1
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Shimizu D, Ishibashi M, Yamada T, Toda Y, Hosogi S, Ashihara E. POLD1 Is Required for Cell Cycle Progression by Overcoming DNA Damage in Malignant Pleural Mesothelioma. Cancer Genomics Proteomics 2024; 21:158-165. [PMID: 38423601 PMCID: PMC10905272 DOI: 10.21873/cgp.20437] [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: 10/19/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND/AIM The prognosis of patients with malignant pleural mesothelioma (MPM) remains poor due to lack of effective therapeutic targets. DNA damage caused by long-time exposure to asbestos fibers has been associated with the development of MPM, with mutations at genes encoding DNA damage repair (DDR)-related molecules frequently expressed in patients with MPM. The present study was designed to identify novel therapeutic targets in MPM using large public databases, such as The Cancer Genome Atlas (TCGA) and Genotype Tissue Expression project (GTEx) focused on DDR pathways. MATERIALS AND METHODS The correlations between mRNA expression levels of DDR-related genes and overall survival (OS) were analyzed in mesothelioma patients in TCGA mesothelioma (TCGA-MESO) datasets. The anti-tumor effects of small interfering RNAs (siRNA) against DDR-related genes associated with OS were subsequently tested in MPM cell lines. RESULTS High levels of mRNA encoding DNA polymerase delta 1, catalytic subunit (POLD1) were significantly associated with reduced OS in patients with MPM (p<0.001, Log-rank test). In addition, siRNA targeting POLD1 (siPOLD1) caused cell cycle arrest at the G1/S checkpoint and induced apoptosis involving accumulation of DNA damage in MPM cell lines. CONCLUSION POLD1 plays essential roles in overcoming DNA damage and cell cycle progression at the G1/S checkpoint in MPM cells. These findings suggest that POLD1 may be a novel therapeutic target in MPM.
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Affiliation(s)
- Daiki Shimizu
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Miku Ishibashi
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Tadaaki Yamada
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuki Toda
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Shigekuni Hosogi
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Eishi Ashihara
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan;
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2
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Mori JO, Keegan J, Flynn RL, Heaphy CM. Alternative lengthening of telomeres: mechanism and the pathogenesis of cancer. J Clin Pathol 2024; 77:82-86. [PMID: 37890990 DOI: 10.1136/jcp-2023-209005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
Telomere maintenance and elongation allows cells to gain replicative immortality and evade cellular senescence during cancer development. While most cancers use telomerase to maintain telomere lengths, a subset of cancers engage the alternative lengthening of telomeres (ALT) pathway for telomere maintenance. ALT is present in 5%-10% of all cancers, although the prevalence is dramatically higher in certain cancer types, including complex karyotype sarcomas, isocitrate dehydrogenase-mutant astrocytoma (WHO grade II-IV), pancreatic neuroendocrine tumours, neuroblastoma and chromophobe hepatocellular carcinomas. ALT is maintained through a homology-directed DNA repair mechanism. Resembling break-induced replication, this aberrant process results in dramatic cell-to-cell telomere length heterogeneity, widespread chromosomal instability and chronic replication stress. Additionally, ALT-positive cancers frequently harbour inactivating mutations in either chromatin remodelling proteins (ATRX, DAXX and H3F3A) or DNA damage repair factors (SMARCAL1 and SLX4IP). ALT can readily be detected in tissue by assessing the presence of unique molecular characteristics, such as large ultrabright nuclear telomeric foci or partially single-stranded telomeric DNA circles (C-circles). Importantly, ALT has been validated as a robust diagnostic and prognostic biomarker for certain cancer types and may even be exploited as a therapeutic target via small molecular inhibitors and/or synthetic lethality approaches.
