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Wu S, Yang P, Geng Z, Li Y, Guo Z, Lou Y, Zhang S, Xiong J, Hu H, Guo X, Pu WT, Zhang Y, Zhu D, Zhang B. Base editing effectively prevents early-onset severe cardiomyopathy in Mybpc3 mutant mice. Cell Res 2024; 34:327-330. [PMID: 38337022 PMCID: PMC10978934 DOI: 10.1038/s41422-024-00930-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/31/2023] [Indexed: 02/12/2024] Open
Affiliation(s)
- Shuo Wu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Yang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yige Li
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhizhao Guo
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingmei Lou
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junhao Xiong
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huan Hu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoling Guo
- Basic Medical Research Center, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
| | - Yan Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Dan Zhu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Bing Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Department of Cardiovascular Surgery, Shanghai Chest Hospital, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute of Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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2
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Tomita A, Sasanuma H, Owa T, Nakazawa Y, Shimada M, Fukuoka T, Ogi T, Nakada S. Inducing multiple nicks promotes interhomolog homologous recombination to correct heterozygous mutations in somatic cells. Nat Commun 2023; 14:5607. [PMID: 37714828 PMCID: PMC10504326 DOI: 10.1038/s41467-023-41048-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 08/22/2023] [Indexed: 09/17/2023] Open
Abstract
CRISPR/Cas9-mediated gene editing has great potential utility for treating genetic diseases. However, its therapeutic applications are limited by unintended genomic alterations arising from DNA double-strand breaks and random integration of exogenous DNA. In this study, we propose NICER, a method for correcting heterozygous mutations that employs multiple nicks (MNs) induced by Cas9 nickase and a homologous chromosome as an endogenous repair template. Although a single nick near the mutation site rarely leads to successful gene correction, additional nicks on homologous chromosomes strongly enhance gene correction efficiency via interhomolog homologous recombination (IH-HR). This process partially depends on BRCA1 and BRCA2, suggesting the existence of several distinct pathways for MN-induced IH-HR. According to a genomic analysis, NICER rarely induces unintended genomic alterations. Furthermore, NICER restores the expression of disease-causing genes in cells derived from genetic diseases with compound heterozygous mutations. Overall, NICER provides a precise strategy for gene correction.
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Affiliation(s)
- Akiko Tomita
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hiroyuki Sasanuma
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-0057, Japan
| | - Tomoo Owa
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, 464-8601, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, 464-8601, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, 464-8601, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, 464-8601, Japan
| | - Takahiro Fukuoka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, 464-8601, Japan
- Genomedia Inc., Tokyo, 113-0033, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, 464-8601, Japan
- Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, 464-8601, Japan
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
- Institute for Advanced Co-Creation Studies, Osaka University, Suita, Osaka, 565-0871, Japan.
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3
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Vaitsiankova A, Burdova K, Sobol M, Gautam A, Benada O, Hanzlikova H, Caldecott KW. PARP inhibition impedes the maturation of nascent DNA strands during DNA replication. Nat Struct Mol Biol 2022; 29:329-338. [PMID: 35332322 PMCID: PMC9010290 DOI: 10.1038/s41594-022-00747-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is implicated in the detection and processing of unligated Okazaki fragments and other DNA replication intermediates, highlighting such structures as potential sources of genome breakage induced by PARP inhibition. Here, we show that PARP1 activity is greatly elevated in chicken and human S phase cells in which FEN1 nuclease is genetically deleted and is highest behind DNA replication forks. PARP inhibitor reduces the integrity of nascent DNA strands in both wild-type chicken and human cells during DNA replication, and does so in FEN1-/- cells to an even greater extent that can be detected as postreplicative single-strand nicks or gaps. Collectively, these data show that PARP inhibitors impede the maturation of nascent DNA strands during DNA replication, and implicate unligated Okazaki fragments and other nascent strand discontinuities in the cytotoxicity of these compounds.
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Affiliation(s)
- Alina Vaitsiankova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Kamila Burdova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Margarita Sobol
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Amit Gautam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Oldrich Benada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, Czech Republic.
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
- Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, Czech Republic.
