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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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2
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Wu H, Han BW, Liu T, Zhang M, Wu Y, Nie J. Epstein-Barr virus deubiquitinating enzyme BPLF1 is involved in EBV carcinogenesis by affecting cellular genomic stability. Neoplasia 2024; 55:101012. [PMID: 38875930 DOI: 10.1016/j.neo.2024.101012] [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: 12/22/2023] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/16/2024]
Abstract
Increased mutational burden and EBV load have been revealed from normal tissues to Epstein-Barr virus (EBV)-associated gastric carcinomas (EBVaGCs). BPLF1, encoded by EBV, is a lytic cycle protein with deubiquitinating activity has been found to participate in disrupting repair of DNA damage. We first confirmed that BPLF1 gene in gastric cancer (GC) significantly increased the DNA double strand breaks (DSBs). Ubiquitination mass spectrometry identified histones as BPLF1 interactors and potential substrates, and co-immunoprecipitation and in vitro experiments verified that BPLF1 regulates H2Bub by targeting Rad6. Over-expressing Rad6 restored H2Bub but partially reduced γ-H2AX, suggesting that other downstream DNA repair processes were affected. mRNA expression of BRCA2 were significantly down-regulated by next-generation sequencing after over-expression of BPLF1, and over-expression of p65 facilitated the repair of DSBs. We demonstrated BPLF1 may lead to the accumulation of DSBs by two pathways, reducing H2B ubiquitination (H2Bub) and blocking homologous recombination which may provide new ideas for the treatment of gastric cancer.
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Affiliation(s)
- Hantao Wu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China; Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Bo-Wei Han
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Tiancai Liu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Min Zhang
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yingsong Wu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Jing Nie
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China.
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3
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Carreira R, Lama-Diaz T, Crugeiras M, Aguado FJ, Sebesta M, Krejci L, Blanco MG. Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors. Nucleic Acids Res 2024:gkae453. [PMID: 38832625 DOI: 10.1093/nar/gkae453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination involves the formation of branched DNA molecules that may interfere with chromosome segregation. To resolve these persistent joint molecules, cells rely on the activation of structure-selective endonucleases (SSEs) during the late stages of the cell cycle. However, the premature activation of SSEs compromises genome integrity, due to untimely processing of replication and/or recombination intermediates. Here, we used a biochemical approach to show that the budding yeast SSEs Mus81 and Yen1 possess the ability to cleave the central recombination intermediate known as the displacement loop or D-loop. Moreover, we demonstrate that, consistently with previous genetic data, the simultaneous action of Mus81 and Yen1, followed by ligation, is sufficient to recreate the formation of a half-crossover precursor in vitro. Our results provide not only mechanistic explanation for the formation of a half-crossover, but also highlight the critical importance for precise regulation of these SSEs to prevent chromosomal rearrangements.
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Affiliation(s)
- Raquel Carreira
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Maria Crugeiras
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - F Javier Aguado
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Marek Sebesta
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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4
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Dvořák Tomaštíková E, Vaculíková J, Štenclová V, Kaduchová K, Pobořilová Z, Paleček JJ, Pecinka A. The interplay of homology-directed repair pathways in the repair of zebularine-induced DNA-protein crosslinks in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38824612 DOI: 10.1111/tpj.16863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/09/2024] [Accepted: 05/16/2024] [Indexed: 06/03/2024]
Abstract
DNA-protein crosslinks (DPCs) are highly toxic DNA lesions represented by proteins covalently bound to the DNA. Persisting DPCs interfere with fundamental genetic processes such as DNA replication and transcription. Cytidine analog zebularine (ZEB) has been shown to crosslink DNA METHYLTRANSFERASE1 (MET1). Recently, we uncovered a critical role of the SMC5/6-mediated SUMOylation in the repair of DPCs. In an ongoing genetic screen, we identified two additional candidates, HYPERSENSITIVE TO ZEBULARINE 2 and 3, that were mapped to REGULATOR OF TELOMERE ELONGATION 1 (RTEL1) and polymerase TEBICHI (TEB), respectively. By monitoring the growth of hze2 and hze3 plants in response to zebularine, we show the importance of homologous recombination (HR) factor RTEL1 and microhomology-mediated end-joining (MMEJ) polymerase TEB in the repair of MET1-DPCs. Moreover, genetic interaction and sensitivity assays showed the interdependency of SMC5/6 complex, HR, and MMEJ in the homology-directed repair of MET1-DPCs in Arabidopsis. Altogether, we provide evidence that MET1-DPC repair in plants is more complex than originally expected.
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Affiliation(s)
- Eva Dvořák Tomaštíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jitka Vaculíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, Olomouc, 77900, Czech Republic
- Faculty of Science, National Center for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Veronika Štenclová
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Kateřina Kaduchová
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Zuzana Pobořilová
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jan J Paleček
- Faculty of Science, National Center for Biomolecular Research, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, Olomouc, 77900, Czech Republic
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5
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Chauvin SD, Ando S, Holley JA, Sugie A, Zhao FR, Poddar S, Kato R, Miner CA, Nitta Y, Krishnamurthy SR, Saito R, Ning Y, Hatano Y, Kitahara S, Koide S, Stinson WA, Fu J, Surve N, Kumble L, Qian W, Polishchuk O, Andhey PS, Chiang C, Liu G, Colombeau L, Rodriguez R, Manel N, Kakita A, Artyomov MN, Schultz DC, Coates PT, Roberson EDO, Belkaid Y, Greenberg RA, Cherry S, Gack MU, Hardy T, Onodera O, Kato T, Miner JJ. Inherited C-terminal TREX1 variants disrupt homology-directed repair to cause senescence and DNA damage phenotypes in Drosophila, mice, and humans. Nat Commun 2024; 15:4696. [PMID: 38824133 PMCID: PMC11144269 DOI: 10.1038/s41467-024-49066-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/22/2024] [Indexed: 06/03/2024] Open
Abstract
Age-related microangiopathy, also known as small vessel disease (SVD), causes damage to the brain, retina, liver, and kidney. Based on the DNA damage theory of aging, we reasoned that genomic instability may underlie an SVD caused by dominant C-terminal variants in TREX1, the most abundant 3'-5' DNA exonuclease in mammals. C-terminal TREX1 variants cause an adult-onset SVD known as retinal vasculopathy with cerebral leukoencephalopathy (RVCL or RVCL-S). In RVCL, an aberrant, C-terminally truncated TREX1 mislocalizes to the nucleus due to deletion of its ER-anchoring domain. Since RVCL pathology mimics that of radiation injury, we reasoned that nuclear TREX1 would cause DNA damage. Here, we show that RVCL-associated TREX1 variants trigger DNA damage in humans, mice, and Drosophila, and that cells expressing RVCL mutant TREX1 are more vulnerable to DNA damage induced by chemotherapy and cytokines that up-regulate TREX1, leading to depletion of TREX1-high cells in RVCL mice. RVCL-associated TREX1 mutants inhibit homology-directed repair (HDR), causing DNA deletions and vulnerablility to PARP inhibitors. In women with RVCL, we observe early-onset breast cancer, similar to patients with BRCA1/2 variants. Our results provide a mechanistic basis linking aberrant TREX1 activity to the DNA damage theory of aging, premature senescence, and microvascular disease.
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Affiliation(s)
- Samuel D Chauvin
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shoichiro Ando
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Joe A Holley
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Atsushi Sugie
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Fang R Zhao
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Subhajit Poddar
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rei Kato
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Cathrine A Miner
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yohei Nitta
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, Japan
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rie Saito
- Department of Pathology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yue Ning
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuya Hatano
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Sho Kitahara
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Shin Koide
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - W Alexander Stinson
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Jiayuan Fu
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nehalee Surve
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lindsay Kumble
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wei Qian
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Oleksiy Polishchuk
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Prabhakar S Andhey
- Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Cindy Chiang
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Guanqun Liu
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Ludovic Colombeau
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Raphaël Rodriguez
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Nicolas Manel
- INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Akiyoshi Kakita
- Department of Pathology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO, USA
| | - David C Schultz
- High-throughput Screening Core, University of Pennsylvania, Philadelphia, PA, USA
| | - P Toby Coates
- Central and Northern Adelaide Renal and Transplantation Service (CNARTS), The Royal Adelaide Hospital, Adelaide, South Australia, Australia
- School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Elisha D O Roberson
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institut Pasteur, Paris, France
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Cherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Tristan Hardy
- Genetics, Repromed, Monash IVF, Dulwich, South Australia, Australia
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Osamu Onodera
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan
- Department of Molecular Neuroscience, Brain Science Branch, Brain Research Institute, Niigata University, Niigata, Japan
| | - Taisuke Kato
- Department of Molecular Neuroscience, Brain Science Branch, Brain Research Institute, Niigata University, Niigata, Japan.
| | - Jonathan J Miner
- Division of Rheumatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- RVCL Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Penn Colton Center for Autoimmunity, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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6
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Hill RM, Li C, Hughes JR, Rocha S, Grundy GJ, Parsons JL. Autophagy is the main driver of radioresistance of HNSCC cells in mild hypoxia. J Cell Mol Med 2024; 28:e18482. [PMID: 38899556 DOI: 10.1111/jcmm.18482] [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: 10/09/2023] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Hypoxia poses a significant challenge to the effectiveness of radiotherapy in head and neck squamous cell carcinoma (HNSCC) patients, and it is imperative to discover novel approaches to overcome this. In this study, we investigated the underlying mechanisms contributing to x-ray radioresistance in HPV-negative HNSCC cells under mild hypoxic conditions (1% oxygen) and explored the potential for autophagy modulation as a promising therapeutic strategy. Our findings show that HNSCC cells exposed to mild hypoxic conditions exhibit increased radioresistance, which is largely mediated by the hypoxia-inducible factor (HIF) pathway. We demonstrate that siRNA knockdown of HIF-1α and HIF-1β leads to increased radiosensitivity in HNSCC cells under hypoxia. Hypoxia-induced radioresistance was not attributed to differences in DNA double strand break repair kinetics, as these remain largely unchanged under normoxic and hypoxic conditions. Rather, we identify autophagy as a critical protective mechanism in HNSCC cells following irradiation under mild hypoxia conditions. Targeting key autophagy genes, such as BECLIN1 and BNIP3/3L, using siRNA sensitizes these cells to irradiation. Whilst autophagy's role in hypoxic radioresistance remains controversial, this study highlights the importance of autophagy modulation as a potential therapeutic approach to enhance the effectiveness of radiotherapy in HNSCC.
