreme stresses. To elucidate the in vivo mechanisms underlying this extraordinary resilience, methods for genetically manipulating tardigrades have long been desired. Despite our prior success in somatic cell gene editing by microinjecting Cas9 ribonucleoproteins (RNPs) into the body cavity of tardigrades, the generation of gene-edited individuals remained elusive. In this study, employing an extremotolerant parthenogenetic tardigrade species, Ramazzottius varieornatus, we established conditions that led to the generation of gene-edited tardigrade individuals. Drawing inspiration from the direct parental CRISPR (DIPA-CRISPR) technique employed in several insects, we simply injected a concentrated Cas9 RNP solution into the body cavity of parental females shortly before their initial oviposition. This approach yielded gene-edited G0 progeny. Notably, only a single allele was predominantly detected at the target locus for each G0 individual, indicative of homozygous mutations. By co-injecting single-stranded oligodeoxynucleotides (ssODNs) with Cas9 RNPs, we achieved the generation of homozygously knocked-in G0 progeny, and these edited alleles were inherited by G1/G2 progeny. This is the first example of heritable gene editing in the entire phylum of Tardigrada. This establishment of a straightforward method for generating homozygous knockout/knock-in individuals not only facilitates in vivo analyses of the molecular mechanisms underpinning extreme tolerance, but also opens up avenues for exploring various topics, including Evo-Devo, in tardigrades.
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Affiliation(s)
- Koyuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Tsudanuma, Narashino, Chiba, Japan
| | - Akihiro Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
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14
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Bisht D, Salave S, Desai N, Gogoi P, Rana D, Biswal P, Sarma G, Benival D, Kommineni N, Desai D. Genome editing and its role in vaccine, diagnosis, and therapeutic advancement. Int J Biol Macromol 2024; 269:131802. [PMID: 38670178 DOI: 10.1016/j.ijbiomac.2024.131802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024]
Abstract
Genome editing involves precise modification of specific nucleotides in the genome using nucleases like CRISPR/Cas, ZFN, or TALEN, leading to increased efficiency of homologous recombination (HR) for gene editing, and it can result in gene disruption events via non-homologous end joining (NHEJ) or homology-driven repair (HDR). Genome editing, particularly CRISPR-Cas9, revolutionizes vaccine development by enabling precise modifications of pathogen genomes, leading to enhanced vaccine efficacy and safety. It allows for tailored antigen optimization, improved vector design, and deeper insights into host genes' impact on vaccine responses, ultimately enhancing vaccine development and manufacturing processes. This review highlights different types of genome editing methods, their associated risks, approaches to overcome the shortcomings, and the diverse roles of genome editing.
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Affiliation(s)
- Deepanker Bisht
- ICAR- Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, India
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Nimeet Desai
- Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India
| | - Purnima Gogoi
- School of Medicine and Public Health, University of Wisconsin and Madison, Madison, WI 53726, USA
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Prachurya Biswal
- College of Veterinary and Animal Sciences, Bihar Animal Sciences University, Kishanganj 855115, Bihar, India
| | - Gautami Sarma
- College of Veterinary & Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, U.S. Nagar, Uttarakhand, India
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India.
| | | | - Dhruv Desai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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15
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Cho H, Yoo M, Pongkulapa T, Rabie H, Muotri AR, Yin PT, Choi J, Lee K. Magnetic Nanoparticle-Assisted Non-Viral CRISPR-Cas9 for Enhanced Genome Editing to Treat Rett Syndrome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306432. [PMID: 38647391 PMCID: PMC11200027 DOI: 10.1002/advs.202306432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/23/2024] [Indexed: 04/25/2024]
Abstract
The CRISPR-Cas9 technology has the potential to revolutionize the treatment of various diseases, including Rett syndrome, by enabling the correction of genes or mutations in human patient cells. However, several challenges need to be addressed before its widespread clinical application. These challenges include the low delivery efficiencies to target cells, the actual efficiency of the genome-editing process, and the precision with which the CRISPR-Cas system operates. Herein, the study presents a Magnetic Nanoparticle-Assisted Genome Editing (MAGE) platform, which significantly improves the transfection efficiency, biocompatibility, and genome-editing accuracy of CRISPR-Cas9 technology. To demonstrate the feasibility of the developed technology, MAGE is applied to correct the mutated MeCP2 gene in induced pluripotent stem cell-derived neural progenitor cells (iPSC-NPCs) from a Rett syndrome patient. By combining magnetofection and magnetic-activated cell sorting, MAGE achieves higher multi-plasmid delivery (99.3%) and repairing efficiencies (42.95%) with significantly shorter incubation times than conventional transfection agents without size limitations on plasmids. The repaired iPSC-NPCs showed similar characteristics as wild-type neurons when they differentiated into neurons, further validating MAGE and its potential for future clinical applications. In short, the developed nanobio-combined CRISPR-Cas9 technology offers the potential for various clinical applications, particularly in stem cell therapies targeting different genetic diseases.
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Affiliation(s)
- Hyeon‐Yeol Cho
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNJ08854USA
- Department of Chemical and Biomolecular EngineeringSogang UniversitySeoul04107South Korea
- Department of Bio and Fermentation Convergence TechnologyKookmin UniversitySeoul02707South Korea
| | - Myungsik Yoo
- W. M. Keck Center for Collaborative Neuroscience and Department of Cell Biology and NeuroscienceRutgers, The State University of New JerseyPiscatawayNJ08854USA
| | - Thanapat Pongkulapa
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNJ08854USA
| | - Hudifah Rabie
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNJ08854USA
| | - Alysson R. Muotri
- School of MedicineDepartment of Pediatrics/Rady Children's Hospital San DiegoDepartment of Cellular and Molecular MedicineStem Cell ProgramLa JollaCA92093USA
| | - Perry T. Yin
- Department of Biomedical EngineeringRutgersThe State University of New JerseyPiscatawayNJ08854USA
| | - Jeong‐Woo Choi
- Department of Chemical and Biomolecular EngineeringSogang UniversitySeoul04107South Korea
| | - Ki‐Bum Lee
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNJ08854USA
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16
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Shi H, Li L, Mu S, Gou S, Liu X, Chen F, Chen M, Jin Q, Lai L, Wang K. Exonuclease editor promotes precision of gene editing in mammalian cells. BMC Biol 2024; 22:119. [PMID: 38769511 PMCID: PMC11107001 DOI: 10.1186/s12915-024-01918-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Many efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing byproducts, which proved to be challenging. RESULTS Here, we have developed a human exonuclease 1-based genome-editing tool, referred to as exonuclease editor. When compared to Cas9, the exonuclease editor gave rise to increased HDR efficiency, reduced NHEJ repair frequency, and significantly elevated HDR/indel ratio. Robust gene editing precision of exonuclease editor was even superior to the fusion of Cas9 with E1B or DN1S, two previously reported precision-enhancing domains. Notably, exonuclease editor inhibited NHEJ at double strand breaks locally rather than globally, reducing indel frequency without compromising genome integrity. The replacement of Cas9 with single-strand DNA break-creating Cas9 nickase further increased the HDR/indel ratio by 453-fold than the original Cas9. In addition, exonuclease editor resulted in high microhomology-mediated end joining efficiency, allowing accurate and flexible deletion of targeted sequences with extended lengths with the aid of paired sgRNAs. Exonuclease editor was further used for correction of DMD patient-derived induced pluripotent stem cells, where 30.0% of colonies were repaired by HDR versus 11.1% in the control. CONCLUSIONS Therefore, the exonuclease editor system provides a versatile and safe genome editing tool with high precision and holds promise for therapeutic gene correction.
