1
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Chu SSH, Xing G, Ling H. The role of human Shu complex in ATP-dependent regulation of RAD51 filaments during homologous recombination-associated DNA damage response. J Biol Chem 2025:110212. [PMID: 40345587 DOI: 10.1016/j.jbc.2025.110212] [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: 02/05/2025] [Revised: 04/25/2025] [Accepted: 05/04/2025] [Indexed: 05/11/2025] Open
Abstract
Error-free DNA lesion bypass is an important pathway in DNA damage tolerance. The Shu complex facilitates this process by promoting homologous recombination (HR) to bypass DNA damage. Biochemical analysis of the human Shu complex homolog, hSWS1-SWSAP1, offers valuable insights into the HR-associated DNA damage response. Here, we biochemically characterized the human Shu complex and examined its interactions with RAD51 filaments, which are essential in HR. Using fluorescence polarization assays, we first revealed that hSWS1-SWSAP1 preferentially binds DNA with an exposed 5' end in the presence of adenine nucleotides. We then investigated and validated the DNA-stimulated ATPase activity of hSWS1-SWSAP1 through site-specific mutagenesis, revealing that DNA with an exposed 5' end is the most efficient in enhancing this activity. Furthermore, we showed that hSWS1-SWSAP1 initially interacts with RAD51 filaments at the 5' end and modulates the properties of the nucleoprotein filaments using fluorescence-based assays. Our findings revealed that hSWS1-SWSAP1 induces conformational changes in RAD51 filaments in an ATP-hydrolysis-dependent manner, while its stabilization of the filaments depends on ATP binding. This work provides mechanistic insights into the regulation of RAD51 filaments in HR-associated DNA damage tolerance.
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Affiliation(s)
- Sam S H Chu
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A 5C1
| | - Guangxin Xing
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A 5C1
| | - Hong Ling
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A 5C1.
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2
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Neal FE, Li W, Uhrig ME, Katz JN, Syed S, Sharma N, Dutta A, Burma S, Hromas R, Mazin AV, Dray E, Libich DS, Olsen SK, Wasmuth EV, Zhao W, Sørensen CS, Wiese C, Kwon Y, Sung P. Distinct roles of the two BRCA2 DNA-binding domains in DNA damage repair and replication fork preservation. Cell Rep 2025; 44:115654. [PMID: 40323719 DOI: 10.1016/j.celrep.2025.115654] [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: 10/03/2024] [Revised: 03/03/2025] [Accepted: 04/15/2025] [Indexed: 05/07/2025] Open
Abstract
Homologous recombination (HR) removes DNA double-strand breaks (DSBs) and preserves stressed DNA replication forks. Successful HR execution requires the tumor suppressor BRCA2, which harbors distinct DNA-binding domains (DBDs): one that possesses three oligonucleotide/oligosaccharide-binding (OB) folds (OB-DBD) and another residing in the C-terminal recombinase binding domain (CTRB-DBD). Here, we employ multi-faceted approaches to delineate the contributions of these domains toward HR and replication fork maintenance. We show that OB-DBD and CTRB-DBD confer single-strand DNA (ssDNA)- and dsDNA-binding capabilities, respectively, and that BRCA2 variants mutated in either domain are impaired in their ability to load the recombinase RAD51 onto ssDNA pre-occupied by RPA. While the CTRB-DBD mutant is modestly affected by DNA break repair, it exhibits a strong defect in the protection of stressed replication forks. In contrast, the OB-DBD is indispensable for both BRCA2 functions. Our study thus defines the unique contributions of the two BRCA2 DBDs in genome maintenance.
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Affiliation(s)
- Francisco E Neal
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Wenjing Li
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Mollie E Uhrig
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA; Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey N Katz
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Shahrez Syed
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Department of Neurosurgery, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Alexander V Mazin
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - David S Libich
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, San Antonio, TX 78229, USA.
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3
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Tavella S, di Lillo A, Conti A, Iannelli F, Mancheno-Ferris A, Matti V, Di Micco R, Fagagna FDD. Weaponizing CRISPR/Cas9 for selective elimination of cells with an aberrant genome. DNA Repair (Amst) 2025; 149:103840. [PMID: 40319546 PMCID: PMC12086175 DOI: 10.1016/j.dnarep.2025.103840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 03/27/2025] [Accepted: 04/23/2025] [Indexed: 05/07/2025]
Abstract
The CRISPR/Cas9 technology is a powerful and versatile tool to disrupt genes' functions by introducing sequence-specific DNA double-strand breaks (DSBs). Here, we repurpose this technology to eradicate aberrant cells by specifically targeting silent and non-functional genomic sequences present only in target cells to be eliminated. Indeed, an intrinsic challenge of most current therapies against cancer and viral infections is the non-specific toxicity that they can induce in normal tissues because of their impact on important cellular mechanisms shared, to different extents, between unhealthy and healthy cells. The CRISPR/Cas9 technology has potential to overcome this limitation; however, so far effectiveness of these approaches was made dependent on the targeting and inactivation of a functional gene product. Here, we generate proof-of-principle evidence by engineering HeLa and RKO cells with a promoterless Green Fluorescent Protein (GFP) construct. The integration of this construct simulates either a genomic alteration, as in cancer cells, or a silent proviral genome. Cas9-mediated DSBs in the GFP sequence activate the DNA damage response (DDR), reduce cell viability and increase mortality. This is associated with increased cell size, multinucleation, cGAS-positive micronuclei accumulation and the activation of an inflammatory response. Pharmacological inhibition of the DNA repair factor DNA-PK enhances cell death. These results demonstrate the therapeutic potential of the CRISPR/Cas9 system in eliminating cells with an aberrant genome, regardless of the expression or the function of the target DNA sequence.
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Affiliation(s)
- Sara Tavella
- Institute of Molecular Genetics (IGM), National Research Institute (CNR), Pavia, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Alessia di Lillo
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Anastasia Conti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Hospital, Milan, Italy
| | - Fabio Iannelli
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Valentina Matti
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Hospital, Milan, Italy; University School of Advanced Studies IUSS, Pavia 27100, Italy
| | - Fabrizio d'Adda di Fagagna
- Institute of Molecular Genetics (IGM), National Research Institute (CNR), Pavia, Italy; IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy; Lead Contact, Italy.
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4
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Huang J, Ding K, Chen J, Fan J, Huang L, Qiu S, Wang L, Du X, Wang C, Pan H, Yuan Z, Liu H, Song H. Comparison of CRISPR-Cas9, CRISPR-Cas12f1, and CRISPR-Cas3 in eradicating resistance genes KPC-2 and IMP-4. Microbiol Spectr 2025:e0257224. [PMID: 40293254 DOI: 10.1128/spectrum.02572-24] [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: 10/10/2024] [Accepted: 02/22/2025] [Indexed: 04/30/2025] Open
Abstract
Bacterial plasmid encoding antibiotic resistance could be eradicated by various CRISPR systems, such as CRISPR-Cas9, Cas12f1, and Cas3. However, the efficacy of these gene editing tools against bacterial resistance has not been systematically assessed and compared. This study eliminates carbapenem resistance genes KPC-2 and IMP-4 via CRISPR-Cas9, Cas12f1, and Cas3 systems, respectively. The eradication efficiency of the three CRISPR systems was evaluated. First, the target sites for the three CRISPR systems were designed within the regions 542-576 bp of the KPC-2 gene and 213-248 bp of the IMP-4 gene, respectively. The recombinant CRISPR plasmids were transformed into Escherichia coli carrying KPC-2 or IMP-4-encoding plasmid. Colony PCR of transformants showed that KPC-2 and IMP-4 were eradicated by the three different CRISPR systems, and the elimination efficacy was both 100.00%. The drug sensitivity test results showed that the resistant E. coli strain was resensitized to ampicillin. In addition, the three CRISPR plasmids could block the horizontal transfer of drug-resistant plasmids, with a blocking rate as high as 99%. Importantly, a qPCR assay was performed to analyze the copy number changes of drug-resistant plasmids in E. coli cells. The results indicated that CRISPR-Cas3 showed higher eradication efficiency than CRISPR-Cas9 and Cas12f1 systems. IMPORTANCE With the continuous development and application of CRISPR-based resistance removal technologies, CRISPR-Cas9, Cas12f1, and Cas3 have gradually come into focus. However, it remains uncertain which system exhibits more potent efficacy in the removal of bacterial resistance. This study verifies that CRISPR-Cas9, Cas12f1, and Cas3 can eradicate the carbapenem-resistant genes KPC-2 and IMP-4 and restore the sensitivity of drug-resistant model bacteria to antibiotics. Among the three CRISPR systems, the CRISPR-Cas3 system showed the highest eradication efficiency. Although each system has its advantages and characteristics, our results provide guidance on the selection of the CRISPR system from the perspective of resistance gene removal efficiency, contributing to the further application of CRISPR-based bacterial resistance removal technologies.
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Affiliation(s)
- Jun Huang
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
- Department of Human Anatomy and Histology, School of Basic Medicine, Capital Medical University, Beijing, China
| | - Kanghui Ding
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Jiahui Chen
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Jiao Fan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Luyao Huang
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Shaofu Qiu
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
| | - Ligui Wang
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
| | - Xinying Du
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
| | - Chao Wang
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
| | - Haifeng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Zhengquan Yuan
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
| | - Hongbo Liu
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Department of Infectious Disease Prevention and Control, Chinese People's Liberation Army Center for Disease Control and Prevention, Beijing, China
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5
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Haider S, Mussolino C. Fine-Tuning Homology-Directed Repair (HDR) for Precision Genome Editing: Current Strategies and Future Directions. Int J Mol Sci 2025; 26:4067. [PMID: 40362308 PMCID: PMC12071731 DOI: 10.3390/ijms26094067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2025] [Revised: 04/19/2025] [Accepted: 04/21/2025] [Indexed: 05/15/2025] Open
Abstract
CRISPR-Cas9 is a powerful genome-editing technology that can precisely target and cleave DNA to induce double-strand breaks (DSBs) at almost any genomic locus. While this versatility holds tremendous therapeutic potential, the predominant cellular pathway for DSB repair-non-homologous end-joining (NHEJ)-often introduces small insertions or deletions that disrupt the target site. In contrast, homology-directed repair (HDR) utilizes exogenous donor templates to enable precise gene modifications, including targeted insertions, deletions, and substitutions. However, HDR remains relatively inefficient compared to NHEJ, especially in postmitotic cells where cell cycle constraints further limit HDR. To address this challenge, numerous methodologies have been explored, ranging from inhibiting key NHEJ factors and optimizing donor templates to synchronizing cells in HDR-permissive phases and engineering HDR-enhancing fusion proteins. These strategies collectively aim to boost HDR efficiency and expand the clinical and research utility of CRISPR-Cas9. In this review, we discuss recent advances in manipulating the balance between NHEJ and HDR, examine the trade-offs and practical considerations of these approaches, and highlight promising directions for achieving high-fidelity genome editing in diverse cell types.
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Affiliation(s)
- Sibtain Haider
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany;
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany;
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
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6
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Li M, Lin Y, Cheng Q, Wei T. Prime Editing: A Revolutionary Technology for Precise Treatment of Genetic Disorders. Cell Prolif 2025; 58:e13808. [PMID: 40014809 PMCID: PMC11969253 DOI: 10.1111/cpr.13808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 12/06/2024] [Accepted: 01/03/2025] [Indexed: 03/01/2025] Open
Abstract
Genetic diseases have long posed significant challenges, with limited breakthroughs in treatment. Recent advances in gene editing technologies offer new possibilities in gene therapy for the treatment of inherited disorders. However, traditional gene editing methods have limitations that hinder their potential for clinical use, such as limited editing capabilities and the production of unintended byproducts. To overcome these limitations, prime editing (PE) has been developed as a powerful tool for precise and efficient genome modification. In this review, we provide an overview of the latest advancements in PE and its potential applications in the treatment of inherited disorders. Furthermore, we examine the current delivery vehicles employed for delivering PE systems in vitro and in vivo, and analyze their respective benefits and limitations. Ultimately, we discuss the challenges that need to be addressed to fully unlock the potential of PE for the remission or cure of genetic diseases.