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Affiliation(s)
- Rhianna M Hill
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Chun Li
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Jonathan R Hughes
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sonia Rocha
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gabrielle J Grundy
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jason L Parsons
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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7
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Tsaridou S, van Vugt MATM. FIRRM and FIGNL1: partners in the regulation of homologous recombination. Trends Genet 2024; 40:467-470. [PMID: 38494375 DOI: 10.1016/j.tig.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
DNA repair through homologous recombination (HR) is of vital importance for maintaining genome stability and preventing tumorigenesis. RAD51 is the core component of HR, catalyzing the strand invasion and homology search. Here, we highlight recent findings on FIRRM and FIGNL1 as regulators of the dynamics of RAD51.
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Affiliation(s)
- Stavroula Tsaridou
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands.
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8
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Chen HW, Yeh HY, Chang CC, Kuo WC, Lin SW, Vrielynck N, Grelon M, Chan NL, Chi P. Biochemical characterization of the meiosis-essential yet evolutionarily divergent topoisomerase VIB-like protein MTOPVIB from Arabidopsis thaliana. Nucleic Acids Res 2024; 52:4541-4555. [PMID: 38499490 PMCID: PMC11077084 DOI: 10.1093/nar/gkae181] [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: 09/06/2023] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Formation of programmed DNA double-strand breaks is essential for initiating meiotic recombination. Genetic studies on Arabidopsis thaliana and Mus musculus have revealed that assembly of a type IIB topoisomerase VI (Topo VI)-like complex, composed of SPO11 and MTOPVIB, is a prerequisite for generating DNA breaks. However, it remains enigmatic if MTOPVIB resembles its Topo VI subunit B (VIB) ortholog in possessing robust ATPase activity, ability to undergo ATP-dependent dimerization, and activation of SPO11-mediated DNA cleavage. Here, we successfully prepared highly pure A. thaliana MTOPVIB and MTOPVIB-SPO11 complex. Contrary to expectations, our findings highlight that MTOPVIB differs from orthologous Topo VIB by lacking ATP-binding activity and independently forming dimers without ATP. Most significantly, our study reveals that while MTOPVIB lacks the capability to stimulate SPO11-mediated DNA cleavage, it functions as a bona fide DNA-binding protein and plays a substantial role in facilitating the dsDNA binding capacity of the MOTOVIB-SPO11 complex. Thus, we illustrate mechanistic divergence between the MTOPVIB-SPO11 complex and classical type IIB topoisomerases.
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Affiliation(s)
- Hsin-Wen Chen
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
| | - Chih-Chiang Chang
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Wei-Chen Kuo
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan
| | - Nathalie Vrielynck
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000,Versailles, France
| | - Mathilde Grelon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000,Versailles, France
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 100233 Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, 10617 Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan
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9
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Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: Recent advances and applications. Biotechnol Adv 2024; 72:108343. [PMID: 38521283 DOI: 10.1016/j.biotechadv.2024.108343] [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: 10/14/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering. MGEs, including DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons, offer various advantages, such as a broad host range, genome-wide mutagenesis, efficient large-size DNA integration, multiplexing capabilities, and in situ single-stranded DNA generation. We focused on the components, mechanisms, and features of each MGE-based tool to highlight their cellular applications. Finally, we discussed the current challenges of MGE-based genome engineering and provided insights into the evolving landscape of this transformative technology. In conclusion, the combination of genome engineering with MGE demonstrates remarkable potential for addressing various challenges and advancing the field of genetic manipulation, and promises to revolutionize our ability to engineer and understand the genomes of diverse organisms.
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Affiliation(s)
- Jaeseong Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea.
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10
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Li J, Wei Y, Liu J, Cheng S, Zhang X, Qiu H, Li J, He C. Integrative analysis of metabolism subtypes and identification of prognostic metabolism-related genes for glioblastoma. Biosci Rep 2024; 44:BSR20231400. [PMID: 38419527 DOI: 10.1042/bsr20231400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/01/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024] Open
Abstract
Increasing evidence has demonstrated that cancer cell metabolism is a critical factor in tumor development and progression; however, its role in glioblastoma (GBM) remains limited. In the present study, we classified GBM into three metabolism subtypes (MC1, MC2, and MC3) through cluster analysis of 153 GBM samples from the RNA-sequencing data of The Cancer Genome Atlas (TCGA) based on 2752 metabolism-related genes (MRGs). We further explored the prognostic value, metabolic signatures, immune infiltration, and immunotherapy sensitivity of the three metabolism subtypes. Moreover, the metabolism scoring model was established to quantify the different metabolic characteristics of the patients. Results showed that MC3, which is associated with a favorable survival outcome, had higher proportions of isocitrate dehydrogenase (IDH) mutations and lower tumor purity and proliferation. The MC1 subtype, which is associated with the worst prognosis, shows a higher number of segments and homologous recombination defects and significantly lower mRNA expression-based stemness index (mRNAsi) and epigenetic-regulation-based mRNAsi. The MC2 subtype has the highest T-cell exclusion score, indicating a high likelihood of immune escape. The results were validated using an independent dataset. Five MRGs (ACSL1, NDUFA2, CYP1B1, SLC11A1, and COX6B1) correlated with survival outcomes were identified based on metabolism-related co-expression module analysis. Laboratory-based validation tests further showed the expression of these MRGs in GBM tissues and how their expression influences cell function. The results provide a reference for developing clinical management approaches and treatments for GBM.
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Affiliation(s)
- Jiahui Li
- Department of Rehabilitation Medicine, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu Province 215228, China
- Center of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Yutian Wei
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Jiali Liu
- Center of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Shupeng Cheng
- Center of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Xia Zhang
- Center of Rehabilitation Medicine, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shanxi Province 710054, China
| | - Huaide Qiu
- Faculty of Rehabilitation Science, Nanjing Normal University of Special Education, Nanjing, Jiangsu Province 210038, China
| | - Jianan Li
- Center of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, China
| | - Chuan He
- Department of Rehabilitation Medicine, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu Province 215228, China
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11
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Rahman R, Shi DD, Reitman ZJ, Hamerlik P, de Groot JF, Haas-Kogan DA, D'Andrea AD, Sulman EP, Tanner K, Agar NYR, Sarkaria JN, Tinkle CL, Bindra RS, Mehta MP, Wen PY. DNA damage response in brain tumors: A Society for Neuro-Oncology consensus review on mechanisms and translational efforts in neuro-oncology. Neuro Oncol 2024:noae072. [PMID: 38770568 DOI: 10.1093/neuonc/noae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
DNA damage response (DDR) mechanisms are critical to maintenance of overall genomic stability, and their dysfunction can contribute to oncogenesis. Significant advances in our understanding of DDR pathways have raised the possibility of developing therapies that exploit these processes. In this expert-driven consensus review, we examine mechanisms of response to DNA damage, progress in development of DDR inhibitors in IDH-wild-type glioblastoma and IDH-mutant gliomas, and other important considerations such as biomarker development, preclinical models, combination therapies, mechanisms of resistance and clinical trial design considerations.
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Affiliation(s)
- Rifaquat Rahman
- Department of Radiation Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Diana D Shi
- Department of Radiation Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Petra Hamerlik
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - John F de Groot
- Division of Neuro-Oncology, University of California San Francisco, San Francisco, California, USA
| | - Daphne A Haas-Kogan
- Department of Radiation Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Erik P Sulman
- Department of Radiation Oncology, New York University, New York, New York, USA
| | - Kirk Tanner
- National Brain Tumor Society, Newton, Massachusetts, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery and Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christopher L Tinkle
- Department of Radiation Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
| | - Minesh P Mehta
- Miami Cancer Institute, Baptist Hospital, Miami, Florida, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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12
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Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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13
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Chen L, Gai X, Yu X. Pre-rRNA facilitates the recruitment of RAD51AP1 to DNA double-strand breaks. J Biol Chem 2024; 300:107115. [PMID: 38403248 PMCID: PMC10959706 DOI: 10.1016/j.jbc.2024.107115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
RAD51-associated protein 1 (RAD51AP1) is known to promote homologous recombination (HR) repair. However, the precise mechanism of RAD51AP1 in HR repair is unclear. Here, we identify that RAD51AP1 associates with pre-rRNA. Both the N terminus and C terminus of RAD51AP1 recognize pre-rRNA. Pre-rRNA not only colocalizes with RAD51AP1 at double-strand breaks (DSBs) but also facilitates the recruitment of RAD51AP1 to DSBs. Consistently, transient inhibition of pre-rRNA synthesis by RNA polymerase I inhibitor suppresses the recruitment of RAD51AP1 as well as HR repair. Moreover, RAD51AP1 forms liquid-liquid phase separation in the presence of pre-rRNA in vitro, which may be the molecular mechanism of RAD51AP1 foci formation. Taken together, our results demonstrate that pre-rRNA mediates the relocation of RAD51AP1 to DSBs for HR repair.
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Affiliation(s)
- Linlin Chen
- School of Life Sciences, Fudan University, Shanghai, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaochen Gai
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
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14
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Kumar N, Taneja A, Ghosh M, Rothweiler U, Sundaresan N, Singh M. Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites. Nucleic Acids Res 2024; 52:1450-1470. [PMID: 38153196 PMCID: PMC10853778 DOI: 10.1093/nar/gkad1208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
The regulator of telomere elongation helicase 1 (RTEL1) plays roles in telomere DNA maintenance, DNA repair, and genome stability by dismantling D-loops and unwinding G-quadruplex structures. RTEL1 comprises a helicase domain, two tandem harmonin homology domains 1&2 (HHD1 and HHD2), and a Zn2+-binding RING domain. In vitro D-loop disassembly by RTEL1 is enhanced in the presence of replication protein A (RPA). However, the mechanism of RTEL1 recruitment at non-telomeric D-loops remains unknown. In this study, we have unravelled a direct physical interaction between RTEL1 and RPA. Under DNA damage conditions, we showed that RTEL1 and RPA colocalise in the cell. Coimmunoprecipitation showed that RTEL1 and RPA interact, and the deletion of HHDs of RTEL1 significantly reduced this interaction. NMR chemical shift perturbations (CSPs) showed that RPA uses its 32C domain to interact with the HHD2 of RTEL1. Interestingly, HHD2 also interacted with DNA in the in vitro experiments. HHD2 structure was determined using X-ray crystallography, and NMR CSPs mapping revealed that both RPA 32C and DNA competitively bind to HHD2 on an overlapping surface. These results establish novel roles of accessory HHDs in RTEL1's functions and provide mechanistic insights into the RPA-mediated recruitment of RTEL1 to DNA repair sites.