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Affiliation(s)
- Joakin O Mori
- Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Joshua Keegan
- Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Rachel L Flynn
- Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Pharmacology, Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Christopher M Heaphy
- Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Pathology and Laboratory Medicine, Boston Medical Center, Boston, Massachusetts, USA
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3
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Cakir MO, Bilge U, Ghanbari A, Ashrafi GH. Regulatory Effect of Ficus carica Latex on Cell Cycle Progression in Human Papillomavirus-Positive Cervical Cancer Cell Lines: Insights from Gene Expression Analysis. Pharmaceuticals (Basel) 2023; 16:1723. [PMID: 38139849 PMCID: PMC10747314 DOI: 10.3390/ph16121723] [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: 11/07/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Cervical cancer presents a significant global health concern with high-risk human papillomaviruses (HPVs) identified as the main cause of this cancer. Although current treatment methods for cervical cancer can eliminate lesions, preventing metastatic spread and minimizing tissue damage remain a major challenge. Therefore, the development of a safer and innovative therapeutic approach is of the utmost importance. Natural products like fig latex, derived from the Ficus carica tree, have demonstrated promising anti-cancer properties when tested on cervical cancer cell lines. However, the specific mechanisms by which fig latex exerts its effects are still unknown. In this study, we conducted RNA-Seq analysis to explore how fig latex may counteract carcinogenesis in HPV-positive cervical cancer cell lines, namely, CaSki (HPV type 16-positive) and HeLa (HPV type 18-positive). Our results from this investigation indicate that fig latex influences the expression of genes associated with the development and progression of cervical cancer, including pathways related to "Nonsense-Mediated Decay (NMD)", "Cell Cycle regulation", "Transcriptional Regulation by TP53", and "Apoptotic Process". This selective impact of fig latex on cancer-related pathways suggests a potential novel therapeutic approach for HPV-related cervical cancer.
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Affiliation(s)
- Muharrem Okan Cakir
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, London KT1 2EE, UK; (M.O.C.); (A.G.)
| | - Ugur Bilge
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Akdeniz University, Antalya 07050, Turkey;
| | - Arshia Ghanbari
- School of Life Sciences, Pharmacy and Chemistry, Kingston University London, London KT1 2EE, UK; (M.O.C.); (A.G.)
| | - G. Hossein Ashrafi
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Akdeniz University, Antalya 07050, Turkey;
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4
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Mehawej C, Chouery E, Azar-Atallah S, Shebaby W, Delague V, Mansour I, Mustapha M, Lefranc G, Megarbane A. POLD3 deficiency is associated with severe combined immunodeficiency, neurodevelopmental delay, and hearing impairment. Clin Immunol 2023; 251:109326. [PMID: 37030525 DOI: 10.1016/j.clim.2023.109326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
Combined immunodeficiency diseases (CID) represent the most severe forms of inborn errors of immunity. Defective T cell development and/or function, leading to an impairment in adaptive immunity are responsible for these diseases. The DNA polymerase δ complex is important for genome duplication and maintenance and consists of the catalytic subunit POLD1, and the accessory subunits POLD2 and POLD3 which stabilizes the complex. Mutations in POLD1 and POLD2 have been recently shown to be associated with a syndromic CID characterized by T cell lymphopenia with or without intellectual deficiency and sensorineural hearing loss. Here we report a homozygous POLD3 variant (NM_006591.3; p.Ile10Thr) in a Lebanese patient, the product of a consanguineous family, presenting with a syndromic severe combined immunodeficiency (SCID) with neurodevelopmental delay and hearing loss. The homozygous POLD3Ile10Thr variant abolishes POLD3 as well as POLD1 and POLD2 expression. Our findings implicate POLD3 deficiency as a novel cause of syndromic SCID.
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Affiliation(s)
- Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon.
| | - Eliane Chouery
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Shirine Azar-Atallah
- Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese American University, Byblos, Lebanon
| | - Wassim Shebaby
- Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese American University, Byblos, Lebanon
| | | | - Issam Mansour
- Molecular Biology Laboratory, Faculty of Health Sciences, American University of Science and Technology, Beirut, Lebanon; Flow Cytometry Departement, Inovie, Fayadieh, Lebanon
| | - Mirna Mustapha
- School of Biosciences, University of Sheffield, Sheffield, UK; Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Gerard Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier, cedex 5, France
| | - Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon; Institut Jérôme Lejeune, Paris, France.