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Affiliation(s)
- Hui Shi
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Lei Li
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangshuang Mu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shixue Gou
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Xiaoyi Liu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Menglong Chen
- Department of Neurology and Stroke Centre, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qin Jin
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
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17
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Selvaraj S, Feist WN, Viel S, Vaidyanathan S, Dudek AM, Gastou M, Rockwood SJ, Ekman FK, Oseghale AR, Xu L, Pavel-Dinu M, Luna SE, Cromer MK, Sayana R, Gomez-Ospina N, Porteus MH. High-efficiency transgene integration by homology-directed repair in human primary cells using DNA-PKcs inhibition. Nat Biotechnol 2024; 42:731-744. [PMID: 37537500 DOI: 10.1038/s41587-023-01888-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Therapeutic applications of nuclease-based genome editing would benefit from improved methods for transgene integration via homology-directed repair (HDR). To improve HDR efficiency, we screened six small-molecule inhibitors of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key protein in the alternative repair pathway of non-homologous end joining (NHEJ), which generates genomic insertions/deletions (INDELs). From this screen, we identified AZD7648 as the most potent compound. The use of AZD7648 significantly increased HDR (up to 50-fold) and concomitantly decreased INDELs across different genomic loci in various therapeutically relevant primary human cell types. In all cases, the ratio of HDR to INDELs markedly increased, and, in certain situations, INDEL-free high-frequency (>50%) targeted integration was achieved. This approach has the potential to improve the therapeutic efficacy of cell-based therapies and broaden the use of targeted integration as a research tool.
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Affiliation(s)
- Sridhar Selvaraj
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - William N Feist
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sebastien Viel
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Immunology Department, Lyon Sud University Hospital, Pierre-Bénite, France
- International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Sriram Vaidyanathan
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Marc Gastou
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sarah J Rockwood
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Freja K Ekman
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Aluya R Oseghale
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Liwen Xu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ruhi Sayana
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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18
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Husser MC, Pham NP, Law C, Araujo FRB, Martin VJJ, Piekny A. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies. eLife 2024; 12:RP92819. [PMID: 38652106 PMCID: PMC11037917 DOI: 10.7554/elife.92819] [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] [Indexed: 04/25/2024] Open
Abstract
Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.
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Affiliation(s)
| | - Nhat P Pham
- Biology Department, Concordia University, Montreal, Canada
| | - Chris Law
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
| | - Flavia R B Araujo
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Biology Department, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Alisa Piekny
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
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19
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Lee BC, Gin A, Wu C, Singh K, Grice M, Mortlock R, Abraham D, Fan X, Zhou Y, AlJanahi A, Choi U, DeRavin SS, Shin T, Hong S, Dunbar CE. Impact of CRISPR/HDR editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques. Cell Stem Cell 2024; 31:455-466.e4. [PMID: 38508195 PMCID: PMC10997443 DOI: 10.1016/j.stem.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) is required. The impact of HDR on true LT-HSC clonal dynamics in a relevant large animal model has not been studied. To track the output and clonality of HDR-edited cells and to provide a comparison to lentivirally transduced HSCs in vivo, we developed a competitive rhesus macaque (RM) autologous transplantation model, co-infusing HSCs transduced with a barcoded GFP-expressing lentiviral vector (LV) and HDR edited at the CD33 locus. CRISPR/HDR-edited cells showed a two-log decrease by 2 months following transplantation, with little improvement via p53 inhibition, in comparison to minimal loss of LV-transduced cells long term. HDR long-term clonality was oligoclonal in contrast to highly polyclonal LV-transduced HSCs. These results suggest marked clinically relevant differences in the impact of current genetic modification approaches on HSCs.
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Affiliation(s)
- Byung-Chul Lee
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Biological Sciences, Sookmyung Women's University, Seoul, Korea; Research Institute of Women's Health, Sookmyung Women's University, Seoul, Korea.
| | - Ashley Gin
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Komudi Singh
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Max Grice
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryland Mortlock
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diana Abraham
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xing Fan
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yifan Zhou
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Aisha AlJanahi
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Uimook Choi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Suk See DeRavin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Taehoon Shin
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Korea
| | - Sogun Hong
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia E Dunbar
- Translational Stem Cell Biology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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20
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Bouchareb A, Biggs D, Alghadban S, Preece C, Davies B. Increasing Knockin Efficiency in Mouse Zygotes by Transient Hypothermia. CRISPR J 2024; 7:111-119. [PMID: 38635329 PMCID: PMC7615915 DOI: 10.1089/crispr.2023.0077] [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] [Indexed: 04/20/2024] Open
Abstract
Integration of a point mutation to correct or edit a gene requires the repair of the CRISPR-Cas9-induced double-strand break by homology-directed repair (HDR). This repair pathway is more active in late S and G2 phases of the cell cycle, whereas the competing pathway of nonhomologous end-joining (NHEJ) operates throughout the cell cycle. Accordingly, modulation of the cell cycle by chemical perturbation or simply by the timing of gene editing to shift the editing toward the S/G2 phase has been shown to increase HDR rates. Using a traffic light reporter in mouse embryonic stem cells and a fluorescence conversion reporter in human-induced pluripotent stem cells, we confirm that a transient cold shock leads to an increase in the rate of HDR, with a corresponding decrease in the rate of NHEJ repair. We then investigated whether a similar cold shock could lead to an increase in the rate of HDR in the mouse embryo. By analyzing the efficiency of gene editing using single nucleotide polymorphism changes and loxP insertion at three different genetic loci, we found that a transient reduction in temperature after zygote electroporation of CRISPR-Cas9 ribonucleoprotein with a single-stranded oligodeoxynucleotide repair template did indeed increase knockin efficiency, without affecting embryonic development. The efficiency of gene editing with and without the cold shock was first assessed by genotyping blastocysts. As a proof of concept, we then confirmed that the modified embryo culture conditions were compatible with live births by targeting the coat color gene tyrosinase and observing the repair of the albino mutation. Taken together, our data suggest that a transient cold shock could offer a simple and robust way to improve knockin outcomes in both stem cells and zygotes.
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Affiliation(s)
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Samy Alghadban
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | | | - Benjamin Davies
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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21
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Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
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Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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22
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Li Z, You L, Hermann A, Bier E. Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier. Nat Commun 2024; 15:2629. [PMID: 38521791 PMCID: PMC10960810 DOI: 10.1038/s41467-024-46479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
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Affiliation(s)
- Zhiqian Li
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lang You
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anita Hermann
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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23
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Hafeez A, Ali S, Javed MA, Iqbal R, Khan MN, Çiğ F, Sabagh AE, Abujamel T, Harakeh S, Ercisli S, Ali B. Breeding for water-use efficiency in wheat: progress, challenges and prospects. Mol Biol Rep 2024; 51:429. [PMID: 38517566 DOI: 10.1007/s11033-024-09345-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/12/2024] [Indexed: 03/24/2024]
Abstract
Drought poses a significant challenge to wheat production globally, leading to substantial yield losses and affecting various agronomic and physiological traits. The genetic route offers potential solutions to improve water-use efficiency (WUE) in wheat and mitigate the negative impacts of drought stress. Breeding for drought tolerance involves selecting desirable plants such as efficient water usage, deep root systems, delayed senescence, and late wilting point. Biomarkers, automated and high-throughput techniques, and QTL genes are crucial in enhancing breeding strategies and developing wheat varieties with improved resilience to water scarcity. Moreover, the role of root system architecture (RSA) in water-use efficiency is vital, as roots play a key role in nutrient and water uptake. Genetic engineering techniques offer promising avenues to introduce desirable RSA traits in wheat to enhance drought tolerance. These technologies enable targeted modifications in DNA sequences, facilitating the development of drought-tolerant wheat germplasm. The article highlighted the techniques that could play a role in mitigating drought stress in wheat.