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Affiliation(s)
- Mengyao Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Lin
- Department of Biomedical Engineering, College of Future TechnologyPeking UniversityBeijingChina
| | - Qiang Cheng
- Department of Biomedical Engineering, College of Future TechnologyPeking UniversityBeijingChina
- Beijing Advanced Center of RNA BiologyPeking UniversityBeijingChina
| | - Tuo Wei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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7
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Amiama-Roig A, Barrientos-Moreno M, Cruz-Zambrano E, López-Ruiz LM, González-Prieto R, Ríos-Orelogio G, Prado F. A Rfa1-MN-based system reveals new factors involved in the rescue of broken replication forks. PLoS Genet 2025; 21:e1011405. [PMID: 40168399 PMCID: PMC11984746 DOI: 10.1371/journal.pgen.1011405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 04/10/2025] [Accepted: 03/10/2025] [Indexed: 04/03/2025] Open
Abstract
The integrity of the replication forks is essential for an accurate and timely completion of genome duplication. However, little is known about how cells deal with broken replication forks. We have generated in yeast a system based on a chimera of the largest subunit of the ssDNA binding complex RPA fused to the micrococcal nuclease (Rfa1-MN) to induce double-strand breaks (DSBs) at replication forks and searched for mutants affected in their repair. Our results show that the core homologous recombination (HR) proteins involved in the formation of the ssDNA/Rad51 filament are essential for the repair of DSBs at forks, whereas non-homologous end joining plays no role. Apart from the endonucleases Mus81 and Yen1, the repair process employs fork-associated HR factors, break-induced replication (BIR)-associated factors and replisome components involved in sister chromatid cohesion and fork stability, pointing to replication fork restart by BIR followed by fork restoration. Notably, we also found factors controlling the length of G1, suggesting that a minimal number of active origins facilitates the repair by converging forks. Our study has also revealed a requirement for checkpoint functions, including the synthesis of Dun1-mediated dNTPs. Finally, our screening revealed minimal impact from the loss of chromatin factors, suggesting that the partially disassembled nucleosome structure at the replication fork facilitates the accessibility of the repair machinery. In conclusion, this study provides an overview of the factors and mechanisms that cooperate to repair broken forks.
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Affiliation(s)
- Ana Amiama-Roig
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Marta Barrientos-Moreno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Esther Cruz-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Luz M. López-Ruiz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Román González-Prieto
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Gabriel Ríos-Orelogio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Félix Prado
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
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8
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Chen X, Chen C, Li Z, Liu C, Lin Z. Punicalagin as an Artemis inhibitor synergizes with photodynamic therapy in tumor suppression. Bioorg Chem 2025; 157:108282. [PMID: 39970756 DOI: 10.1016/j.bioorg.2025.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 01/22/2025] [Accepted: 02/13/2025] [Indexed: 02/21/2025]
Abstract
Photodynamic therapy (PDT) is a minimally invasive treatment that utilizes a photosensitizer, specific light wavelengths, and oxygen to generate reactive oxygen species (ROS), causing oxidative damage and tumor cell death. However, the effectiveness of PDT can be reduced by the intrinsic antioxidant and DNA repair mechanisms of tumor cells. Artemis (SNM1C/DCLRE1C) is an endonuclease essential for repairing DNA double-strand breaks (DSBs) via non-homologous end-joining (NHEJ). Herein, we conducted a high-throughput small-molecule screening and identified Punicalagin (PUG), a natural polyphenol from pomegranate, as a novel Artemis inhibitor with an IC50 value of 296.1 nM. We also investigated the effects of PUG combined with PDT in tumor treatment, using the pentalysine β-carbonylphthalocyanine zinc (ZnPc5K) as the photosensitizer. In HeLa cells, ZnPc5K-based PDT induced significant DSBs, which could be repaired by the intrinsic DNA repair mechanisms within 12 h. Co-treatment with PUG compromised DNA repair, promoted cell apoptosis, inhibited cell invasion, and suppressed the growth of various tumor cells. Furthermore, in a mouse xenograft model, the combination of PUG and ZnPc5K-PDT effectively inhibited tumor growth with minimal side effects. These findings suggest that PUG, as an Artemis inhibitor, can enhance the therapeutic efficacy of PDT in tumor suppression by impairing DNA repair through the NHEJ pathway.
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Affiliation(s)
- Xuening Chen
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Changkun Chen
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Zuoan Li
- Shengli Clinical Medical College of Fujian Medical University, Department of Emergency, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, China
| | - Chun Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou, China.
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9
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Vats A, Laimins L. How human papillomavirus (HPV) targets DNA repair pathways for viral replication: from guardian to accomplice. Microbiol Mol Biol Rev 2025; 89:e0015323. [PMID: 39868790 PMCID: PMC11948491 DOI: 10.1128/mmbr.00153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025] Open
Abstract
SUMMARYHuman papillomaviruses (HPVs) are small DNA viruses that are responsible for significant disease burdens worldwide, including cancers of the cervix, anogenital tract, and oropharynx. HPVs infect stratified epithelia at a variety of body locations and link their productive life cycles to the differentiation of the host cell. These viruses have evolved sophisticated mechanisms to exploit cellular pathways, such as DNA damage repair (DDR), to regulate their life cycles. HPVs activate key DDR pathways such as ATM, ATR, and FA, which are critical for maintaining genomic integrity but are often dysregulated in cancers. Importantly, these DDR pathways are essential for HPV replication in undifferentiated cells and amplification upon differentiation. The ability to modulate these DDR pathways not only enables HPV persistence but also contributes to cellular transformation. In this review, we discuss the recent advances in understanding the mechanisms by which HPV manipulates the host DDR pathways and how these depend upon enhanced topoisomerase activity and R-loop formation. Furthermore, the strategies to manipulate DDR pathways utilized by high-risk HPVs are compared with those used by other DNA viruses that exhibit similarities and distinct differences.
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Affiliation(s)
- Arushi Vats
- Department of Microbiology-Immunology, Northwestern University, Chicago, Illinois, USA
| | - Laimonis Laimins
- Department of Microbiology-Immunology, Northwestern University, Chicago, Illinois, USA
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10
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Shin Y, Petassi MT, Jessop AM, Kim SY, Matei R, Morse K, Raina VB, Roy U, Greene EC. Structural basis for Rad54- and Hed1-mediated regulation of Rad51 during the transition from mitotic to meiotic recombination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.26.645561. [PMID: 40196570 PMCID: PMC11974805 DOI: 10.1101/2025.03.26.645561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Rad51 catalyzes the DNA pairing reactions that take place during homologous recombination (HR), and HR must be tightly regulated to ensure physiologically appropriate outcomes. Rad54 is an ATP-dependent DNA motor protein that stimulates Rad51 activity during mitosis. In meiosis Rad51 is downregulated by the protein Hed1, which blocks Rad54 binding to Rad51, and allows Dmc1 to function as the active recombinase. We currently have a poor understanding of the regulatory interplay between Rad54, Hed1, Rad51 and Dmc1. Here, we identify a conserved Rad51 interaction motif within Rad54, and we solve a CryoEM structure of this motif bound to Rad51. We also identify a distinct Rad51 interaction motif within Hed1 and solve its structure bound to Rad51. These structures explain how Rad54 engages Rad51 to promote recombination between sister chromatids during mitosis and how Rad51 is downregulated by Hed1 upon entry into meiosis such that its meiosis-specific homolog Dmc1 can promote recombination between homologous chromosomes.
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Affiliation(s)
- Yeonoh Shin
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Michael T Petassi
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Aidan M Jessop
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Stefan Y Kim
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Razvan Matei
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Katherine Morse
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Vivek B Raina
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Upasana Roy
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
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11
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Bhat A, Bhan S, Kabiraj A, Pandita RK, Ramos KS, Nandi S, Sopori S, Sarkar PS, Dhar A, Pandita S, Kumar R, Das C, Tainer JA, Pandita TK. A predictive chromatin architecture nexus regulates transcription and DNA damage repair. J Biol Chem 2025; 301:108300. [PMID: 39947477 PMCID: PMC11931391 DOI: 10.1016/j.jbc.2025.108300] [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: 09/02/2024] [Revised: 12/16/2024] [Accepted: 01/16/2025] [Indexed: 03/28/2025] Open
Abstract
Genomes are blueprints of life essential for an organism's survival, propagation, and evolutionary adaptation. Eukaryotic genomes comprise of DNA, core histones, and several other nonhistone proteins, packaged into chromatin in the tiny confines of nucleus. Chromatin structural organization restricts transcription factors to access DNA, permitting binding only after specific chromatin remodeling events. The fundamental processes in living cells, including transcription, replication, repair, and recombination, are thus regulated by chromatin structure through ATP-dependent remodeling, histone variant incorporation, and various covalent histone modifications including phosphorylation, acetylation, and ubiquitination. These modifications, particularly involving histone variant H2AX, furthermore play crucial roles in DNA damage responses by enabling repair protein's access to damaged DNA. Chromatin also stabilizes the genome by regulating DNA repair mechanisms while suppressing damage from endogenous and exogenous sources. Environmental factors such as ionizing radiations induce DNA damage, and if repair is compromised, can lead to chromosomal abnormalities and gene amplifications as observed in several tumor types. Consequently, chromatin architecture controls the genome fidelity and activity: it orchestrates correct gene expression, genomic integrity, DNA repair, transcription, replication, and recombination. This review considers connecting chromatin organization to functional outcomes impacting transcription, DNA repair and genomic integrity as an emerging grand challenge for predictive molecular cell biology.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu and Kashmir, India.
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu and Kashmir, India
| | - Aindrila Kabiraj
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, BARC Training School Complex, Mumbai, Maharashtra, India
| | - Raj K Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Keneth S Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, BARC Training School Complex, Mumbai, Maharashtra, India
| | - Shreya Sopori
- Centre for Molecular Biology, Central University of Jammu, Jammu and Kashmir, India
| | - Parthas S Sarkar
- Department of Neurobiology and Neurology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Arti Dhar
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Telangana, India
| | | | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, BARC Training School Complex, Mumbai, Maharashtra, India.
| | - John A Tainer
- Department of Molecular & Cellular Oncology and Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, Texas, USA
| | - Tej K Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA.
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12
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Yuan Z. From Origin to the Present: Establishment, Mechanism, Evolutions and Biomedical Applications of the CRISPR/Cas-Based Macromolecular System in Brief. Molecules 2025; 30:947. [PMID: 40005257 PMCID: PMC11858448 DOI: 10.3390/molecules30040947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/10/2025] [Accepted: 02/17/2025] [Indexed: 02/27/2025] Open
Abstract
Advancements in biological and medical science are intricately linked to the biological central dogma. In recent years, gene editing techniques, especially CRISPR/Cas systems, have emerged as powerful tools for modifying genetic information, supplementing the central dogma and holding significant promise for disease diagnosis and treatment. Extensive research has been conducted on the continuously evolving CRISPR/Cas systems, particularly in relation to challenging diseases, such as cancer and HIV infection. Consequently, the integration of CRISPR/Cas-based techniques with contemporary medical approaches and therapies is anticipated to greatly enhance healthcare outcomes for humans. This review begins with a brief overview of the discovery of the CRISPR/Cas system. Subsequently, using CRISPR/Cas9 as an example, a clear description of the classical molecular mechanism underlying the CRISPR/Cas system was given. Additionally, the development of the CRISPR/Cas system and its applications in gene therapy and high-sensitivity disease diagnosis were discussed. Furthermore, we address the prospects for clinical applications of CRISPR/Cas-based gene therapy, highlighting the ethical considerations associated with altering genetic information. This brief review aims to enhance understanding of the CRISPR/Cas macromolecular system and provide insight into the potential of genetic macromolecular drugs for therapeutic purposes.
