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Liao H, Wu J, VanDusen NJ, Li Y, Zheng Y. CRISPR-Cas9-mediated homology-directed repair for precise gene editing. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102344. [PMID: 39494147 PMCID: PMC11531618 DOI: 10.1016/j.omtn.2024.102344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2024]
Abstract
CRISPR-Cas9-mediated homology-directed repair (HDR) is a versatile platform for creating precise site-specific DNA insertions, deletions, and substitutions. These precise edits are made possible through the use of exogenous donor templates that carry the desired sequence. CRISPR-Cas9-mediated HDR can be widely used to study protein functions, disease modeling, and gene therapy. However, HDR is limited by its low efficiency, especially in postmitotic cells. Here, we review CRISPR-Cas9-mediated HDR, with a focus on methodologies for boosting HDR efficiency, and applications of precise editing via HDR. First, we describe two common mechanisms of DNA repair, non-homologous end joining (NHEJ), and HDR, and discuss their impact on CRISPR-Cas9-mediated precise genome editing. Second, we discuss approaches for improving HDR efficiency through inhibition of the NHEJ pathway, activation of the HDR pathway, modification of donor templates, and delivery of Cas9/sgRNA reagents. Third, we summarize the applications of HDR for protein labeling in functional studies, disease modeling, and ex vivo and in vivo gene therapies. Finally, we discuss alternative precise editing platforms and their limitations, and describe potential avenues to improving CRISPR-Cas9-mediated HDR efficiency and fidelity in future research.
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Affiliation(s)
- Hongyu Liao
- 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
| | - Jiahao Wu
- 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
| | - Nathan J. VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - 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
| | - 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
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2
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Arnaoutova I, Aratyn-Schaus Y, Zhang L, Packer MS, Chen HD, Lee C, Gautam S, Gregoire FM, Leboeuf D, Boule S, Fernandez TP, Huang V, Cheng LI, Lung G, Bannister B, Decker J, Leete T, Shuang LS, Bock C, Kothiyal P, Grayson P, Mok KW, Quinn JJ, Young L, Barrera L, Ciaramella G, Mansfield BC, Chou JY. Base-editing corrects metabolic abnormalities in a humanized mouse model for glycogen storage disease type-Ia. Nat Commun 2024; 15:9729. [PMID: 39523369 PMCID: PMC11551175 DOI: 10.1038/s41467-024-54108-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024] Open
Abstract
Glycogen storage disease type-Ia patients, deficient in the G6PC1 gene encoding glucose-6-phosphatase-α, lack blood glucose control, resulting in life-threatening hypoglycemia. Here we show our humanized mouse model, huR83C, carrying the pathogenic G6PC1-R83C variant displays the phenotype of glycogen storage disease type-Ia and dies prematurely. We evaluate the efficacy of BEAM-301, a formulation of lipid nanoparticles containing a newly-engineered adenine base editor, to correct the G6PC1-R83C variant in huR83C mice and monitor phenotypic correction through one year. BEAM-301 can correct up to ~60% of the G6PC1-R83C variant in liver cells, restores blood glucose control, improves metabolic abnormalities of the disease, and confers long-term survival to the mice. Interestingly, just ~10% base correction is therapeutic. The durable pharmacological efficacy of base editing in huR83C mice supports the development of BEAM-301 as a potential therapeutic for homozygous and compound heterozygous glycogen storage disease type-Ia patients carrying the G6PC1-R83C variant.
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Affiliation(s)
- Irina Arnaoutova
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Lisa Zhang
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Hung-Dar Chen
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cheol Lee
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sudeep Gautam
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | | | | | | | | | - Lo-I Cheng
- BEAM Therapeutics, Cambridge, MA, 02142, USA
| | | | | | | | | | | | | | | | | | - Ka W Mok
- BEAM Therapeutics, Cambridge, MA, 02142, USA
| | | | | | | | | | - Brian C Mansfield
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Janice Y Chou
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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3
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Merlin JPJ, Abrahamse H. Optimizing CRISPR/Cas9 precision: Mitigating off-target effects for safe integration with photodynamic and stem cell therapies in cancer treatment. Biomed Pharmacother 2024; 180:117516. [PMID: 39332185 DOI: 10.1016/j.biopha.2024.117516] [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: 07/12/2024] [Revised: 09/22/2024] [Accepted: 09/25/2024] [Indexed: 09/29/2024] Open
Abstract
CRISPR/Cas9 precision genome editing has revolutionized cancer treatment by introducing specific alterations to the cancer genome. But the therapeutic potential of CRISPR/Cas9 is limited by off-target effects, which can cause undesired changes to genomic regions and create major safety concerns. The primary emphasis lies in their implications within the realm of cancer photodynamic therapy (PDT), where precision is paramount. PDT is a promising cancer treatment method; nevertheless, its effectiveness is severely limited and readily leads to recurrence due to the therapeutic resistance of cancer stem cells (CSCs). With a focus on targeted genome editing into cancer cells during PDT and stem cell treatment (SCT), the review aims to further the ongoing search for safer and more accurate CRISPR/Cas9-mediated methods. At the core of this exploration are recent advancements and novel techniques that offer promise in mitigating the risks associated with off-target effects. With a focus on cancer PDT and SCT, this review critically assesses the landscape of off-target effects in CRISPR/Cas9 applications, offering a comprehensive knowledge of their nature and prevalence. A key component of the review is the assessment of cutting-edge delivery methods, such as technologies based on nanoparticles (NPs), to optimize the distribution of CRISPR components. Additionally, the study delves into the intricacies of guide RNA design, focusing on advancements that bolster specificity and minimize off-target effects, crucial elements in ensuring the precision required for effective cancer PDT and SCT. By synthesizing insights from various methodologies, including the exploration of innovative genome editing tools and leveraging robust validation methods and bioinformatics tools, the review aspires to chart a course towards more reliable and precise CRISPR-Cas9 applications in cancer PDT and SCT. For safe PDT and SCT integration in cancer therapy, CRISPR/Cas9 precision optimization is essential. Utilizing sophisticated molecular and computational techniques to address off-target effects is crucial to realizing the therapeutic promise of these technologies, which will ultimately lead to the development of individualized and successful cancer treatment strategies. Our long-term goals are to improve precision genome editing for more potent cancer therapy approaches by refining the way CRISPR/Cas9 is integrated with photodynamic and stem cell therapies.
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Affiliation(s)
- J P Jose Merlin
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, South Africa.
| | - Heidi Abrahamse
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, South Africa
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4
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Legere NJ, Hinson JT. Emerging CRISPR Therapies for Precision Gene Editing and Modulation in the Cardiovascular Clinic. Curr Cardiol Rep 2024; 26:1231-1240. [PMID: 39287778 DOI: 10.1007/s11886-024-02125-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/21/2024] [Indexed: 09/19/2024]
Abstract
PURPOSE OF REVIEW Outline the growing suite of novel genome editing tools powered by CRISPR-Cas9 technology that are rapidly advancing towards the clinic for the treatment of cardiovascular disorders. RECENT FINDINGS A diversity of new genome editors and modulators are being developed for therapies across myriad human diseases. Recent breakthroughs have improved the efficacy, safety, specificity, and delivery of CRISPR-mediated therapies that could impact heart disease in the next decade, though several challenges remain. Many iterations of the original CRISPR system have been developed seeking to leverage its vast therapeutic potential. As examples, nuclease-free editing, precision single-nucleotide editing, gene expression regulation, and epigenomic modifications are now feasible with the current CRISPR-mediated suite of enzymes. These emerging tools will be indispensable for the development of novel cardiovascular therapeutics as demonstrated by recent successes in both basic research laboratories and pre-clinical models. Here, we provide an overview of current and emerging CRISPR-mediated technologies as they pertain to the cardiovascular system, highlighting successful implementations and future challenges.
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Affiliation(s)
| | - J Travis Hinson
- University of Connecticut Health Center, Farmington, CT, USA.
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Calhoun Cardiology Center, UConn Health, Farmington, CT, USA.
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5
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Liu J, Zhu L. PlmCas12e Utilizes Glu662 to Prevent Cleavage Site Occupation by Positively Charged Residues Before Target Strand Cleavage. Molecules 2024; 29:5036. [PMID: 39519677 PMCID: PMC11547573 DOI: 10.3390/molecules29215036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 10/19/2024] [Accepted: 10/19/2024] [Indexed: 11/16/2024] Open
Abstract
CRISPR-Cas12e is a recently identified gene-editing tool mainly known because its relatively small size benefits cell delivery. Drastically different from Cas9, it creates a blunt-end double-strand breakage of the DNA via two cleavage sites; Cas12e produces a sticky-end double-strand breakage of the DNA through only one cleavage site in its RuvC domain, meaning two consecutive cleavage events first on the non-target strand (ntsDNA) and then the target strand (tsDNA). Though crucial for Cas12e's cleavage efficiency, the mechanism by which Cas12e loads tsDNA for the second cleavage remains elusive. Through molecular dynamics simulations and our recently matured traveling-salesman-based automated path-searching (TAPS) algorithm, we identified a series of positively charged residues (Arg856TSL, Arg768RuvC, Lys898TSL, Arg904TSL, Arg764RuvC) that guide the tsDNA backbone toward the cleavage site of wild-type PlmCas12e. Further simulations of the R856L and R904L mutants supported such observations. More interestingly, we found the key role of Glu662RuvC in coordinating Arg764RuvC, preventing its occupation of the cleavage site, and facilitating tsDNA cleavage. Additional simulations confirmed that mutating Glu662RuvC to valine disabled such coordination and created a stable intermediate state with Arg764RuvC occupying the cleavage site before tsDNA loading. These insights, revealing an elaborate mechanism of cleavage facilitation, offer essential guiding principles for future rational engineering of Cas12e into more efficient gene-editing tools.
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Affiliation(s)
| | - Lizhe Zhu
- School of Medicine, and Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China;
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6
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Rose EP, Osterberg VR, Gorbunova V, Unni VK. Alpha-synuclein modulates the repair of genomic DNA double-strand breaks in a DNA-PK cs-regulated manner. Neurobiol Dis 2024; 201:106675. [PMID: 39306014 PMCID: PMC11556349 DOI: 10.1016/j.nbd.2024.106675] [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: 02/27/2024] [Revised: 08/22/2024] [Accepted: 09/18/2024] [Indexed: 09/25/2024] Open
Abstract
α-synuclein (αSyn) is a presynaptic and nuclear protein that aggregates in important neurodegenerative diseases such as Parkinson's Disease (PD), Parkinson's Disease Dementia (PDD) and Lewy Body Dementia (LBD). Our past work suggests that nuclear αSyn may regulate forms of DNA double-strand break (DSB) repair in HAP1 cells after DNA damage induction with the chemotherapeutic agent bleomycin1. Here, we report that genetic deletion of αSyn specifically impairs the non-homologous end-joining (NHEJ) pathway of DSB repair using an extrachromosomal plasmid-based repair assay in HAP1 cells. Notably, induction of a single DSB at a precise genomic location using a CRISPR/Cas9 lentiviral approach also showed the importance of αSyn in regulating NHEJ in HAP1 cells and primary mouse cortical neuron cultures. This modulation of DSB repair is regulated by the activity of the DNA damage response signaling kinase DNA-PKcs, since the effect of αSyn loss-of-function is reversed by DNA-PKcs inhibition. Together, these findings suggest that αSyn plays an important physiologic role in regulating DSB repair in both a transformed cell line and in primary cortical neurons. Loss of this nuclear function may contribute to the neuronal genomic instability detected in PD, PDD and LBD and points to DNA-PKcs as a potential therapeutic target.