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Affiliation(s)
- Aqsa Hafeez
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shehzad Ali
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63000, Pakistan
| | - Muhammad Nauman Khan
- Department of Botany, Islamia College Peshawar, Peshawar, 25120, Pakistan
- Biology Laboratory, University Public School, University of Peshawar, Peshawar, 25120, Pakistan
| | - Fatih Çiğ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, 56100, Turkey
| | - Ayman El Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, 56100, Turkey
| | - Turki Abujamel
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum, 25240, Türkiye
- HGF Agro, Ata Teknokent, Erzurum, 25240, Türkiye
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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24
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Chen X, Du J, Yun S, Xue C, Yao Y, Rao S. Recent advances in CRISPR-Cas9-based genome insertion technologies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102138. [PMID: 38379727 PMCID: PMC10878794 DOI: 10.1016/j.omtn.2024.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Programmable genome insertion (or knock-in) is vital for both fundamental and translational research. The continuously expanding number of CRISPR-based genome insertion strategies demonstrates the ongoing development in this field. Common methods for site-specific genome insertion rely on cellular double-strand breaks repair pathways, such as homology-directed repair, non-homologous end-joining, and microhomology-mediated end joining. Recent advancements have further expanded the toolbox of programmable genome insertion techniques, including prime editing, integrase coupled with programmable nuclease, and CRISPR-associated transposon. These tools possess their own capabilities and limitations, promoting tremendous efforts to enhance editing efficiency, broaden targeting scope and improve editing specificity. In this review, we first summarize recent advances in programmable genome insertion techniques. We then elaborate on the cons and pros of each technique to assist researchers in making informed choices when using these tools. Finally, we identify opportunities for future improvements and applications in basic research and therapeutics.
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Affiliation(s)
- Xinwen Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingjing Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shaowei Yun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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25
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Wang J, Torres IM, Shang M, Al-Armanazi J, Dilawar H, Hettiarachchi DU, Paladines-Parrales A, Chambers B, Pottle K, Soman M, Su B, Dunham RA. One-step knock-in of two antimicrobial peptide transgenes at multiple loci of catfish by CRISPR/Cas9-mediated multiplex genome engineering. Int J Biol Macromol 2024; 260:129384. [PMID: 38224812 DOI: 10.1016/j.ijbiomac.2024.129384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/23/2023] [Accepted: 01/01/2024] [Indexed: 01/17/2024]
Abstract
CRISPR/Cas9-mediated multiplex genome editing (MGE) conventionally uses multiple single-guide RNAs (sgRNAs) for gene-targeted mutagenesis via the non-homologous end joining (NHEJ) pathway. MGE has been proven to be highly efficient for functional gene disruption/knockout (KO) at multiple loci in mammalian cells or organisms. However, in the absence of a DNA donor, this approach is limited to small indels without transgene integration. Here, we establish the linear double-stranded DNA (dsDNA) and double-cut plasmid (dcPlasmid) combination-assisted MGE in channel catfish (Ictalurus punctatus), allowing combinational deletion mutagenesis and transgene knock-in (KI) at multiple sites through NHEJ/homology-directed repair (HDR) pathway in parallel. In this study, we used single-sgRNA-based genome editing (ssGE) and multi-sgRNA-based MGE (msMGE) to replace the luteinizing hormone (lh) and melanocortin-4 receptor (mc4r) genes with the cathelicidin (As-Cath) transgene and the myostatin (two target sites: mstn1, mstn2) gene with the cecropin (Cec) transgene, respectively. A total of 9000 embryos were microinjected from three families, and 1004 live fingerlings were generated and analyzed. There was no significant difference in hatchability (all P > 0.05) and fry survival (all P > 0.05) between ssGE and msMGE. Compared to ssGE, CRISPR/Cas9-mediated msMGE assisted by the mixture of dsDNA and dcPlasmid donors yielded a higher knock-in (KI) efficiency of As-Cath (19.93 %, [59/296] vs. 12.96 %, [45/347]; P = 0.018) and Cec (22.97 %, [68/296] vs. 10.80 %, [39/361]; P = 0.003) transgenes, respectively. The msMGE strategy can be used to generate transgenic fish carrying two transgenes at multiple loci. In addition, double and quadruple mutant individuals can be produced with high efficiency (36.3 % ∼ 71.1 %) in one-step microinjection. In conclusion, we demonstrated that the CRISPR/Cas9-mediated msMGE allows the one-step generation of simultaneous insertion of the As-Cath and Cec transgenes at four sites, and the simultaneous disruption of the lh, mc4r, mstn1 and mstn2 alleles. This msMGE system, aided by the mixture donors, promises to pioneer a new dimension in the drive and selection of multiple designated traits in other non-model organisms.
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Affiliation(s)
- Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America.
| | - Indira Medina Torres
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Jacob Al-Armanazi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Hamza Dilawar
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Darshika U Hettiarachchi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Abel Paladines-Parrales
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Barrett Chambers
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Kate Pottle
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Misha Soman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America.
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
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26
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Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [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: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
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Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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27
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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28
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Leal AF, Herreno-Pachón AM, Benincore-Flórez E, Karunathilaka A, Tomatsu S. Current Strategies for Increasing Knock-In Efficiency in CRISPR/Cas9-Based Approaches. Int J Mol Sci 2024; 25:2456. [PMID: 38473704 PMCID: PMC10931195 DOI: 10.3390/ijms25052456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Since its discovery in 2012, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system has supposed a promising panorama for developing novel and highly precise genome editing-based gene therapy (GT) alternatives, leading to overcoming the challenges associated with classical GT. Classical GT aims to deliver transgenes to the cells via their random integration in the genome or episomal persistence into the nucleus through lentivirus (LV) or adeno-associated virus (AAV), respectively. Although high transgene expression efficiency is achieved by using either LV or AAV, their nature can result in severe side effects in humans. For instance, an LV (NCT03852498)- and AAV9 (NCT05514249)-based GT clinical trials for treating X-linked adrenoleukodystrophy and Duchenne Muscular Dystrophy showed the development of myelodysplastic syndrome and patient's death, respectively. In contrast with classical GT, the CRISPR/Cas9-based genome editing requires the homologous direct repair (HDR) machinery of the cells for inserting the transgene in specific regions of the genome. This sophisticated and well-regulated process is limited in the cell cycle of mammalian cells, and in turn, the nonhomologous end-joining (NHEJ) predominates. Consequently, seeking approaches to increase HDR efficiency over NHEJ is crucial. This manuscript comprehensively reviews the current alternatives for improving the HDR for CRISPR/Cas9-based GTs.