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Affiliation(s)
- Niranjan Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Arushi Taneja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Meenakshi Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Ulli Rothweiler
- The Norwegian Structural Biology Centre, Department of Chemistry, The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
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15
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Qian H, Margaretha Plat A, Jonker A, Hoebe RA, Krawczyk P. Super-resolution GSDIM microscopy unveils distinct nanoscale characteristics of DNA repair foci under diverse genotoxic stress. DNA Repair (Amst) 2024; 134:103626. [PMID: 38232606 DOI: 10.1016/j.dnarep.2024.103626] [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: 09/07/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
DNA double-strand breaks initiate the DNA damage response (DDR), leading to the accumulation of repair proteins at break sites and the formation of the-so-called foci. Various microscopy methods, such as wide-field, confocal, electron, and super-resolution microscopy, have been used to study these structures. However, the impact of different DNA-damaging agents on their (nano)structure remains unclear. Utilising GSDIM super-resolution microscopy, here we investigated the distribution of fluorescently tagged DDR proteins (53BP1, RNF168, MDC1) and γH2AX in U2OS cells treated with γ-irradiation, etoposide, cisplatin, or hydroxyurea. Our results revealed that both foci structure and their nanoscale ultrastructure, including foci size, nanocluster characteristics, fluorophore density and localisation, can be significantly altered by different inducing agents, even ones with similar mechanisms. Furthermore, distinct behaviours of DDR proteins were observed under the same treatment. These findings have implications for cancer treatment strategies involving these agents and provide insights into the nanoscale organisation of the DDR.
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Affiliation(s)
- Haibin Qian
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Audrey Margaretha Plat
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Ard Jonker
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Ron A Hoebe
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Przemek Krawczyk
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands.
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16
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Chen J, Potlapalli R, Quan H, Chen L, Xie Y, Pouriyeh S, Sakib N, Liu L, Xie Y. Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights. BIOTECH 2024; 13:3. [PMID: 38247733 PMCID: PMC10801582 DOI: 10.3390/biotech13010003] [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: 10/29/2023] [Revised: 11/21/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the past decade, substantial progress and pivotal discoveries have been achieved in DNA damage and repair. This comprehensive review paper consolidates research efforts, focusing on DNA repair mechanisms, computational research methods, and associated databases. Our work is a valuable resource for scientists and researchers engaged in computational DNA research, offering the latest insights into DNA-related proteins, diseases, and cutting-edge methodologies. The review addresses key questions, including the major types of DNA damage, common DNA repair mechanisms, the availability of reliable databases for DNA damage and associated diseases, and the predominant computational research methods for enzymes involved in DNA damage and repair.
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Affiliation(s)
- Jiawei Chen
- College of Letter and Science, University of California, Berkeley, CA 94720, USA;
| | - Ravi Potlapalli
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Heng Quan
- Department of Civil and Urban Engineering, New York University, New York, NY 11201, USA;
| | - Lingtao Chen
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Ying Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Seyedamin Pouriyeh
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Nazmus Sakib
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
| | - Lichao Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA;
| | - Yixin Xie
- College of Computing and Software Engineering, Kennesaw State University, Marietta, GA 30060, USA; (L.C.); (R.P.); (Y.X.); (S.P.); (N.S.)
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17
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Zhou Y, Mouw KW. DNA repair deficiency and the immune microenvironment: A pathways perspective. DNA Repair (Amst) 2024; 133:103594. [PMID: 37980867 PMCID: PMC10841828 DOI: 10.1016/j.dnarep.2023.103594] [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: 07/10/2023] [Revised: 09/18/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
Timely and accurate repair of DNA damage is required for genomic stability, but DNA repair pathways are often lost or altered in tumors. In addition to directly impacting tumor cell response to DNA damage, DNA repair deficiency can also alter the immune microenvironment via changes in innate and adaptive immune signaling. In some settings, these changes can lead to increased sensitivity to immune checkpoint inhibitors (ICIs). In this review, we discuss the impact of specific DNA repair pathway dysfunction on immune contexture and ICI response in solid tumors.
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Affiliation(s)
- Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Radiation Oncology, Brigham & Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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18
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Park CS, Habib O, Lee Y, Hur JK. Applications of CRISPR technologies to the development of gene and cell therapy. BMB Rep 2024; 57:2-11. [PMID: 38178651 PMCID: PMC10828430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
Advancements in gene and cell therapy have resulted in novel therapeutics for diseases previously considered incurable or challenging to treat. Among the various contributing technologies, genome editing stands out as one of the most crucial for the progress in gene and cell therapy. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the subsequent evolution of genetic engineering technology have markedly expanded the field of target-specific gene editing. Originally studied in the immune systems of bacteria and archaea, the CRISPR system has demonstrated wide applicability to effective genome editing of various biological systems including human cells. The development of CRISPR-based base editing has enabled directional cytosine-tothymine and adenine-to-guanine substitutions of select DNA bases at the target locus. Subsequent advances in prime editing further elevated the flexibility of the edit multiple consecutive bases to desired sequences. The recent CRISPR technologies also have been actively utilized for the development of in vivo and ex vivo gene and cell therapies. We anticipate that the medical applications of CRISPR will rapidly progress to provide unprecedented possibilities to develop novel therapeutics towards various diseases. [BMB Reports 2024; 57(1): 2-11].
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Affiliation(s)
- Chul-Sung Park
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
| | - Omer Habib
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Younsu Lee
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Junho K. Hur
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
- Department of Genetics, College of Medicine, Hanyang University, Seoul 04763, Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea
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19
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Alvaro-Aranda L, Petitalot A, Djeghmoum Y, Panigada D, Singh JK, Ehlén Å, Vugic D, Martin C, Miron S, Contreras-Perez A, Nhiri N, Boucherit V, Lafitte P, Dumoulin I, Rouleau E, Jacquet E, Feliubadaló L, Del Valle J, Stoppa-Lyonnet D, Zinn-Justin S, Lázaro C, Caputo SM, Carreira A. The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination. Nucleic Acids Res 2023:gkad1222. [PMID: 38142462 DOI: 10.1093/nar/gkad1222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023] Open
Abstract
BRCA2 tumor suppressor protein ensures genome integrity by mediating DNA repair via homologous recombination (HR). This function is executed in part by its canonical DNA binding domain located at the C-terminus (BRCA2CTD), the only folded domain of the protein. Most germline pathogenic missense variants are located in this highly conserved region which binds to single-stranded DNA (ssDNA) and to the acidic protein DSS1. These interactions are essential for the HR function of BRCA2. Here, we report that the variant R2645G, identified in breast cancer and located at the DSS1 interface, unexpectedly increases the ssDNA binding activity of BRCA2CTDin vitro. Human cells expressing this variant display a hyper-recombination phenotype, chromosomal instability in the form of chromatid gaps when exposed to DNA damage, and increased PARP inhibitor sensitivity. In mouse embryonic stem cells (mES), this variant alters viability and confers sensitivity to cisplatin and Mitomycin C. These results suggest that BRCA2 interaction with ssDNA needs to be tightly regulated to limit HR and prevent chromosomal instability and we propose that this control mechanism involves DSS1. Given that several missense variants located within this region have been identified in breast cancer patients, these findings might have clinical implications for carriers.
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Affiliation(s)
- Lucia Alvaro-Aranda
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Yasmina Djeghmoum
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Davide Panigada
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Jenny Kaur Singh
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Åsa Ehlén
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Domagoj Vugic
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Charlotte Martin
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Simona Miron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, 91190 Gif-sur-Yvette, France
| | - Aida Contreras-Perez
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, Paris-Saclay University, CNRS, 91190 Gif-sur-Yvette, France
| | - Virginie Boucherit
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Philippe Lafitte
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Isaac Dumoulin
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Etienne Rouleau
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, Paris-Saclay University, CNRS, 91190 Gif-sur-Yvette, France
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris 75005, France
- Paris-Cité University, Paris, France
- INSERM U830, Institut Curie, Paris 75005, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, 91190 Gif-sur-Yvette, France
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Aura Carreira
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
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20
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Amritha PP, Shah JM. Essential role of the BRCA2B gene in somatic homologous recombination in Arabidopsis thaliana. BIOTECHNOLOGIA 2023; 104:371-380. [PMID: 38213474 PMCID: PMC10777725 DOI: 10.5114/bta.2023.132773] [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: 01/30/2023] [Revised: 06/15/2023] [Accepted: 08/29/2023] [Indexed: 01/13/2024] Open
Abstract
Constant exposure to various environmental and endogenous stresses can cause structural DNA damage, resulting in genome instability. Higher eukaryotic cells deploy conserved DNA repair systems, which include various DNA repair pathways, to maintain genome stability. Homologous recombination (HR), one of these repair pathways, involves multiple proteins. BRCA2, one of the proteins in the HR pathway, is of substantial research interest in humans because it is an oncogene. However, the study of this gene is limited due to the lack of availability of homozygous BRCA2-knockout mutants in mammals, which results in embryonic lethality. Arabidopsis thaliana has two copies of the BRCA2 homologs: BRCA2A and BRCA2B . Therefore, the single mutants remain nonlethal and fertile in Arabidopsis. The BRCA2A homolog, which plays a significant role in the HR pathway of germline cells and during the defense response, is well-studied in Arabidopsis. Our study focuses on the functional characterization of the BRCA2B homolog in the somatic cells of Arabidopsis, using the homozygous ΔBRCA2B mutant line. The phenotypic differences of ΔBRCA2B mutants were characterized and compared with wild Arabidopsis plants. The role of BRCA2B in spontaneous somatic HR (SHR) was studied using the ΔBRCA2B-gus detector line. ΔBRCA2B plants have a 6.3-fold lower SHR frequency than the control detector plants. Expression of four other HR pathway genes, including BRE, BRCC36A, RAD50, and RAD54, was significantly reduced in ΔBRCA2B mutants. Thus, our findings convey that the BRCA2B homolog plays an important role in maintaining spontaneous SHR rates and has a direct or indirect regulatory effect on the expression of other HR-related genes.
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Affiliation(s)
| | - Jasmine M. Shah
- Department of Plant Science, Central University of Kerala, Kasaragod, Kerala, India
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21
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Yoon S, Lee BK, Kim KP. Caffeine enhances chemosensitivity to irinotecan in the treatment of colorectal cancer. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 121:155120. [PMID: 37806154 DOI: 10.1016/j.phymed.2023.155120] [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: 03/26/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common types of cancer. This disease arises from gene mutations and epigenetic alterations that transform colonic epithelial cells into colon adenocarcinoma cells, which display a unique gene expression pattern compared to normal cells. Specifically, CRC cells exhibit significantly higher expression levels of genes involved in DNA repair or replication, which is attributed to the accumulation of DNA breakage resulting from rapid cell cycle progression. PURPOSE This study aimed to investigate the in vivo effects of caffeine on CRC cells and evaluate its impact on the sensitivity of these cells to irinotecan, a topoisomerase I inhibitor widely used for CRC treatment. METHODS Two CRC cell lines, HCT116 and HT29, were treated with irinotecan and caffeine. Western blot analysis assessed protein expression levels in caffeine/irinotecan-treated CRC cells. Immunofluorescence staining determined protein localization, measured DNA breaks, and explored the effects of DNA damage reagents during cell cycle progression and flow cytometry analysis was used to measure cell viability. Fiber assays investigated DNA synthesis in DNA-damaged cells during S-phase, while the comet assay assessed DNA fragmentation caused by DNA breaks. RESULTS Our findings demonstrated that the combination of irinotecan and caffeine exhibits a synergistic effect in suppressing CRC cell proliferation and inducing cell death. Compared to treatment with only irinotecan or caffeine, the combined irinotecan and caffeine treatment was more effective in inducing DNA lesions by displacing RAD51 from DNA break sites and inhibiting DNA repair progression, leading to cell cycle arrest. This combination also resulted in more severe effects, including DNA fragmentation and mitotic catastrophe. CONCLUSION Caffeine could enhance the effectiveness of an existing drug for CRC treatment despite having little impact on the cell survival rate of CRC cells. Our findings suggest that the beneficial adjuvant effects of caffeine may not only be applicable to CRC but also to various other types of cancers at different stages of development.