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Affiliation(s)
- Elizabeth P Rose
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239, United States of America; Neuroscience Graduate Program, Vollum Institute, Oregon Health & Science University, Portland, OR 97239, United States of America
| | - Valerie R Osterberg
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239, United States of America
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY 14620, United States of America
| | - Vivek K Unni
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239, United States of America; OHSU Parkinson Center, Department of Neurology, Oregon Health & Science University, Portland, OR 97239, United States of America.
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7
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Aguilar G, Bauer M, Vigano MA, Schnider ST, Brügger L, Jiménez-Jiménez C, Guerrero I, Affolter M. Seamless knockins in Drosophila via CRISPR-triggered single-strand annealing. Dev Cell 2024; 59:2672-2686.e5. [PMID: 38971155 DOI: 10.1016/j.devcel.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/06/2023] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
CRISPR-Cas greatly facilitated the integration of exogenous sequences into specific loci. However, knockin generation in multicellular animals remains challenging, partially due to the complexity of insertion screening. Here, we describe SEED/Harvest, a method to generate knockins in Drosophila, based on CRISPR-Cas and the single-strand annealing (SSA) repair pathway. In SEED (from "scarless editing by element deletion"), a switchable cassette is first integrated into the target locus. In a subsequent CRISPR-triggered repair event, resolved by SSA, the cassette is seamlessly removed. Germline excision of SEED cassettes allows for fast and robust knockin generation of both fluorescent proteins and short protein tags in tandem. Tissue-specific expression of Cas9 results in somatic cassette excision, conferring spatiotemporal control of protein labeling and the conditional rescue of mutants. Finally, to achieve conditional protein labeling and manipulation of short tag knockins, we developed a genetic toolbox by functionalizing the ALFA nanobody.
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Affiliation(s)
- Gustavo Aguilar
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Milena Bauer
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - M Alessandra Vigano
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Sophie T Schnider
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Lukas Brügger
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Carlos Jiménez-Jiménez
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Isabel Guerrero
- Tissue and Organ Homeostasis, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Nicolás Cabrera 1, Madrid, Spain
| | - Markus Affolter
- Growth & Development, Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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8
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Maruta G, Maeoka H, Tsunoda T, Akiyoshi K, Takagi S, Shirasawa S, Ishikura S. RAD52-mediated repair of DNA double-stranded breaks at inactive centromeres leads to subsequent apoptotic cell death. Nucleic Acids Res 2024:gkae852. [PMID: 39360606 DOI: 10.1093/nar/gkae852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/12/2024] [Accepted: 09/18/2024] [Indexed: 10/04/2024] Open
Abstract
Centromeres, where the kinetochore complex binds, are susceptible to damages including DNA double-stranded breaks (DSBs). Here, we report the functional significance and the temporally and spatially distinct regulation of centromeric DSB repair via the three pathways of non-homologous end joining (NHEJ), homologous recombination (HR) and single-strand annealing (SSA). The SSA factor RAD52 is most frequently recruited to centromeric DSB sites compared with the HR factor RAD51 and the NHEJ factor DNA ligase IV (LIG4), indicating that SSA plays predominant roles in centromeric DSB repair. Upon centromeric DSB induction, LIG4 is recruited to both active centromeres, where kinetochore complex binds, and inactive centromeres. In contrast, RAD51 and RAD52 are recruited only to inactive centromeres. These results indicate that DSBs at active centromeres are repaired through NHEJ, whereas the three pathways of NHEJ, HR and SSA are involved in DSB repair at inactive centromeres. Furthermore, siRNA-mediated depletion of either LIG4 or RAD51 promotes cell death after centromeric DSB induction, whereas RAD52 depletion inhibits it, suggesting that HR and NHEJ are required for appropriate centromeric DSB repair, whereas SSA-mediated centromeric DSB repair leads to subsequent cell death. Thus, SSA-mediated DSB repair at inactive centromeres may cause centromere dysfunction through error-prone repair.
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Affiliation(s)
- Gen Maruta
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Department of Anesthesiology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Hisanori Maeoka
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Center for Advanced Molecular Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Kozaburo Akiyoshi
- Department of Anesthesiology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Satoshi Takagi
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Center for Advanced Molecular Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
- Center for Advanced Molecular Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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9
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Zhen T, Sun T, Xiong B, Liu H, Wang L, Chen Y, Sun H. New insight into targeting the DNA damage response in the treatment of glioblastoma. Chin J Nat Med 2024; 22:869-886. [PMID: 39428180 DOI: 10.1016/s1875-5364(24)60694-1] [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: 06/21/2024] [Indexed: 10/22/2024]
Abstract
Glioblastoma (GBM) is the most common invasive malignant tumor in human brain tumors, representing the most severe grade of gliomas. Despite existing therapeutic approaches, patient prognosis remains dismal, necessitating the exploration of novel strategies to enhance treatment efficacy and extend survival. Due to the restrictive nature of the blood-brain barrier (BBB), small-molecule inhibitors are prioritized in the treatment of central nervous system tumors. Among these, DNA damage response (DDR) inhibitors have garnered significant attention due to their potent therapeutic potential across various malignancies. This review provides a detailed analysis of DDR pathways as therapeutic targets in GBM, summarizes recent advancements, therapeutic strategies, and ongoing clinical trials, and offers perspectives on future directions in this rapidly evolving field. The goal is to present a comprehensive outlook on the potential of DDR inhibitors in improving GBM management and outcomes.
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Affiliation(s)
- Tengfei Zhen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Tianyu Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Baichen Xiong
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Hui Liu
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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10
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Ajit K, Gullerova M. From silence to symphony: transcriptional repression and recovery in response to DNA damage. Transcription 2024:1-15. [PMID: 39353089 DOI: 10.1080/21541264.2024.2406717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/10/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Genotoxic stress resulting from DNA damage is resolved through a signaling cascade known as the DNA Damage Response (DDR). The repair of damaged DNA is essential for cell survival, often requiring the DDR to attenuate other cellular processes such as the cell cycle, DNA replication, and transcription of genes not involved in DDR. The complex relationship between DDR and transcription has only recently been investigated. Transcription can facilitate the DDR in response to double-strand breaks (DSBs) and stimulate nucleotide excision repair (NER). However, transcription may need to be reduced to prevent potential interference with the repair machinery. In this review, we discuss various mechanisms that regulate transcription repression in response to different types of DNA damage, categorizing them by their range and duration of effect. Finally, we explore various models of transcription recovery following DNA damage-induced repression.
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Affiliation(s)
- Kamal Ajit
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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11
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Downs JA, Gasser SM. Chromatin remodeling and spatial concerns in DNA double-strand break repair. Curr Opin Cell Biol 2024; 90:102405. [PMID: 39083951 DOI: 10.1016/j.ceb.2024.102405] [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: 04/08/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024]
Abstract
The substrate for the repair of DNA damage in living cells is not DNA but chromatin. Chromatin bears a range of modifications, which in turn bind ligands that compact or open chromatin structure, and determine its spatial organization within the nucleus. In some cases, RNA in the form of RNA:DNA hybrids or R-loops modulates DNA accessibility. Each of these parameters can favor particular pathways of repair. Chromatin or nucleosome remodelers are key regulators of chromatin structure, and a number of remodeling complexes are implicated in DNA repair. We cover novel insights into the impact of chromatin structure, nuclear organization, R-loop formation, nuclear actin, and nucleosome remodelers in DNA double-strand break repair, focusing on factors that alter repair functional upon ablation.
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Affiliation(s)
- Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Susan M Gasser
- ISREC Foundation, and University of Lausanne, Agora Cancer Research Center, Rue du Bugnon 25a, 1005 Lausanne, Switzerland.
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12
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Puspita L, Juwono VB, Shim JW. Advances in human pluripotent stem cell reporter systems. iScience 2024; 27:110856. [PMID: 39290832 PMCID: PMC11407076 DOI: 10.1016/j.isci.2024.110856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
The capability of human pluripotent stem cells (hPSCs) to self-renew and differentiate into any cell type has greatly contributed to the advancement of biomedicine. Reporter lines derived from hPSCs have played a crucial role in elucidating the mechanisms underlying human development and diseases by acting as an alternative reporter system that cannot be used in living humans. To bring hPSCs closer to clinical application in transplantation, scientists have generated reporter lines for isolating the desired cell populations, as well as improving graft quality and treatment outcomes. This review presents an overview of the applications of hPSC reporter lines and the important variables in designing a reporter system, including options for gene delivery and editing tools, design of reporter constructs, and selection of reporter genes. It also provides insights into the prospects of hPSC reporter lines and the challenges that must be overcome to maximize the potential of hPSC reporter lines.
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Affiliation(s)
- Lesly Puspita
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si 31151, Korea
| | - Virginia Blessy Juwono
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
| | - Jae-Won Shim
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
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Vercauteren S, Fiesack S, Maroc L, Verstraeten N, Dewachter L, Michiels J, Vonesch SC. The rise and future of CRISPR-based approaches for high-throughput genomics. FEMS Microbiol Rev 2024; 48:fuae020. [PMID: 39085047 PMCID: PMC11409895 DOI: 10.1093/femsre/fuae020] [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: 05/08/2024] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 08/02/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) has revolutionized the field of genome editing. To circumvent the permanent modifications made by traditional CRISPR techniques and facilitate the study of both essential and nonessential genes, CRISPR interference (CRISPRi) was developed. This gene-silencing technique employs a deactivated Cas effector protein and a guide RNA to block transcription initiation or elongation. Continuous improvements and a better understanding of the mechanism of CRISPRi have expanded its scope, facilitating genome-wide high-throughput screens to investigate the genetic basis of phenotypes. Additionally, emerging CRISPR-based alternatives have further expanded the possibilities for genetic screening. This review delves into the mechanism of CRISPRi, compares it with other high-throughput gene-perturbation techniques, and highlights its superior capacities for studying complex microbial traits. We also explore the evolution of CRISPRi, emphasizing enhancements that have increased its capabilities, including multiplexing, inducibility, titratability, predictable knockdown efficacy, and adaptability to nonmodel microorganisms. Beyond CRISPRi, we discuss CRISPR activation, RNA-targeting CRISPR systems, and single-nucleotide resolution perturbation techniques for their potential in genome-wide high-throughput screens in microorganisms. Collectively, this review gives a comprehensive overview of the general workflow of a genome-wide CRISPRi screen, with an extensive discussion of strengths and weaknesses, future directions, and potential alternatives.
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Affiliation(s)
- Silke Vercauteren
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Simon Fiesack
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Laetitia Maroc
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Natalie Verstraeten
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Liselot Dewachter
- de Duve Institute, Université catholique de Louvain, Hippokrateslaan 75, 1200 Brussels, Belgium
| | - Jan Michiels
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
| | - Sibylle C Vonesch
- Center for Microbiology, VIB - KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, box 2460, 3001 Leuven, Belgium
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Pallaseni A, Peets EM, Girling G, Crepaldi L, Kuzmin I, Moor M, Muñoz-Subirana N, Schimmel J, Serçin Ö, Mardin BR, Tijsterman M, Peterson H, Kosicki M, Parts L. The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.28.546891. [PMID: 37425722 PMCID: PMC10326969 DOI: 10.1101/2023.06.28.546891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Mutagenic outcomes of CRISPR/Cas9-generated double-stranded breaks depend on both the sequence flanking the cut and cellular DNA damage repair. The interaction of these features has been largely unexplored, limiting our ability to understand and manipulate the outcomes. Here, we measured how the absence of 18 repair genes changed frequencies of 83,680 unique mutational outcomes generated by Cas9 double-stranded breaks at 2,838 synthetic target sequences in mouse embryonic stem cells. This large scale survey allowed us to classify the outcomes in an unbiased way, generating hypotheses about new modes of double-stranded break repair. Our data indicate a specialised role for Prkdc (DNA-PKcs protein) and Polm (Polμ) in creating 1bp insertions that match the nucleotide on the proximal side of the Cas9 cut with respect to the protospacer-adjacent motif (PAM), a variable involvement of Nbn (NBN) and Polq (Polθ) in the creation of different deletion outcomes, and a unique class of uni-directional deletion outcomes that are dependent on both end-protection gene Xrcc5 (Ku80) and the resection gene Nbn (NBN). We used the knowledge of the reproducible variation across repair milieus to build predictive models of the mutagenic outcomes of Cas9 scission that outperform the current standards. This work improves our understanding of DNA repair gene function, and provides avenues for more precise modulation of CRISPR/Cas9-generated mutations.