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Affiliation(s)
- Andrés Felipe Leal
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Angelica María Herreno-Pachón
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Eliana Benincore-Flórez
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
| | - Amali Karunathilaka
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
| | - Shunji Tomatsu
- Nemours Children’s Health, Wilmington, DE 19803, USA; (A.F.L.); (A.M.H.-P.); (E.B.-F.); (A.K.)
- Faculty of Arts and Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501-1194, Japan
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19144, USA
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29
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Hochstoeger T, Papasaikas P, Piskadlo E, Chao JA. Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5'TOP mRNAs. SCIENCE ADVANCES 2024; 10:eadi7830. [PMID: 38363833 PMCID: PMC10871529 DOI: 10.1126/sciadv.adi7830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
A central mechanism of mTOR complex 1 (mTORC1) signaling is the coordinated translation of ribosomal protein and translation factor mRNAs mediated by the 5'-terminal oligopyrimidine motif (5'TOP). Recently, La-related protein 1 (LARP1) was proposed to be the specific regulator of 5'TOP mRNA translation downstream of mTORC1, while eIF4E-binding proteins (4EBP1/2) were suggested to have a general role in translational repression of all transcripts. Here, we use single-molecule translation site imaging of 5'TOP and canonical mRNAs to study the translation of single mRNAs in living cells. Our data reveal that 4EBP1/2 has a dominant role in repression of translation of both 5'TOP and canonical mRNAs during pharmacological inhibition of mTOR. In contrast, we find that LARP1 selectively protects 5'TOP mRNAs from degradation in a transcriptome-wide analysis of mRNA half-lives. Our results clarify the roles of 4EBP1/2 and LARP1 in regulating 5'TOP mRNAs and provide a framework to further study how these factors control cell growth during development and disease.
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Affiliation(s)
- Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
| | | | - Ewa Piskadlo
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jeffrey A. Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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30
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Li X, Wirtz T, Weber T, Lebedin M, Lowenstein ED, Sommermann T, Zach A, Yasuda T, de la Rosa K, Chu VT, Schulte JH, Müller I, Kocks C, Rajewsky K. Precise CRISPR-Cas9 gene repair in autologous memory T cells to treat familial hemophagocytic lymphohistiocytosis. Sci Immunol 2024; 9:eadi0042. [PMID: 38306418 DOI: 10.1126/sciimmunol.adi0042] [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: 03/30/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Familial hemophagocytic lymphohistiocytosis (FHL) is an inherited, often fatal immune deficiency characterized by severe systemic hyperinflammation. Although allogeneic bone marrow transplantation can be curative, more effective therapies are urgently needed. FHL is caused by inactivating mutations in proteins that regulate cellular immunity. Here, we used an adeno-associated virus-based CRISPR-Cas9 system with an inhibitor of nonhomologous end joining to repair such mutations in potentially long-lived T cells ex vivo. Repaired CD8 memory T cells efficiently cured lethal hyperinflammation in a mouse model of Epstein-Barr virus-triggered FHL2, a subtype caused by perforin-1 (Prf1) deficiency. Furthermore, repair of PRF1 and Munc13-4 (UNC13D)-whose deficiency causes the FHL subtype FHL3-in mutant memory T cells from two critically ill patients with FHL restored T cell cytotoxicity. These results provide a starting point for the treatment of genetic T cell immune dysregulation syndromes with repaired autologous T cells.
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Affiliation(s)
- Xun Li
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Tristan Wirtz
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Timm Weber
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Mikhail Lebedin
- Immune Mechanisms and Human Antibodies, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 10117 Berlin, Germany
| | - Elijah D Lowenstein
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Thomas Sommermann
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Andreas Zach
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 10117 Berlin, Germany
| | - Tomoharu Yasuda
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Kathrin de la Rosa
- Immune Mechanisms and Human Antibodies, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Center of Biological Design, Berlin Institute of Health (BIH) at Charité, 13125 Berlin, Germany
| | - Van Trung Chu
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Genome Engineering & Disease Models, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), 10117 Berlin, Germany
| | - Ingo Müller
- Division of Pediatric Stem Cell Transplantation and Immunology, Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christine Kocks
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Klaus Rajewsky
- Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
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31
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Evmenov K, Pustogarov N, Panteleev D, Safin A, Alkalaeva E. An Efficient Expression and Purification Protocol for SpCas9 Nuclease and Evaluation of Different Delivery Methods of Ribonucleoprotein. Int J Mol Sci 2024; 25:1622. [PMID: 38338898 PMCID: PMC10855156 DOI: 10.3390/ijms25031622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system is a revolutionary tool for precise genome editing across various cell types. Ribonucleoproteins (RNPs), encompassing the Cas9 protein and guide RNA (gRNA), have emerged as a promising technique due to their increased specificity and reduced off-target effects. This method eliminates the need for plasmid DNA introduction, thereby preventing potential integration of foreign DNA into the target cell genome. Given the requirement for large quantities of highly purified protein in various Cas9 studies, we present an efficient and simple method for the preparation of recombinant Streptococcus pyogenes Cas9 (SpCas9) protein. This method leverages the Small Ubiquitin Like Modifier(SUMO) tag system, which includes metal-affinity chromatography followed by anion-exchange chromatography purification. Furthermore, we compare two methods of CRISPR-Cas9 system delivery into cells: transfection with plasmid DNA encoding the CRISPR-Cas9 system and RNP transfection with the Cas9-gRNA complex. We estimate the efficiency of genomic editing and protein lifespan post-transfection. Intriguingly, we found that RNP treatment of cells, even in the absence of a transfection system, is a relatively efficient method for RNP delivery into cell culture. This discovery is particularly promising as it can significantly reduce cytotoxicity, which is crucial for certain cell cultures such as induced pluripotent stem cells (iPSCs).
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Affiliation(s)
- Konstantin Evmenov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (K.E.); (N.P.)
| | - Nikolay Pustogarov
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (K.E.); (N.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Biology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Dmitri Panteleev
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia;
| | - Artur Safin
- Department of Biology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; (K.E.); (N.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
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32
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Verma N, Renauer PA, Dong C, Xin S, Lin Q, Zhang F, Glazer PM, Chen S. Genome scale CRISPR screens identify actin capping proteins as key modulators of therapeutic responses to radiation and immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.14.575614. [PMID: 38293095 PMCID: PMC10827061 DOI: 10.1101/2024.01.14.575614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Radiotherapy (RT), is a fundamental treatment for malignant tumors and is used in over half of cancer patients. As radiation can promote anti-tumor immune effects, a promising therapeutic strategy is to combine radiation with immune checkpoint inhibitors (ICIs). However, the genetic determinants that impact therapeutic response in the context of combination therapy with radiation and ICI have not been systematically investigated. To unbiasedly identify the tumor intrinsic genetic factors governing such responses, we perform a set of genome-scale CRISPR screens in melanoma cells for cancer survival in response to low-dose genotoxic radiation treatment, in the context of CD8 T cell co-culture and with anti-PD1 checkpoint blockade antibody. Two actin capping proteins, Capza3 and Capg, emerge as top hits that upon inactivation promote the survival of melanoma cells in such settings. Capza3 and Capg knockouts (KOs) in mouse and human cancer cells display persistent DNA damage due to impaired homology directed repair (HDR); along with increased radiation, chemotherapy, and DNA repair inhibitor sensitivity. However, when cancer cells with these genes inactivated were exposed to sublethal radiation, inactivation of such actin capping protein promotes activation of the STING pathway, induction of inhibitory CEACAM1 ligand expression and resistance to CD8 T cell killing. Patient cancer genomics analysis reveals an increased mutational burden in patients with inactivating mutations in CAPG and/or CAPZA3, at levels comparable to other HDR associated genes. There is also a positive correlation between CAPG expression and activation of immune related pathways and CD8 T cell tumor infiltration. Our results unveil the critical roles of actin binding proteins for efficient HDR within cancer cells and demonstrate a previously unrecognized regulatory mechanism of therapeutic response to radiation and immunotherapy.