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Affiliation(s)
- Zheng Yuan
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100022, China
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13
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Shao C, Zhou H, Chen C, Dettman EJ, Ren Y, Cristescu R, Gozman A, Jin F. Prevalence of Homologous Recombination Repair Mutations and Association with Clinical Outcomes in Patients with Solid Tumors: A Study Using the AACR Project GENIE Dataset. Cancers (Basel) 2025; 17:577. [PMID: 40002171 PMCID: PMC11852487 DOI: 10.3390/cancers17040577] [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: 12/17/2024] [Revised: 01/28/2025] [Accepted: 02/04/2025] [Indexed: 02/27/2025] Open
Abstract
BACKGROUND/OBJECTIVES Mutations in BRCA1 and/or BRCA2 (BRCAm) and other homologous recombination repair genes (HRRm) are associated with several cancers. We evaluated the prevalence and association with overall survival (OS) of somatic BRCAm and HRRm among patients with advanced solid tumors. METHODS We used deidentified data from the AACR GENIE Biopharma Collaborative dataset derived from patients with tumors genotyped using next-generation sequencing between 1 January 2014 and 31 December 2017. Eligible patients were aged ≥18 years diagnosed with non-small-cell lung, colorectal, breast, bladder, prostate, or pancreatic cancer, with documented BRCA/HRR somatic mutation status. The primary analysis was OS (censored at the start of poly[ADP ribose] polymerase inhibitors [PARPi]/immunotherapy) after initiation of second-line therapy since most patients had sequencing after first-line therapy. RESULTS Among eligible patients, 242/7022 (3.4%) had BRCAm and 477/5474 (8.7%) had HRRm. Adjusted OS HRs (95% CI) for the primary analysis (using the initiation of second-line therapy as index date) were 0.79 (0.61-1.03) with/without BRCAm (n = 116/n = 3394) and 0.83 (0.69-0.99) with/without HRRm (n = 247/n = 2656); in sensitivity analysis of patients with stage IV disease, HRs were 0.97 (0.68-1.38) with/without BRCAm (n = 58/n = 1847) and 0.92 (0.73-1.18) with/without HRRm (n = 132/n = 1488). CONCLUSIONS Overall, BRCAm and HRRm did not show a strong association with OS, with a trend toward longer OS among patients receiving standard second-line therapies excluding PARPi/immunotherapy.
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Affiliation(s)
- Changxia Shao
- Merck & Co., Inc., Rahway, NJ 07065, USA; (H.Z.); (C.C.); (E.J.D.); (Y.R.); (R.C.); (A.G.); (F.J.)
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14
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Lu H, Wise SS, Toyoda JH, Speer RM, Croom-Perez TJ, Meaza I, Kouokam JC, Wise JY, Hoyle G, Chen N, Wise JP, Kondo K, Toba H, Takizawa H, Wise JP. Particulate hexavalent chromium exposure induces DNA double-strand breaks and inhibits homologous recombination repair in rat and human lung tissues. CHEMOSPHERE 2025; 370:143982. [PMID: 39701314 PMCID: PMC11750071 DOI: 10.1016/j.chemosphere.2024.143982] [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: 06/05/2024] [Revised: 12/04/2024] [Accepted: 12/16/2024] [Indexed: 12/21/2024]
Abstract
Lung cancer is an important human health concern because of its high mortality rate, with many cases caused by environmental chemicals other than tobacco. Particulate hexavalent chromium [Cr(VI)] is a well-established human lung carcinogen, but how Cr(VI) induces lung cancer is poorly understood. Chromosome instability, a hallmark of lung cancer, is considered a major driving factor in Cr(VI)-induced lung cancer. Our previous studies in cultured human lung cells showed that particulate Cr(VI) induces DNA double-strand breaks during the late S and G2 phases of the cell cycle, which are repaired by homologous recombination, one of the main repair pathways of DNA double-strand breaks. Our previous data showed that prolonged exposure to Cr(VI) inhibits homologous recombination repair by targeting RAD51, a key protein that mediates homologous recombination. Therefore, particulate Cr(VI)-induced DNA damage combined with failure of DNA repair can lead to chromosome instability. In this study we translated these results to rat lung tissue and lung tumor tissue from Cr(VI)-exposed workers. Wistar rats were exposed to zinc chromate in a saline solution or saline alone by oropharyngeal aspiration with a single dose repeated weekly for 90 days. We observed DNA double-strand breaks increased in a concentration-dependent manner, but homologous recombination repair decreased in rat lungs after 90 days of exposure. Notably, these effects were more pronounced in bronchioles than alveoli. We also considered these effects in Cr(VI)-associated human lung tumors and observed increased DNA double-strand breaks and reduced RAD51 levels in lung tumor tissue compared with adjacent normal lung tissue. Thus, Cr(VI)-induced induction of DNA double-strand breaks, and inhibition of homologous recombination repair translates from cultured cells to experimental animals, normal lung tissue adjacent to the tumor, and Cr(VI)-associated human lung tumors.
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Affiliation(s)
- Haiyan Lu
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - Sandra S. Wise
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - Jennifer H. Toyoda
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - Rachel M. Speer
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - Tayler J Croom-Perez
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - Idoia Meaza
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - J. Calvin Kouokam
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - Jamie Young Wise
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292
| | - Gary Hoyle
- Environmental and Occupational Health Sciences, University of Louisville, Louisville, Kentucky 40292
| | - Ning Chen
- Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, Division of Environmental Medicine, Department of Medicine, University of Louisville, Louisville, Kentucky 40292
| | - John Pierce Wise
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292
- Pediatric Research Institute, University of Louisville, Louisville, Kentucky 40292
| | - Kazuya Kondo
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University Tokushima, Japan
| | - Hiroaki Toba
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University Tokushima, Japan
| | - Hiromitsu Takizawa
- Department of Thoracic, Endocrine Surgery and Oncology, Graduate School of Biomedical Sciences, Tokushima University Tokushima, Japan
| | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky 40292
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292
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15
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Liu J, Gore S, Heyer WD. Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments. Nucleic Acids Res 2025; 53:gkaf052. [PMID: 39898551 PMCID: PMC11788929 DOI: 10.1093/nar/gkaf052] [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: 05/08/2024] [Revised: 01/16/2025] [Accepted: 01/24/2025] [Indexed: 02/04/2025] Open
Abstract
Homologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and DNA strand exchange in recombinational DNA repair. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) to ascertain the density map of the wild-type budding yeast Rad51-ssDNA filament bound to ADP-AlF3, achieving a resolution of 2.35 Å without imposing helical symmetry. The model assigned 6 Rad51 protomers, 24 nt of DNA, and 6 bound ADP-AlF3. It shows 6-fold symmetry implying monomeric building blocks, unlike the structure of the Rad51-I345T mutant filament with three-fold symmetry implying dimeric building blocks, for which the structural comparisons provide a satisfying mechanistic explanation. This image analysis enables comprehensive comparisons of individual Rad51 protomers within the filament and reveals local conformational movements of amino acid side chains. Notably, R293 in Loop 1 adopts multiple conformations to facilitate L296 and V331 in separating and twisting the DNA triplets. We also analyzed the crystal structure of Rad51-I345T and the predicted structure of yeast Rad51-K342E using the Rad51-ssDNA structure from this study as a reference.
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Affiliation(s)
- Jie Liu
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA 95616-8665, United States
| | - Steven K Gore
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA 95616-8665, United States
| | - Wolf-Dietrich Heyer
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA 95616-8665, United States
- Department of Molecular & Cellular Biology, University of California, Davis, Davis CA 95616-8665, United States
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16
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Corrigan RR, Mashburn-Warren LM, Yoon H, Bedrosian TA. Somatic Mosaicism in Brain Disorders. ANNUAL REVIEW OF PATHOLOGY 2025; 20:13-32. [PMID: 39227323 DOI: 10.1146/annurev-pathmechdis-111523-023528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Research efforts over the past decade have defined the genetic landscape of somatic variation in the brain. Neurons accumulate somatic mutations from development through aging with potentially profound functional consequences. Recent studies have revealed the contribution of somatic mosaicism to various brain disorders including focal epilepsy, neuropsychiatric disease, and neurodegeneration. One notable finding is that the effect of somatic mosaicism on clinical outcomes can vary depending on contextual factors, such as the developmental origin of a variant or the number and type of cells affected. In this review, we highlight current knowledge regarding the role of somatic mosaicism in brain disorders and how biological context can mediate phenotypes. First, we identify the origins of brain somatic variation throughout the lifespan of an individual. Second, we explore recent discoveries that suggest somatic mosaicism contributes to various brain disorders. Finally, we discuss neuropathological associations of brain mosaicism in different biological contexts and potential clinical utility.
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Affiliation(s)
- Rachel R Corrigan
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA;
| | | | - Hyojung Yoon
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA;
| | - Tracy A Bedrosian
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA;
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17
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Samsa WE, Zhang Z, Gong Z. CBFβ Regulates RUNX3 ADP-Ribosylation to Mediate Homologous Recombination Repair. J Cell Physiol 2025; 240:e31503. [PMID: 39696918 DOI: 10.1002/jcp.31503] [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: 07/17/2024] [Revised: 11/09/2024] [Accepted: 12/02/2024] [Indexed: 12/20/2024]
Abstract
RUNX3 is a master developmental transcriptional factor that has been implicated as a tumor suppressor in many cancers. However, the exact role of RUNX3 in cancer pathogenesis remains to be completely elucidated. Recently, it has emerged that RUNX3 is involved in the DNA damage response. Here, we demonstrate that heterodimerization of RUNX3 with CBFβ is necessary for its stability by protecting RUNX3 from RUNX3 ADP-ribosylation-dependent ubiquitination and degradation. We further identify new amino acid residues that are targets for PARylation and demonstrate that RUNX3 PARylation at these residues is necessary for localization of RUNX3 to DNA double strand break sites (DBSs). We also demonstrate that both RUNX3 PARylation and CBFβ heterodimerization with RUNX3 positively regulates homologous recombination (HR) repair, in part by promoting the recruitment of CtIP and phospho-RPA2 to the DBSs to mediate HR repair. In summary, we provide evidence that RUNX3 regulates HR repair activity in a PARylation-dependent manner.
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Affiliation(s)
- William E Samsa
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Zhen Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
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18
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Fan J, Wei PL, Li Y, Zhang S, Ren Z, Li W, Yin WB. Developing filamentous fungal chassis for natural product production. BIORESOURCE TECHNOLOGY 2025; 415:131703. [PMID: 39477163 DOI: 10.1016/j.biortech.2024.131703] [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: 06/18/2024] [Revised: 10/09/2024] [Accepted: 10/23/2024] [Indexed: 11/07/2024]
Abstract
The growing demand for green and sustainable production of high-value chemicals has driven the interest in microbial chassis. Recent advances in synthetic biology and metabolic engineering have reinforced filamentous fungi as promising chassis cells to produce bioactive natural products. Compared to the most used model organisms, Escherichia coli and Saccharomyces cerevisiae, most filamentous fungi are natural producers of secondary metabolites and possess an inherent pre-mRNA splicing system and abundant biosynthetic precursors. In this review, we summarize recent advances in the application of filamentous fungi as chassis cells. Emphasis is placed on strategies for developing a filamentous fungal chassis, including the establishment of mature genetic manipulation and efficient genetic tools, the catalogue of regulatory elements, and the optimization of endogenous metabolism. Furthermore, we provide an outlook on the advanced techniques for further engineering and application of filamentous fungal chassis.