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Affiliation(s)
- Ananth Pallaseni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elin Madli Peets
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gareth Girling
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Luca Crepaldi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ivan Kuzmin
- Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Marilin Moor
- Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Núria Muñoz-Subirana
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Özdemirhan Serçin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 515, Heidelberg, Germany
| | - Balca R. Mardin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 515, Heidelberg, Germany
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Hedi Peterson
- Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Michael Kosicki
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Computer Science, University of Tartu, Tartu, Estonia
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15
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Jeon Y, Lu Y, Ferrari MM, Channagiri T, Xu P, Meers C, Zhang Y, Balachander S, Park VS, Marsili S, Pursell ZF, Jonoska N, Storici F. RNA-mediated double-strand break repair by end-joining mechanisms. Nat Commun 2024; 15:7935. [PMID: 39261460 PMCID: PMC11390984 DOI: 10.1038/s41467-024-51457-9] [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: 11/16/2022] [Accepted: 08/07/2024] [Indexed: 09/13/2024] Open
Abstract
Double-strand breaks (DSBs) in DNA are challenging to repair. Cells employ at least three DSB-repair mechanisms, with a preference for non-homologous end joining (NHEJ) over homologous recombination (HR) and microhomology-mediated end joining (MMEJ). While most eukaryotic DNA is transcribed into RNA, providing complementary genetic information, much remains unknown about the direct impact of RNA on DSB-repair outcomes and its role in DSB-repair via end joining. Here, we show that both sense and antisense-transcript RNAs impact DSB repair in a sequence-specific manner in wild-type human and yeast cells. Depending on its sequence complementarity with the broken DNA ends, a transcript RNA can promote repair of a DSB or a double-strand gap in its DNA gene via NHEJ or MMEJ, independently from DNA synthesis. The results demonstrate a role of transcript RNA in directing the way DSBs are repaired in DNA, suggesting that RNA may directly modulate genome stability and evolution.
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Affiliation(s)
- Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Fredrick, MD, USA
| | - Yilin Lu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Margherita Maria Ferrari
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, USA
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada
| | - Tejasvi Channagiri
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, USA
| | - Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Columbia University Irving Medical Center, New York, NY, USA
| | - Yiqi Zhang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Program for Lung and Vascular Biology, Section for Injury Repair and Regeneration Research, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Division of Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Emory University, Atlanta, GA, USA
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA, USA
| | - Stefania Marsili
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA, USA
| | - Nataša Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, USA.
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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16
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van der Merwe NC, Buccimazza I, Rossouw B, Araujo M, Ntaita KS, Schoeman M, Vorster K, Napo K, Kotze MJ, Oosthuizen J. Clinical relevance of double heterozygosity revealed by next-generation sequencing of homologous recombination repair pathway genes in South African breast cancer patients. Breast Cancer Res Treat 2024; 207:331-342. [PMID: 38814507 PMCID: PMC11297091 DOI: 10.1007/s10549-024-07362-2] [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: 03/22/2024] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
PURPOSE Genetically predisposed breast cancer (BC) patients represent a minor but clinically meaningful subgroup of the disease, with 25% of all cases associated with actionable variants in BRCA1/2. Diagnostic implementation of next-generation sequencing (NGS) resulted in the rare identification of BC patients with double heterozygosity for deleterious variants in genes partaking in homologous recombination repair of DNA. As clinical heterogeneity poses challenges for genetic counseling, this study focused on the occurrence and clinical relevance of double heterozygous BC in South Africa. METHODS DNA samples were diagnostically screened using the NGS-based Oncomine™ BRCA Expanded Research Assay. Data was generated on the Ion GeneStudio S5 system and analyzed using the Torrent Suite™ and reporter software. The clinical significance of the variants detected was determined using international variant classification guidelines and treatment implications. RESULTS Six of 1600 BC patients (0.375%) tested were identified as being bi-allelic for two germline likely pathogenic or pathogenic variants. Most of the variants were present in BRCA1/2, including two founder-related small deletions in three cases, with family-specific variants detected in ATM, BARD1, FANCD2, NBN, and TP53. The scientific interpretation and clinical relevance were based on the clinical and tumor characteristics of each case. CONCLUSION This study increased current knowledge of the risk implications associated with the co-occurrence of more than one pathogenic variant in the BC susceptibility genes, confirmed to be a rare condition in South Africa. Further molecular pathology-based studies are warranted to determine whether clinical decision-making is affected by the detection of a second pathogenic variant in BRCA1/2 and TP53 carriers.
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Affiliation(s)
- Nerina C van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa.
| | - Ines Buccimazza
- Genetics Unit, Inkosi Albert Luthuli General Hospital, Durban, South Africa
- Department of Surgery, Nelson R Mandela School of Medicine, Inkosi Albert Luthuli General Hospital, Durban, South Africa
| | - Bianca Rossouw
- Division of Human Genetics, National Health Laboratory Service, Braamfontein, Johannesburg, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Monica Araujo
- Division of Human Genetics, National Health Laboratory Service, Braamfontein, Johannesburg, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kholiwe S Ntaita
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Mardelle Schoeman
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Karin Vorster
- Department of Oncology, Free State Department of Health, Universitas Annex Hospital, Bloemfontein, South Africa
- Department of Oncology, Faculty of Health Science, University of the Free State, Bloemfontein, South Africa
| | - Kgabo Napo
- Department of Oncology, Free State Department of Health, Universitas Annex Hospital, Bloemfontein, South Africa
- Department of Oncology, Faculty of Health Science, University of the Free State, Bloemfontein, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jaco Oosthuizen
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
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17
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Li W, Hao Y. Polo-Like Kinase 1 and DNA Damage Response. DNA Cell Biol 2024; 43:430-437. [PMID: 38959179 DOI: 10.1089/dna.2024.0018] [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: 07/05/2024] Open
Abstract
Polo-like kinase 1 (Plk1), an evolutionarily conserved serine/threonine protein kinase, is a key regulator involved in the mitotic process of the cell cycle. Mounting evidence suggests that Plk1 is also involved in a variety of nonmitotic events, including the DNA damage response, DNA replication, cytokinesis, embryonic development, apoptosis, and immune regulation. The DNA damage response (DDR) includes activation of the DNA checkpoint, DNA damage recovery, DNA repair, and apoptosis. Plk1 is not only an important target of the G2/M DNA damage checkpoint but also negatively regulates the G2/M checkpoint commander Ataxia telangiectasia-mutated (ATM), promotes G2/M phase checkpoint recovery, and regulates homologous recombination repair by interacting with Rad51 and BRCA1, the key factors of homologous recombination repair. This article briefly reviews the function of Plk1 in response to DNA damage.
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Affiliation(s)
- Wei Li
- Laboratory of Nuclear and Radiation Damage, Characteristic Medical Center, PLA Rocket Force, Beijing, China
- Department of Disease Prevention and Control, Characteristic Medical Center, PLA Rocket Force, Beijing, China
| | - Yongjian Hao
- Department of Disease Prevention and Control, Characteristic Medical Center, PLA Rocket Force, Beijing, China
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18
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Du Z, Lin M, Li Q, Guo D, Xue Y, Liu W, Shi H, Chen T, Dan J. The totipotent 2C-like state safeguards genomic stability of mouse embryonic stem cells. J Cell Physiol 2024; 239:e31337. [PMID: 38860420 DOI: 10.1002/jcp.31337] [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: 01/09/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Mouse embryonic stem cells (mESCs) sporadically transition to a transient totipotent state that resembles blastomeres of the two-cell (2C) embryo stage, which has been proposed to contribute to exceptional genomic stability, one of the key features of mESCs. However, the biological significance of the rare population of 2C-like cells (2CLCs) in ESC cultures remains to be tested. Here we generated an inducible reporter cell system for specific elimination of 2CLCs from the ESC cultures to disrupt the equilibrium between ESCs and 2CLCs. We show that removing 2CLCs from the ESC cultures leads to dramatic accumulation of DNA damage, genomic mutations, and rearrangements, indicating impaired genomic instability. Furthermore, 2CLCs removal results in increased apoptosis and reduced proliferation of mESCs in both serum/LIF and 2i/LIF culture conditions. Unexpectedly, p53 deficiency results in defective response to DNA damage, leading to early accumulation of DNA damage, micronuclei, indicative of genomic instability, cell apoptosis, and reduced self-renewal capacity of ESCs when devoid of 2CLCs in cultures. Together, our data reveal that transition to the privileged 2C-like state is a major component of the intrinsic mechanisms that maintain the exceptional genomic stability of mESCs for long-term self-renewal.
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Affiliation(s)
- Zeling Du
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Meiqi Lin
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Qiaohua Li
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Dan Guo
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Yanna Xue
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Wei Liu
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jiameng Dan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
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Yang Q, Abebe JS, Mai M, Rudy G, Kim SY, Devinsky O, Long C. T4 DNA polymerase prevents deleterious on-target DNA damage and enhances precise CRISPR editing. EMBO J 2024; 43:3733-3751. [PMID: 39039289 PMCID: PMC11377749 DOI: 10.1038/s44318-024-00158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 07/24/2024] Open
Abstract
Unintended on-target chromosomal alterations induced by CRISPR/Cas9 in mammalian cells are common, particularly large deletions and chromosomal translocations, and present a safety challenge for genome editing. Thus, there is still an unmet need to develop safer and more efficient editing tools. We screened diverse DNA polymerases of distinct origins and identified a T4 DNA polymerase derived from phage T4 that strongly prevents undesired on-target damage while increasing the proportion of precise 1- to 2-base-pair insertions generated during CRISPR/Cas9 editing (termed CasPlus). CasPlus induced substantially fewer on-target large deletions while increasing the efficiency of correcting common frameshift mutations in DMD and restored higher level of dystrophin expression than Cas9-alone in human cardiomyocytes. Moreover, CasPlus greatly reduced the frequency of on-target large deletions during mouse germline editing. In multiplexed guide RNAs mediating gene editing, CasPlus repressed chromosomal translocations while maintaining gene disruption efficiency that was higher or comparable to Cas9 in primary human T cells. Therefore, CasPlus offers a safer and more efficient gene editing strategy to treat pathogenic variants or to introduce genetic modifications in human applications.
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Affiliation(s)
- Qiaoyan Yang
- NYU Cardiovascular Research Center, Leon H. Charney Division of Cardiology, Department of Medicine, NYU Langone Health, New York, NY, USA
| | - Jonathan S Abebe
- NYU Cardiovascular Research Center, Leon H. Charney Division of Cardiology, Department of Medicine, NYU Langone Health, New York, NY, USA
| | - Michelle Mai
- NYU Cardiovascular Research Center, Leon H. Charney Division of Cardiology, Department of Medicine, NYU Langone Health, New York, NY, USA
| | - Gabriella Rudy
- NYU Cardiovascular Research Center, Leon H. Charney Division of Cardiology, Department of Medicine, NYU Langone Health, New York, NY, USA
| | - Sang Y Kim
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Orrin Devinsky
- New York University Langone Comprehensive Epilepsy Center, NYU Langone Health, New York, NY, USA
| | - Chengzu Long
- NYU Cardiovascular Research Center, Leon H. Charney Division of Cardiology, Department of Medicine, NYU Langone Health, New York, NY, USA.