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Affiliation(s)
- Nipun Verma
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
| | - Paul A. Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Chuanpeng Dong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Shan Xin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Qianqian Lin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Feifei Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Immunobiology Program, Yale University, New Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, Connecticut, USA
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Farley KO, Forbes CA, Shaw NC, Kuzminski E, Ward M, Baynam G, Lassmann T, Fear VS. CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction. HGG ADVANCES 2024; 5:100257. [PMID: 38007613 PMCID: PMC10787298 DOI: 10.1016/j.xhgg.2023.100257] [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: 09/01/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023] Open
Abstract
An estimated 3.5%-5.9% of the global population live with rare diseases, and approximately 80% of these diseases have a genetic cause. Rare genetic diseases are difficult to diagnose, with some affected individuals experiencing diagnostic delays of 5-30 years. Next-generation sequencing has improved clinical diagnostic rates to 33%-48%. In a majority of cases, novel variants potentially causing the disease are discovered. These variants require functional validation in specialist laboratories, resulting in a diagnostic delay. In the interim, the finding is classified as a genetic variant of uncertain significance (VUS) and the affected individual remains undiagnosed. A VUS (PTCHD1 c. 2489T>G) was identified in a child with autistic behavior, global developmental delay, and hypotonia. Loss of function mutations in PTCHD1 are associated with autism spectrum disorder and intellectual disability; however, the molecular function of PTCHD1 and its role in neurodevelopmental disease is unknown. Here, we apply CRISPR gene editing and induced pluripotent stem cell (iPSC) neural disease modeling to assess the variant. During differentiation from iPSCs to neural progenitors, we detect subtle but significant gene signatures in synaptic transmission and muscle contraction pathways. Our work supports the causal link between the genetic variant and the child's phenotype, providing evidence for the variant to be considered a pathogenic variant according to the American College of Medical Genetics and Genomics guidelines. In addition, our study provides molecular data on the role of PTCHD1 in the context of other neurodevelopmental disorders.
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Affiliation(s)
- Kathryn O Farley
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia.
| | - Catherine A Forbes
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicole C Shaw
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Emma Kuzminski
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Michelle Ward
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco WA 6008, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA 6008, Australia; Undiagnosed Diseases Program, Genetic Services of WA, Subiaco WA 6008, Australia; Rare Care Centre, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Timo Lassmann
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Vanessa S Fear
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
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34
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Shumega AR, Pavlov YI, Chirinskaite AV, Rubel AA, Inge-Vechtomov SG, Stepchenkova EI. CRISPR/Cas9 as a Mutagenic Factor. Int J Mol Sci 2024; 25:823. [PMID: 38255897 PMCID: PMC10815272 DOI: 10.3390/ijms25020823] [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: 11/15/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The discovery of the CRISPR/Cas9 microbial adaptive immune system has revolutionized the field of genetics, by greatly enhancing the capacity for genome editing. CRISPR/Cas9-based editing starts with DNA breaks (or other lesions) predominantly at target sites and, unfortunately, at off-target genome sites. DNA repair systems differing in accuracy participate in establishing desired genetic changes but also introduce unwanted mutations, that may lead to hereditary, oncological, and other diseases. New approaches to alleviate the risks associated with genome editing include attenuating the off-target activity of editing complex through the use of modified forms of Cas9 nuclease and single guide RNA (sgRNA), improving delivery methods for sgRNA/Cas9 complex, and directing DNA lesions caused by the sgRNA/Cas9 to non-mutagenic repair pathways. Here, we have described CRISPR/Cas9 as a new powerful mutagenic factor, discussed its mutagenic properties, and reviewed factors influencing the mutagenic activity of CRISPR/Cas9.
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Affiliation(s)
- Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Sergey G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
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35
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Gim GM, Jang G. Outlook on genome editing application to cattle. J Vet Sci 2024; 25:e10. [PMID: 38311323 PMCID: PMC10839183 DOI: 10.4142/jvs.23133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/04/2023] [Accepted: 08/20/2023] [Indexed: 02/07/2024] Open
Abstract
In livestock industry, there is growing interest in methods to increase the production efficiency of livestock to address food shortages, given the increasing global population. With the advancements in gene engineering technology, it is a valuable tool and has been intensively utilized in research specifically focused on human disease. In historically, this technology has been used with livestock to create human disease models or to produce recombinant proteins from their byproducts. However, in recent years, utilizing gene editing technology, cattle with identified genes related to productivity can be edited, thereby enhancing productivity in response to climate change or specific disease instead of producing recombinant proteins. Furthermore, with the advancement in the efficiency of gene editing, it has become possible to edit multiple genes simultaneously. This cattle breed improvement has been achieved by discovering the genes through the comprehensive analysis of the entire genome of cattle. The cattle industry has been able to address gene bottlenecks that were previously impossible through conventional breeding systems. This review concludes that gene editing is necessary to expand the cattle industry, improving productivity in the future. Additionally, the enhancement of cattle through gene editing is expected to contribute to addressing environmental challenges associated with the cattle industry. Further research and development in gene editing, coupled with genomic analysis technologies, will significantly contribute to solving issues that conventional breeding systems have not been able to address.
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Affiliation(s)
| | - Goo Jang
- LARTBio Inco, Seoul 06221, Korea
- Laboratory of Theriogenology and Biotechnology, Department of Veterinary Clinical Science, College of Veterinary Medicine and the Research Institute of Veterinary Science, Seoul National University, Seoul 08826, Korea
- Comparative medicine Disease Research Center, Seoul National University, Seoul 08826, Korea
- Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia.
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36
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Mishra G, Srivastava K, Rais J, Dixit M, Kumari Singh V, Chandra Mishra L. CRISPR-Cas9: A Potent Gene-editing Tool for the Treatment of Cancer. Curr Mol Med 2024; 24:191-204. [PMID: 36788695 DOI: 10.2174/1566524023666230213094308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 02/16/2023]
Abstract
The prokaryotic adaptive immune system has clustered regularly interspaced short palindromic repeat. CRISPR-associated protein (CRISPR-Cas) genome editing systems have been harnessed. A robust programmed technique for efficient and accurate genome editing and gene targeting has been developed. Engineered cell therapy, in vivo gene therapy, animal modeling, and cancer diagnosis and treatment are all possible applications of this ground-breaking approach. Multiple genetic and epigenetic changes in cancer cells induce malignant cell growth and provide chemoresistance. The capacity to repair or ablate such mutations has enormous potential in the fight against cancer. The CRISPR-Cas9 genome editing method has recently become popular in cancer treatment research due to its excellent efficiency and accuracy. The preceding study has shown therapeutic potential in expanding our anticancer treatments by using CRISPR-Cas9 to directly target cancer cell genomic DNA in cellular and animal cancer models. In addition, CRISPR-Cas9 can combat oncogenic infections and test anticancer medicines. It may design immune cells and oncolytic viruses for cancer immunotherapeutic applications. In this review, these preclinical CRISPRCas9- based cancer therapeutic techniques are summarised, along with the hurdles and advancements in converting therapeutic CRISPR-Cas9 into clinical use. It will increase their applicability in cancer research.