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Affiliation(s)
- Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University of Albany-State University of New York, Rensselaer, NY, USA
| | - Keun Pil Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea.
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22
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Hurley KE, Banerjee SK, Stephens AC, Scribner MR, Cooper VS, Richardson AR. The contribution of DNA repair pathways to Staphylococcus aureus fitness and fidelity during nitric oxide stress. mBio 2023; 14:e0215623. [PMID: 37948342 PMCID: PMC10746251 DOI: 10.1128/mbio.02156-23] [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: 08/15/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023] Open
Abstract
Staphylococcus aureus is a major human pathogen that causes a variety of illnesses, ranging from minor skin and soft tissue infections to more severe systemic infections. Although the primary host immune response can typically clear bacterial infections, S. aureus is uniquely resistant to inflammation. For instance, our laboratory has determined that S. aureus is highly resistant to nitric oxide (NO⋅), an important component of the innate immune response that plays a role in both immunomodulatory and antibacterial processes. Additionally, NO⋅ and its derivatives can cause damage to S. aureus DNA, more specifically, deamination and/or oxidation of DNA bases; however, regulation and repair mechanisms of DNA in S. aureus are understudied. Thus, we hypothesize that several DNA repair mechanisms may account for the replication fidelity of S. aureus and may contribute to fitness in the presence of NO⋅. Here, we show the role of several DNA repair mechanisms in S. aureus. More specifically, we found that recombinational repair genes recJ, recG, and polA may play a role in the repair of NO⋅-induced replication fork collapses. We also show the role of the base excision repair pathway protein, MutY, in reducing NO⋅-mediated mutagenesis. Overall, our results suggest that NO⋅ leads to DNA damage, which subsequently induces the activity of several DNA repair pathways, contributing to the replication fidelity and fitness of S. aureus.IMPORTANCEPathogenic bacteria must evolve various mechanisms in order to evade the host immune response that they are infecting. One aspect of the primary host immune response to an infection is the production of an inflammatory effector component, nitric oxide (NO⋅). Staphylococcus aureus has uniquely evolved a diverse array of strategies to circumvent the inhibitory activity of nitric oxide. One such mechanism by which S. aureus has evolved allows the pathogen to survive and maintain its genomic integrity in this environment. For instance, here, our results suggest that S. aureus employs several DNA repair pathways to ensure replicative fitness and fidelity under NO⋅ stress. Thus, our study presents evidence of an additional strategy that allows S. aureus to evade the cytotoxic effects of host NO⋅.
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Affiliation(s)
- Kelly E. Hurley
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Srijon K. Banerjee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amelia C. Stephens
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michelle R. Scribner
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anthony R. Richardson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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23
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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24
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Abbasi SF, Mahjabeen I, Parveen N, Qamar I, Haq MFU, Shafique R, Saeed N, Ashraf NS, Kayani MA. Exploring homologous recombination repair and base excision repair pathway genes for possible diagnostic markers in hematologic malignancies. Mol Genet Genomics 2023; 298:1527-1543. [PMID: 37861816 DOI: 10.1007/s00438-023-02078-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
Hematologic malignancies (HMs) are a collection of malignant transformations, originating from the cells in the bone marrow and lymphoid organs. HMs comprise three main types; leukemia, lymphoma, and multiple myeloma. Globally, HMS accounts for approximately 10% of newly diagnosed cancer. DNA repair pathways defend the cells from recurrent DNA damage. Defective DNA repair mechanisms such as homologous recombination repair (HRR), nucleotide excision repair (NER), and base excision repair (BER) pathways may lead to genomic instability, which initiates HM progression and carcinogenesis. Expression deregulation of HRR, NER, and BER has been investigated in various malignancies. However, no studies have been reported to assess the differential expression of selected DNA repair genes combinedly in HMs. The present study was designed to assess the differential expression of HRR and BER pathway genes including RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 in blood cancer patients to highlight their significance as diagnostic/ prognostic marker in hematological malignancies. The study cohort comprised of 210 blood cancer patients along with an equal number of controls. For expression analysis, q-RT PCR was performed. DNA damage was measured in blood cancer patients and controls using the comet assay and LORD Q-assay. Data analysis showed significant downregulation of selected genes in blood cancer patients compared to healthy controls. To check the diagnostic value of selected genes, the Area under curve (AUC) was calculated and 0.879 AUC was observed for RAD51 (p < 0.0001) and 0.830 (p < 0.0001) for APEX1. Kaplan-Meier analysis showed that downregulation of RAD51 (p < 0.0001), XRCC3 (p < 0.02), and APEX1 (p < 0.0001) was found to be associated with a significant decrease in survival of blood cancer patients. Cox regression analysis showed that deregulation of RAD51 (p < 0.0001), XRCC2 (p < 0.02), XRCC3 (p < 0.003), and APEX1 (p < 0.00001) was found to be associated with the poor prognosis of blood cancer patients. Comet assay showed an increased number of comets in blood cancer patients compared to controls. These results are confirmed by performing the LORD q-assay and an increased frequency of lesions/Kb was observed in selected genes in cancer patients compared to controls. Our results showed significant downregulation of RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 genes with increased DNA damage in blood cancer patients. The findings of the current research suggested that deregulated expression of HRR and BER pathway genes can act as a diagnostic/prognostic marker in hematologic malignancies.
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Affiliation(s)
- Sumaira Fida Abbasi
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan.
| | - Neelam Parveen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Imama Qamar
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Maria Fazal Ul Haq
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Rabia Shafique
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nadia Saeed
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nida Sarosh Ashraf
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
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25
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Tur-Planells V, García-Sastre A, Cuadrado-Castano S, Nistal-Villan E. Engineering Non-Human RNA Viruses for Cancer Therapy. Vaccines (Basel) 2023; 11:1617. [PMID: 37897020 PMCID: PMC10611381 DOI: 10.3390/vaccines11101617] [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: 09/08/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Alongside the development and progress in cancer immunotherapy, research in oncolytic viruses (OVs) continues advancing novel treatment strategies to the clinic. With almost 50 clinical trials carried out over the last decade, the opportunities for intervention using OVs are expanding beyond the old-fashioned concept of "lytic killers", with promising breakthrough therapeutic strategies focused on leveraging the immunostimulatory potential of different viral platforms. This review presents an overview of non-human-adapted RNA viruses engineered for cancer therapy. Moreover, we describe the diverse strategies employed to manipulate the genomes of these viruses to optimize their therapeutic capabilities. By focusing on different aspects of this particular group of viruses, we describe the insights into the promising advancements in the field of virotherapy and its potential to revolutionize cancer treatment.
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Affiliation(s)
- Vicent Tur-Planells
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Cuadrado-Castano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute (IGI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Estanislao Nistal-Villan
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
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26
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Butkiewicz D, Krześniak M, Gdowicz-Kłosok A, Składowski K, Rutkowski T. DNA Double-Strand Break Response and Repair Gene Polymorphisms May Influence Therapy Results and Prognosis in Head and Neck Cancer Patients. Cancers (Basel) 2023; 15:4972. [PMID: 37894339 PMCID: PMC10605140 DOI: 10.3390/cancers15204972] [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: 09/18/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Radiotherapy and cisplatin-based chemotherapy belong to the main treatment modalities for head and neck squamous cell carcinoma (HNSCC) and induce cancer cell death by generating DNA damage, including the most severe double-strand breaks (DSBs). Alterations in DSB response and repair genes may affect individual DNA repair capacity and treatment sensitivity, contributing to the therapy resistance and poor prognosis often observed in HNSCC. In this study, we investigated the association of a panel of single-nucleotide polymorphisms (SNPs) in 20 DSB signaling and repair genes with therapy results and prognosis in 505 HNSCC patients treated non-surgically with DNA damage-inducing therapies. In the multivariate analysis, there were a total of 14 variants associated with overall, locoregional recurrence-free or metastasis-free survival. Moreover, we identified 10 of these SNPs as independent predictors of therapy failure and unfavorable prognosis in the whole group or in two treatment subgroups. These were MRE11 rs2155209, XRCC5 rs828907, RAD51 rs1801321, rs12593359, LIG4 rs1805388, CHEK1 rs558351, TP53 rs1042522, ATM rs1801516, XRCC6 rs2267437 and NBN rs2735383. Only CHEK1 rs558351 remained statistically significant after correcting for multiple testing. These results suggest that specific germline variants related to DSB response and repair may be potential genetic modifiers of therapy effects and disease progression in HNSCC treated with radiotherapy and cisplatin-based chemoradiation.
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Affiliation(s)
- Dorota Butkiewicz
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Małgorzata Krześniak
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Agnieszka Gdowicz-Kłosok
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Krzysztof Składowski
- I Radiation and Clinical Oncology Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
| | - Tomasz Rutkowski
- I Radiation and Clinical Oncology Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
- Radiotherapy Department, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
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27
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Li L, Vasan L, Kartono B, Clifford K, Attarpour A, Sharma R, Mandrozos M, Kim A, Zhao W, Belotserkovsky A, Verkuyl C, Schmitt-Ulms G. Advances in Recombinant Adeno-Associated Virus Vectors for Neurodegenerative Diseases. Biomedicines 2023; 11:2725. [PMID: 37893099 PMCID: PMC10603849 DOI: 10.3390/biomedicines11102725] [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: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors are gene therapy delivery tools that offer a promising platform for the treatment of neurodegenerative diseases. Keeping up with developments in this fast-moving area of research is a challenge. This review was thus written with the intention to introduce this field of study to those who are new to it and direct others who are struggling to stay abreast of the literature towards notable recent studies. In ten sections, we briefly highlight early milestones within this field and its first clinical success stories. We showcase current clinical trials, which focus on gene replacement, gene augmentation, or gene suppression strategies. Next, we discuss ongoing efforts to improve the tropism of rAAV vectors for brain applications and introduce pre-clinical research directed toward harnessing rAAV vectors for gene editing applications. Subsequently, we present common genetic elements coded by the single-stranded DNA of rAAV vectors, their so-called payloads. Our focus is on recent advances that are bound to increase treatment efficacies. As needed, we included studies outside the neurodegenerative disease field that showcased improved pre-clinical designs of all-in-one rAAV vectors for gene editing applications. Finally, we discuss risks associated with off-target effects and inadvertent immunogenicity that these technologies harbor as well as the mitigation strategies available to date to make their application safer.