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5
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Rai R, Biju K, Sun W, Sodeinde T, Al-Hiyasat A, Morgan J, Ye X, Li X, Chen Y, Chang S. Homology directed telomere clustering, ultrabright telomere formation and nuclear envelope rupture in cells lacking TRF2 B and RAP1. Nat Commun 2023; 14:2144. [PMID: 37059728 PMCID: PMC10104862 DOI: 10.1038/s41467-023-37761-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
Double-strand breaks (DSBs) due to genotoxic stress represent potential threats to genome stability. Dysfunctional telomeres are recognized as DSBs and are repaired by distinct DNA repair mechanisms. RAP1 and TRF2 are telomere binding proteins essential to protect telomeres from engaging in homology directed repair (HDR), but how this occurs remains unclear. In this study, we examined how the basic domain of TRF2 (TRF2B) and RAP1 cooperate to repress HDR at telomeres. Telomeres lacking TRF2B and RAP1 cluster into structures termed ultrabright telomeres (UTs). HDR factors localize to UTs, and UT formation is abolished by RNaseH1, DDX21 and ADAR1p110, suggesting that they contain DNA-RNA hybrids. Interaction between the BRCT domain of RAP1 and KU70/KU80 is also required to repress UT formation. Expressing TRF2∆B in Rap1-/- cells resulted in aberrant lamin A localization in the nuclear envelope and dramatically increased UT formation. Expressing lamin A phosphomimetic mutants induced nuclear envelope rupturing and aberrant HDR-mediated UT formation. Our results highlight the importance of shelterin and proteins in the nuclear envelope in repressing aberrant telomere-telomere recombination to maintain telomere homeostasis.
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Affiliation(s)
- Rekha Rai
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
| | - Kevin Biju
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Wenqi Sun
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tori Sodeinde
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Amer Al-Hiyasat
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Jaida Morgan
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA
| | - Xianwen Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Xueqing Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China
| | - Sandy Chang
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, 330 Cedar Street, CT, 06520, USA.
- Department of Pathology, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar Street, New Haven, CT, 06520, USA.
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6
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Tosato V, Rossi B, Sims J, Bruschi CV. Timing of Chromosome DNA Integration throughout the Yeast Cell Cycle. Biomolecules 2023; 13:biom13040614. [PMID: 37189362 DOI: 10.3390/biom13040614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
The dynamic mechanism of cell uptake and genomic integration of exogenous linear DNA still has to be completely clarified, especially within each phase of the cell cycle. We present a study of integration events of double-stranded linear DNA molecules harboring at their ends sequence homologies to the host’s genome, all throughout the cell cycle of the model organism Saccharomyces cerevisiae, comparing the efficiency of chromosomal integration of two types of DNA cassettes tailored for site-specific integration and bridge-induced translocation. Transformability increases in S phase regardless of the sequence homologies, while the efficiency of chromosomal integration during a specific cycle phase depends upon the genomic targets. Moreover, the frequency of a specific translocation between chromosomes XV and VIII strongly increased during DNA synthesis under the control of Pol32 polymerase. Finally, in the null POL32 double mutant, different pathways drove the integration in the various phases of the cell cycle and bridge-induced translocation was possible outside the S phase even without Pol32. The discovery of this cell-cycle dependent regulation of specific pathways of DNA integration, associated with an increase of ROS levels following translocation events, is a further demonstration of a sensing ability of the yeast cell in determining a cell-cycle-related choice of DNA repair pathways under stress.
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7
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Nappi A, Miro C, Pezone A, Tramontano A, Di Cicco E, Sagliocchi S, Cicatiello AG, Murolo M, Torabinejad S, Abbotto E, Caiazzo G, Raia M, Stornaiuolo M, Antonini D, Fabbrocini G, Salvatore D, Avvedimento VE, Dentice M. Loss of p53 activates thyroid hormone via type 2 deiodinase and enhances DNA damage. Nat Commun 2023; 14:1244. [PMID: 36871014 PMCID: PMC9985592 DOI: 10.1038/s41467-023-36755-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
The Thyroid Hormone (TH) activating enzyme, type 2 Deiodinase (D2), is functionally required to elevate the TH concentration during cancer progression to advanced stages. However, the mechanisms regulating D2 expression in cancer still remain poorly understood. Here, we show that the cell stress sensor and tumor suppressor p53 silences D2 expression, thereby lowering the intracellular THs availability. Conversely, even partial loss of p53 elevates D2/TH resulting in stimulation and increased fitness of tumor cells by boosting a significant transcriptional program leading to modulation of genes involved in DNA damage and repair and redox signaling. In vivo genetic deletion of D2 significantly reduces cancer progression and suggests that targeting THs may represent a general tool reducing invasiveness in p53-mutated neoplasms.