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Affiliation(s)
- Gauri Mishra
- Department of Zoology, Swami Shraddhanand College, University of Delhi-110036, Delhi, India
- Division Radiopharmaceuticals and Radiation Biology, Institute of Nuclear Medicine and Allied Sciences, Brig SK Mazumdar Road, Delhi-110054, India
| | - Kamakshi Srivastava
- Department of Zoology, Swami Shraddhanand College, University of Delhi-110036, Delhi, India
| | - Juhi Rais
- Department of Nuclear Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, India
| | - Manish Dixit
- Department of Nuclear Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, India
| | - Vandana Kumari Singh
- Department of Zoology, Hansraj College, University of Delhi- 110007, Dehli, India
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Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH. Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. Nat Biotechnol 2024; 42:87-98. [PMID: 36991112 PMCID: PMC10620015 DOI: 10.1038/s41587-023-01748-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Conventional genome engineering with CRISPR-Cas9 creates double-strand breaks (DSBs) that lead to undesirable byproducts and reduce product purity. Here we report an approach for programmable integration of large DNA sequences in human cells that avoids the generation of DSBs by using Type I-F CRISPR-associated transposases (CASTs). We optimized DNA targeting by the QCascade complex through protein design and developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase TnsC to genomic sites targeted by QCascade. After initial detection of plasmid-based integration, we screened 15 additional CAST systems from a wide range of bacterial hosts, identified a homolog from Pseudoalteromonas that exhibits improved activity and further increased integration efficiencies. Finally, we discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, likely by promoting active disassembly of the post-integration CAST complex, akin to its known role in Mu transposition. Our work highlights the ability to reconstitute complex, multi-component machineries in human cells and establishes a strong foundation to exploit CRISPR-associated transposases for eukaryotic genome engineering.
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Affiliation(s)
- George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Rebeca T King
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tyler S Halpin-Healy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Marcus I Hogan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Vertex Pharmaceuticals, Inc., Boston, MA, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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Hawley RG, Hawley TS. CRISPR-Cas9-Mediated Bioluminescent Tagging of Endogenous Proteins by Fluorescent Protein-Assisted Cell Sorting. Methods Mol Biol 2024; 2779:273-286. [PMID: 38526790 DOI: 10.1007/978-1-0716-3738-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Oncogenic fusion genes are attractive therapeutic targets because of their tumor-specific expression and central "driver" roles in various human cancers. However, oncogenic fusions involving transcription factors such as PAX3-FOXO1 in alveolar fusion gene-positive rhabdomyosarcoma (FP-RMS) have been difficult to inhibit due to the apparent lack of tractable drug-like binding sites comparable to that recognized by Gleevec (imatinib mesylate) on the BCR-ABL1 tyrosine kinase fusion protein. Toward the identification of novel small molecules that selectively target PAX3-FOXO1, we used CRISPR-Cas9-mediated knock-in to append the pro-luminescent HiBiT tag onto the carboxy terminus of the endogenous PAX3-FOXO1 fusion protein in two human FP-RMS cell lines (RH4 and SCMC). HiBiT is an 11-amino acid peptide derived from the NanoLuc luciferase that produces a luminescence signal which is ~100-fold brighter than firefly or Renilla luciferases through high-affinity binding to a complementary NanoLuc peptide fragment called LgBiT. To facilitate single-cell clonal isolation of knock-ins, the homology-directed repair template encoding HiBiT was followed by a P2A self-cleaving peptide for coexpression of an mCherry fluorescent protein as a fluorescence-activated cell sorter (FACS)-selectable marker. HiBiT tagging thus allows highly sensitive luminescence detection of endogenous PAX3-FOXO1 levels permitting quantitative high-throughput screening of large compound libraries for the discovery of PAX3-FOXO1 inhibitors and degraders.
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Affiliation(s)
- Robert G Hawley
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
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Williams L, Larsen J. Nanoparticle-mediated delivery of non-viral gene editing technology to the brain. Prog Neurobiol 2024; 232:102547. [PMID: 38042249 PMCID: PMC10872436 DOI: 10.1016/j.pneurobio.2023.102547] [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: 07/18/2023] [Revised: 11/01/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Neurological disorders pose a significant burden on individuals and society, affecting millions worldwide. These disorders, including but not limited to Alzheimer's disease, Parkinson's disease, and Huntington's disease, often have limited treatment options and can lead to progressive degeneration and disability. Gene editing technologies, including Zinc Finger Nucleases (ZFN), Transcription Activator-Like Effector Nucleases (TALEN), and Clustered Regularly Interspaced Short Palindromic Repeats-associated Protein 9 (CRISPR-Cas9), offer a promising avenue for potential cures by targeting and correcting the underlying genetic mutations responsible for neurologic disorders. However, efficient delivery methods are crucial for the successful application of gene editing technologies in the context of neurological disorders. The central nervous system presents unique challenges to treatment development due to the blood-brain barrier, which restricts the entry of large molecules. While viral vectors are traditionally used for gene delivery, nonviral delivery methods, such as nanoparticle-mediated delivery, offer safer alternatives that can efficiently transport gene editing components. Herein we aim to introduce the three main gene editing nucleases as nonviral treatments for neurologic disorders, the delivery barriers associated with brain targeting, and the current nonviral techniques used for brain-specific delivery. We highlight the challenges and opportunities for future research in this exciting and growing field that could lead to blood-brain barrier bypassing therapeutic gene editing.
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Affiliation(s)
- Lucian Williams
- Department of Bioengineering, Clemson University, Clemson, SC 29631, USA
| | - Jessica Larsen
- Department of Bioengineering, Clemson University, Clemson, SC 29631, USA; Department of Chemical Engineering, Clemson University, Clemson, SC 29631, USA.
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40
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Cortina C, Cañellas-Socias A. CRISPR Knock-Ins in Organoids to Track Tumor Cell Subpopulations. Methods Mol Biol 2024; 2811:137-154. [PMID: 39037655 DOI: 10.1007/978-1-0716-3882-8_10] [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: 07/23/2024]
Abstract
The integration of CRISPR/Cas9 genome editing techniques with organoid technology has revolutionized the field of tumor modeling, enabling the creation of diverse tumor models with distinct mutational profiles. This protocol details the application of CRISPR knock-ins to engineer tumor organoids with reporter cassettes, which are regulated by endogenous promoters of specific genes of interest. This approach facilitates the precise fluorescent labeling, isolation, and subsequent manipulation of targeted tumor cell subpopulations. The utilization of these knock-in reporter cassettes not only allows the visualization and purification of specific tumor cell subsets but also enables conditional cell ablation and lineage tracing studies. In this chapter, we provide a comprehensive guide for the design, construction, delivery, and validation of CRISPR/Cas9 tools tailored for knock-in reporter cassette integration into specific marker genes of interest. By following this protocol, researchers can harness the potential of engineered tumor organoids to decipher intricate tumor heterogeneity, track metastatic trajectories, and unveil novel therapeutic vulnerabilities linked to specific tumor cell subpopulations.