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Affiliation(s)
- Jie Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
| | - Peng-Lin Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuanyuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shengquan Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zedong Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China.
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19
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Yoshioka S, Kurazono H, Ohshita K, Fukui K, Takemura M, Kato SI, Ohnishi K, Yano T, Wakamatsu T. The HNH endonuclease domain of the giant virus MutS7 specifically binds to branched DNA structures with single-stranded regions. DNA Repair (Amst) 2025; 145:103804. [PMID: 39742574 DOI: 10.1016/j.dnarep.2024.103804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 12/12/2024] [Accepted: 12/20/2024] [Indexed: 01/03/2025]
Abstract
Most giant viruses including Mimiviridae family build large viral factories within the host cytoplasms. These giant viruses are presumed to possess specific genes that enable the rapid and massive replication of their large double-stranded DNA genomes within viral factories. It has been revealed that a functionally uncharacterized protein, MutS7, is expressed during the operational phase of the viral factory. MutS7 contains an N-terminal mismatched DNA-binding domain, which is similar to the mismatched DNA-recognizing protein MutS1, and a unique C-terminal HNH endonuclease domain absent in other MutS family proteins. MutS7 gene of the genus Mimivirus of the family Mimiviridae is encoded in the locus that is responsible for resistance against infection of a virophage. In the present study, we characterized the MutS7 HNH domain of Mimivirus shirakomae. The HNH domain preferentially bound to branched DNA structures containing single-stranded regions, especially the displacement-loop structure, which is a primary intermediate in homologous/homeologous recombination, rather than to linear DNAs and branched DNAs lacking single-stranded regions. However, the HNH domain exhibited no endonuclease activity. The site-directed mutagenesis analysis revealed that the Cys4-type zinc finger of the HNH domain was not essential, but was important for the DNA binding. Given that giant virus MutS7 contains a mismatch-binding domain in addition to the HNH domain, we propose that giant virus MutS7 may suppress homeologous recombination in the viral factory.
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Affiliation(s)
- Satoshi Yoshioka
- Agriculture and Marine Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Hirochika Kurazono
- Agriculture and Marine Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Koki Ohshita
- Agricultural Science, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Kenji Fukui
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka 569-8686, Japan
| | - Masaharu Takemura
- Department of Mathematics and Science Education, Graduate School of Science, Tokyo University of Science, Shinjuku, Tokyo 162-8601, Japan
| | - Shin-Ichiro Kato
- Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka 569-8686, Japan
| | - Taisuke Wakamatsu
- Agriculture and Marine Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan; Agricultural Science, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
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20
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Choi S, Shin M, Kim WY. Targeting the DNA damage response (DDR) of cancer cells with natural compounds derived from Panax ginseng and other plants. J Ginseng Res 2025; 49:1-11. [PMID: 39872282 PMCID: PMC11764321 DOI: 10.1016/j.jgr.2024.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 01/30/2025] Open
Abstract
DNA damage is a driver of cancer formation, leading to the impairment of repair mechanisms in cancer cells and rendering them susceptible to DNA-damaging therapeutic approaches. The concept of "synthetic lethality" in cancer clinics has emerged, particularly with the use of PARP inhibitors and the identification of DNA damage response (DDR) mutation biomarkers, emphasizing the significance of targeting DDR in cancer therapy. Novel approaches aimed at genome maintenance machinery are under development to further enhance the efficacy of cancer treatments. Natural compounds from traditional medicine, renowned for their anti-aging and anticarcinogenic properties, have garnered attention. Ginseng-derived compounds, in particular, exhibit anti-carcinogenic effects by suppressing reactive oxygen species (ROS) and protecting cells from DNA damage-induced carcinogenesis. However, the anticancer therapeutic effect of ginseng compounds has also been demonstrated by inducing DNA damage and blocking DDR. This review concentrates on the biphasic effects of ginseng compounds on DNA mutations-both inhibiting mutation accumulation and impairing DNA repair. Additionally, it explores other natural compounds targeting DDR directly, providing potential insights into enhancing cancer therapy efficacy.
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Affiliation(s)
- SeokGyeong Choi
- College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Minwook Shin
- College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Woo-Young Kim
- College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
- Muscle Physiome Research Center, Sookmyung Women's University, Seoul, Republic of Korea
- Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea
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21
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Chu SSH, Xing G, Jha VK, Ling H. The Shu complex is an ATPase that regulates Rad51 filaments during homologous recombination in the DNA damage response. DNA Repair (Amst) 2025; 145:103792. [PMID: 39647428 DOI: 10.1016/j.dnarep.2024.103792] [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: 06/05/2024] [Revised: 11/15/2024] [Accepted: 11/24/2024] [Indexed: 12/10/2024]
Abstract
Rad51 filaments are Rad51-coated single-stranded DNA and essential in homologous recombination (HR). The yeast Shu complex (Shu) is a conserved regulator of homologous recombination, working through its modulation on Rad51 filaments to direct HR-associated DNA damage response. However, the biochemical properties of Shu remain unclear, which hinders molecular insights into Shu's role in HR and the DNA damage response. In this work, we biochemically characterized Shu and analyzed its molecular actions on single-stranded DNA and Rad51 filaments. First, we revealed that Shu preferentially binds fork-shaped DNA with 20nt ssDNA components. Then, we identified and validated, through site-specific mutagenesis, that Shu is an ATPase and hydrolyzes ATP in a DNA-dependent manner. Furthermore, we showed that Shu interacts with ssDNA and Rad51 filaments and alters the properties of ssDNA and the filaments with a 5'-3' polarity. The alterations depend on the ATP hydrolysis of Shu, suggesting that the ATPase activity of Shu is important in regulating its functions. The preference of Shu for acting on the 5' end of Rad51 filaments aligns with the observation that Shu promotes lesion bypass at the lagging strand of a replication fork. Our work on Shu, a prototype modulator of Rad51 filaments in eukaryotes, provides a general molecular mechanism for Rad51-mediated error-free DNA lesion bypass.
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Affiliation(s)
- Sam S H Chu
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Guangxin Xing
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Vikash K Jha
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Hong Ling
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada.
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22
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Tang J, Nakamura M, Ng WY, Feng N, Ueno M. Novel pof1 mutation suppresses the sensitivity to DNA replication inhibitor in fission yeast RecQ helicase mutant. Biochem Biophys Res Commun 2024; 741:151014. [PMID: 39580958 DOI: 10.1016/j.bbrc.2024.151014] [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: 11/08/2024] [Accepted: 11/15/2024] [Indexed: 11/26/2024]
Abstract
Homologous recombination is vital for DNA double-strand break repair. Dysfunction in homologous recombination can lead to cell death, mutations, and cancer. In fission yeast (Schizosaccharomyces pombe), RecQ helicase Rqh1 resolves recombination intermediates. We found that rqh1-hd strain impaired growth in media containing hydroxyurea and thiabendazole. Using this condition, we identified a novel pof1 mutation (pof1-A81T) that suppress the poor growth of the rqh1-hd strain on the plate containing hydroxyurea and thiabendazole. Compared to rqh1-hd, rqh1-hd pof1-A81T cells displayed reduced Replication Protein A foci on chromosome bridges after hydroxyurea treatment. This suggests that pof1-A81T mutation suppresses the accumulation of recombination intermediates in hydroxyurea-treated rqh1-hd cells. Additionally, pof1-A81T mutation rescued the segregation defect of nucleolar protein Gar2 observed in hydroxyurea-treated rqh1-hd cells, potentially by mitigating recombination intermediate accumulation in rDNA. These results suggest that the pof1-A81T mutation suppresses the accumulation of recombination intermediates, particularly in rDNA, and alleviates the rqh1 deficiency phenotype in S. pombe.
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Affiliation(s)
- Jiashen Tang
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Mikio Nakamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Wai Yee Ng
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Naiwen Feng
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Masaru Ueno
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan.
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23
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Gehrke L, Gonçalves VDR, Andrae D, Rasko T, Ho P, Einsele H, Hudecek M, Friedel SR. Current Non-Viral-Based Strategies to Manufacture CAR-T Cells. Int J Mol Sci 2024; 25:13685. [PMID: 39769449 PMCID: PMC11728233 DOI: 10.3390/ijms252413685] [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: 11/19/2024] [Revised: 12/12/2024] [Accepted: 12/14/2024] [Indexed: 01/16/2025] Open
Abstract
The successful application of CAR-T cells in the treatment of hematologic malignancies has fundamentally changed cancer therapy. With increasing numbers of registered CAR-T cell clinical trials, efforts are being made to streamline and reduce the costs of CAR-T cell manufacturing while improving their safety. To date, all approved CAR-T cell products have relied on viral-based gene delivery and genomic integration methods. While viral vectors offer high transfection efficiencies, concerns regarding potential malignant transformation coupled with costly and time-consuming vector manufacturing are constant drivers in the search for cheaper, easier-to-use, safer, and more efficient alternatives. In this review, we examine different non-viral gene transfer methods as alternatives for CAR-T cell production, their advantages and disadvantages, and examples of their applications. Transposon-based gene transfer methods lead to stable but non-targeted gene integration, are easy to handle, and achieve high gene transfer rates. Programmable endonucleases allow targeted integration, reducing the potential risk of integration-mediated malignant transformation of CAR-T cells. Non-integrating CAR-encoding vectors avoid this risk completely and achieve only transient CAR expression. With these promising alternative techniques for gene transfer, all avenues are open to fully exploiting the potential of next-generation CAR-T cell therapy and applying it in a wide range of applications.
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Affiliation(s)
- Leon Gehrke
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Vasco Dos Reis Gonçalves
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Dominik Andrae
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Tamas Rasko
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Patrick Ho
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
| | - Michael Hudecek
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
- Fraunhofer-Institut für Zelltherapie und Immunologie, Außenstelle Zelluläre Immuntherapie, 97070 Würzburg, Germany
| | - Sabrina R. Friedel
- Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum Würzburg, 97080 Würzburg, Germany
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24
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Zhai Z, Cui Z, Zhang Y, Song P, Wu J, Tan Z, Lin S, Ma X, Guan F, Kang H. Integrated pan-cancer analysis and experimental verification of the roles of meiotic nuclear divisions 1 in breast cancer. Biochem Biophys Res Commun 2024; 739:150600. [PMID: 39191147 DOI: 10.1016/j.bbrc.2024.150600] [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: 07/11/2024] [Revised: 08/08/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION The aberrant up-regulation of meiotic nuclear division 1 (MND1) in somatic cells is considered as one of the driving factors of oncogenesis, whereas its expression and role in breast invasive cancer (BRCA) remain unclear. Hence, this study embarked on a comprehensive evaluation of MND1 across various cancers and identified its roles in BRCA. METHODS Based on publicly available databases, including but not limited to UCSC Xena, TCGA, GTEx, GEO, STRING, GeneMANIA, and CancerSEA, we evaluated the expression patterns, genomic features, and biological functions of MND1 from a pan-cancer viewpoint and delved into the implications of MND1 in the prognosis and treatment of BRCA. Further molecular biology experiments were undertaken to identify the role of MND1 in proliferation, migration, and apoptosis in BRCA cells. RESULTS Elevated levels of MND1 were notably observed in a wide array of tumor types, especially in BRCA, COAD, HNSC, LIHC, LUAD, LUSC, STAD, and UCEC. Elevated MND1 expression was markedly associated with shortened OS in several tumors, including BRCA (HR = 1.52 [95%CI, 1.10-2.09], P = 0.011). The up-regulation of MND1 in BRCA was validated in external cohorts and clinical samples. Survival analyses demonstrated that elevated MND1 expression was associated with decreased survival for patients with BRCA. Co-expressed genes of MND1 were identified, and subsequent pathway analyses based on significantly associated genes indicated that MND1 plays key roles in DNA replication, cell cycle regulation, and DNA damage repair. The observed abnormal elevation and activation of MND1 led to increased proliferation and migration, along with decreased apoptosis in BRCA cells. CONCLUSIONS MND1 emerges as a promising biomarker for diagnostic and therapeutic targeting in various cancers, including BRCA. The abnormal up-regulation and activation of MND1 are linked to carcinogenesis and poor prognosis among BRCA patients, which may be attributed to its involvement in HR-dependent ALT, warranting further scrutiny.