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20
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van de Kamp G, Heemskerk T, Kanaar R, Essers J. Synergistic Roles of Non-Homologous End Joining and Homologous Recombination in Repair of Ionizing Radiation-Induced DNA Double Strand Breaks in Mouse Embryonic Stem Cells. Cells 2024; 13:1462. [PMID: 39273031 PMCID: PMC11393957 DOI: 10.3390/cells13171462] [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: 07/24/2024] [Revised: 08/23/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
DNA double strand breaks (DSBs) are critical for the efficacy of radiotherapy as they lead to cell death if not repaired. DSBs caused by ionizing radiation (IR) initiate histone modifications and accumulate DNA repair proteins, including 53BP1, which forms distinct foci at damage sites and serves as a marker for DSBs. DSB repair primarily occurs through Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). NHEJ directly ligates DNA ends, employing proteins such as DNA-PKcs, while HR, involving proteins such as Rad54, uses a sister chromatid template for accurate repair and functions in the S and G2 phases of the cell cycle. Both pathways are crucial, as illustrated by the IR sensitivity in cells lacking DNA-PKcs or Rad54. We generated mouse embryonic stem (mES) cells which are knockout (KO) for DNA-PKcs and Rad54 to explore the combined role of HR and NHEJ in DSB repair. We found that cells lacking both DNA-PKcs and Rad54 are hypersensitive to X-ray radiation, coinciding with impaired 53BP1 focus resolution and a more persistent G2 phase cell cycle block. Additionally, mES cells deficient in DNA-PKcs or both DNA-PKcs and Rad54 exhibit an increased nuclear size approximately 18-24 h post-irradiation. To further explore the role of Rad54 in the absence of DNA-PKcs, we generated DNA-PKcs KO mES cells expressing GFP-tagged wild-type (WT) or ATPase-defective Rad54 to track the Rad54 foci over time post-irradiation. Cells lacking DNA-PKcs and expressing ATPase-defective Rad54 exhibited a similar phenotypic response to IR as those lacking both DNA-PKcs and Rad54. Despite a strong G2 phase arrest, live-cell imaging showed these cells eventually progress through mitosis, forming micronuclei. Additionally, mES cells lacking DNA-PKcs showed increased Rad54 foci over time post-irradiation, indicating an enhanced reliance on HR for DSB repair without DNA-PKcs. Our findings underscore the essential roles of HR and NHEJ in maintaining genomic stability post-IR in mES cells. The interplay between these pathways is crucial for effective DSB repair and cell cycle progression, highlighting potential targets for enhancing radiotherapy outcomes.
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Affiliation(s)
- Gerarda van de Kamp
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Tim Heemskerk
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Jeroen Essers
- Oncode Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
- Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
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21
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Albaqami WF, Alshamrani AA, Almubarak AA, Alotaibi FE, Alotaibi BJ, Alanazi AM, Alotaibi MR, Alhoshani A, As Sobeai HM. Genetic and Epigenetic Biomarkers Associated with Early Relapse in Pediatric Acute Lymphoblastic Leukemia: A Focused Bioinformatics Study on DNA-Repair Genes. Biomedicines 2024; 12:1766. [PMID: 39200230 PMCID: PMC11351110 DOI: 10.3390/biomedicines12081766] [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: 06/30/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 09/02/2024] Open
Abstract
Genomic instability is one of the main drivers of tumorigenesis and the development of hematological malignancies. Cancer cells can remedy chemotherapeutic-induced DNA damage by upregulating DNA-repair genes and ultimately inducing therapy resistance. Nevertheless, the association between the DNA-repair genes, drug resistance, and disease relapse has not been well characterized in acute lymphoblastic leukemia (ALL). This study aimed to explore the role of the DNA-repair machinery and the molecular mechanisms by which it is regulated in early- and late-relapsing pediatric ALL patients. We performed secondary data analysis on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)-ALL expansion phase II trial of 198 relapsed pediatric precursor B-cell ALL. Comprehensive genetic and epigenetic investigations of 147 DNA-repair genes were conducted in the study. Gene expression was assessed using Microarray and RNA-sequencing platforms. Genomic alternations, methylation status, and miRNA transcriptome were investigated for the candidate DNA-repair genes. We identified three DNA-repair genes, ALKBH3, NHEJ1, and PARP1, that were upregulated in early relapsers compared to late relapsers (p < 0.05). Such upregulation at diagnosis was significantly associated with disease-free survival and overall survival in precursor-B-ALL (p < 0.05). Moreover, PARP1 upregulation accompanied a significant downregulation of its targeting miRNA, miR-1301-3p (p = 0.0152), which was strongly linked with poorer disease-free and overall survivals. Upregulation of DNA-repair genes, PARP1 in particular, increases the likelihood of early relapse of precursor-B-ALL in children. The observation that PARP1 was upregulated in early relapsers relative to late relapsers might serve as a valid rationale for proposing alternative treatment approaches, such as using PARP inhibitors with chemotherapy.
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Affiliation(s)
- Walaa F. Albaqami
- Department of Science, Prince Sultan Military College of Health Sciences, Dhahran 31932, Saudi Arabia;
| | - Ali A. Alshamrani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Ali A. Almubarak
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Faris E. Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Basil Jamal Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Abdulrahman M. Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
- Pharmaceutical Care Division, King Faisal Specialist Hospital & Research Centre, Madinah 42523, Saudi Arabia
| | - Moureq R. Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Ali Alhoshani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
| | - Homood M. As Sobeai
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (A.A.A.); (F.E.A.); (B.J.A.); (A.M.A.); (M.R.A.); (A.A.)
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22
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Özdemir C, Purkey LR, Sanchez A, Miller KM. PARticular MARks: Histone ADP-ribosylation and the DNA damage response. DNA Repair (Amst) 2024; 140:103711. [PMID: 38924925 DOI: 10.1016/j.dnarep.2024.103711] [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: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Cellular and molecular responses to DNA damage are highly orchestrated and dynamic, acting to preserve the maintenance and integrity of the genome. Histone proteins bind DNA and organize the genome into chromatin. Post-translational modifications of histones have been shown to play an essential role in orchestrating the chromatin response to DNA damage by regulating the DNA damage response pathway. Among the histone modifications that contribute to this intricate network, histone ADP-ribosylation (ADPr) is emerging as a pivotal component of chromatin-based DNA damage response (DDR) pathways. In this review, we survey how histone ADPr is regulated to promote the DDR and how it impacts chromatin and other histone marks. Recent advancements have revealed histone ADPr effects on chromatin structure and the regulation of DNA repair factor recruitment to DNA lesions. Additionally, we highlight advancements in technology that have enabled the identification and functional validation of histone ADPr in cells and in response to DNA damage. Given the involvement of DNA damage and epigenetic regulation in human diseases including cancer, these findings have clinical implications for histone ADPr, which are also discussed. Overall, this review covers the involvement of histone ADPr in the DDR and highlights potential future investigations aimed at identifying mechanisms governed by histone ADPr that participate in the DDR, human diseases, and their treatments.
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Affiliation(s)
- Cem Özdemir
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laura R Purkey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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23
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Collins VJ, Ludwig KR, Nelson AE, Rajan SS, Yeung C, Vulikh K, Isanogle KA, Mendoza A, Difilippantonio S, Karim BO, Caplen NJ, Heske CM. Enhancing Standard of Care Chemotherapy Efficacy Using DNA-Dependent Protein Kinase (DNA-PK) Inhibition in Preclinical Models of Ewing Sarcoma. Mol Cancer Ther 2024; 23:1109-1123. [PMID: 38657228 PMCID: PMC11293986 DOI: 10.1158/1535-7163.mct-23-0641] [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: 09/21/2023] [Revised: 01/26/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
Disruption of DNA damage repair via impaired homologous recombination is characteristic of Ewing sarcoma (EWS) cells. We hypothesize that this disruption results in increased reliance on nonhomologous end joining to repair DNA damage. In this study, we investigated if pharmacologic inhibition of the enzyme responsible for nonhomologous end joining, the DNA-PK holoenzyme, alters the response of EWS cells to genotoxic standard of care chemotherapy. We used analyses of cell viability and proliferation to investigate the effects of clinical DNA-PK inhibitors (DNA-PKi) in combination with six therapeutic or experimental agents for EWS. We performed calculations of synergy using the Loewe additivity model. Immunoblotting evaluated treatment effects on DNA-PK, DNA damage, and apoptosis. Flow cytometric analyses evaluated effects on cell cycle and fate. We used orthotopic xenograft models to interrogate tolerability, drug mechanism, and efficacy in vivo. DNA-PKi demonstrated on-target activity, reducing phosphorylated DNA-PK levels in EWS cells. DNA-PKi sensitized EWS cell lines to agents that function as topoisomerase 2 (TOP2) poisons and enhanced the DNA damage induced by TOP2 poisons. Nanomolar concentrations of single-agent TOP2 poisons induced G2M arrest and little apoptotic response while adding DNA-PKi-mediated apoptosis. In vivo, the combination of AZD7648 and etoposide had limited tolerability but resulted in enhanced DNA damage, apoptosis, and EWS tumor shrinkage. The combination of DNA-PKi with standard of care TOP2 poisons in EWS models is synergistic, enhances DNA damage and cell death, and may form the basis of a promising future therapeutic strategy for EWS.
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Affiliation(s)
- Victor J. Collins
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ariana E. Nelson
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Choh Yeung
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ksenia Vulikh
- Molecular Histopathology Lab, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Kristine A. Isanogle
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Arnulfo Mendoza
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Simone Difilippantonio
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Baktiar O. Karim
- Molecular Histopathology Lab, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Christine M. Heske
- Translational Sarcoma Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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24
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Lee JJ, Kang HJ, Kim D, Lim SO, Kim SS, Kim G, Kim S, Lee JK, Kim J. expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer. BMC Bioinformatics 2024; 25:236. [PMID: 38997639 PMCID: PMC11241885 DOI: 10.1186/s12859-024-05854-y] [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: 11/10/2023] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Homologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy and poly ADP-ribose polymerase (PARP) inhibitors. One of the conventional approaches to HRD prognostication has generally centered on identifying deleterious mutations within the BRCA1/2 genes, along with quantifying the genomic scars, such as Genomic Instability Score (GIS) estimation with scarHRD. However, the scarHRD method has limitations in scenarios involving tumors bereft of corresponding germline data. Although several RNA-seq-based HRD prediction algorithms have been developed, they mainly support cohort-wise classification, thereby yielding HRD status without furnishing an analogous quantitative metric akin to scarHRD. This study introduces the expHRD method, which operates as a novel transcriptome-based framework tailored to n-of-1-style HRD scoring. RESULTS The prediction model has been established using the elastic net regression method in the Cancer Genome Atlas (TCGA) pan-cancer training set. The bootstrap technique derived the HRD geneset for applying the expHRD calculation. The expHRD demonstrated a notable correlation with scarHRD and superior performance in predicting HRD-high samples. We also performed intra- and extra-cohort evaluations for clinical feasibility in the TCGA-OV and the Genomic Data Commons (GDC) ovarian cancer cohort, respectively. The innovative web service designed for ease of use is poised to extend the realms of HRD prediction across diverse malignancies, with ovarian cancer standing as an emblematic example. CONCLUSIONS Our novel approach leverages the transcriptome data, enabling the prediction of HRD status with remarkable precision. This innovative method addresses the challenges associated with limited available data, opening new avenues for utilizing transcriptomics to inform clinical decisions.
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Affiliation(s)
- Jae Jun Lee
- Computational Cancer Genomics Groups, Spanish Cancer Research Center (CNIO), Madrid, Spain
| | - Hyun Ju Kang
- Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea
| | - Donghyo Kim
- Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Si On Lim
- Department of Biomedical Sciences, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea
| | - Stephanie S Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital (SNUBH), Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Gahyun Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital (SNUBH), Seongnam, Gyeonggi-do, 13620, Republic of Korea
| | - Sanguk Kim
- Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea.
| | - Jin-Ku Lee
- Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea.