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Affiliation(s)
- Carme Cortina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
| | - Adrià Cañellas-Socias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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41
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Liu J, Li W, Jin X, Lin F, Han J, Zhang Y. Optimal tagging strategies for illuminating expression profiles of genes with different abundance in zebrafish. Commun Biol 2023; 6:1300. [PMID: 38129658 PMCID: PMC10739737 DOI: 10.1038/s42003-023-05686-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
CRISPR-mediated knock-in (KI) technology opens a new era of fluorescent-protein labeling in zebrafish, a preferred model organism for in vivo imaging. We described here an optimized zebrafish gene-tagging strategy, which enables easy and high-efficiency KI, ensures high odds of obtaining seamless KI germlines and is suitable for wide applications. Plasmid donors for 3'-labeling were optimized by shortening the microhomologous arms and by reducing the number and reversing the sequence of the consensus Cas9/sgRNA binding sites. To allow for scar-less KI across the genome, linearized dsDNA donors with 5'-chemical modifications were generated and successfully incorporated into our method. To refine the germline screen workflow and expedite the screen process, we combined fluorescence enrichment and caudal-fin junction-PCR. Furthermore, to trace proteins expressed at a low abundance, we developed a fluorescent signal amplifier using the transcriptional activation strategy. Together, our strategies enable efficient gene-tagging and sensitive expression detection for almost every gene in zebrafish.
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Affiliation(s)
- Jiannan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Wenyuan Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Xuepu Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Fanjia Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
- Laboratory Animal Center, Xiamen University, 361102, Xiamen, Fujian, China.
- Research Unit of Cellular Stress of CAMS, Cancer Research Center of Xiamen University, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Yingying Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
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42
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Lee BC, Gin A, Wu C, Singh K, Grice M, Mortlock R, Abraham D, Fan X, Zhou Y, AlJanahi A, Choi U, de Ravin SS, Shin T, Hong S, Dunbar CE. Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571396. [PMID: 38168153 PMCID: PMC10760194 DOI: 10.1101/2023.12.13.571396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34 + cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34 + cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively. CD33 knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction in CD33 KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP + cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.
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43
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Chen Z, Kwan SY, Mir A, Hazeltine M, Shin M, Liang SQ, Chan IL, Kelly K, Ghanta KS, Gaston N, Cao Y, Xie J, Gao G, Xue W, Sontheimer EJ, Watts JK. A Fluorescent Reporter Mouse for In Vivo Assessment of Genome Editing with Diverse Cas Nucleases and Prime Editors. CRISPR J 2023; 6:570-582. [PMID: 38108517 PMCID: PMC10753986 DOI: 10.1089/crispr.2023.0048] [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: 07/27/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
CRISPR-based genome-editing technologies, including nuclease editing, base editing, and prime editing, have recently revolutionized the development of therapeutics targeting disease-causing mutations. To advance the assessment and development of genome editing tools, a robust mouse model is valuable, particularly for evaluating in vivo activity and delivery strategies. In this study, we successfully generated a knock-in mouse line carrying the Traffic Light Reporter design known as TLR-multi-Cas variant 1 (TLR-MCV1). We comprehensively validated the functionality of this mouse model for both in vitro and in vivo nuclease and prime editing. The TLR-MCV1 reporter mouse represents a versatile and powerful tool for expediting the development of editing technologies and their therapeutic applications.
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Affiliation(s)
- Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Suet-Yan Kwan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Max Hazeltine
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Io Long Chan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Krishna S. Ghanta
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Yueying Cao
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Jun Xie
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Viral Vector Core, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Guangping Gao
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Viral Vector Core, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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Jose B, Punetha M, Tripathi MK, Khanna S, Yadav V, Singh AK, Kumar B, Singh K, Chouhan VS, Sarkar M. CRISPR/Cas mediated disruption of BMPR-1B gene and introduction of FecB mutation into the Caprine embryos using Easi-CRISPR strategy. Theriogenology 2023; 211:125-133. [PMID: 37619525 DOI: 10.1016/j.theriogenology.2023.08.008] [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: 05/07/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Bone Morphogenetic Proteins play a significant role in ovarian physiology and contribute to the reproductive fitness of mammals. The BMPR-1B/FecB mutation, a loss of function mutation increases litter size by 1-2 with each number of mutated alleles in sheep. Considering demand-supply gap of the meat industry, and low replacement rate of indigenous caprine species, the conservative BMPR-1B locus can be explored, and FecB mutated goats can be produced. The experiment one produced CRISPR/Cas mediated KO transferable caprine embryos, and experiment two generated caprine embryos with desired FecB mutation using Easi-CRISPR strategy. In the KO experiment, Cas9 and BMPR-1B guide RNA (100:100ng/ul) were electroporated into single stage caprine zygotes at 750V, 10 ms and 1pulse using Neon transfection system. In the second experiment, phosphorothioate (PS) modified single-stranded oligodeoxynucleotide (ssODN) was used as an HDR template along with CRISPR components (100:100ng/ul, ssODN 100ng/ul). The precise time and method of electroporation, RNP format of CRISPR components and PS modified asymmetric ssODN were the factors that affected the production of mosaicism free BMPR-1B edited caprine embryos. The editing efficiency of KO and KI experiments was 68.52 and 63.16% respectively, and successful production of goats with higher mean ovulation rate can be realized with addition of embryo transfer technology to these experiments.
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Affiliation(s)
- Bosco Jose
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Meeti Punetha
- Division of Animal Physiology and Reproduction, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India.
| | - Manoj Kumar Tripathi
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Shivani Khanna
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Vijay Yadav
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Amit Kumar Singh
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Brijesh Kumar
- Division of Animal Reproduction, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Kiranjeet Singh
- Division of Surgery, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Vikrant Singh Chouhan
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Mihir Sarkar
- Physiology & Climatology Division, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
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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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46
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Lewis MM, Soto MR, Maier EY, Wulfe SD, Bakheet S, Obregon H, Ghosh D. Optimization of ionizable lipids for aerosolizable mRNA lipid nanoparticles. Bioeng Transl Med 2023; 8:e10580. [PMID: 38023707 PMCID: PMC10658486 DOI: 10.1002/btm2.10580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 06/17/2023] [Accepted: 07/10/2023] [Indexed: 12/01/2023] Open
Abstract
Although mRNA lipid nanoparticles (LNPs) are highly effective as vaccines, their efficacy for pulmonary delivery has not yet fully been established. A major barrier to this therapeutic goal is their instability during aerosolization for local delivery. This imparts a shear force that degrades the mRNA cargo and therefore reduces cell transfection. In addition to remaining stable upon aerosolization, mRNA LNPs must also possess the aerodynamic properties to achieve deposition in clinically relevant areas of the lungs. We addressed these challenges by formulating mRNA LNPs with SM-102, the clinically approved ionizable lipid in the Spikevax COVID-19 vaccine. Our lead candidate, B-1, had the highest mRNA expression in both a physiologically relevant air-liquid interface (ALI) human lung cell model and in healthy mice lungs upon aerosolization. Further, B-1 showed selective transfection in vivo of lung epithelial cells compared to immune cells and endothelial cells. These results show that the formulation can target therapeutically relevant cells in pulmonary diseases such as cystic fibrosis. Morphological studies of B-1 revealed differences in the surface structure compared to LNPs with lower transfection efficiency. Importantly, the formulation maintained critical aerodynamic properties in simulated human airways upon next generation impaction. Finally, structure-function analysis of SM-102 revealed that small changes in the number of carbons can improve upon mRNA delivery in ALI human lung cells. Overall, our study expands the application of SM-102 and its analogs to aerosolized pulmonary delivery and identifies a potent lead candidate for future therapeutically active mRNA therapies.