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Affiliation(s)
- Leyao Li
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
| | - Lakshmy Vasan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Bryan Kartono
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Kevan Clifford
- Institute of Medical Science, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Centre for Addiction and Mental Health (CAMH), 250 College St., Toronto, ON M5T 1R8, Canada
| | - Ahmadreza Attarpour
- Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Raghav Sharma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Matthew Mandrozos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ain Kim
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Wenda Zhao
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ari Belotserkovsky
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Claire Verkuyl
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Centre, 6th Floor, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, 6th Floor, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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28
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Rastokina A, Cebrián J, Mozafari N, Mandel NH, Smith CI, Lopes M, Zain R, Mirkin S. Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers. Nucleic Acids Res 2023; 51:8532-8549. [PMID: 37216608 PMCID: PMC10484681 DOI: 10.1093/nar/gkad441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/02/2023] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Friedreich's ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron of the human FXN gene that occur during both intergenerational transmissions and in somatic cells. Here we describe an experimental system to analyze large-scale repeat expansions in cultured human cells. It employs a shuttle plasmid that can replicate from the SV40 origin in human cells or be stably maintained in S. cerevisiae utilizing ARS4-CEN6. It also contains a selectable cassette allowing us to detect repeat expansions that accumulated in human cells upon plasmid transformation into yeast. We indeed observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system to study large-scale repeat expansions in human cells. Further, GAA•TTC repeats stall replication fork progression, while the frequency of repeat expansions appears to depend on proteins implicated in replication fork stalling, reversal, and restart. Locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers, which interfere with triplex formation at GAA•TTC repeats in vitro, prevented the expansion of these repeats in human cells. We hypothesize, therefore, that triplex formation by GAA•TTC repeats stall replication fork progression, ultimately leading to repeat expansions during replication fork restart.
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Affiliation(s)
| | - Jorge Cebrián
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | | | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
- Center for Rare Diseases, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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29
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Shi M, Hou J, Liang W, Li Q, Shao S, Ci S, Shu C, Zhao X, Zhao S, Huang M, Wu C, Hu Z, He L, Guo Z, Pan F. GAPDH facilitates homologous recombination repair by stabilizing RAD51 in an HDAC1-dependent manner. EMBO Rep 2023; 24:e56437. [PMID: 37306047 PMCID: PMC10398663 DOI: 10.15252/embr.202256437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/13/2023] Open
Abstract
Homologous recombination (HR), a form of error-free DNA double-strand break (DSB) repair, is important for the maintenance of genomic integrity. Here, we identify a moonlighting protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as a regulator of HR repair, which is mediated through HDAC1-dependent regulation of RAD51 stability. Mechanistically, in response to DSBs, Src signaling is activated and mediates GAPDH nuclear translocation. Then, GAPDH directly binds with HDAC1, releasing it from its suppressor. Subsequently, activated HDAC1 deacetylates RAD51 and prevents it from undergoing proteasomal degradation. GAPDH knockdown decreases RAD51 protein levels and inhibits HR, which is re-established by overexpression of HDAC1 but not SIRT1. Notably, K40 is an important acetylation site of RAD51, which facilitates stability maintenance. Collectively, our findings provide new insights into the importance of GAPDH in HR repair, in addition to its glycolytic activity, and they show that GAPDH stabilizes RAD51 by interacting with HDAC1 and promoting HDAC1 deacetylation of RAD51.
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Affiliation(s)
- Munan Shi
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Jiajia Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Weichu Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qianwen Li
- Department of Radiotherapy, Taikang Xianlin Drum Tower HospitalNanjing UniversityNanjingChina
| | - Shan Shao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Shusheng Ci
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Chuanjun Shu
- Department of Bioinformatics, School of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjingChina
| | - Xingqi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Shanmeizi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Miaoling Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Congye Wu
- Department of Oncology, Nanjing First HospitalNanjing Medical UniversityNanjingChina
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
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Gupta P, Sambyal V, Guleria K, Uppal MS, Sudan M. Association of RAD51, XRCC1, XRCC2, and XRCC3 Polymorphisms with Risk of Breast Cancer. Genet Test Mol Biomarkers 2023; 27:205-214. [PMID: 37522793 DOI: 10.1089/gtmb.2023.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Background: DNA repair genes are among the low-penetrance genes implicated in breast cancer. However variants of DNA repair genes may alter their protein function thus leading to carcinogenesis. Breast cancer is the most common cancer among women in India. The aim of the present study was to identify association, if any, of single nucleotide polymorphisms (SNP's) in four genes involved in DNA repair pathways including, RAD51 rs1801320, XRCC1 rs25487, XRCC2 rs3218536, and XRCC3 rs861539 with the risk of breast cancer. Materials and Methods: In this case-control study 611 female subjects (311 breast cancer patients and 300 healthy controls) were screened for four SNPs using polymerase chain reaction-restriction fragment length polymorphism analyses. Multifactor dimensionality reduction (MDR) analysis was performed to estimate the gene-gene interaction. Protein-protein interaction network analysis were studied using the STRING database. Results: The GC genotype (p = 0.018) and the combined GC+CC (p = 0.03) genotypes of RAD51 rs1801320 were significantly associated with reduced risk of breast cancer. The CT genotype (p = 0.0001), the combined CT+TT genotypes (p = 0.0002), and the T allele (p = 0.0019) of XRCC3 rs861539 polymorphism were associated with reduced risk of the breast cancer. No association of XRCC1 rs25487 and XRCC2 rs3218536 polymorphisms with breast cancer was observed. MDR analysis indicated a positive interaction between XRCC3 and XRCC2. String network analysis showed that the RAD51, XRCC1, XRCC2, and XRCC3 proteins are in strong interaction with each other and other breast cancer-related proteins such as BRCA2. Conclusion: RAD51 rs1801320 and XRCC3 rs861539 polymorphisms were associated with reduced risk of breast cancer. There is evidence of positive interactions among XRCC1, XRCC2, XRCC3, and RAD51.
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Affiliation(s)
- Priyanka Gupta
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - Vasudha Sambyal
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - Kamlesh Guleria
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, India
| | - Manjit Singh Uppal
- Department of Surgery and Sri Guru Ram Das Institute of Medical Sciences and Research, Amritsar, India
| | - Meena Sudan
- Department of Radiotherapy, Sri Guru Ram Das Institute of Medical Sciences and Research, Amritsar, India
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Yu C, Hou L, Huang Y, Cui X, Xu S, Wang L, Yan S. The multi-BRCT domain protein DDRM2 promotes the recruitment of RAD51 to DNA damage sites to facilitate homologous recombination. THE NEW PHYTOLOGIST 2023; 238:1073-1084. [PMID: 36727295 DOI: 10.1111/nph.18787] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
DNA double-strand breaks (DSBs) are the most toxic form of DNA damage in cells. Homologous recombination (HR) is an error-free repair mechanism for DSBs as well as a basis for gene targeting using genome-editing techniques. Despite the importance of HR, the HR mechanism in plants is poorly understood. Through genetic screens for DNA damage response mutants (DDRMs), we find that the Arabidopsis ddrm2 mutant is hypersensitive to DSB-inducing reagents. DDRM2 encodes a protein with four BRCA1 C-terminal (BRCT) domains and is highly conserved in plants including bryophytes, the earliest land plant lineage. The plant-specific transcription factor SOG1 binds to the promoter of DDRM2 and activates its expression. In consistence, the expression of DDRM2 is induced by DSBs in a SOG1-dependent manner. In support, genetic analysis suggests that DDRM2 functions downstream of SOG1. Similar to the sog1 mutant, the ddrm2 mutant shows dramatically reduced HR efficiency. Mechanistically, DDRM2 interacts with the core HR protein RAD51 and is required for the recruitment of RAD51 to DSB sites. Our study reveals that SOG1-DDRM2-RAD51 is a novel module for HR, providing a potential target for improving the efficiency of gene targeting.
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Affiliation(s)
- Chen Yu
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Longhui Hou
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiaoyu Cui
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shijun Xu
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
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32
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Chen R, Feng S, Ren J, Kang H, Yang Y, Xia N, Fang F, Wei B. Enzymatic Assembly of DNA Nanostructures and Fragments with Sequence Overlaps. J Am Chem Soc 2023; 145:9176-9181. [PMID: 37125454 DOI: 10.1021/jacs.3c01214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Homologous recombination, an evolutionarily conserved DNA double-strand break repair pathway to protect genome stability, has long been exploited for the in vivo and in vitro assembly of multiple DNA duplex fragments in molecular cloning. Whether such methods can also be applied in the self-assembly of DNA nanostructures remains underexplored. Here, we report an enzymatic approach for the self-assembly of high-order DNA constructs with overlapping segments. In our system, a DNA polymerase with exonuclease activity was introduced to produce ssDNA overhangs for specific sticky end cohesion, and as many as 25 DNA structural units were designed to be hierarchically assembled. Using this approach, we successfully constructed a variety of high-order DNA nanostructures, including tubes and extended oligomers, from homogeneous assembly and custom multimers from heterogeneous assembly. Our strategy expands the construction toolbox of complex DNA nanostructures and highlights the potential to enhance the assembly of duplex fragments in molecular cloning.
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Affiliation(s)
- Rong Chen
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Shuang Feng
- CodeR Therapeutics, Ltd., Hefei, Anhui 230000, China
| | - Jieling Ren
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Hong Kang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yufan Yang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Ninuo Xia
- CodeR Therapeutics, Ltd., Hefei, Anhui 230000, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Fang Fang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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Tang H, Kulkarni S, Peters C, Eddison J, Al-Ani M, Madhusudan S. The Current Status of DNA-Repair-Directed Precision Oncology Strategies in Epithelial Ovarian Cancers. Int J Mol Sci 2023; 24:ijms24087293. [PMID: 37108451 PMCID: PMC10138422 DOI: 10.3390/ijms24087293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Survival outcomes for patients with advanced ovarian cancer remain poor despite advances in chemotherapy and surgery. Platinum-based systemic chemotherapy can result in a response rate of up to 80%, but most patients will have recurrence and die from the disease. Recently, the DNA-repair-directed precision oncology strategy has generated hope for patients. The clinical use of poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA germ-line-deficient and/or platinum-sensitive epithelial ovarian cancers has improved survival. However, the emergence of resistance is an ongoing clinical challenge. Here, we review the current clinical state of PARP inhibitors and other clinically viable targeted approaches in epithelial ovarian cancers.