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine (SNUCM), Seoul, 03080, Republic of Korea.
| | - Jinho Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital (SNUBH), Seongnam, Gyeonggi-do, 13620, Republic of Korea.
- Department of Genomic Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, 13620, Republic of Korea.
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Gyeonggi-do, 13620, Republic of Korea.
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25
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Li Y, Li L, Wang X, Zhao F, Yang Y, Zhou Y, Zhang J, Wang L, Jiang Z, Zhang Y, Chen Y, Wu C, Li K, Zhang T, Wang P, Mao Z, Zhu W, Xu X, Liang S, Lou Z, Yuan J. USP25 Elevates SHLD2-Mediated DNA Double-Strand Break Repair and Regulates Chemoresponse in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2403485. [PMID: 38803048 PMCID: PMC11267380 DOI: 10.1002/advs.202403485] [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: 04/03/2024] [Indexed: 05/29/2024]
Abstract
DNA damage plays a significant role in the tumorigenesis and progression of the disease. Abnormal DNA repair affects the therapy and prognosis of cancer. In this study, it is demonstrated that the deubiquitinase USP25 promotes non-homologous end joining (NHEJ), which in turn contributes to chemoresistance in cancer. It is shown that USP25 deubiquitinates SHLD2 at the K64 site, which enhances its binding with REV7 and promotes NHEJ. Furthermore, USP25 deficiency impairs NHEJ-mediated DNA repair and reduces class switch recombination (CSR) in USP25-deficient mice. USP25 is overexpressed in a subset of colon cancers. Depletion of USP25 sensitizes colon cancer cells to IR, 5-Fu, and cisplatin. TRIM25 is also identified, an E3 ligase, as the enzyme responsible for degrading USP25. Downregulation of TRIM25 leads to an increase in USP25 levels, which in turn induces chemoresistance in colon cancer cells. Finally, a peptide that disrupts the USP25-SHLD2 interaction is successfully identified, impairing NHEJ and increasing sensitivity to chemotherapy in PDX model. Overall, these findings reveal USP25 as a critical effector of SHLD2 in regulating the NHEJ repair pathway and suggest its potential as a therapeutic target for cancer therapy.
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Affiliation(s)
- Yunhui Li
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Cancer CenterTongji University School of MedicineShanghai200331China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
| | - Lei Li
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Cancer CenterTongji University School of MedicineShanghai200331China
| | - Xinshu Wang
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
| | - Fei Zhao
- College of BiologyHunan UniversityChangsha410082China
| | - Yuntong Yang
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
| | - Yujuan Zhou
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
| | - Jiyuan Zhang
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
| | - Li Wang
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
| | - Zeshan Jiang
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
| | - Yuanyuan Zhang
- Department of General Surgery and Colorectal SurgeryShanghai East HospitalTongji University School of MedicineShanghai200120China
| | - Yuping Chen
- Cancer CenterTongji University School of MedicineShanghai200331China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
- Translational Research Institute of Brain and Brain‐Like IntelligenceShanghai Fourth People's HospitalSchool of MedicineTongji UniversityShanghai200080China
| | - Chenming Wu
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Cancer CenterTongji University School of MedicineShanghai200331China
| | - Ke Li
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Medicinal BiotechnologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100050China
| | - Tingting Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesInstitute of Medicinal BiotechnologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100050China
| | - Ping Wang
- Tongji University Cancer CenterShanghai Tenth People's HospitalSchool of MedicineShanghai200072China
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal‐Fetal MedicineClinical and Translational Research Center of Shanghai First Maternity and Infant HospitalFrontier Science Center for Stem Cell ResearchTongji University School of MedicineShanghai200040China
| | - Weiguo Zhu
- International Cancer CenterGuangdong Key Laboratory of Genome Instability and Human Disease PreventionMarshall Laboratory of Biomedical EngineeringDepartment of Biochemistry and Molecular BiologyShenzhen University Medical SchoolShenzhen518037China
| | - Xingzhi Xu
- The Sixth Affiliated Hospital of Shenzhen UniversityGuangdong Key Laboratory for Genome Stability and Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University School of MedicineShenzhen518055China
| | - Shikang Liang
- School of Biomedical SciencesLKS Faculty of MedicineThe University of Hong KongHong Kong SAR999077Hong Kong
| | - Zhenkun Lou
- Department of OncologyMayo ClinicRochesterMNUSA
| | - Jian Yuan
- Medical Innovation CenterShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Cancer CenterTongji University School of MedicineShanghai200331China
- Department of Biochemistry and Molecular BiologyTongji University School of MedicineShanghai200331China
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26
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Weber JA, Lang JF, Carrell EM, Alameh MG, Davidson BL. Temporal restriction of Cas9 expression improves CRISPR-mediated deletion efficacy and fidelity. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102172. [PMID: 38978694 PMCID: PMC11229411 DOI: 10.1016/j.omtn.2024.102172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/08/2024] [Indexed: 07/10/2024]
Abstract
Clinical application of CRISPR-Cas9 technology for large deletions of somatic mutations is inefficient, and methods to improve utility suffer from our inability to rapidly assess mono- vs. biallelic deletions. Here we establish a model system for investigating allelic heterogeneity at the single-cell level and identify indel scarring from non-simultaneous nuclease activity at gRNA cut sites as a major barrier to CRISPR-del efficacy both in vitro and in vivo. We show that non-simultaneous nuclease activity is partially prevented via restriction of CRISPR-Cas9 expression via inducible adeno-associated viruses (AAVs) or lipid nanoparticles (LNPs). Inducible AAV-based expression of CRISPR-del machinery significantly improved mono- and biallelic deletion frequency in vivo, supporting the use of the Xon cassette over traditional constitutively expressing AAV approaches. These data depicting improvements to deletions and insight into allelic heterogeneity after CRISPR-del will inform therapeutic approaches for phenotypes that require either large mono- or biallelic deletions, such as autosomal recessive diseases or where mutant allele-specific gRNAs are not readily available, or in situations where the targeted sequence for excision is located multiple times in a genome.
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Affiliation(s)
- Jesse A Weber
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan F Lang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA, USA
| | - Ellie M Carrell
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mohamad-Gabriel Alameh
- Penn Institute for RNA Innovation, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
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27
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Singh PK, Devanna BN, Dubey H, Singh P, Joshi G, Kumar R. The potential of genome editing to create novel alleles of resistance genes in rice. Front Genome Ed 2024; 6:1415244. [PMID: 38933684 PMCID: PMC11201548 DOI: 10.3389/fgeed.2024.1415244] [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: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.
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Affiliation(s)
- Pankaj Kumar Singh
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India
| | | | - Himanshu Dubey
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | - Prabhakar Singh
- Botany Department, Banaras Hindu University, Varanasi, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal (A Central University), Tehri Garhwal, Uttarakhand, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
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28
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Vijayakumar S, Yesudhason BV, Anandharaj JL, Sathyaraj WV, Selvan Christyraj JRS. Impact of double-strand breaks induced by uv radiation on neuroinflammation and neurodegenerative disorders. Mol Biol Rep 2024; 51:725. [PMID: 38851636 DOI: 10.1007/s11033-024-09693-1] [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: 01/17/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Exposure to UV affects the development and growth of a wide range of organisms. Nowadays, researchers are focusing on the impact of UV radiation and its underlying molecular mechanisms, as well as devising strategies to mitigate its harmful effects. Different forms of UV radiation, their typical exposure effects, the impact of UV on DNA integrity, and the deterioration of genetic material are discussed in this review; furthermore, we also review the effects of UV radiation that affect the biological functions of the organisms. Subsequently, we address the processes that aid organisms in navigating the damage in genetic material, neuroinflammation, and neurodegeneration brought on by UV-mediated double-strand breaks. To emphasize the molecular pathways, we conclude the review by going over the animal model studies that highlight the genes and proteins that are impacted by UV radiation.
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Affiliation(s)
- Srilakshmi Vijayakumar
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Beryl Vedha Yesudhason
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.
| | - Jenif Leo Anandharaj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Weslen Vedakumari Sathyaraj
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamilnadu, India
| | - Johnson Retnaraj Samuel Selvan Christyraj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.
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29
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Osborne HC, Foster BM, Al-Hazmi H, Meyer S, Larrosa I, Schmidt CK. Small-Molecule Inhibition of CBX4/7 Hypersensitises Homologous Recombination-Impaired Cancer to Radiation by Compromising CtIP-Mediated DNA End Resection. Cancers (Basel) 2024; 16:2155. [PMID: 38893273 PMCID: PMC11172190 DOI: 10.3390/cancers16112155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
The therapeutic targeting of DNA repair pathways is an emerging concept in cancer treatment. Compounds that target specific DNA repair processes, such as those mending DNA double-strand breaks (DSBs), are therefore of therapeutic interest. UNC3866 is a small molecule that targets CBX4, a chromobox protein, and a SUMO E3 ligase. As a key modulator of DNA end resection-a prerequisite for DSB repair by homologous recombination (HR)-CBX4 promotes the functions of the DNA resection factor CtIP. Here, we show that treatment with UNC3866 markedly sensitises HR-deficient, NHEJ-hyperactive cancer cells to ionising radiation (IR), while it is non-toxic in selected HR-proficient cells. Consistent with UNC3866 targeting CtIP functions, it inhibits end-resection-dependent DNA repair including HR, alternative end joining (alt-EJ), and single-strand annealing (SSA). These findings raise the possibility that the UNC3866-mediated inhibition of end resection processes we define highlights a distinct vulnerability for the selective killing of HR-ineffective cancers.
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Affiliation(s)
- Hugh C. Osborne
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health (FBMH), University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK; (H.C.O.); (B.M.F.); (H.A.-H.); (S.M.)
| | - Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health (FBMH), University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK; (H.C.O.); (B.M.F.); (H.A.-H.); (S.M.)
| | - Hazim Al-Hazmi
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health (FBMH), University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK; (H.C.O.); (B.M.F.); (H.A.-H.); (S.M.)
| | - Stefan Meyer
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health (FBMH), University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK; (H.C.O.); (B.M.F.); (H.A.-H.); (S.M.)
- Department of Paediatric and Adolescent Oncology, Royal Manchester Children’s Hospital, Manchester M13 9WL, UK
- Department of Adolescent Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Igor Larrosa
- Department of Chemistry, University of Manchester, Chemistry Building, Oxford Road, Manchester M13 9PL, UK;
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health (FBMH), University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK; (H.C.O.); (B.M.F.); (H.A.-H.); (S.M.)
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Wang D, Luo H, Chen Y, Ou Y, Dong M, Chen J, Liu R, Wang X, Zhang Q. 14-3-3σ downregulation sensitizes pancreatic cancer to carbon ions by suppressing the homologous recombination repair pathway. Aging (Albany NY) 2024; 16:9727-9752. [PMID: 38843383 PMCID: PMC11210243 DOI: 10.18632/aging.205896] [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: 11/20/2023] [Accepted: 04/15/2024] [Indexed: 06/22/2024]
Abstract
This study explored the role of 14-3-3σ in carbon ion-irradiated pancreatic adenocarcinoma (PAAD) cells and xenografts and clarified the underlying mechanism. The clinical significance of 14-3-3σ in patients with PAAD was explored using publicly available databases. 14-3-3σ was silenced or overexpressed and combined with carbon ions to measure cell proliferation, cell cycle, and DNA damage repair. Immunoblotting and immunofluorescence (IF) assays were used to determine the underlying mechanisms of 14-3-3σ toward carbon ion radioresistance. We used the BALB/c mice to evaluate the biological behavior of 14-3-3σ in combination with carbon ions. Bioinformatic analysis revealed that PAAD expressed higher 14-3-3σ than normal pancreatic tissues; its overexpression was related to invasive clinicopathological features and a worse prognosis. Knockdown or overexpression of 14-3-3σ demonstrated that 14-3-3σ promoted the survival of PAAD cells after carbon ion irradiation. And 14-3-3σ was upregulated in PAAD cells during DNA damage (carbon ion irradiation, DNA damaging agent) and promotes cell recovery. We found that 14-3-3σ resulted in carbon ion radioresistance by promoting RPA2 and RAD51 accumulation in the nucleus in PAAD cells, thereby increasing homologous recombination repair (HRR) efficiency. Blocking the HR pathway consistently reduced 14-3-3σ overexpression-induced carbon ion radioresistance in PAAD cells. The enhanced radiosensitivity of 14-3-3σ depletion on carbon ion irradiation was also demonstrated in vivo. Altogether, 14-3-3σ functions in tumor progression and can be a potential target for developing biomarkers and treatment strategies for PAAD along with incorporating carbon ion irradiation.