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Affiliation(s)
- Zhen Zhai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Zhiwei Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi' an, China
| | - Yu Zhang
- Department of Infectious Diseases, Honghui-hospital, Xi'an Jiaotong University, Shanghua Road, Xi'an, China
| | - Ping Song
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 157, West Fifth Road, Xi'an, China
| | - Jinpeng Wu
- College of Life Sciences, Northwest University, No. 229, Taibai North Road, Xi'an, China
| | - Zengqi Tan
- Institute of Hematology, Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, No. 229, Taibai North Road, Xi'an, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China
| | - Feng Guan
- College of Life Sciences, Northwest University, No. 229, Taibai North Road, Xi'an, China.
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China; Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, West Fifth Road, Xi'an, China.
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25
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Kyriukha Y, Watkins MB, Redington JM, Chintalapati N, Ganti A, Dastvan R, Uversky VN, Hopkins JB, Pozzi N, Korolev S. The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction. iScience 2024; 27:111259. [PMID: 39584160 PMCID: PMC11582789 DOI: 10.1016/j.isci.2024.111259] [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: 06/12/2024] [Revised: 08/21/2024] [Accepted: 10/23/2024] [Indexed: 11/26/2024] Open
Abstract
The partner and localizer of BRCA2 (PALB2) is a scaffold protein linking BRCA1 with BRCA2 and RAD51 during homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR in cells, while the PALB2 DNA-binding domain (PALB2-DBD) supports DNA strand exchange in vitro. We determined that PALB2-DBD is intrinsically disordered beyond a single N-terminal α-helix. Coiled-coil mediated dimerization is stabilized by interaction between intrinsically disordered regions (IDRs) leading to a 2-fold structural compaction. Single-stranded (ss)DNA binding promotes additional structural compaction and protein tetramerization. Using confocal single-molecule FRET, we observed bimodal and oligomerization-dependent compaction of ssDNA bound to PALB2-DBD, suggesting a novel strand exchange mechanism. Bioinformatics analysis and preliminary observations indicate that PALB2 forms protein-nucleic acids condensates. Intrinsically disordered DBDs are prevalent in the human proteome. PALB2-DBD and similar IDRs may use a chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.
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Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | - Maxwell B. Watkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Jennifer M. Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | - Nithya Chintalapati
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | - Abhishek Ganti
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jesse B. Hopkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, USA
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26
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Mazzarotti G, Cuomo M, Ragosta MC, Russo A, D’Angelo M, Medugno A, Napolitano GM, Iannuzzi CA, Forte IM, Camerlingo R, Burk S, Errichiello F, Frusciante L, Forino M, Campitiello MR, De Laurentiis M, Giordano A, Alfano L. Oleanolic Acid Modulates DNA Damage Response to Camptothecin Increasing Cancer Cell Death. Int J Mol Sci 2024; 25:13475. [PMID: 39769237 PMCID: PMC11676975 DOI: 10.3390/ijms252413475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/04/2025] Open
Abstract
Targeting DNA damage response (DDR) pathways represents one of the principal approaches in cancer therapy. However, defects in DDR mechanisms, exhibited by various tumors, can also promote tumor progression and resistance to therapy, negatively impacting patient survival. Therefore, identifying new molecules from natural extracts could provide a powerful source of novel compounds for cancer treatment strategies. In this context, we investigated the role of oleanolic acid (OA), identified in fermented Aglianico red grape pomace, in modulating the DDR in response to camptothecin (CPT), an inhibitor of topoisomerase I. Specifically, we found that OA can influence the choice of DNA repair pathway upon CPT treatment, shifting the repair process from homologous recombination gene conversion to single-strand annealing. Moreover, our data demonstrate that combining sub-lethal concentrations of OA with CPT enhances the efficacy of topoisomerase I inhibition compared to CPT alone. Overall, these findings highlight a new role for OA in the DDR, leading to a more mutagenic DNA repair pathway and increased sensitivity in the HeLa cancer cell line.
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Affiliation(s)
- Giulio Mazzarotti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Maria Cuomo
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | | | - Andrea Russo
- Clinical and Translational Oncology Program, Scuola Superiore Meridionale (SSM, School of Advanced Studies), University of Naples Federico II, 80131 Naples, Italy
| | - Margherita D’Angelo
- Unit of Dietetics and Sports Medicine, Department of Experimental Medicine, Section of Human Physiology, Università degli Studi della Campania “Luigi Vanvitelli”, 80122 Naples, Italy
| | - Annamaria Medugno
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Giuseppe Maria Napolitano
- Clinical and Translational Oncology Program, Scuola Superiore Meridionale (SSM, School of Advanced Studies), University of Naples Federico II, 80131 Naples, Italy
| | - Carmelina Antonella Iannuzzi
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Iris Maria Forte
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Rosa Camerlingo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Sharon Burk
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesco Errichiello
- Department of Agricultural Sciences, Grape and Wine Science Division, University of Napoli Federico II, 83100 Avellino, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, Grape and Wine Science Division, University of Napoli Federico II, 83100 Avellino, Italy
| | - Martino Forino
- Department of Agricultural Sciences, Grape and Wine Science Division, University of Napoli Federico II, 83100 Avellino, Italy
| | - Maria Rosaria Campitiello
- Department of Obstetrics and Gynecology and Physiopathology of Human Reproduction, ASL Salerno, 84124 Salerno, Italy
| | - Michelino De Laurentiis
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Bldg. Suite 333, 1900 N 12th Street, Philadelphia, PA 19122, USA
| | - Luigi Alfano
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
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27
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Uchigashima M, Mikuni T. Single-cell synaptome mapping: its technical basis and applications in critical period plasticity research. Front Neural Circuits 2024; 18:1523614. [PMID: 39726910 PMCID: PMC11670323 DOI: 10.3389/fncir.2024.1523614] [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: 11/06/2024] [Accepted: 11/28/2024] [Indexed: 12/28/2024] Open
Abstract
Our brain adapts to the environment by optimizing its function through experience-dependent cortical plasticity. This plasticity is transiently enhanced during a developmental stage, known as the "critical period," and subsequently maintained at lower levels throughout adulthood. Thus, understanding the mechanism underlying critical period plasticity is crucial for improving brain adaptability across the lifespan. Critical period plasticity relies on activity-dependent circuit remodeling through anatomical and functional changes at individual synapses. However, it remains challenging to identify the molecular signatures of synapses responsible for critical period plasticity and to understand how these plasticity-related synapses are spatiotemporally organized within a neuron. Recent advances in genetic tools and genome editing methodologies have enabled single-cell endogenous protein labeling in the brain, allowing for comprehensive molecular profiling of individual synapses within a neuron, namely "single-cell synaptome mapping." This promising approach can facilitate insights into the spatiotemporal organization of synapses that are sparse yet functionally important within single neurons. In this review, we introduce the basics of single-cell synaptome mapping and discuss its methodologies and applications to investigate the synaptic and cellular mechanisms underlying circuit remodeling during the critical period.
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Affiliation(s)
- Motokazu Uchigashima
- Department of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Takayasu Mikuni
- Department of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan
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28
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Khodyreva SN, Dyrkheeva NS, Lavrik OI. Proteins Associated with Neurodegenerative Diseases: Link to DNA Repair. Biomedicines 2024; 12:2808. [PMID: 39767715 PMCID: PMC11673744 DOI: 10.3390/biomedicines12122808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/15/2024] [Accepted: 11/20/2024] [Indexed: 01/11/2025] Open
Abstract
The nervous system is susceptible to DNA damage and DNA repair defects, and if DNA damage is not repaired, neuronal cells can die, causing neurodegenerative diseases in humans. The overall picture of what is known about DNA repair mechanisms in the nervous system is still unclear. The current challenge is to use the accumulated knowledge of basic science on DNA repair to improve the treatment of neurodegenerative disorders. In this review, we summarize the current understanding of the function of DNA damage repair, in particular, the base excision repair and double-strand break repair pathways as being the most important in nervous system cells. We summarize recent data on the proteins involved in DNA repair associated with neurodegenerative diseases, with particular emphasis on PARP1 and ND-associated proteins, which are involved in DNA repair and have the ability to undergo liquid-liquid phase separation.
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Affiliation(s)
- Svetlana N. Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva pr., Novosibirsk 630090, Russia;
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva pr., Novosibirsk 630090, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva pr., Novosibirsk 630090, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez pr., St. Petersburg 194223, Russia
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29
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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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30
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Joudeh LA, Schuck PL, Van NM, DiCintio AJ, Stewart JA, Waldman AS. Progerin can induce DNA damage in the absence of global changes in replication or cell proliferation. PLoS One 2024; 19:e0315084. [PMID: 39636792 PMCID: PMC11620420 DOI: 10.1371/journal.pone.0315084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 11/15/2024] [Indexed: 12/07/2024] Open
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by features of accelerated aging, and individuals with HGPS seldom live beyond their mid-teens. The syndrome is commonly caused by a point mutation in the LMNA gene which codes for lamin A and its splice variant lamin C, components of the nuclear lamina. The mutation causing HGPS leads to production of a truncated, farnesylated form of lamin A referred to as "progerin." Progerin is also expressed at low levels in healthy individuals and appears to play a role in normal aging. HGPS is associated with an accumulation of genomic DNA double-strand breaks (DSBs) and alterations in the nature of DSB repair. The source of DSBs in HGPS is often attributed to stalling and subsequent collapse of replication forks in conjunction with faulty recruitment of repair factors to damage sites. In this work, we used a model system involving immortalized human cell lines to investigate progerin-induced genomic damage. Using an immunofluorescence approach to visualize phosphorylated histone H2AX foci which mark sites of genomic damage, we report that cells engineered to express progerin displayed a significant elevation of endogenous damage in the absence of any change in the cell cycle profile or doubling time of cells. Genomic damage was enhanced and persistent in progerin-expressing cells treated with hydroxyurea. Overexpression of wild-type lamin A did not elicit the outcomes associated with progerin expression. Our results show that DNA damage caused by progerin can occur independently from global changes in replication or cell proliferation.