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Demétrio de Souza França P, Guru N, Roberts S, Kossatz S, Mason C, Abrahão M, Ghossein RA, Patel SG, Reiner T. Fluorescence-guided resection of tumors in mouse models of oral cancer. Sci Rep 2020; 10:11175. [PMID: 32636416 PMCID: PMC7341853 DOI: 10.1038/s41598-020-67958-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022] Open
Abstract
Complete removal and negative margins are the goal of any surgical resection of primary oral cavity carcinoma. Current approaches to determine tumor boundaries rely heavily on surgeons' expertise, and final histopathological reports are usually only available days after surgery, precluding contemporaneous re-assessment of positive margins. Intraoperative optical imaging could address this unmet clinical need. Using mouse models of oral cavity carcinoma, we demonstrated that PARPi-FL, a fluorescent PARP inhibitor targeting the enzyme PARP1/2, can delineate oral cancer and accurately identify positive margins, both macroscopically and at cellular resolution. PARPi-FL also allowed identification of compromised margins based on fluorescence hotspots, which were not seen in margin-negative resections and control tongues. PARPi-FL was further able to differentiate tumor from low-grade dysplasia. Intravenous injection of PARPi-FL has significant potential for clinical translation and could aid surgeons in assessing oral cancer margins in vivo.
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Affiliation(s)
- Paula Demétrio de Souza França
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Otorhinolaryngology and Head and Neck Surgery, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Navjot Guru
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Sheryl Roberts
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Susanne Kossatz
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Nuclear Medicine, School of Medicine, Technische Universität München, Munich, Germany
| | - Christian Mason
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Marcio Abrahão
- Department of Otorhinolaryngology and Head and Neck Surgery, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Ronald A Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Snehal G Patel
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Otorhinolaryngology, Weill Cornell Medical College, New York, NY, USA
| | - Thomas Reiner
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Otorhinolaryngology, Weill Cornell Medical College, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Islam MR, Ihenacho K, Park JW, Islam IS. Plasmid DNA nicking- a Novel Activity of Soybean Trypsin Inhibitor and Bovine Aprotinin. Sci Rep 2019; 9:11596. [PMID: 31406183 PMCID: PMC6690959 DOI: 10.1038/s41598-019-48068-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 07/16/2019] [Indexed: 11/09/2022] Open
Abstract
Protease inhibitors, such as trypsin inhibitor, serum alpha-1 antitrypsin, or liver aprotinin, are a class of proteins that competitively bind and block the catalytic activity of proteolytic enzymes with wide ranging biological functions. A significant number of protease inhibitors have also been shown to possess antimicrobial activity, presumed to contribute in defense against pathogenic microorganisms as plants with higher levels of protease inhibitors tend to exhibit increased resistance towards pathogens. Two proposed mechanisms for the antimicrobial activity are combating microbial proteases that play roles in disease development and disruption of microbial cell wall & membrane necessary for survival. Here we show for the first time a novel activity of soybean trypsin inhibitor and bovine aprotinin that they nick supercoiled, circular plasmid DNA. A number of experiments conducted to demonstrate the observed DNA nicking activity is inherent, rather than a co-purified, contaminating nuclease. The nicking of the plasmid results in markedly reduced efficiencies in transformation of E. coli and transfection of HEK293T cells. Thus, this work reveals yet a new mechanism for the antimicrobial activity by protease inhibitors.
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Affiliation(s)
- M Rafiq Islam
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America.
| | - Kelvin Ihenacho
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America
| | - Jae Whan Park
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America
| | - I Sakif Islam
- Laboratory of Biochemistry, Northwest Missouri State University, 7314 N. Tullis Ave, Kansas City, Missouri, 64158, United States of America
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Abstract
Replication-dependent chromosomal breakage suggests that replication forks occasionally run into nicks in template DNA and collapse, generating double-strand ends. To model replication fork collapse in vivo, I constructed phage lambda chromosomes carrying the nicking site of M13 bacteriophage and infected with these substrates Escherichia coli cells, producing M13 nicking enzyme. I detected double-strand breaks at the nicking sites in lambda DNA purified from these cells. The double-strand breakage depends on (i) the presence of the nicking site; (ii) the production of the nicking enzyme; and (iii) replication of the nick-containing chromosome. Replication fork collapse at nicks in template DNA explains diverse phenomena, including eukaryotic cell killing by DNA topoisomerase inhibitors and inviability of recombination-deficient vertebrate cell lines.
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Affiliation(s)
- A Kuzminov
- Department of Microbiology, University of Illinois, Urbana-Champaign, B103 C&LSL, 601 South Goodwin Avenue, Urbana, IL 61801-3709.
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