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Affiliation(s)
- Dandan Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, People’s Republic of China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
| | - Hongtao Luo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
- Graduate School, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yanliang Chen
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, People’s Republic of China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
| | - Yuhong Ou
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, People’s Republic of China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
| | - Meng Dong
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, People’s Republic of China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
| | - Junru Chen
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, People’s Republic of China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
| | - Ruifeng Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
- Graduate School, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiaohu Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, People’s Republic of China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
- Graduate School, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Qiuning Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of China
- Graduate School, University of Chinese Academy of Sciences, Beijing, People’s Republic of China
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31
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Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [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: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
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Mohammedali A, Biernacka K, Barker RM, Holly JMP, Perks CM. The Role of Insulin-like Growth Factor Binding Protein (IGFBP)-2 in DNA Repair and Chemoresistance in Breast Cancer Cells. Cancers (Basel) 2024; 16:2113. [PMID: 38893232 PMCID: PMC11171178 DOI: 10.3390/cancers16112113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The role if insulin-like growth factor binding protein-2 (IGFBP-2) in mediating chemoresistance in breast cancer cells has been demonstrated, but the mechanism of action is unclear. This study aimed to further investigate the role of IGFBP-2 in the DNA damage response induced by etoposide in MCF-7, T47D (ER+ve), and MDA-MB-231 (ER-ve) breast cancer cell lines. In the presence or absence of etoposide, IGFBP-2 was silenced using siRNA in the ER-positive cell lines, or exogenous IGFBP-2 was added to the ER-negative MDA-MB-231 cells. Cell number and death were assessed using trypan blue dye exclusion assay, changes in abundance of proteins were monitored using Western blotting of whole cell lysates, and localization and abundance were determined using immunofluorescence and cell fractionation. Results from ER-positive cell lines demonstrated that upon exposure to etoposide, loss of IGFBP-2 enhanced cell death, and this was associated with a reduction in P-DNA-PKcs and an increase in γH2AX. Conversely, with ER-negative cells, the addition of IGFBP-2 in the presence of etoposide resulted in cell survival, an increase in P-DNA-PKcs, and a reduction in γH2AX. In summary, IGFBP-2 is a survival factor for breast cancer cells that is associated with enhancement of the DNA repair mechanism.
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Affiliation(s)
- Alaa Mohammedali
- Cancer Endocrinology Group, Learning and Research Building, Southmead Hospital, Translational Health Sciences, Bristol Medical School, Bristol BS10 5NB, UK; (A.M.); (K.B.); (R.M.B.)
| | - Kalina Biernacka
- Cancer Endocrinology Group, Learning and Research Building, Southmead Hospital, Translational Health Sciences, Bristol Medical School, Bristol BS10 5NB, UK; (A.M.); (K.B.); (R.M.B.)
| | - Rachel M. Barker
- Cancer Endocrinology Group, Learning and Research Building, Southmead Hospital, Translational Health Sciences, Bristol Medical School, Bristol BS10 5NB, UK; (A.M.); (K.B.); (R.M.B.)
| | - Jeff M. P. Holly
- Translational Health Sciences, Bristol Medical School, Bristol BS10 5NB, UK;
| | - Claire M. Perks
- Cancer Endocrinology Group, Learning and Research Building, Southmead Hospital, Translational Health Sciences, Bristol Medical School, Bristol BS10 5NB, UK; (A.M.); (K.B.); (R.M.B.)
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Morozumi R, Shimizu N, Tamura K, Nakamura M, Suzuki A, Ishiniwa H, Ide H, Tsuda M. Changes in repair pathways of radiation-induced DNA double-strand breaks at the midblastula transition in Xenopus embryo. JOURNAL OF RADIATION RESEARCH 2024; 65:315-322. [PMID: 38648785 PMCID: PMC11115444 DOI: 10.1093/jrr/rrae012] [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: 12/04/2023] [Revised: 01/25/2024] [Indexed: 04/25/2024]
Abstract
Ionizing radiation (IR) causes DNA damage, particularly DNA double-strand breaks (DSBs), which have significant implications for genome stability. The major pathways of repairing DSBs are homologous recombination (HR) and nonhomologous end joining (NHEJ). However, the repair mechanism of IR-induced DSBs in embryos is not well understood, despite extensive research in somatic cells. The externally developing aquatic organism, Xenopus tropicalis, serves as a valuable model for studying embryo development. A significant increase in zygotic transcription occurs at the midblastula transition (MBT), resulting in a longer cell cycle and asynchronous cell divisions. This study examines the impact of X-ray irradiation on Xenopus embryos before and after the MBT. The findings reveal a heightened X-ray sensitivity in embryos prior to the MBT, indicating a distinct shift in the DNA repair pathway during embryo development. Importantly, we show a transition in the dominant DSB repair pathway from NHEJ to HR before and after the MBT. These results suggest that the MBT plays a crucial role in altering DSB repair mechanisms, thereby influencing the IR sensitivity of developing embryos.
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Affiliation(s)
- Ryosuke Morozumi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Naoto Shimizu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Kouhei Tamura
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Makoto Nakamura
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Department of Physiology, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atsushi Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Hiroko Ishiniwa
- Institute of Environmental Radioactivity, Fukushima University, Fukushima, 960-1296, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Masataka Tsuda
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
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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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Iglesias-Corral D, García-Valles P, Arroyo-Garrapucho N, Bueno-Martínez E, Ruiz-Robles JM, Ovejero-Sánchez M, González-Sarmiento R, Herrero AB. Chloroquine-induced DNA damage synergizes with DNA repair inhibitors causing cancer cell death. Front Oncol 2024; 14:1390518. [PMID: 38803536 PMCID: PMC11128598 DOI: 10.3389/fonc.2024.1390518] [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: 02/23/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Background Cancer is a global health problem accounting for nearly one in six deaths worldwide. Conventional treatments together with new therapies have increased survival to this devastating disease. However, the persistent challenges of treatment resistance and the limited therapeutic arsenal available for specific cancer types still make research in new therapeutic strategies an urgent need. Methods Chloroquine was tested in combination with different drugs (Panobinostat, KU-57788 and NU-7026) in 8 human-derived cancer cells lines (colorectal: HCT116 and HT29; breast: MDA-MB-231 and HCC1937; glioblastoma: A-172 and LN-18; head and neck: CAL-33 and 32816). Drug´s effect on proliferation was tested by MTT assays and cell death was assessed by Anexin V-PI apoptosis assays. The presence of DNA double-strand breaks was analyzed by phospho-H2AX fluorescent staining. To measure homologous recombination efficiency the HR-GFP reporter was used, which allows flow cytometry-based detection of HR stimulated by I-SceI endonuclease-induced DSBs. Results The combination of chloroquine with any of the drugs employed displayed potent synergistic effects on apoptosis induction, with particularly pronounced efficacy observed in glioblastoma and head and neck cancer cell lines. We found that chloroquine produced DNA double strand breaks that depended on reactive oxygen species formation, whereas Panobinostat inhibited DNA double-strand breaks repair by homologous recombination. Cell death caused by chloroquine/Panobinostat combination were significantly reduced by N-Acetylcysteine, a reactive oxygen species scavenger, underscoring the pivotal role of DSB generation in CQ/LBH-induced lethality. Based on these data, we also explored the combination of CQ with KU-57788 and NU-7026, two inhibitors of the other main DSB repair pathway, nonhomologous end joining (NHEJ), and again synergistic effects on apoptosis induction were observed. Conclusion Our data provide a rationale for the clinical investigation of CQ in combination with DSB inhibitors for the treatment of different solid tumors.
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Affiliation(s)
- Diego Iglesias-Corral
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Paula García-Valles
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Nuria Arroyo-Garrapucho
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Elena Bueno-Martínez
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Juan Manuel Ruiz-Robles
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - María Ovejero-Sánchez
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Rogelio González-Sarmiento
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Ana Belén Herrero
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
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Ping N, Zuo K, Cai J, Rong C, Yu Z, Zhang X, Wang G, Ma C, Yang H, Li J, Wang X, Zhao D. Apigenin protects against ischemic stroke by increasing DNA repair. Front Pharmacol 2024; 15:1362301. [PMID: 38746012 PMCID: PMC11091408 DOI: 10.3389/fphar.2024.1362301] [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: 12/28/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
Background and Objective Oxidative stress is an important pathological process in ischemic stroke (IS). Apigenin (APG) is a natural product with favorable antioxidative effects, and some studies have already demonstrated the antioxidative mechanism of APG in the treatment of IS. However, the mechanism of APG on DNA damage and repair after IS is not clear. The aim of this study was to investigate the mechanism of APG on DNA repair after IS. Methods Male Sprague-Dawley rats were used to establish a model of permanent middle cerebral artery occlusion (pMCAO) on one side, and were pre-treated with gavage of APG (30, 60, or 120 mg/kg) for 7 days. One day after pMCAO, the brain tissues were collected. Cerebral infarct volume, brain water content, HE staining and antioxidant index were analyzed to evaluated the brain damage. Molecular Docking, molecular dynamics (MD) simulation, immunohistochemistry, and Western blot were used to explore the potential proteins related to DNA damage repair. Results APG has a low binding score with DNA repair-related proteins. APG treatment has improved the volume of cerebral infarction and neurological deficits, reduced brain edema, and decreased parthanatos and apoptosis by inhibiting PARP1/AIF pathway. In addition, APG improved the antioxidative capacity through reducing reactive oxygen species and malondialdehyde, and increasing glutathione and superoxide dismutase. Also, APG has reduced DNA damage- and cell death-related proteins such as PARP1, γH2A.X, 53BP1, AIF, cleaved caspase3, Cytochrome c, and increased DNA repair by BRCA1 and RAD51 through homologous recombination repair, and reduced non-homologous end link repair by KU70. Conclusion APG can improve nerve damage after IS, and these protective effects were realized by reducing oxidative stress and DNA damage, and improving DNA repair.
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Affiliation(s)
- Niu Ping
- Department of Encephalopathy, Hospital of Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Kuiyang Zuo
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Jiahan Cai
- Traditional Chinese Medicine College, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Chunshu Rong
- Department of Encephalopathy, Hospital of Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Ziqiao Yu
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Xu Zhang
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Gaihua Wang
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Chunyu Ma
- Department of Encephalopathy, Hospital of Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Huirong Yang
- Department of Encephalopathy, Hospital of Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Jinhua Li
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Xu Wang
- Department of Encephalopathy, Hospital of Changchun University of Chinese Medicine, Changchun, Jilin, China
- School of Public Health, Jilin University, Changchun, Jilin, China
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Dexi Zhao
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
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37
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Herrick J. DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity? Genes (Basel) 2024; 15:520. [PMID: 38674454 PMCID: PMC11049855 DOI: 10.3390/genes15040520] [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: 03/17/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
DNA damage causes the mutations that are the principal source of genetic variation. DNA damage detection and repair mechanisms therefore play a determining role in generating the genetic diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at a rate set by the level of standing allelic diversity in a population. The process of speciation is driven by a combination of two evolutionary forces: genetic drift and ecological selection. Genetic drift takes place under the conditions of relaxed selection, and results in a balance between the rates of mutation and the rates of genetic substitution. These two processes, drift and selection, are necessarily mediated by a variety of mechanisms guaranteeing genome stability in any given species. One of the outstanding questions in evolutionary biology concerns the origin of the widely varying phylogenetic distribution of biodiversity across the Tree of Life and how the forces of drift and selection contribute to shaping that distribution. The following examines some of the molecular mechanisms underlying genome stability and the adaptive radiations that are associated with biodiversity and the widely varying species richness and evenness in the different eukaryotic lineages.