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Affiliation(s)
- Hiu Tang
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Sanat Kulkarni
- Department of Medicine, Sandwell and West Birmingham Hospitals, Lyndon, West Bromwich B71 4HJ, UK
| | - Christina Peters
- Department of Oncology, Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton BN2 5BD, UK
| | - Jasper Eddison
- College of Medical & Dental Sciences, University of Birmingham Medical School, Birmingham B15 2TT, UK
| | - Maryam Al-Ani
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Srinivasan Madhusudan
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham NG7 3RD, UK
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34
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Chang T, Lian Z, Ma S, Liang Z, Ma X, Wen X, Wang Y, Liu R. Combination with vorinostat enhances the antitumor activity of cisplatin in castration-resistant prostate cancer by inhibiting DNA damage repair pathway and detoxification of GSH. Prostate 2023; 83:470-486. [PMID: 36576015 DOI: 10.1002/pros.24479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Like DNA methylation, histone modifications are considered important processes for epigenetic alterations in gene function, and abnormally high expression of histone deacetylases (HDACs) plays a key role in many human diseases. In addition to regulating the acetylation levels of histone and non-histone proteins and gene transcription, HDAC inhibitors as antitumor drugs can also affect the DNA damage repair (DDR) pathway in tumor cells. Prostate cancer (PCa) is one of the most heritable malignancies in which DDR pathway defects can be detected in a considerable proportion of cases. Such defects are more prevalent in castration-resistant prostate cancer (CRPC) and are highly enriched in metastatic lesions. There is currently evidence that DDR pathway-deficient PCa is associated with high-risk biological behaviors and response sensitivity to platinum-based chemotherapy. Platinum-based drugs have been used in multiple clinical trials as monotherapy or in combination with other chemotherapeutic agents for the treatment of CRPC. METHODS This study evaluated the combined anticancer effect of (cisplatin) CDDP and the HDAC inhibitors vorinostat (SAHA) on three androgen-dependent cell lines PC-3, DU-145, and C4-2B in vitro. The efficacy and safety of SAHA combined with CDDP in the treatment of CRPC were further verified through animal experiments. RESULTS The combination of the two drugs increases cytotoxic effects by increasing DNA damage. Our results showed that the SAHA could not only reduce the expression of homologous recombinant repair proteins BRCA2, BRCA1, PARP1, and RAD51, but also decrease enzymes that Reduce the key enzymes of GSH biosynthesis, GSS and GCLC, and GSTP1 which can catalyze the binding of GSH to cisplatin. The intracellular GSH level also decreased with the increase of SAHA concentration, at the same time, the content of intracellular Pt element. CONCLUSION The combination of CDDP and SAHA can produce synergistic anticancer effects in androgen-independent PCa cells in vitro and in vivo. Our results open up a new avenue for the effective treatment of CRPC. To optimize the chemotherapy regimen for patients with advanced PCa, it is necessary to further study the molecular mechanism of platinum drugs, HDAC inhibitors, and their combined action.
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Affiliation(s)
- Taihao Chang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhenpeng Lian
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Urology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Shenfei Ma
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhengxin Liang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xudong Ma
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xiaodong Wen
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yanming Wang
- Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin, China
| | - Ranlu Liu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
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Kang Y, Zhang Q, Feng YX, Yang L, Yu XZ. Exogenous proline activated an integrated response of NER and HR pathways to reduce DNA damage in rice seedlings under chromium stress. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:51792-51803. [PMID: 36820975 DOI: 10.1007/s11356-023-26009-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The DNA damage induced by hexavalent chromium [Cr(VI)] pollutant causes a genotoxic effect on rice seedlings. Hereby, we examined the effects of exogenous proline (Pro) on the alleviation of DNA damage in rice seedlings under different effective concentrations of Cr(VI). Our results revealed that Cr(VI) stress induced reactive oxygen species (ROS), i.e., H2O2 and O2·- accumulation in rice seedlings, repressed genes expression activated in the homologous recombination (HR) and nucleotide excision repair (NER) pathways, and caused DNA damage. Exogenous application of Pro increased Cr accumulation in rice roots, but decreased Cr accumulation in rice shoots, wherein Pro application decreased ROS accumulation in both tissues of rice seedlings. The comet assays suggested that exogenous application of Pro significantly alleviated the DNA damage in rice seedlings during Cr(VI) treatments, judged by the Olive tail moment and tail DNA. Transcriptional assays revealed that exogenous Pro upregulated the expression level of genes associated with the HR and NER pathways and triggered coordinated actions of both repairing pathways to modulate DNA lesion in rice plants during exposure to Cr(VI). Calculations from gene expression variation factors showed that regulative effect of exogenous application of Pro on DNA repair pathways was highly activated at 2.0 mg Cr/L. The current study revealed that Cr(VI) affect rice plants and exogenous Pro rescue these effects by the activation of HR and NER pathways.
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Affiliation(s)
- Yi Kang
- The Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology|, Guilin, 541004, People's Republic of China
| | - Qing Zhang
- The Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology|, Guilin, 541004, People's Republic of China
| | - Yu-Xi Feng
- The Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology|, Guilin, 541004, People's Republic of China
| | - Li Yang
- The Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology|, Guilin, 541004, People's Republic of China
| | - Xiao-Zhang Yu
- The Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology|, Guilin, 541004, People's Republic of China.
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Tisseverasinghe S, Bahoric B, Anidjar M, Probst S, Niazi T. Advances in PARP Inhibitors for Prostate Cancer. Cancers (Basel) 2023; 15:cancers15061849. [PMID: 36980735 PMCID: PMC10046616 DOI: 10.3390/cancers15061849] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Poly-adenosine diphosphate-ribose polymerase plays an essential role in cell function by regulating apoptosis, genomic stability and DNA repair. PARPi is a promising drug class that has gained significant traction in the last decade with good outcomes in different cancers. Several trials have sought to test its effectiveness in metastatic castration resistant prostate cancer (mCRPC). We conducted a comprehensive literature review to evaluate the current role of PARPi in this setting. To this effect, we conducted queries in the PubMed, Embase and Cochrane databases. We reviewed and compared all major contemporary publications on the topic. In particular, recent phase II and III studies have also demonstrated the benefits of olaparib, rucaparib, niraparib, talazoparib in CRPC. Drug effectiveness has been assessed through radiological progression or overall response. Given the notion of synthetic lethality and potential synergy with other oncological therapies, several trials are looking to integrate PARPi in combined therapies. There remains ongoing controversy on the need for genetic screening prior to treatment initiation as well as the optimal patient population, which would benefit most from PARPi. PARPi is an important asset in the oncological arsenal for mCRPC. New combinations with PARPi may improve outcomes in earlier phases of prostate cancer.
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Affiliation(s)
| | - Boris Bahoric
- Department of Radiation Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Maurice Anidjar
- Department of Urology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Stephan Probst
- Department of Nuclear Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Tamim Niazi
- Department of Radiation Oncology, McGill University, Montreal, QC H3A 0G4, Canada
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37
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Concannon K, Morris BB, Gay CM, Byers LA. Combining targeted DNA repair inhibition and immune-oncology approaches for enhanced tumor control. Mol Cell 2023; 83:660-680. [PMID: 36669489 PMCID: PMC9992136 DOI: 10.1016/j.molcel.2022.12.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/08/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023]
Abstract
Targeted therapy and immunotherapy have revolutionized cancer treatment. However, the ability of cancer to evade the immune system remains a major barrier for effective treatment. Related to this, several targeted DNA-damage response inhibitors (DDRis) are being tested in the clinic and have been shown to potentiate anti-tumor immune responses. Seminal studies have shown that these agents are highly effective in a pan-cancer class of tumors with genetic defects in key DNA repair genes such as BRCA1/2, BRCA-related genes, ataxia telangiectasia mutated (ATM), and others. Here, we review the molecular consequences of targeted DDR inhibition, from tumor cell death to increased engagement of the anti-tumor immune response. Additionally, we discuss mechanistic and clinical rationale for pairing targeted DDRis with immunotherapy for enhanced tumor control. We also review biomarkers for patient selection and promising new immunotherapy approaches poised to form the foundation of next-generation DDRi and immunotherapy combinations.
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Affiliation(s)
- Kyle Concannon
- Department of Hematology/Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin B Morris
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carl M Gay
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren A Byers
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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38
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Kaur J, Mojumdar A. A mechanistic overview of spinal cord injury, oxidative DNA damage repair and neuroprotective therapies. Int J Neurosci 2023; 133:307-321. [PMID: 33789065 DOI: 10.1080/00207454.2021.1912040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Despite substantial development in medical treatment strategies scientists are struggling to find a cure against spinal cord injury (SCI) which causes long term disability and paralysis. The prime rationale behind it is the enlargement of primary lesion due to an initial trauma to the spinal cord which spreads to the neighbouring spinal tissues It begins from the time of traumatic event happened and extends to hours and even days. It further causes series of biological and functional alterations such as inflammation, excitotoxicity and ischemia, and promotes secondary lesion to the cord which worsens the life of individuals affected by SCI. Oxidative DNA damage is a stern consequence of oxidative stress linked with secondary injury causes oxidative base alterations and strand breaks, which provokes cell death in neurons. It is implausible to stop primary damage however it is credible to halt the secondary lesion and improve the quality of the patient's life to some extent. Therefore it is crucial to understand the hidden perspectives of cell and molecular biology affecting the pathophysiology of SCI. Thus the focus of the review is to connect the missing links and shed light on the oxidative DNA damages and the functional repair mechanisms, as a consequence of the injury in neurons. The review will also probe the significance of neuroprotective strategies in the present scenario. HIGHLIGHTSSpinal cord injury, a pernicious condition, causes excitotoxicity and ischemia, ultimately leading to cell death.Oxidative DNA damage is a consequence of oxidative stress linked with secondary injury, provoking cell death in neurons.Base excision repair (BER) is one of the major repair pathways that plays a crucial role in repairing oxidative DNA damages.Neuroprotective therapies curbing SCI and boosting BER include the usage of pharmacological drugs and other approaches.