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Affiliation(s)
- Liza A. Joudeh
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - P. Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Nina M. Van
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Alannah J. DiCintio
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Jason A. Stewart
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Alan S. Waldman
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
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31
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Gilioli G, Lankester AC, de Kivit S, Staal FJT, Ott de Bruin LM. Gene therapy strategies for RAG1 deficiency: Challenges and breakthroughs. Immunol Lett 2024; 270:106931. [PMID: 39303994 DOI: 10.1016/j.imlet.2024.106931] [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: 07/23/2024] [Revised: 09/14/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
Mutations in the recombination activating genes (RAG) cause various forms of immune deficiency. Hematopoietic stem cell transplantation (HSCT) is the only cure for patients with severe manifestations of RAG deficiency; however, outcomes are suboptimal with mismatched donors. Gene therapy aims to correct autologous hematopoietic stem and progenitor cells (HSPC) and is emerging as an alternative to allogeneic HSCT. Gene therapy based on viral gene addition exploits viral vectors to add a correct copy of a mutated gene into the genome of HSPCs. Only recently, after a prolonged phase of development, viral gene addition has been approved for clinical testing in RAG1-SCID patients. In the meantime, a new technology, CRISPR/Cas9, has made its debut to compete with viral gene addition. Gene editing based on CRISPR/Cas9 allows to perform targeted genomic integrations of a correct copy of a mutated gene, circumventing the risk of virus-mediated insertional mutagenesis. In this review, we present the biology of the RAG genes, the challenges faced during the development of viral gene addition for RAG1-SCID, and the current status of gene therapy for RAG1 deficiency. In particular, we highlight the latest advances and challenges in CRISPR/Cas9 gene editing and their potential for the future of gene therapy.
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Affiliation(s)
- Giorgio Gilioli
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arjan C Lankester
- Department of Pediatrics, Pediatric Stem Cell Transplantation Program and Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, the Netherlands
| | - Sander de Kivit
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Lisa M Ott de Bruin
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands; Department of Pediatrics, Pediatric Stem Cell Transplantation Program and Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, the Netherlands
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32
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Chen J, Miao Z, Kong D, Zhang A, Wang F, Liu G, Yu X, Luo L, Liu Y. Application of CRISPR/Cas9 Technology in Rice Germplasm Innovation and Genetic Improvement. Genes (Basel) 2024; 15:1492. [PMID: 39596692 PMCID: PMC11593773 DOI: 10.3390/genes15111492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 11/11/2024] [Accepted: 11/19/2024] [Indexed: 11/29/2024] Open
Abstract
Improving the efficiency of germplasm innovation has always been the aim of rice breeders. Traditional hybrid breeding methods for variety selection rarely meet the practical needs of rice production. The emergence of genome-editing technologies, such as CRISPR/Cas9, provides a new approach to the genetic improvement of crops such as rice. The number of published scientific papers related to "gene editing" and "CRISPR/Cas9" retrievable on websites both from China and other countries exhibited an increasing trend, year by year, from 2014 to 2023. Research related to gene editing in rice accounts for 33.4% and 12.3% of all the literature on gene editing published in China and other countries, respectively, much higher than that on maize and wheat. This article reviews recent research on CRISPR/Cas9 gene-editing technology in rice, especially germplasm innovation and genetic improvement of commercially promoted varieties with improved traits such as disease, insect, and herbicide resistance, salt tolerance, quality, nutrition, and safety. The aim is to provide a reference for the precise and efficient development of new rice cultivars that meet market demand.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yi Liu
- Shanghai Agrobiological Gene Center, Shanghai 201106, China; (J.C.); (Z.M.)
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Zhang L, Wang D, Li Z, Lin G, Li J, Zhang R. Interlaboratory consistency of SDC2 promoter methylation detection in colorectal cancer using the post-optimized materials. iScience 2024; 27:111177. [PMID: 39569371 PMCID: PMC11577190 DOI: 10.1016/j.isci.2024.111177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/05/2024] [Accepted: 10/14/2024] [Indexed: 11/22/2024] Open
Abstract
Fecal DNA-based Syndecan 2 (SDC2) methylation detection is a promising non-invasive strategy for early colorectal cancer (CRC) screening. In China, commercial assays for SDC2 methylation detection vary in sensitivity and specificity, yet there is no standardized external quality assessment (EQA) to ensure accuracy. This study utilized CRISPR-Cas9 and homology-directed repair (HDR) technologies to edit the SDC2 promoter in 293T cells, creating hypermethylated and heterogeneous cell lines. These cell lines were used to develop an EQA panel for SDC2 methylation. We established a 10-sample panel, encompassing a range of methylation levels, and conducted an EQA across 140 laboratories. Among 1,400 results, 0.57% were incorrect. The optimized EQA materials effectively monitor the accuracy of SDC2 methylation detection in CRC, supporting reliable and consistent clinical testing and contributing to early CRC screening and diagnosis in China.
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Affiliation(s)
- Lijing Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Ziqiang Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, Beijing, P.R. China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
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34
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Watanabe K, Yamamoto T, Fujita T, Hino S, Hino Y, Yamazaki K, Ohashi Y, Sakuraba S, Kono H, Nakao M, Ochiai K, Dan S, Saitoh N. Metabolically inducing defects in DNA repair sensitizes BRCA-wild-type cancer cells to replication stress. Sci Signal 2024; 17:eadl6445. [PMID: 39531517 DOI: 10.1126/scisignal.adl6445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/29/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024]
Abstract
Metabolic reprogramming from oxidative respiration to glycolysis is generally considered to be advantageous for tumor initiation and progression. However, we found that breast cancer cells forced to perform glycolysis acquired a vulnerability to PARP inhibitors. Small-molecule inhibition of mitochondrial respiration-using glyceollin I, metformin, or phenformin-induced overproduction of the oncometabolite lactate, which acidified the extracellular milieu and repressed the expression of homologous recombination (HR)-associated DNA repair genes. These serial events created so-called "BRCAness," in which cells exhibit an HR deficiency phenotype despite lacking germline mutations in HR genes such as BRCA1 and BRCA2, and, thus, sensitized the cancer cells to clinically available poly(ADP-ribose) polymerase inhibitors. The increase in lactate repressed HR-associated gene expression by decreasing histone acetylation. These effects were selective to breast cancer cells; normal epithelial cells retained HR proficiency and cell viability. These mechanistic insights into the BRCAness-prone properties of breast cancer cells support the therapeutic utility and cancer cell-specific potential of mitochondria-targeting drugs.
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Affiliation(s)
- Kenji Watanabe
- Division of Cancer Biology, Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Tatsuro Yamamoto
- Division of Cancer Biology, Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Tomoko Fujita
- Division of Cancer Biology, Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yuko Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Kanami Yamazaki
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Yoshimi Ohashi
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Shun Sakuraba
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 265-8522, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 265-8522, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Koji Ochiai
- PhytoMol-Tech Inc., 3-14-3 Minami-Kumamoto, Chuo-ku, Kumamoto City, Kumamoto 860-0812, Japan
| | - Shingo Dan
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
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Palermo V, Malacaria E, Semproni M, Camerini S, Casella M, Perdichizzi B, Valenzisi P, Sanchez M, Marini F, Pellicioli A, Franchitto A, Pichierri P. Switch-like phosphorylation of WRN integrates end-resection with RAD51 metabolism at collapsed replication forks. Nucleic Acids Res 2024; 52:12334-12350. [PMID: 39315694 PMCID: PMC11551760 DOI: 10.1093/nar/gkae807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/25/2024] [Accepted: 09/03/2024] [Indexed: 09/25/2024] Open
Abstract
Replication-dependent DNA double-strand breaks are harmful lesions preferentially repaired by homologous recombination (HR), a process that requires processing of DNA ends to allow RAD51-mediated strand invasion. End resection and subsequent repair are two intertwined processes, but the mechanism underlying their execution is still poorly appreciated. The WRN helicase is one of the crucial factors for end resection and is instrumental in selecting the proper repair pathway. Here, we reveal that ordered phosphorylation of WRN by the CDK1, ATM and ATR kinases defines a complex regulatory layer essential for correct long-range end resection, connecting it to repair by HR. We establish that long-range end resection requires an ATM-dependent phosphorylation of WRN at Ser1058 and that phosphorylation at Ser1141, together with dephosphorylation at the CDK1 site Ser1133, is needed for the proper metabolism of RAD51 foci and RAD51-dependent repair. Collectively, our findings suggest that regulation of WRN by multiple kinases functions as a molecular switch to allow timely execution of end resection and repair at replication-dependent DNA double-strand breaks.
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Affiliation(s)
- Valentina Palermo
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Eva Malacaria
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Maurizio Semproni
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Serena Camerini
- FAST, Core Facilities Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marialuisa Casella
- FAST, Core Facilities Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Benedetta Perdichizzi
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Pasquale Valenzisi
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Sanchez
- FAST, Core Facilities Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Federica Marini
- Department of Biosciences, Genomic Instability and Human Pathologies Section, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Achille Pellicioli
- Department of Biosciences, Genomic Instability and Human Pathologies Section, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milan, Italy
| | - Annapaola Franchitto
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Department of Environment and Health, Mechanisms, Biomarkers and Models Section, Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, Viale delle Medaglie d’Oro 305, 00134 Rome, Italy
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36
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Deveryshetty J, Mistry A, Pangeni S, Ghoneim M, Tokmina-Lukaszewska M, Kaushik V, Taddei A, Ha T, Bothner B, Antony E. Rad52 sorts and stacks Rad51 at the DNA junction to promote homologous recombination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.07.622519. [PMID: 39574592 PMCID: PMC11580989 DOI: 10.1101/2024.11.07.622519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2025]
Abstract
Homologous recombination (HR) repairs double-stranded DNA breaks (DSBs). The DSBs are resected to yield single-stranded DNA (ssDNA) that are coated by Replication Protein A (RPA). Rad51 is a recombinase and catalyzes strand invasion and the search for homology. However, it binds to ssDNA with lower affinity than RPA. Thus, mediator proteins such as Rad52/BRCA2 are required to promote Rad51 binding to RPA-coated ssDNA, but the underlying mechanisms remain poorly understood. Saccharomyces cerevisiae Rad52 interacts with Rad51 through two distinct binding modes. We here uncover that the Rad51-binding site in the disordered C-terminus of Rad52 (mode-1) sorts polydisperse Rad51 into discrete monomers. The second Rad51 binding site resides in the ordered N-terminal ring of Rad52 (mode-2), but this interaction occurs at only one position on the ring. In single molecule confocal fluorescence microscopy combined with optical tweezer analysis, we directly visualize filament formation using fluorescent-Rad51. Rad52 catalyzes Rad51 loading onto RPA-coated ssDNA, with a distinct preference for junctions, but no filament growth is observed. Deletion of the C-terminus of Rad52 results in loss of Rad51 sorting and abrogates Rad51 binding to RPA-coated DNA. While BRCA2 and Rad52 are structurally unrelated, many of these functional features are conserved. We describe a concerted Sort & Stack mechanism for mediator proteins in promoting HR.
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Affiliation(s)
- Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | - Ayush Mistry
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | - Sushil Pangeni
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21205
| | - Mohamed Ghoneim
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | | | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
| | - Angela Taddei
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Taekjip Ha
- Program in Cellular and Molecular Medicine, Childrens Hospital, Boston, MA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO 63104
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37
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Thomas MS, Pillai GS, Butler MA, Fernandez J, LaRocque JR. The epistatic relationship of Drosophila melanogaster CtIP and Rif1 in homology-directed repair of DNA double-strand breaks. G3 (BETHESDA, MD.) 2024; 14:jkae210. [PMID: 39397376 PMCID: PMC11540315 DOI: 10.1093/g3journal/jkae210] [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: 07/09/2024] [Accepted: 08/26/2024] [Indexed: 10/15/2024]
Abstract
Double-strand breaks (DSBs) are genotoxic DNA lesions that pose significant threats to genomic stability, necessitating precise and efficient repair mechanisms to prevent cell death or mutations. DSBs are repaired through nonhomologous end-joining (NHEJ) or homology-directed repair (HDR), which includes homologous recombination (HR) and single-strand annealing (SSA). CtIP and Rif1 are conserved proteins implicated in DSB repair pathway choice, possibly through redundant roles in promoting DNA end-resection required for HDR. Although the roles of these proteins have been well-established in other organisms, the role of Rif1 and its potential redundancies with CtIP in Drosophila melanogaster remain elusive. To examine the roles of DmCtIP and DmRif1 in DSB repair, this study employed the direct repeat of white (DR-white) assay, tracking across indels by decomposition (TIDE) analysis, and P{wIw_2 kb 3'} assay to track repair outcomes in HR, NHEJ, and SSA, respectively. These experiments were performed in DmCtIPΔ/Δ single mutants, DmRif1Δ/Δ single mutants, and DmRif1Δ/Δ; DmCtIPΔ/Δ double mutants. This work demonstrates significant defects in both HR and SSA repair in DmCtIPΔ/Δ and DmRif1Δ/Δ single mutants. However, experiments in DmRif1Δ/Δ; DmCtIPΔ/Δ double mutants reveal that DmCtIP is epistatic to DmRif1 in promoting HDR. Overall, this study concludes that DmRif1 and DmCtIP do not perform their activities in a redundant pathway, but rather DmCtIP is the main driver in promoting HR and SSA, most likely through its role in end resection.