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Affiliation(s)
- John Herrick
- Independent Researcher at 3, Rue des Jeûneurs, 75002 Paris, France
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38
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Jurkovic CM, Boisvert FM. Evolution of techniques and tools for replication fork proteome and protein interaction studies. Biochem Cell Biol 2024; 102:135-144. [PMID: 38113480 DOI: 10.1139/bcb-2023-0215] [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: 12/21/2023] Open
Abstract
Understanding the complex network of protein-protein interactions (PPI) that govern cellular functions is essential for unraveling the molecular basis of biological processes and diseases. Mass spectrometry (MS) has emerged as a powerful tool for studying protein dynamics, enabling comprehensive analysis of protein function, structure, post-translational modifications, interactions, and localization. This article provides an overview of MS techniques and their applications in proteomics studies, with a focus on the replication fork proteome. The replication fork is a multi-protein assembly involved in DNA replication, and its proper functioning is crucial for maintaining genomic integrity. By combining quantitative MS labeling techniques with various data acquisition methods, researchers have made significant strides in elucidating the complex processes and molecular mechanisms at the replication fork. Overall, MS has revolutionized our understanding of protein dynamics, offering valuable insights into cellular processes and potential targets for therapeutic interventions.
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Affiliation(s)
- Carla-Marie Jurkovic
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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Yin L, Hu X, Pei G, Tang M, Zhou Y, Zhang H, Huang M, Li S, Zhang J, Citu C, Zhao Z, Debeb BG, Feng X, Chen J. Genome-wide CRISPR screen reveals the synthetic lethality between BCL2L1 inhibition and radiotherapy. Life Sci Alliance 2024; 7:e202302353. [PMID: 38316463 PMCID: PMC10844523 DOI: 10.26508/lsa.202302353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Radiation therapy (RT) is one of the most commonly used anticancer therapies. However, the landscape of cellular response to irradiation, especially to a single high-dose irradiation, remains largely unknown. In this study, we performed a whole-genome CRISPR loss-of-function screen and revealed temporal inherent and acquired responses to RT. Specifically, we found that loss of the IL1R1 pathway led to cellular resistance to RT. This is in part because of the involvement of radiation-induced IL1R1-dependent transcriptional regulation, which relies on the NF-κB pathway. Moreover, the mitochondrial anti-apoptotic pathway, particularly the BCL2L1 gene, is crucially important for cell survival after radiation. BCL2L1 inhibition combined with RT dramatically impeded tumor growth in several breast cancer cell lines and syngeneic models. Taken together, our results suggest that the combination of an apoptosis inhibitor such as a BCL2L1 inhibitor with RT may represent a promising anticancer strategy for solid cancers including breast cancer.
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Affiliation(s)
- Ling Yin
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoding Hu
- https://ror.org/04twxam07 Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- https://ror.org/04twxam07 Morgan Welch Inflammatory Breast Cancer Clinic and Research Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangsheng Pei
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mengfan Tang
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - You Zhou
- https://ror.org/04twxam07 Department of Pediatrics Research, Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huimin Zhang
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Min Huang
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siting Li
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie Zhang
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Citu Citu
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhongming Zhao
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bisrat G Debeb
- https://ror.org/04twxam07 Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- https://ror.org/04twxam07 Morgan Welch Inflammatory Breast Cancer Clinic and Research Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xu Feng
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Junjie Chen
- https://ror.org/04twxam07 Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Alfano L, Iannuzzi CA, Barone D, Forte IM, Ragosta MC, Cuomo M, Mazzarotti G, Dell'Aquila M, Altieri A, Caporaso A, Roma C, Marra L, Boffo S, Indovina P, De Laurentiis M, Giordano A. CDK9-55 guides the anaphase-promoting complex/cyclosome (APC/C) in choosing the DNA repair pathway choice. Oncogene 2024; 43:1263-1273. [PMID: 38433256 DOI: 10.1038/s41388-024-02982-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
DNA double-strand breaks (DSBs) contribute to genome instability, a key feature of cancer. DSBs are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ). We investigated the role of an isoform of the multifunctional cyclin-dependent kinase 9, CDK9-55, in DNA repair, by generating CDK9-55-knockout HeLa clones (through CRISPR-Cas9), which showed potential HR dysfunction. A phosphoproteomic screening in these clones treated with camptothecin revealed that CDC23 (cell division cycle 23), a component of the E3-ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome), is a new substrate of CDK9-55, with S588 being its putative phosphorylation site. Mutated non-phosphorylatable CDC23(S588A) affected the repair pathway choice by impairing HR and favouring error-prone NHEJ. This CDK9 role should be considered when designing CDK-inhibitor-based cancer therapies.
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Affiliation(s)
- Luigi Alfano
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy.
| | - Carmelina Antonella Iannuzzi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Daniela Barone
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Iris Maria Forte
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | | | - Maria Cuomo
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulio Mazzarotti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Milena Dell'Aquila
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Angela Altieri
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Antonella Caporaso
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Laura Marra
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Silvia Boffo
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Paola Indovina
- Sbarro Research Health Organization, Candiolo, Torino, Italy
| | - Michelino De Laurentiis
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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41
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Merker L, Feller L, Dorn A, Puchta H. Deficiency of both classical and alternative end-joining pathways leads to a synergistic defect in double-strand break repair but not to an increase in homology-dependent gene targeting in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:242-254. [PMID: 38179887 DOI: 10.1111/tpj.16604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/13/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
In eukaryotes, double-strand breaks (DSBs) are either repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ). In somatic plant cells, HR is very inefficient. Therefore, the vast majority of DSBs are repaired by two different pathways of NHEJ. The classical (cNHEJ) pathway depends on the heterodimer KU70/KU80, while polymerase theta (POLQ) is central to the alternative (aNHEJ) pathway. Surprisingly, Arabidopsis plants are viable, even when both pathways are impaired. However, they exhibit severe growth retardation and reduced fertility. Analysis of mitotic anaphases indicates that the double mutant is characterized by a dramatic increase in chromosome fragmentation due to defective DSB repair. In contrast to the single mutants, the double mutant was found to be highly sensitive to the DSB-inducing genotoxin bleomycin. Thus, both pathways can complement for each other efficiently in DSB repair. We speculated that in the absence of both NHEJ pathways, HR might be enhanced. This would be especially attractive for gene targeting (GT) in which predefined changes are introduced using a homologous template. Unexpectedly, the polq single mutant as well as the double mutant showed significantly lower GT frequencies in comparison to wildtype plants. Accordingly, we were able to show that elimination of both NHEJ pathways does not pose an attractive approach for Agrobacterium-mediated GT. However, our results clearly indicate that a loss of cNHEJ leads to an increase in GT frequency, which is especially drastic and attractive for practical applications, in which the in planta GT strategy is used.
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Affiliation(s)
- Laura Merker
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Laura Feller
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Annika Dorn
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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42
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Graham EL, Fernandez J, Gandhi S, Choudhry I, Kellam N, LaRocque JR. The impact of developmental stage, tissue type, and sex on DNA double-strand break repair in Drosophila melanogaster. PLoS Genet 2024; 20:e1011250. [PMID: 38683763 PMCID: PMC11057719 DOI: 10.1371/journal.pgen.1011250] [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: 12/15/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Accurate repair of DNA double-strand breaks (DSBs) is essential for the maintenance of genome integrity, as failure to repair DSBs can result in cell death. The cell has evolved two main mechanisms for DSB repair: non-homologous end-joining (NHEJ) and homology-directed repair (HDR), which includes single-strand annealing (SSA) and homologous recombination (HR). While certain factors like age and state of the chromatin are known to influence DSB repair pathway choice, the roles of developmental stage, tissue type, and sex have yet to be elucidated in multicellular organisms. To examine the influence of these factors, DSB repair in various embryonic developmental stages, larva, and adult tissues in Drosophila melanogaster was analyzed through molecular analysis of the DR-white assay using Tracking across Indels by DEcomposition (TIDE). The proportion of HR repair was highest in tissues that maintain the canonical (G1/S/G2/M) cell cycle and suppressed in both terminally differentiated and polyploid tissues. To determine the impact of sex on repair pathway choice, repair in different tissues in both males and females was analyzed. When molecularly examining tissues containing mostly somatic cells, males and females demonstrated similar proportions of HR and NHEJ. However, when DSB repair was analyzed in male and female premeiotic germline cells utilizing phenotypic analysis of the DR-white assay, there was a significant decrease in HR in females compared to males. This study describes the impact of development, tissue-specific cycling profile, and, in some cases, sex on DSB repair outcomes, underscoring the complexity of repair in multicellular organisms.
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Affiliation(s)
- Elizabeth L. Graham
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Joel Fernandez
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Shagun Gandhi
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Iqra Choudhry
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Natalia Kellam
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Jeannine R. LaRocque
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, District of Columbia, United States of America
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43
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Wang YJ, Cao JB, Yang J, Liu T, Yu HL, He ZX, Bao SL, He XX, Zhu XJ. PRMT5-mediated homologous recombination repair is essential to maintain genomic integrity of neural progenitor cells. Cell Mol Life Sci 2024; 81:123. [PMID: 38459149 PMCID: PMC10923982 DOI: 10.1007/s00018-024-05154-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: 11/14/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
Maintaining genomic stability is a prerequisite for proliferating NPCs to ensure genetic fidelity. Though histone arginine methylation has been shown to play important roles in safeguarding genomic stability, the underlying mechanism during brain development is not fully understood. Protein arginine N-methyltransferase 5 (PRMT5) is a type II protein arginine methyltransferase that plays a role in transcriptional regulation. Here, we identify PRMT5 as a key regulator of DNA repair in response to double-strand breaks (DSBs) during NPC proliferation. Prmt5F/F; Emx1-Cre (cKO-Emx1) mice show a distinctive microcephaly phenotype, with partial loss of the dorsal medial cerebral cortex and complete loss of the corpus callosum and hippocampus. This phenotype is resulted from DSBs accumulation in the medial dorsal cortex followed by cell apoptosis. Both RNA sequencing and in vitro DNA repair analyses reveal that PRMT5 is required for DNA homologous recombination (HR) repair. PRMT5 specifically catalyzes H3R2me2s in proliferating NPCs in the developing mouse brain to enhance HR-related gene expression during DNA repair. Finally, overexpression of BRCA1 significantly rescues DSBs accumulation and cell apoptosis in PRMT5-deficient NSCs. Taken together, our results show that PRMT5 maintains genomic stability by regulating histone arginine methylation in proliferating NPCs.
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Affiliation(s)
- Ya-Jun Wang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jian-Bo Cao
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jing Yang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Tong Liu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Hua-Li Yu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Zi-Xuan He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Shi-Lai Bao
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Xiao He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China.
| | - Xiao-Juan Zhu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China.