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Affiliation(s)
- Jaspreet Kaur
- Department of Neuroscience, University of Copenhagen, Copenhagen N, Denmark
| | - Aditya Mojumdar
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
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Yu N, Qin H, Zhang F, Liu T, Cao K, Yang Y, Chen Y, Cai J. The role and mechanism of long non-coding RNAs in homologous recombination repair of radiation-induced DNA damage. J Gene Med 2023; 25:e3470. [PMID: 36537017 DOI: 10.1002/jgm.3470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks can seriously damage the genetic information that organisms depend on for survival and reproduction. Therefore, cells require a robust DNA damage response mechanism to repair the damaged DNA. Homologous recombination (HR) allows error-free repair, which is key to maintaining genomic integrity. Long non-coding RNAs (lncRNAs) are RNA molecules that are longer than 200 nucleotides. In recent years, a number of studies have found that lncRNAs can act as regulators of gene expression and DNA damage response mechanisms, including HR repair. Moreover, they have significant effects on the occurrence, development, invasion and metastasis of tumor cells, as well as the sensitivity of tumors to radiotherapy and chemotherapy. These studies have therefore begun to expose the great potential of lncRNAs for clinical applications. In this review, we focus on the regulatory roles of lncRNAs in HR repair.
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Affiliation(s)
- Nanxi Yu
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
| | - Hongran Qin
- Department of Nuclear Radiation, Shanghai Pulmonary Hospital,School of Medicine, Tongji University, Shanghai, China
| | - Fangxiao Zhang
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China
| | - Tingting Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Kun Cao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Yuanyuan Chen
- South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China.,Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, China
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, China
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Johnston CHG, Hope R, Soulet AL, Dewailly M, De Lemos D, Polard P. The RecA-directed recombination pathway of natural transformation initiates at chromosomal replication forks in the pneumococcus. Proc Natl Acad Sci U S A 2023; 120:e2213867120. [PMID: 36795748 PMCID: PMC9974461 DOI: 10.1073/pnas.2213867120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/09/2022] [Indexed: 02/17/2023] Open
Abstract
Homologous recombination (HR) is a crucial mechanism of DNA strand exchange that promotes genetic repair and diversity in all kingdoms of life. Bacterial HR is driven by the universal recombinase RecA, assisted in the early steps by dedicated mediators that promote its polymerization on single-stranded DNA (ssDNA). In bacteria, natural transformation is a prominent HR-driven mechanism of horizontal gene transfer specifically dependent on the conserved DprA recombination mediator. Transformation involves internalization of exogenous DNA as ssDNA, followed by its integration into the chromosome by RecA-directed HR. How DprA-mediated RecA filamentation on transforming ssDNA is spatiotemporally coordinated with other cellular processes remains unknown. Here, we tracked the localization of fluorescent fusions to DprA and RecA in Streptococcus pneumoniae and revealed that both accumulate in an interdependent manner with internalized ssDNA at replication forks. In addition, dynamic RecA filaments were observed emanating from replication forks, even with heterologous transforming DNA, which probably represent chromosomal homology search. In conclusion, this unveiled interaction between HR transformation and replication machineries highlights an unprecedented role for replisomes as landing pads for chromosomal access of tDNA, which would define a pivotal early HR step for its chromosomal integration.
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Affiliation(s)
- Calum H. G. Johnston
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - Rachel Hope
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
- Department of Life Sciences, Imperial College, SW7 2AZLondon, UK
| | - Anne-Lise Soulet
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - Marie Dewailly
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - David De Lemos
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, 31062Toulouse, France
- Université Paul Sabatier (Toulouse III), 31062Toulouse, France
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Through the Looking Glass: Updated Insights on Ovarian Cancer Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13040713. [PMID: 36832201 PMCID: PMC9955065 DOI: 10.3390/diagnostics13040713] [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: 12/05/2022] [Revised: 01/30/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the deadliest gynaecological malignancy and the eighth most prevalent cancer in women, with an abysmal mortality rate of two million worldwide. The existence of multiple overlapping symptoms with other gastrointestinal, genitourinary, and gynaecological maladies often leads to late-stage diagnosis and extensive extra-ovarian metastasis. Due to the absence of any clear early-stage symptoms, current tools only aid in the diagnosis of advanced-stage patients, wherein the 5-year survival plummets further to less than 30%. Therefore, there is a dire need for the identification of novel approaches that not only allow early diagnosis of the disease but also have a greater prognostic value. Toward this, biomarkers provide a gamut of powerful and dynamic tools to allow the identification of a spectrum of different malignancies. Both serum cancer antigen 125 (CA-125) and human epididymis 4 (HE4) are currently being used in clinics not only for EOC but also peritoneal and GI tract cancers. Screening of multiple biomarkers is gradually emerging as a beneficial strategy for early-stage diagnosis, proving instrumental in administration of first-line chemotherapy. These novel biomarkers seem to exhibit an enhanced potential as a diagnostic tool. This review summarizes existing knowledge of the ever-growing field of biomarker identification along with potential future ones, especially for ovarian cancer.
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Song W, Li A, Sha QQ, Liu SY, Zhou Y, Zhou CY, Zhang X, Li XZ, Jiang JX, Li F, Li C, Schatten H, Ou XH, Sun QY. Maternal exposure to 4-vinylcyclohexene diepoxide during pregnancy induces subfertility and birth defects of offspring in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160431. [PMID: 36423845 DOI: 10.1016/j.scitotenv.2022.160431] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/13/2022] [Accepted: 11/19/2022] [Indexed: 06/16/2023]
Abstract
4-vinylcyclohexene diepoxide (VCD), widely used in industry, is a hazardous compound that can cause premature ovarian failure, but whether maternal VCD exposure affects the health and reproduction of offspring is unknown. Here we focused on the effects of VCD on fertility and physical health of F1 and F2 offspring in mice. The pregnant mice were injected intraperitoneally with different dosages of VCD once every day from 6.5 to 18.5 days post-coitus (dpc). We showed that maternal exposure to VCD during pregnancy significantly reduced the litter size and ovarian reserve, while increasing microtia occurrences of F1 mice. The cytospread staining showed a significant inhibition of meiotic prophase I progression from the zygotene stage to the pachytene stage. Mechanistically, the expression level of DNA damage marker (γ-H2AX) and BAX/BCL2 ratios were significantly increased, and RAD51 and DMC1 were extensively recruited to DNA double strand breaks sites in the oocytes of offspring from VCD-exposed mothers. Overall, our results provide solid evidence showing that maternal exposure to VCD during pregnancy has intergenerational deleterious effects on the offspring.
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Affiliation(s)
- Wei Song
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China; College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ang Li
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Qian-Qian Sha
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Shao-Yuan Liu
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Yong Zhou
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Chang-Yin Zhou
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Xue Zhang
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Xiao-Zhen Li
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Jia-Xin Jiang
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Fei Li
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Chao Li
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Xiang-Hong Ou
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China.
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China; College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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43
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Sang W, Liu J, Xing Y, Feng C, Hu Q, Lang Y, Li X, Bao J, Jiang H. Transcriptome analysis of hepatopancreas of Chinese grass shrimp, Palaemonetes sinensis, infected by Enterocytospora artemiae. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108557. [PMID: 36669602 DOI: 10.1016/j.fsi.2023.108557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The emergence of the microsporidian, Enterocytospora artemiae, has caused serious economic losses to the aquaculture industry of Palaemonetes sinensis. The hepatopancreas is the main digestive and immune organ of P. sinensis, and the main site of E. artemiae infection. We used next-generation sequencing to determine the effects of E. artemiae parasitism on the hepatopancreas of P. sinensis at the transcriptome level. The hepatopancreas of P. sinensis was parasitized by E. artemiae, and 881 differentially expressed genes (DEGs) were obtained, of which 643 were upregulated and 238 were downregulated. These DEGs are mainly involved in DNA replication, transcription, translation, immunity, and metabolism. Among them, the cellular processes of DNA replication, transcription and translation are significantly strengthened, which may be related to the use of host ATP and nucleic acid by E. artemiae to achieve proliferation and damage to host cells to enhance DNA replication and repair. Moreover, to defend against E. artemiae, some immune genes related to antioxidation, such as glutathione metabolism, seleno compound metabolism, and cytochrome p450 2L1, were significantly upregulated, but simultaneously, tumor necrosis factor, NF-κB inhibitor α, and other immune-related genes were significantly down regulated, indicating that the parasitism of E. artemiae led to a significant decline in the immune defense ability of P. sinensis. From the perspective of metabolism, the metabolism-related DEGs of retinol, glycine, serine, and threonine metabolism, were significantly downregulated, resulting in insufficient nutrient absorption and decreased energy supply of the P. sinensis, which in turn affected their growth. The differential genes and pathways identified in this study can provide a reference basis to further elucidate the pathogenic mechanism of P. sinensis infected with E. artemiae and the prevention and control of microsporidia disease.
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Affiliation(s)
- Wenjia Sang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jun Liu
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuenan Xing
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chengcheng Feng
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingbiao Hu
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuxi Lang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaodong Li
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jie Bao
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
| | - Hongbo Jiang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
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Sokolova A, Johnstone KJ, McCart Reed AE, Simpson PT, Lakhani SR. Hereditary breast cancer: syndromes, tumour pathology and molecular testing. Histopathology 2023; 82:70-82. [PMID: 36468211 PMCID: PMC10953374 DOI: 10.1111/his.14808] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 12/09/2022]
Abstract
Hereditary factors account for a significant proportion of breast cancer risk. Approximately 20% of hereditary breast cancers are attributable to pathogenic variants in the highly penetrant BRCA1 and BRCA2 genes. A proportion of the genetic risk is also explained by pathogenic variants in other breast cancer susceptibility genes, including ATM, CHEK2, PALB2, RAD51C, RAD51D and BARD1, as well as genes associated with breast cancer predisposition syndromes - TP53 (Li-Fraumeni syndrome), PTEN (Cowden syndrome), CDH1 (hereditary diffuse gastric cancer), STK11 (Peutz-Jeghers syndrome) and NF1 (neurofibromatosis type 1). Polygenic risk, the cumulative risk from carrying multiple low-penetrance breast cancer susceptibility alleles, is also a well-recognised contributor to risk. This review provides an overview of the established breast cancer susceptibility genes as well as breast cancer predisposition syndromes, highlights distinct genotype-phenotype correlations associated with germline mutation status and discusses molecular testing and therapeutic implications in the context of hereditary breast cancer.