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Affiliation(s)
- Annarita Nappi
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Caterina Miro
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Antonio Pezone
- Department of Biology, University of Naples "Federico II", 80126, Naples, Italy
| | - Alfonso Tramontano
- Department of Precision Medicine, University of Campania "L. Vanvitelli", 80138, Naples, Italy
| | - Emery Di Cicco
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Serena Sagliocchi
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | | | - Melania Murolo
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Sepehr Torabinejad
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Elena Abbotto
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy
| | - Giuseppina Caiazzo
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Maddalena Raia
- CEINGE, Biotecnologie Avanzate S.c.a.r.l., 80131, Naples, Italy
| | - Mariano Stornaiuolo
- Department of Pharmacy, University of Naples "Federico II", 80149, Naples, Italy
| | - Dario Antonini
- Department of Biology, University of Naples "Federico II", 80126, Naples, Italy
| | - Gabriella Fabbrocini
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy
| | - Domenico Salvatore
- CEINGE, Biotecnologie Avanzate S.c.a.r.l., 80131, Naples, Italy.,Department of Public Health, University of Naples "Federico II", 80131, Naples, Italy
| | - Vittorio Enrico Avvedimento
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", 80131, Naples, Italy
| | - Monica Dentice
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", 80131, Naples, Italy. .,CEINGE, Biotecnologie Avanzate S.c.a.r.l., 80131, Naples, Italy.
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Murdocca M, Spitalieri P, D'Apice MR, Novelli G, Sangiuolo F. From cue to meaning: The involvement of POLD1 gene in DNA replication, repair and aging. Mech Ageing Dev 2023; 211:111790. [PMID: 36764464 DOI: 10.1016/j.mad.2023.111790] [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: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Aging is an extremely complex biological process. Aging, cancer and inflammation represent a trinity, object of many interesting researches. The accumulation of DNA damage and its consequences progressively interfere with cellular function and increase susceptibility to developing aging condition. DNA Polymerase delta (Pol δ), encoded by POLD1 gene (MIM#174761) on 19q13.3, is well implicated in many steps of the replication program and repair. Thanks to its exonuclease and polymerase activities, the enzyme is involved in the regulation of the cell cycle, DNA synthesis, and DNA damage repair processes. Damaging variants within the exonuclease domain predispose to cancers, while those occurring in the polymerase active site cause the autosomal dominant Progeroid Syndrome called MDPL, Mandibular hypoplasia, Deafness and Progeroid features with concomitant Lipodystrophy Since DNA damage represents the main cause of ageing and age-related pathologies, an overview of critical Pol δ activities will allow to better understand the associations between DNA damage and nearly every aspect of the ageing process, helping the researchers to counteract all the ageing-pathologies at the same time.
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Affiliation(s)
- Michela Murdocca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
| | - Paola Spitalieri
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
| | | | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy; University of Nevada, Department of Pharmacology, Reno, USA; Neuromed Institute, IRCCS, Pozzilli, IS, Italy.