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Affiliation(s)
- Makenzie S Thomas
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, D.C. 20057, USA
| | - Gautham S Pillai
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, D.C. 20057, USA
| | - Margaret A Butler
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, D.C. 20057, USA
| | - Joel Fernandez
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, D.C. 20057, USA
| | - Jeannine R LaRocque
- Department of Human Science, School of Health, Georgetown University Medical Center, Washington, D.C. 20057, USA
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38
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Hong S, Lee J, Kim Y, Kim E, Shin K. AAVS1-targeted, stable expression of ChR2 in human brain organoids for consistent optogenetic control. Bioeng Transl Med 2024; 9:e10690. [PMID: 39545087 PMCID: PMC11558186 DOI: 10.1002/btm2.10690] [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: 02/16/2024] [Revised: 04/30/2024] [Accepted: 05/23/2024] [Indexed: 11/17/2024] Open
Abstract
Self-organizing brain organoids provide a promising tool for studying human development and disease. Here we created human forebrain organoids with stable and homogeneous expression of channelrhodopsin-2 (ChR2) by generating AAVS1 safe harbor locus-targeted, ChR2 knocked-in human pluripotent stem cells (hPSCs), followed by the differentiation of these genetically engineered hPSCs into forebrain organoids. The resulting ChR2-expressing human forebrain organoids showed homogeneous cellular expression of ChR2 throughout entire regions without any structural and functional perturbations and displayed consistent and robust neural activation upon light stimulation, allowing for the non-virus mediated, spatiotemporal optogenetic control of neural activities. Furthermore, in the hybrid platform in which brain organoids are connected with spinal cord organoids and skeletal muscle spheroids, ChR2 knocked-in forebrain organoids induced strong and consistent muscle contraction upon brain-specific optogenetic stimulation. Our study thus provides a novel, non-virus mediated, preclinical human organoid system for light-inducible, consistent control of neural activities to study neural circuits and dynamics in normal and disease-specific human brains as well as neural connections between brain and other peripheral tissues.
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Affiliation(s)
- Soojung Hong
- School of Biological Sciences, College of Natural Sciences, Seoul National UniversitySeoulRepublic of Korea
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoulRepublic of Korea
| | - Juhee Lee
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoulRepublic of Korea
| | - Yunhee Kim
- School of Biological Sciences, College of Natural Sciences, Seoul National UniversitySeoulRepublic of Korea
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoulRepublic of Korea
| | - Eunjee Kim
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoulRepublic of Korea
| | - Kunyoo Shin
- School of Biological Sciences, College of Natural Sciences, Seoul National UniversitySeoulRepublic of Korea
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoulRepublic of Korea
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39
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Herrera Sandoval C, Borchers C, Aoki ST. An effective Caenorhabditis elegans CRISPR training module for high school and undergraduate summer research experiences in molecular biology. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 52:656-665. [PMID: 39072870 PMCID: PMC11568952 DOI: 10.1002/bmb.21856] [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: 09/16/2023] [Revised: 06/21/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
Engaging in research experiences as a high school or undergraduate student interested in science, technology, engineering, and mathematics (STEM) is pivotal for their academic and professional development. A structured teaching framework can help cultivate a student's curiosity and passion for learning and research. In this study, an eight-week training program was created to encompass fundamental molecular biology principles and hands-on laboratory activities. This curriculum focuses on using clustered regularly interspaced short palindromic repeats (CRISPR) gene editing in the Caenorhabditis elegans model organism. Through pre- and post-program assessments, enhancements in students' molecular biology proficiency and enthusiasm for scientific exploration were observed. Overall, this training module demonstrated its accessibility and ability to engage inexperienced students in molecular biology and gene editing methodologies.
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Affiliation(s)
- Carmen Herrera Sandoval
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
- Indiana BioMedical Gateway (IBMG) Program, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
| | - Christopher Borchers
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
- Indiana BioMedical Gateway (IBMG) Program, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
| | - Scott T Aoki
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University-Indianapolis, Indianapolis, Indiana, USA
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40
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Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse A, Sigurdsson S, Biswas G, Levy Y, Bothner B, Cooley R, Mehl R, Dastvan R, Origanti S, Antony E. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res 2024; 52:11626-11640. [PMID: 38989614 PMCID: PMC11514480 DOI: 10.1093/nar/gkae584] [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: 04/01/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and double electron-electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
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Affiliation(s)
- Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Iram Munir Ahmad
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Gargi Biswas
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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41
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Peng JC, Chang HY, Sun YL, Prentiss M, Li HW, Chi P. Hop2-Mnd1 functions as a DNA sequence fidelity switch in Dmc1-mediated DNA recombination. Nat Commun 2024; 15:9266. [PMID: 39463417 PMCID: PMC11514202 DOI: 10.1038/s41467-024-53641-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 10/17/2024] [Indexed: 10/29/2024] Open
Abstract
Homologous recombination during meiosis is critical for chromosome segregation and also gives rise to genetic diversity. Genetic exchange between homologous chromosomes during meiosis is mediated by the recombinase Dmc1, which is capable of recombining DNA sequences with mismatches. The Hop2-Mnd1 complex mediates Dmc1 activity. Here, we reveal a regulatory role for Hop2-Mnd1 in restricting substrate selection. Specifically, Hop2-Mnd1 upregulates Dmc1 activity with DNA substrates that are either fully homologous or contain DNA mismatches, and it also acts against DNA strand exchange between substrates solely harboring microhomology. By isolating and examining salient Hop2-Mnd1 separation-of-function variants, we show that suppressing illegitimate DNA recombination requires the Dmc1 filament interaction attributable to Hop2-Mnd1 but not its DNA binding activity. Our study provides mechanistic insights into how Hop2-Mnd1 helps maintain meiotic recombination fidelity.
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Affiliation(s)
- Jo-Ching Peng
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yuting Liang Sun
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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42
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He M, Jiang H, Li S, Xue M, Wang H, Zheng C, Tong J. The crosstalk between DNA-damage responses and innate immunity. Int Immunopharmacol 2024; 140:112768. [PMID: 39088918 DOI: 10.1016/j.intimp.2024.112768] [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: 05/20/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024]
Abstract
DNA damage is typically caused during cell growth by DNA replication stress or exposure to endogenous or external toxins. The accumulation of damaged DNA causes genomic instability, which is the root cause of many serious disorders. Multiple cellular organisms utilize sophisticated signaling pathways against DNA damage, collectively known as DNA damage response (DDR) networks. Innate immune responses are activated following cellular abnormalities, including DNA damage. Interestingly, recent studies have indicated that there is an intimate relationship between the DDR network and innate immune responses. Diverse kinds of cytosolic DNA sensors, such as cGAS and STING, recognize damaged DNA and induce signals related to innate immune responses, which link defective DDR to innate immunity. Moreover, DDR components operate in immune signaling pathways to induce IFNs and/or a cascade of inflammatory cytokines via direct interactions with innate immune modulators. Consistently, defective DDR factors exacerbate the innate immune imbalance, resulting in severe diseases, including autoimmune disorders and tumorigenesis. Here, the latest progress in understanding crosstalk between the DDR network and innate immune responses is reviewed. Notably, the dual function of innate immune modulators in the DDR network may provide novel insights into understanding and developing targeted immunotherapies for DNA damage-related diseases, even carcinomas.
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Affiliation(s)
- Mei He
- College of Life Sciences, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hua Jiang
- Department of Hematology, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200000, China
| | - Shun Li
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610041, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China.
| | - Huiqing Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
| | - Jie Tong
- College of Life Sciences, Hebei University, Baoding 071002, China.
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43
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D'Andrea VD, Magnani CJ, Ernandez J, Bellmunt J, Mossanen M, Clinton TN, Carvalho FLF, Mouw KW. Impact of DNA Repair Deficiency in the Evolving Treatment Landscape of Bladder Cancer. Curr Urol Rep 2024; 26:12. [PMID: 39382743 DOI: 10.1007/s11934-024-01242-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2024] [Indexed: 10/10/2024]
Abstract
PURPOSE OF REVIEW This review explores the current landscape of treatments which target the DNA damage response (DDR) in metastatic and muscle-invasive bladder cancer. It emphasizes recent clinical trials which integrate DDR inhibitors with standard chemotherapy and immunotherapy. RECENT FINDINGS Noteworthy findings include the ATLANTIS trial, which demonstrated prolonged progression-free survival (PFS) in DDR biomarker-selected patients using PARP inhibitors as maintenance after standard chemotherapy. Trials such as BAYOU, which combined immunotherapy with PARP inhibition, similarly suggested a potential therapeutic benefit in DDR biomarker-selected patients with bladder cancer. Efforts to develop bladder-sparing treatment regimens based on DDR-associated mutational profiles, such as the RETAIN and HCRN 16-257 trials, have had mixed outcomes to date. There are now ongoing efforts to combine DDR inhibitors with the newest bladder cancer therapies, such as antibody-drug conjugates. This review highlights the most recent advances in targeting DNA repair deficiency in the evolving treatment landscape of bladder cancer.
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Affiliation(s)
- Vincent D D'Andrea
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Christopher J Magnani
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - John Ernandez
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Joaquim Bellmunt
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mossanen
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Timothy N Clinton
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Filipe L F Carvalho
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kent W Mouw
- Brigham & Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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44
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Sfeir A, Tijsterman M, McVey M. Microhomology-Mediated End-Joining Chronicles: Tracing the Evolutionary Footprints of Genome Protection. Annu Rev Cell Dev Biol 2024; 40:195-218. [PMID: 38857538 DOI: 10.1146/annurev-cellbio-111822-014426] [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: 06/12/2024]
Abstract
The fidelity of genetic information is essential for cellular function and viability. DNA double-strand breaks (DSBs) pose a significant threat to genome integrity, necessitating efficient repair mechanisms. While the predominant repair strategies are usually accurate, paradoxically, error-prone pathways also exist. This review explores recent advances and our understanding of microhomology-mediated end joining (MMEJ), an intrinsically mutagenic DSB repair pathway conserved across organisms. Central to MMEJ is the activity of DNA polymerase theta (Polθ), a specialized polymerase that fuels MMEJ mutagenicity. We examine the molecular intricacies underlying MMEJ activity and discuss its function during mitosis, where the activity of Polθ emerges as a last-ditch effort to resolve persistent DSBs, especially when homologous recombination is compromised. We explore the promising therapeutic applications of targeting Polθ in cancer treatment and genome editing. Lastly, we discuss the evolutionary consequences of MMEJ, highlighting its delicate balance between protecting genome integrity and driving genomic diversity.