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Affiliation(s)
- A Sokolova
- Sullivan and Nicolaides PathologyBrisbane
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - K J Johnstone
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
| | - A E McCart Reed
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - P T Simpson
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - S R Lakhani
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
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Legartová S, Fagherazzi P, Goswami P, Brazda V, Lochmanová G, Koutná I, Bártová E. Irradiation potentiates p53 phosphorylation and p53 binding to the promoter and coding region of the TP53 gene. Biochimie 2023; 204:154-168. [PMID: 36167255 DOI: 10.1016/j.biochi.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/08/2022] [Accepted: 09/21/2022] [Indexed: 01/12/2023]
Abstract
An essential factor of the DNA damage response is 53BP1, a multimeric protein that inhibits the resection-dependent double-strand break (DBS) repair. The p53 protein is a tumor suppressor known as a guardian of the genome. Although the interaction between 53BP1 and its p53 partner is well-known in regulating gene expression, a question remains whether genome injury can affect the interaction between 53BP1 and p53 proteins or p53 binding to DNA. Here, using mass spectrometry, we determine post-translational modifications and interaction properties of 53BP1 and p53 proteins in non-irradiated and γ-irradiated cells. In addition, we used Atomic Force Microscopy (AFM) and Fluorescent Lifetime Imaging Microscopy combined with Fluorescence Resonance Energy Transfer (FLIM-FRET) for studies of p53 binding to DNA. Also, we used local laser microirradiation as a tool of advanced confocal microscopy, showing selected protein accumulation at locally induced DNA lesions. We observed that 53BP1 and p53 proteins accumulate at microirradiated chromatin but with distinct kinetics. The density of 53BP1 (53BP1pS1778) phosphorylated form was lower in DNA lesions than in the non-specified form. By mass spectrometry, we found 22 phosphorylations, 4 acetylation sites, and methylation of arginine 1355 within the DNA-binding domain of the 53BP1 protein (aa1219-1711). The p53 protein was phosphorylated on 8 amino acids and acetylated on the N-terminal domain. Post-translational modifications (PTMs) of 53BP1 were not changed in cells exposed to γ-radiation, while γ-rays increased the level of S6ph and S15ph in p53. Interaction analysis showed that 53BP1 and p53 proteins have 54 identical interaction protein partners, and AFM revealed that p53 binds to both non-specific and TP53-specific sequences (AGACATGCCTA GGCATGTCT). Irradiation by γ-rays enhanced the density of the p53 protein at the AGACATGCCTAGGCATGTCT region, and the binding of p53 S15ph to the TP53 promoter was potentiated in irradiated cells. These findings show that γ-irradiation, in general, strengthens the binding of phosphorylated p53 protein to the encoding gene.
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Affiliation(s)
- Soňa Legartová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Paolo Fagherazzi
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Pratik Goswami
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Vaclav Brazda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Gabriela Lochmanová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Irena Koutná
- The International Clinical Research Center of St. Anne's University Hospital in Brno (FNUSA-ICRC), Pekařská 53, 656 91, Brno, Czech Republic
| | - Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Xing D, Li S, Shang M, Wang W, Zhang Q, Wang J, Hasin T, Hettiarachchi D, Alston V, Bern L, Parrales AP, Lu C, Coogan M, Johnson A, Qin Z, Su B, Dunham R. A New Strategy for Increasing Knock-in Efficiency: Multiple Elongase and Desaturase Transgenes Knock-in by Targeting Long Repeated Sequences. ACS Synth Biol 2022; 11:4210-4219. [PMID: 36332126 DOI: 10.1021/acssynbio.2c00252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CRISPR/Cas9-mediated knock-in (KI) has a wide application in gene therapy, gene function study, and transgenic breeding programs. Unlike gene therapy, which requires accurate KI to correct gene mutation, transgenic breeding programs can accept robust KI as long as integration does not interrupt normal gene functions and result in any negative pleiotropic effects. High KI efficiency is required to reduce the breeding cost and shorten the breeding period, especially in transferring multiple foreign genes to a single individual. To elevate the KI efficacy and achieve multiple gene KIs simultaneously, we introduced a new strategy that enables transgene integration into numerous sites of the genome by targeting long repeated sequences (LRSs). Using this simple strategy, for the first time we successfully generated transgenic fish carrying the masu salmon (Oncorhynchus masou) elovl2 gene and rabbitfish (Siganus canaliculatus) Δ4 fad and Δ6 fad genes, and achieved robust target KI of elovl2 and Δ6 fad genes at multiple sites of LRS1 and LRS3, respectively, in the initial generation. This demonstrated that donor plasmid homology arms, which were nearly identical but not completely the same as the genome sequence, still led to on-target KI. Although the target KI efficiencies at LRS1, LRS2, and LRS3 sites were still relatively low in the current study, it is very promising that 100% KI efficiency in the future could be realized and perfected by selection of better LRSs and optimization of sgRNAs.
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Affiliation(s)
- De Xing
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Shangjia Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Wenwen Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Qin Zhang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Tasnuba Hasin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Darshika Hettiarachchi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Veronica Alston
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Logan Bern
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Abel Paladines Parrales
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Cuiyu Lu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Michael Coogan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Andrew Johnson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao266003, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, Alabama36849, United States
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van der Merwe NC, Ntaita KS, Stofberg H, Combrink HM, Oosthuizen J, Kotze MJ. Implementation of multigene panel testing for breast and ovarian cancer in South Africa: A step towards excellence in oncology for the public sector. Front Oncol 2022; 12:938561. [PMID: 36568162 PMCID: PMC9768488 DOI: 10.3389/fonc.2022.938561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
Translation of genomic knowledge into public health benefits requires the implementation of evidence-based recommendations in clinical practice. In this study, we moved beyond BRCA1/2 susceptibility testing in breast and ovarian cancer patients to explore the application of pharmacogenetics across multiple genes participating in homologous recombination DNA damage repair. This involved the utilisation of next-generation sequencing (NGS) at the intersection of research and service delivery for development of a comprehensive genetic testing platform in South Africa. Lack of international consensus regarding risk categorization of established cancer susceptibility genes and the level of evidence required for prediction of drug response supported the development of a central database to facilitate clinical interpretation. Here we demonstrate the value of this approach using NGS to 1) determine the variant spectrum applicable to targeted therapy and implementation of prevention strategies using the 15-gene Oncomine™ BRCA Expanded Panel, and 2) searched for novel and known pathogenic variants in uninformative cases using whole exome sequencing (WES). Targeted NGS performed as a routine clinical service in 414 South African breast and/or ovarian cancer patients resulted in the detection of 48 actionable variants among 319 (15%) cases. BRCA1/2-associated cancers were identified in 70.8% of patients (34/48, including two double-heterozygotes), with the majority (35.3%, 12/34) representing known South African founder variants. Detection of actionable variants in established non-BRCA1/2 risk genes contributed 29% to the total percentage (14/48), distributed amongst ATM, CHEK2, BARD1, BRIP1, PALB2 and TP53. Experimental WES using a virtually constructed multi-cancer NGS panel in 16 genetically unresolved cases (and four controls) revealed novel protein truncating variants in the basal cell carcinoma gene PTCH1 (c.4187delG) and the signal transmission and transduction gene KIT (c.930delA) involved in crucial cellular processes. Based on these findings, the most cost-effective approach would be to perform BRCA1/2 founder variant testing at referral, followed by targeted multigene panel testing if clinically indicated and addition of WES in unresolved cases. This inventive step provides a constant flow of new knowledge into the diagnostic platform via a uniquely South African pathology-supported genetic approach implemented for the first time in this context to integrate research with service delivery.
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Affiliation(s)
- Nerina C. van der Merwe
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa,*Correspondence: Nerina C. van der Merwe,
| | - Kholiwe S. Ntaita
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Hanri Stofberg
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Herkulaas MvE. Combrink
- Office of the Dean, Economic and Management Sciences, University of the Free State, Bloemfontein, South Africa,Interdisciplinary Centre for Digital Futures, University of the Free State, Bloemfontein, South Africa
| | - Jaco Oosthuizen
- Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa,Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Maritha J. Kotze
- Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa,Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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FOXO3a Mediates Homologous Recombination Repair (HRR) via Transcriptional Activation of MRE11, BRCA1, BRIP1, and RAD50. Molecules 2022; 27:molecules27238623. [PMID: 36500714 PMCID: PMC9741359 DOI: 10.3390/molecules27238623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
To test whether homologous recombination repair (HRR) depends on FOXO3a, a cellular aging model of human dermal fibroblast (HDF) and tet-on flag-h-FOXO3a transgenic mice were studied. HDF cells transfected with over-expression of wt-h-FOXO3a increased the protein levels of MRE11, BRCA1, BRIP1, and RAD50, while knock-down with siFOXO3a decreased them. The protein levels of MRE11, BRCA1, BRIP1, RAD50, and RAD51 decreased during cellular aging. Chromatin immunoprecipitation (ChIP) assay was performed on FOXO3a binding accessibility to FOXO consensus sites in human MRE11, BRCA1, BRIP1, and RAD50 promoters; the results showed FOXO3a binding decreased during cellular aging. When the tet-on flag-h-FOXO3a mice were administered doxycycline orally, the protein and mRNA levels of flag-h-FOXO3a, MRE11, BRCA1, BRIP1, and RAD50 increased in a doxycycline-dose-dependent manner. In vitro HRR assays were performed by transfection with an HR vector and I-SceI vector. The mRNA levels of the recombined GFP increased after doxycycline treatment in MEF but not in wt-MEF, and increased in young HDF comparing to old HDF, indicating that FOXO3a activates HRR. Overall, these results demonstrate that MRE11, BRCA1, BRIP1, and RAD50 are transcriptional target genes for FOXO3a, and HRR activity is increased via transcriptional activation of MRE11, BRCA1, BRIP1, and RAD50 by FOXO3a.
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49
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DNA Damage Response in Cancer Therapy and Resistance: Challenges and Opportunities. Int J Mol Sci 2022; 23:ijms232314672. [PMID: 36499000 PMCID: PMC9735783 DOI: 10.3390/ijms232314672] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Resistance to chemo- and radiotherapy is a common event among cancer patients and a reason why new cancer therapies and therapeutic strategies need to be in continuous investigation and development. DNA damage response (DDR) comprises several pathways that eliminate DNA damage to maintain genomic stability and integrity, but different types of cancers are associated with DDR machinery defects. Many improvements have been made in recent years, providing several drugs and therapeutic strategies for cancer patients, including those targeting the DDR pathways. Currently, poly (ADP-ribose) polymerase inhibitors (PARP inhibitors) are the DDR inhibitors (DDRi) approved for several cancers, including breast, ovarian, pancreatic, and prostate cancer. However, PARPi resistance is a growing issue in clinical settings that increases disease relapse and aggravate patients' prognosis. Additionally, resistance to other DDRi is also being found and investigated. The resistance mechanisms to DDRi include reversion mutations, epigenetic modification, stabilization of the replication fork, and increased drug efflux. This review highlights the DDR pathways in cancer therapy, its role in the resistance to conventional treatments, and its exploitation for anticancer treatment. Biomarkers of treatment response, combination strategies with other anticancer agents, resistance mechanisms, and liabilities of treatment with DDR inhibitors are also discussed.
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50
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A novel homozygous variant in homologous recombination repair gene ZSWIM7 causes azoospermia in males and primary ovarian insufficiency in females. Eur J Med Genet 2022; 65:104629. [DOI: 10.1016/j.ejmg.2022.104629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/18/2022] [Accepted: 09/25/2022] [Indexed: 11/18/2022]
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