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
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Bonjoch L, Soares de Lima Y, Díaz-Gay M, Dotti I, Muñoz J, Moreira L, Carballal S, Ocaña T, Cuatrecasas M, Ortiz O, Castells A, Pellisé M, Balaguer F, Salas A, Alexandrov LB, Castellví-Bel S. Unraveling the impact of a germline heterozygous POLD1 frameshift variant in serrated polyposis syndrome. Front Mol Biosci 2023; 10:1119900. [PMID: 36756361 PMCID: PMC9900627 DOI: 10.3389/fmolb.2023.1119900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Serrated polyposis syndrome (SPS) is one of the most frequent polyposis syndromes characterized by an increased risk for developing colorectal cancer (CRC). Although SPS etiology has been mainly associated with environmental factors, germline predisposition to SPS could also be relevant for cases with familial aggregation or a family history of SPS/CRC. After whole-exome sequencing of 39 SPS patients from 16 families, we identified a heterozygous germline frameshift variant in the POLD1 gene (c.1941delG, p.(Lys648fs*46)) in a patient with SPS and CRC. Tumor presented an ultra-hypermutated phenotype and microsatellite instability. The POLD1 germline variant segregated in three additional SPS-affected family members. We attempted to create yeast and cellular models for this variant but were no viable. Alternatively, we generated patient-derived organoids (PDOs) from healthy rectal tissue of the index case, as well as from a control donor. Then, we challenged PDOs with a DNA-damaging agent to induce replication stress. No significant differences were observed in the DNA damage response between control and POLD1-Lys648fs PDOs, nor specific mutational signatures were observed. Our results do not support the pathogenicity of the analyzed POLD1 frameshift variant. One possible explanation is that haplosufficiency of the wild-type allele may be compensating for the absence of expression of the frameshift allele. Overall, future work is required to elucidate if functional consequences could be derived from POLD1 alterations different from missense variants in their proofreading domain. To our knowledge, our study presents the first organoid model for germline POLD1 variants and establishes the basis for its use as a model for disease in SPS, CRC and other malignancies.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Isabella Dotti
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Sabela Carballal
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Oswaldo Ortiz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Maria Pellisé
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
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10
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RAD18 opposes transcription-associated genome instability through FANCD2 recruitment. PLoS Genet 2022; 18:e1010309. [DOI: 10.1371/journal.pgen.1010309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/20/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
DNA replication is a vulnerable time for genome stability maintenance. Intrinsic stressors, as well as oncogenic stress, can challenge replication by fostering conflicts with transcription and stabilizing DNA:RNA hybrids. RAD18 is an E3 ubiquitin ligase for PCNA that is involved in coordinating DNA damage tolerance pathways to preserve genome stability during replication. In this study, we show that RAD18 deficient cells have higher levels of transcription-replication conflicts and accumulate DNA:RNA hybrids that induce DNA double strand breaks and replication stress. We find that these effects are driven in part by failure to recruit the Fanconi Anemia protein FANCD2 at difficult to replicate and R-loop prone genomic sites. FANCD2 activation caused by splicing inhibition or aphidicolin treatment is critically dependent on RAD18 activity. Thus, we highlight a RAD18-dependent pathway promoting FANCD2-mediated suppression of R-loops and transcription-replication conflicts.
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11
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Singh M, Zhang S, Perez AM, Lee EYC, Lee MYWT, Zhang D. POLDIP3: At the Crossroad of RNA and DNA Metabolism. Genes (Basel) 2022; 13:1921. [PMID: 36360158 PMCID: PMC9690394 DOI: 10.3390/genes13111921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
POLDIP3 was initially identified as a DNA polymerase delta (Pol δ) interacting protein almost twenty years ago. Intriguingly, it also interacts with proteins involved in a variety of RNA related biological processes, such as transcription, pre-mRNA splicing, mRNA export, and translation. Studies in recent years revealed that POLDIP3 also plays critical roles in disassembling genome wide R-loop formation and activating the DNA damage checkpoint in vivo. Here, we review the functions of POLDIP3 in various RNA and DNA related cellular processes. We then propose a unified model to illustrate how POLDIP3 plays such a versatile role at the crossroad of the RNA and DNA metabolism.