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Affiliation(s)
- Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA;
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center; Institute of Biology Leiden, Leiden University, Leiden, The Netherlands;
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts, USA;
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45
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Neal F, Li W, Uhrig ME, Sharma N, Syed S, Burma S, Hromas R, Mazin A, Dray E, Libich D, Olsen S, Wasmuth E, Zhao W, Sørensen CS, Wiese C, Kwon Y, Sung P. Distinct roles of the two BRCA2 DNA binding domains in DNA damage repair and replication fork preservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614752. [PMID: 39386664 PMCID: PMC11463483 DOI: 10.1101/2024.09.24.614752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Homologous recombination (HR) is a highly conserved tool for the removal of DNA double-strand breaks (DSBs) and the preservation of stalled and damaged DNA replication forks. Successful completion of HR requires the tumor suppressor BRCA2. Germline mutations in BRCA2 lead to familial breast, ovarian, and other cancers, underscoring the importance of this protein for maintaining genome stability. BRCA2 harbors two distinct DNA binding domains, one that possesses three oligonucleotide/oligosaccharide binding (OB) folds (known as the OB-DBD), and with the other residing in the C-terminal recombinase binding domain (termed the CTRB-DBD) encoded by the last gene exon. Here, we employ a combination of genetic, biochemical, and cellular approaches to delineate contributions of these two DNA binding domains toward HR and the maintenance of stressed DNA replication forks. We show that OB-DBD and CTRB-DBD confer ssDNA and dsDNA binding capabilities to BRCA2, respectively, and that BRCA2 variants mutated in either DNA binding domain are impaired in the ability to load the recombinase RAD51 onto ssDNA pre-occupied by RPA. While the CTRB-DBD mutant is modestly affected for HR, it exhibits a strong defect in the protection of stressed replication forks. In contrast, the OB-DBD is indispensable for both BRCA2 functions. Our study thus defines the unique contributions of the two BRCA2 DNA binding domains in genome maintenance.
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Sun L, Lai M, Ghouri F, Nawaz MA, Ali F, Baloch FS, Nadeem MA, Aasim M, Shahid MQ. Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence-A Critical Review. PLANTS (BASEL, SWITZERLAND) 2024; 13:2676. [PMID: 39409546 PMCID: PMC11478383 DOI: 10.3390/plants13192676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/08/2024] [Accepted: 09/22/2024] [Indexed: 10/20/2024]
Abstract
With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops' audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research.
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Affiliation(s)
- Lixia Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.S.); (M.L.); (F.G.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Mingyu Lai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.S.); (M.L.); (F.G.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.S.); (M.L.); (F.G.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Amjad Nawaz
- Education Scientific Center of Nanotechnology, Far Eastern Federal University, 690091 Vladivostok, Russia;
| | - Fawad Ali
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China;
| | - Faheem Shehzad Baloch
- Dapartment of Biotechnology, Faculty of Science, Mersin University, Mersin 33343, Türkiye;
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye; (M.A.N.); (M.A.)
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Türkiye; (M.A.N.); (M.A.)
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; (L.S.); (M.L.); (F.G.)
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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Liang F, Rai R, Sodeinde T, Chang S. TRF2-RAP1 represses RAD51-dependent homology-directed telomere repair by promoting BLM-mediated D-loop unwinding and inhibiting BLM-DNA2-dependent 5'-end resection. Nucleic Acids Res 2024; 52:9695-9709. [PMID: 39082275 PMCID: PMC11381343 DOI: 10.1093/nar/gkae642] [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: 05/07/2024] [Revised: 06/26/2024] [Accepted: 07/12/2024] [Indexed: 09/10/2024] Open
Abstract
Inappropriate homology-directed repair (HDR) of telomeres results in catastrophic telomere loss and aberrant chromosome fusions, leading to genome instability. We have previously shown that the TRF2-RAP1 heterodimer protects telomeres from engaging in aberrant telomere HDR. Cells lacking the basic domain of TRF2 and functional RAP1 display HDR-mediated telomere clustering, resulting in the formation of ultrabright telomeres (UTs) and massive chromosome fusions. Using purified proteins, we uncover three distinct molecular pathways that the TRF2-RAP1 heterodimer utilizes to protect telomeres from engaging in aberrant HDR. We show mechanistically that TRF2-RAP1 inhibits RAD51-initiated telomeric D-loop formation. Both the TRF2 basic domain and RAP1-binding to TRF2 are required to block RAD51-mediated homology search. TRF2 recruits the BLM helicase to telomeres through its TRFH domain to promote BLM-mediated unwinding of telomere D-loops. In addition, TRF2-RAP1 inhibits BLM-DNA2-mediated 5' telomere end resection, preventing the generation of 3' single-stranded telomere overhangs necessary for RAD51-dependent HDR. Importantly, cells expressing BLM mutants unable to interact with TRF2 accumulate telomere D-loops and UTs. Our findings uncover distinct molecular mechanisms coordinated by TRF2-RAP1 to protect telomeres from engaging in aberrant HDR.
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Affiliation(s)
- Fengshan Liang
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
| | - Rekha Rai
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
| | - Tori Sodeinde
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
| | - Sandy Chang
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
- Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
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48
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Gál Z, Boukoura S, Oxe KC, Badawi S, Nieto B, Korsholm LM, Geisler SB, Dulina E, Rasmussen AV, Dahl C, Lv W, Xu H, Pan X, Arampatzis S, Stratou DE, Galanos P, Lin L, Guldberg P, Bartek J, Luo Y, Larsen DH. Hyper-recombination in ribosomal DNA is driven by long-range resection-independent RAD51 accumulation. Nat Commun 2024; 15:7797. [PMID: 39242676 PMCID: PMC11379943 DOI: 10.1038/s41467-024-52189-6] [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: 09/29/2023] [Accepted: 08/28/2024] [Indexed: 09/09/2024] Open
Abstract
Ribosomal DNA (rDNA) encodes the ribosomal RNA genes and represents an intrinsically unstable genomic region. However, the underlying mechanisms and implications for genome integrity remain elusive. Here, we use Bloom syndrome (BS), a rare genetic disease characterized by DNA repair defects and hyper-unstable rDNA, as a model to investigate the mechanisms leading to rDNA instability. We find that in Bloom helicase (BLM) proficient cells, the homologous recombination (HR) pathway in rDNA resembles that in nuclear chromatin; it is initiated by resection, replication protein A (RPA) loading and BRCA2-dependent RAD51 filament formation. However, BLM deficiency compromises RPA-loading and BRCA1/2 recruitment to rDNA, but not RAD51 accumulation. RAD51 accumulates at rDNA despite depletion of long-range resection nucleases and rDNA damage results in micronuclei when BLM is absent. In summary, our findings indicate that rDNA is permissive to RAD51 accumulation in the absence of BLM, leading to micronucleation and potentially global genomic instability.
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Affiliation(s)
- Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Stavroula Boukoura
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Kezia Catharina Oxe
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Sara Badawi
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Lea Milling Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | | | - Christina Dahl
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Wei Lv
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Huixin Xu
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Xiaoguang Pan
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | | | | | - Panagiotis Galanos
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
| | - Per Guldberg
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, 5000, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm, Sweden
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark.
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49
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Lu H, Wise SS, Speer RM, Croom-Perez TJ, Toyoda JH, Meaza I, Williams A, Wise JP, Kouokam JC, Young Wise J, Hoyle GW, Zhu C, Ali AM, Wise JP. Acute particulate hexavalent chromium exposure induces DNA double-strand breaks and activates homologous recombination repair in rat lung tissue. Toxicol Sci 2024; 201:1-13. [PMID: 38867691 PMCID: PMC11347773 DOI: 10.1093/toxsci/kfae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
Hexavalent chromium [Cr(VI)] is an established human lung carcinogen, but the carcinogenesis mechanism is poorly understood. Chromosome instability, a hallmark of lung cancer, is considered a major driver of Cr(VI)-induced lung cancer. Unrepaired DNA double-strand breaks are the underlying cause, and homologous recombination repair is the primary mechanism preventing Cr(VI)-induced DNA breaks from causing chromosome instability. Cell culture studies show acute Cr(VI) exposure causes DNA double-strand breaks and increases homologous recombination repair activity. However, the ability of Cr(VI)-induced DNA breaks and repair impact has only been reported in cell culture studies. Therefore, we investigated whether acute Cr(VI) exposure could induce breaks and homologous recombination repair in rat lungs. Male and female Wistar rats were acutely exposed to either zinc chromate particles in a saline solution or saline alone by oropharyngeal aspiration. This exposure route resulted in increased Cr levels in each lobe of the lung. We found Cr(VI) induced DNA double-strand breaks in a concentration-dependent manner, with females being more susceptible than males, and induced homologous recombination repair at similar levels in both sexes. Thus, these data show this driving mechanism discovered in cell culture indeed translates to lung tissue in vivo.
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Affiliation(s)
- Haiyan Lu
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Sandra S Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Rachel M Speer
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Tayler J Croom-Perez
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Jennifer H Toyoda
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Idoia Meaza
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Aggie Williams
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - John Pierce Wise
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Pediatric Research Institute, University of Louisville, Louisville, KY 40292, United States
| | - J Calvin Kouokam
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Jamie Young Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
| | - Gary W Hoyle
- Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40292, United States
| | - Cairong Zhu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610044, China
| | - Abdul-Mehdi Ali
- Earth and Planetary Sciences Department, The University of New Mexico, Albuquerque, NM 87131, United States
| | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292, United States
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50
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Huang Y, Li W, Foo T, Ji JH, Wu B, Tomimatsu N, Fang Q, Gao B, Long M, Xu J, Maqbool R, Mukherjee B, Ni T, Alejo S, He Y, Burma S, Lan L, Xia B, Zhao W. DSS1 restrains BRCA2's engagement with dsDNA for homologous recombination, replication fork protection, and R-loop homeostasis. Nat Commun 2024; 15:7081. [PMID: 39152168 PMCID: PMC11329725 DOI: 10.1038/s41467-024-51557-6] [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: 01/03/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024] Open
Abstract
DSS1, essential for BRCA2-RAD51 dependent homologous recombination (HR), associates with the helical domain (HD) and OB fold 1 (OB1) of the BRCA2 DSS1/DNA-binding domain (DBD) which is frequently targeted by cancer-associated pathogenic variants. Herein, we reveal robust ss/dsDNA binding abilities in HD-OB1 subdomains and find that DSS1 shuts down HD-OB1's DNA binding to enable ssDNA targeting of the BRCA2-RAD51 complex. We show that C-terminal helix mutations of DSS1, including the cancer-associated R57Q mutation, disrupt this DSS1 regulation and permit dsDNA binding of HD-OB1/BRCA2-DBD. Importantly, these DSS1 mutations impair BRCA2/RAD51 ssDNA loading and focus formation and cause decreased HR efficiency, destabilization of stalled forks and R-loop accumulation, and hypersensitize cells to DNA-damaging agents. We propose that DSS1 restrains the intrinsic dsDNA binding of BRCA2-DBD to ensure BRCA2/RAD51 targeting to ssDNA, thereby promoting optimal execution of HR, and potentially replication fork protection and R-loop suppression.
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Affiliation(s)
- Yuxin Huang
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Wenjing Li
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Tzeh Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Jae-Hoon Ji
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Bo Wu
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Nozomi Tomimatsu
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Qingming Fang
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Boya Gao
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Melissa Long
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Jingfei Xu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Rouf Maqbool
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Bipasha Mukherjee
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Tengyang Ni
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Salvador Alejo
- Department of Obstetrics & Gynecology, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Li Lan
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA.
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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