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Affiliation(s)
- Mae M. Lewis
- Department of Biomedical EngineeringThe University of Texas at AustinAustinTexasUSA
| | - Melissa R. Soto
- Division of Molecular Pharmaceutics and Drug Delivery, College of PharmacyThe University of Texas at AustinAustinTexasUSA
| | - Esther Y. Maier
- Drug Dynamics InstituteThe University of Texas at AustinAustinTexasUSA
| | - Steven D. Wulfe
- Division of Molecular Pharmaceutics and Drug Delivery, College of PharmacyThe University of Texas at AustinAustinTexasUSA
| | - Sandy Bakheet
- Division of Molecular Pharmaceutics and Drug Delivery, College of PharmacyThe University of Texas at AustinAustinTexasUSA
| | - Hannah Obregon
- Division of Molecular Pharmaceutics and Drug Delivery, College of PharmacyThe University of Texas at AustinAustinTexasUSA
| | - Debadyuti Ghosh
- Division of Molecular Pharmaceutics and Drug Delivery, College of PharmacyThe University of Texas at AustinAustinTexasUSA
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47
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Yoon C, Baek KE, Kim D, Lee GM. Mitigating transcriptional bottleneck using a constitutively active transcription factor, VP16-CREB, in mammalian cells. Metab Eng 2023; 80:33-44. [PMID: 37709006 DOI: 10.1016/j.ymben.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 07/13/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
High-level expression of recombinant proteins in mammalian cells has long been an area of interest. Inefficient transcription machinery is often an obstacle in achieving high-level expression of recombinant proteins in mammalian cells. Synthetic promoters have been developed to improve the transcription efficiency, but have achieved limited success due to the limited availability of transcription factors (TFs). Here, we present a TF-engineering approach to mitigate the transcriptional bottlenecks of recombinant proteins. This includes: (i) identification of cAMP response element binding protein (CREB) as a candidate TF by searching for TFs enriched in the cytomegalovirus (CMV) promoter-driven high-producing recombinant Chinese hamster ovary (rCHO) cell lines via transcriptome analysis, (ii) confirmation of transcriptional limitation of active CREB in rCHO cell lines, and (iii) direct activation of the transgene promoter by expressing constitutively active CREB at non-cytotoxic levels in rCHO cell lines. With the expression of constitutively active VP16-CREB, the production of therapeutic proteins, such as monoclonal antibody and etanercept, in CMV promoter-driven rCHO cell lines was increased up to 3.9-fold. VP16-CREB was also used successfully with synthetic promoters containing cAMP response elements. Taken together, this strategy to introduce constitutively active TFs into cells is a useful means of overcoming the transcriptional limitations in recombinant mammalian cells.
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Affiliation(s)
- Chansik Yoon
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Kyoung Eun Baek
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Dongil Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea.
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48
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Cao K, Cui Y, Sun F, Zhang H, Fan J, Ge B, Cao Y, Wang X, Zhu X, Wei Z, Yao Q, Ma J, Wang Y, Meng C, Gao Z. Metabolic engineering and synthetic biology strategies for producing high-value natural pigments in Microalgae. Biotechnol Adv 2023; 68:108236. [PMID: 37586543 DOI: 10.1016/j.biotechadv.2023.108236] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/16/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Microalgae are microorganisms capable of producing bioactive compounds using photosynthesis. Microalgae contain a variety of high value-added natural pigments such as carotenoids, phycobilins, and chlorophylls. These pigments play an important role in many areas such as food, pharmaceuticals, and cosmetics. Natural pigments have a health value that is unmatched by synthetic pigments. However, the current commercial production of natural pigments from microalgae is not able to meet the growing market demand. The use of metabolic engineering and synthetic biological strategies to improve the production performance of microalgal cell factories is essential to promote the large-scale production of high-value pigments from microalgae. This paper reviews the health and economic values, the applications, and the synthesis pathways of microalgal pigments. Overall, this review aims to highlight the latest research progress in metabolic engineering and synthetic biology in constructing engineered strains of microalgae with high-value pigments and the application of CRISPR technology and multi-omics in this context. Finally, we conclude with a discussion on the bottlenecks and challenges of microalgal pigment production and their future development prospects.
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Affiliation(s)
- Kai Cao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China; School of Life Sciences and medicine, Shandong University of Technology, Zibo 255049, China
| | - Yulin Cui
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Fengjie Sun
- Department of Biological Sciences, School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Hao Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Jianhua Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Yujiao Cao
- School of Foreign Languages, Shandong University of Technology, Zibo 255090, China
| | - Xiaodong Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Xiangyu Zhu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China; School of Life Sciences and medicine, Shandong University of Technology, Zibo 255049, China
| | - Zuoxi Wei
- School of Life Sciences and medicine, Shandong University of Technology, Zibo 255049, China
| | - Qingshou Yao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Jinju Ma
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Yu Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Chunxiao Meng
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
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49
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Rose JC, Wong ITL, Daniel B, Jones MG, Yost KE, Hung KL, Curtis EJ, Mischel PS, Chang HY. Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563489. [PMID: 37961138 PMCID: PMC10634728 DOI: 10.1101/2023.10.22.563489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.8 Mb ecDNA both reaching 15%. We show non-homologous end joining and microhomology mediated end joining both contribute to ecDNA formation, while inhibition of DNA-PKcs and ATM have opposing impacts on ecDNA formation. EcDNA and the corresponding chromosomal excision scar form at significantly different rates and respond differently to DNA-PKcs and ATM inhibition. Taken together, our results support a model of ecDNA formation in which double strand break ends dissociate from their legitimate ligation partners prior to joining of illegitimate ends to form the ecDNA and excision scar.
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Affiliation(s)
- John C Rose
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew G Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ellis J Curtis
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul S Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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50
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Wang M, Ding F, Wang H, Li L, Dai Y, Sun Z, Li N. Versatile generation of precise gene edits in bovines using SEGCPN. BMC Biol 2023; 21:226. [PMID: 37864194 PMCID: PMC10589966 DOI: 10.1186/s12915-023-01677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/07/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Gene knockout and knock-in have been widely performed in large farm animals based on genome editing systems. However, many types of precise gene editing, including targeted deletion, gene tagging, and large gene fragment replacement, remain a challenge in large farm animals. RESULTS Here, we established versatile self-excising gene-targeting technology in combination with programmable nucleases (SEGCPN) to efficiently generate various types of precise gene editing in bovine. First, we used this versatile method to successfully generate bovine embryos with point mutations and 11-bp deletions at the MSTN locus. Second, we successfully generated bulls with EGFP labeling at the SRY locus. Finally, we successfully generated humanized cows in which the endogenous 18-kb α-casein gene was replaced with a 2.6-kb human α-lactalbumin gene. CONCLUSIONS In summary, our new SEGCPN method offers unlimited possibilities for various types of precise gene editing in large animals for application both in agriculture and disease models.
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Affiliation(s)
- Ming Wang
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China
| | - Fangrong Ding
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Haiping Wang
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Ling Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Yunping Dai
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
| | - ZhaoLin Sun
- College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China.
| | - Ning Li
- College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China.
- Beijing Capital Agribusiness Future Biotechnology Co., Ltd, No. 75 Bingjiaokou Hutong, Beijing, 100088, China.
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