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44
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Rose EP, Osterberg VR, Banga JS, Gorbunova V, Unni VK. Alpha-synuclein regulates the repair of genomic DNA double-strand breaks in a DNA-PK cs-dependent manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582819. [PMID: 38496612 PMCID: PMC10942394 DOI: 10.1101/2024.02.29.582819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
α-synuclein (αSyn) is a presynaptic and nuclear protein that aggregates in important neurodegenerative diseases such as Parkinson's Disease (PD), Parkinson's Disease Dementia (PDD) and Lewy Body Dementia (LBD). Our past work suggests that nuclear αSyn may regulate forms of DNA double-strand break (DSB) repair in HAP1 cells after DNA damage induction with the chemotherapeutic agent bleomycin1. Here, we report that genetic deletion of αSyn specifically impairs the non-homologous end-joining (NHEJ) pathway of DSB repair using an extrachromosomal plasmid-based repair assay in HAP1 cells. Importantly, induction of a single DSB at a precise genomic location using a CRISPR/Cas9 lentiviral approach also showed the importance of αSyn in regulating NHEJ in HAP1 cells and primary mouse cortical neuron cultures. This modulation of DSB repair is dependent on the activity of the DNA damage response signaling kinase DNA-PKcs, since the effect of αSyn loss-of-function is reversed by DNA-PKcs inhibition. Using in vivo multiphoton imaging in mouse cortex after induction of αSyn pathology, we find an increase in longitudinal cell survival of inclusion-bearing neurons after Polo-like kinase (PLK) inhibition, which is associated with an increase in the amount of aggregated αSyn within inclusions. Together, these findings suggest that αSyn plays an important physiologic role in regulating DSB repair in both a transformed cell line and in primary cortical neurons. Loss of this nuclear function may contribute to the neuronal genomic instability detected in PD, PDD and DLB and points to DNA-PKcs and PLK as potential therapeutic targets.
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Affiliation(s)
- Elizabeth P. Rose
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239
- Neuroscience Graduate Program, Vollum Institute, Oregon Health & Science University, Portland, OR 97239
| | - Valerie R. Osterberg
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239
| | - Jovin S. Banga
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, 14620
| | - Vivek K. Unni
- Jungers Center for Neurosciences Research, Oregon Health & Science University, Portland, OR 97239
- OHSU Parkinson Center, Department of Neurology, Oregon Health & Science University, Portland, OR 97239
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45
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Chen W, Chen Z, Jia Y, Guo Y, Zheng L, Yao S, Shao Y, Li M, Mao R, Jiang Y. Circ_0008657 regulates lung DNA damage induced by hexavalent chromium through the miR-203a-3p/ATM axis. ENVIRONMENT INTERNATIONAL 2024; 185:108515. [PMID: 38394914 DOI: 10.1016/j.envint.2024.108515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/17/2023] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Hexavalent chromium [Cr (VI)] is an important environmental pollutant and may cause lung injury when inhaled into the human body. Cr (VI) is genotoxic and can cause DNA damage, although the underlying epigenetic mechanisms remain unclear. To simulate the real-life workplace exposure to Cr (VI), we used a novel exposure dose calculation method. We evaluated the effect of Cr (VI) on DNA damage in human bronchial epithelial cells (16HBE and BEAS-2B) by calculating the equivalent real-time exposure dose of Cr (VI) (0 to 10 μM) in an environmental population. Comet experiments and olive tail moment measurements revealed increased DNA damage in cells exposed to Cr (VI). Cr (VI) treatment increased nuclear γ-H2AX foci and γ-H2AX protein expression, and caused DNA damage in the lung tissues of mice. An effective Cr (VI) dose (6 μM) was determined and used for cell treatment. Cr (VI) exposure upregulated circ_0008657, and knockdown of circ_0008657 decreased Cr (VI)-induced DNA damage, whereas circ_0008657 overexpression had the opposite effect. Mechanistically, we found that circ_0008657 binds to microRNA (miR)-203a-3p and subsequently regulates ATM serine/threonine kinase (ATM), a key protein involved in homologous recombination repair downstream of miR-203a-3p, thereby regulating DNA damage induced by Cr (VI). The present findings suggest that circ_0008657 competitively binds to miR-203a-3p to activate the ATM pathway and regulate the DNA damage response after environmental chemical exposure in vivo and in vitro.
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Affiliation(s)
- Wei Chen
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Zehao Chen
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Yangyang Jia
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Yaozheng Guo
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Liting Zheng
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Shuwei Yao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Yueting Shao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Meizhen Li
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Rulin Mao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Yiguo Jiang
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China.
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46
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Abdi Ghavidel A, Aghamiri S, Raee P, Mohammadi-Yeganeh S, Noori E, Bandehpour M, Kazemi B, Jajarmi V. Recent Advances in CRISPR/Cas9-Mediated Genome Editing in Leishmania Strains. Acta Parasitol 2024; 69:121-134. [PMID: 38127288 DOI: 10.1007/s11686-023-00756-0] [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: 06/04/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Genome manipulation of Leishmania species and the creation of modified strains are widely employed strategies for various purposes, including gene function studies, the development of live attenuated vaccines, and the engineering of host cells for protein production. OBJECTIVE Despite the introduction of novel manipulation approaches like CRISPR/Cas9 technology with significant advancements in recent years, the development of a reliable protocol for efficiently and precisely altering the genes of Leishmania strains remains a challenging endeavor. Following the successful adaptation of the CRISPR/Cas9 system for higher eukaryotic cells, several research groups have endeavored to apply this system to manipulate the genome of Leishmania. RESULTS Despite the substantial differences between Leishmania and higher eukaryotes, the CRISPR/Cas9 system has been effectively tested and applied in Leishmania. CONCLUSION: This comprehensive review summarizes all the CRISPR/Cas9 systems that have been employed in Leishmania, providing details on their methods and the expression systems for Cas9 and gRNA. The review also explores the various applications of the CRISPR system in Leishmania, including the deletion of multicopy gene families, the development of the Leishmania vaccine, complete gene deletions, investigations into chromosomal translocations, protein tagging, gene replacement, large-scale gene knockout, genome editing through cytosine base replacement, and its innovative use in the detection of Leishmania. In addition, the review offers an up-to-date overview of all double-strand break repair mechanisms in Leishmania.
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Affiliation(s)
- Afshin Abdi Ghavidel
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Aghamiri
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Effat Noori
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Jajarmi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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47
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Tao L, Xia X, Kong S, Wang T, Fan F, Wang W. Natural pentacyclic triterpenoid from Pristimerin sensitizes p53-deficient tumor to PARP inhibitor by ubiquitination of Chk1. Pharmacol Res 2024; 201:107091. [PMID: 38316371 DOI: 10.1016/j.phrs.2024.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Inhibition of checkpoint kinase 1 (Chk1) has shown to overcome resistance to poly (ADP-ribose) polymerase (PARP) inhibitors and expand the clinical utility of PARP inhibitors in a broad range of human cancers. Pristimerin, a naturally occurring pentacyclic triterpenoid, has been the focus of intensive studies for its anticancer potential. However, it is not yet known whether low dose of pristimerin can be combined with PARP inhibitors by targeting Chk1 signaling pathway. In this study, we investigated the efficacy, safety and molecular mechanisms of the synergistic effect produced by the combination olaparib and pristimerin in TP53-deficient and BRCA-proficient cell models. As a result, an increased expression of Chk1 was correlated with TP53 mutation, and pristimerin preferentially sensitized p53-defective cells to olaparib. The combination of olaparib and pristimerin resulted in a more pronounced abrogation of DNA synthesis and induction of DNA double-strand breaks (DSBs). Moreover, pristimerin disrupted the constitutional levels of Chk1 and DSB repair activities. Mechanistically, pristimerin promoted K48-linked polyubiquitination and proteasomal degradation of Chk1 while not affecting its kinase domain and activity. Importantly, combinatorial therapy led to a higher rate of tumor growth inhibition without apparent hematological toxicities. In addition, pristimerin suppressed olaparib-induced upregulation of Chk1 and enhanced olaparib-induced DSB marker γΗ2ΑΧ in vivo. Taken together, inhibition of Chk1 by pristimerin has been observed to induce DNA repair deficiency, which may expand the application of olaparib in BRCA-proficient cancers harboring TP53 mutations. Thus, pristimerin can be combined for PARP inhibitor-based therapy.
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Affiliation(s)
- Li Tao
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Xiangyu Xia
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shujing Kong
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Tingye Wang
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Fangtian Fan
- Anhui Engineering Technology Research Center of Biochemical Pharmaceuticals, School of Pharmacy, Bengbu Medical College, Bengbu, Anhui 233003, China
| | - Weimin Wang
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China; Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yixing, Jiangsu 214200, China.
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48
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Rajendra E, Grande D, Mason B, Di Marcantonio D, Armstrong L, Hewitt G, Elinati E, Galbiati A, Boulton SJ, Heald RA, Smith GCM, Robinson HMR. Quantitative, titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells. Nucleic Acids Res 2024; 52:1736-1752. [PMID: 38109306 PMCID: PMC10899754 DOI: 10.1093/nar/gkad1196] [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: 05/25/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
Repair of DNA damage is essential for the maintenance of genome stability and cell viability. DNA double strand breaks (DSBs) constitute a toxic class of DNA lesion and multiple cellular pathways exist to mediate their repair. Robust and titratable assays of cellular DSB repair (DSBR) are important to functionally interrogate the integrity and efficiency of these mechanisms in disease models as well as in response to genetic or pharmacological perturbations. Several variants of DSBR reporters are available, however these are often limited by throughput or restricted to specific cellular models. Here, we describe the generation and validation of a suite of extrachromosomal reporter assays that can efficiently measure the major DSBR pathways of homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single strand annealing (SSA). We demonstrate that these assays can be adapted to a high-throughput screening format and that they are sensitive to pharmacological modulation, thus providing mechanistic and quantitative insights into compound potency, selectivity, and on-target specificity. We propose that these reporter assays can serve as tools to dissect the interplay of DSBR pathway networks in cells and will have broad implications for studies of DSBR mechanisms in basic research and drug discovery.
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Affiliation(s)
- Eeson Rajendra
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Diego Grande
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Bethany Mason
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Lucy Armstrong
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Elias Elinati
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Simon J Boulton
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Robert A Heald
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Graeme C M Smith
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
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49
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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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50
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Leslie AR, Ning S, Armstrong CM, D’Abronzo LS, Sharifi M, Schaaf ZA, Lou W, Liu C, Evans CP, Lombard AP, Gao AC. IGFBP3 promotes resistance to Olaparib via modulating EGFR signaling in advanced prostate cancer. iScience 2024; 27:108984. [PMID: 38327800 PMCID: PMC10847745 DOI: 10.1016/j.isci.2024.108984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/07/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Olaparib is a pioneering PARP inhibitor (PARPi) approved for treating castration-resistant prostate cancer (CRPC) tumors harboring DNA repair defects, but clinical resistance has been documented. To study acquired resistance, we developed Olaparib-resistant (OlapR) cell lines through chronic Olaparib treatment of LNCaP and C4-2B cell lines. Here, we found that IGFBP3 is highly expressed in acquired (OlapR) and intrinsic (Rv1) models of Olaparib resistance. We show that IGFBP3 expression promotes Olaparib resistance by enhancing DNA repair capacity through activation of EGFR and DNA-PKcs. IGFBP3 depletion enhances efficacy of Olaparib by promoting DNA damage accumulation and subsequently, cell death in resistant models. Mechanistically, we show that silencing IGFBP3 or EGFR expression reduces cell viability and resensitizes OlapR cells to Olaparib treatment. Inhibition of EGFR by Gefitinib suppressed growth of OlapR cells and improved Olaparib sensitivity, thereby phenocopying IGFBP3 inhibition. Collectively, our results highlight IGFBP3 and EGFR as critical mediators of Olaparib resistance.
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Affiliation(s)
- Amy R. Leslie
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Shu Ning
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | | | | | - Masuda Sharifi
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Zachary A. Schaaf
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Wei Lou
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
| | - Chengfei Liu
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
| | - Christopher P. Evans
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
| | - Alan P. Lombard
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Allen C. Gao
- Department of Urologic Surgery, University of California Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
- VA Northern California Health Care System, Sacramento, CA, USA
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