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Affiliation(s)
- Manrose Singh
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Alexis M. Perez
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
| | - Ernest Y. C. Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Marietta Y. W. T. Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
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12
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Tang H, You T, Sun Z, Bai C. A Comprehensive Prognostic Analysis of POLD1 in Hepatocellular Carcinoma. BMC Cancer 2022; 22:197. [PMID: 35189839 PMCID: PMC8862270 DOI: 10.1186/s12885-022-09284-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 02/09/2022] [Indexed: 12/11/2022] Open
Abstract
Background DNA polymerase delta 1 catalytic subunit (POLD1) plays a key role in DNA replication and damage repair. A defective DNA proofreading function caused by POLD1 mutation contributes to carcinogenesis, while POLD1 overexpression predicts poor prognosis in cancers. However, the effect of POLD1 in hepatocellular carcinoma (HCC) is not well-understood. Methods Expression patterns of POLD1 were evaluated in TCGA and the HPA databases. Kaplan-Meier curves and Cox regression were used to examine the prognostic value of POLD1. The prognostic and predictive value of POLD1 was further validated by another independent cohort from ICGC database. The influences of DNA copy number variation, methylation and miRNA on POLD1 mRNA expression were examined. The correlation between infiltrating immune cells and POLD1 expression was analyzed. GO and KEGG enrichment analyses were performed to detect biological pathways associated with POLD1 expression in HCC. Results POLD1 was overexpressed in HCC (n = 369) compared with adjacent normal liver (n = 50). POLD1 upregulation was significantly correlated with positive serum AFP and advanced TNM stage. Kaplan–Meier and multivariate analyses suggested that POLD1 overexpression predicts poor prognosis in HCC. DNA copy gain, low POLD1 methylation, and miR‑139-3p downregulation were associated with POLD1 overexpression. Besides, POLD1 expression was associated with the infiltration levels of dendritic cell, macrophage, B cell, and CD4 + T cell in HCC. Functional enrichment analysis suggested “DNA replication”, “mismatch repair” and “cell cycle” pathways might be involved in the effect of POLD1 on HCC pathogenesis. Additionally, POLD1 mRNA expression was significantly associated with tumor mutation burden, microsatellite instability, and prognosis in various tumors. Conclusions POLD1 may be a potential prognostic marker and promising therapeutic target in HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09284-y.
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Affiliation(s)
- Hui Tang
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, 100730, Beijing, China
| | - Tingting You
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, 100730, Beijing, China
| | - Zhao Sun
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, 100730, Beijing, China
| | - Chunmei Bai
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, 100730, Beijing, China.
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13
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Di Genova A, Nardocci G, Maldonado-Agurto R, Hodar C, Valdivieso C, Morales P, Gajardo F, Marina R, Gutiérrez RA, Orellana A, Cambiazo V, González M, Glavic A, Mendez MA, Maass A, Allende ML, Montecino MA. Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life. Genomics 2021; 114:305-315. [PMID: 34954349 DOI: 10.1016/j.ygeno.2021.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/26/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022]
Abstract
Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to G-protein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.
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Affiliation(s)
- Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Gino Nardocci
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Maldonado-Agurto
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Pamela Morales
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Felipe Gajardo
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Raquel Marina
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile; Department of Molecular Genetics and Microbiology, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile; Center of Plant Biotechnology, Universidad Andres Bello, Santiago, Chile
| | - Veronica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Alvaro Glavic
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Marco A Mendez
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Chile; Institute of Ecology and Biodiversity, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile.
| | - Martin A Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
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14
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Reint G, Li Z, Labun K, Keskitalo S, Soppa I, Mamia K, Tolo E, Szymanska M, Meza-Zepeda LA, Lorenz S, Cieslar-Pobuda A, Hu X, Bordin DL, Staerk J, Valen E, Schmierer B, Varjosalo M, Taipale J, Haapaniemi E. Rapid genome editing by CRISPR-Cas9-POLD3 fusion. eLife 2021; 10:75415. [PMID: 34898428 PMCID: PMC8747517 DOI: 10.7554/elife.75415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein-Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.
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Affiliation(s)
- Ganna Reint
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Zhuokun Li
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Kornel Labun
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Salla Keskitalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Inkeri Soppa
- Centre for Molecular Medicine, University of Oslo, Oslo, Finland
| | - Katariina Mamia
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eero Tolo
- Faculty of Social Sciences, University of Helsinki, Oslo, Finland
| | | | - Leonardo A Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Xian Hu
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Diana L Bordin
- Department of Clinical Molecular Biology, Akershus University Hospital, Oslo, Norway
| | - Judith Staerk
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eivind Valen
- Center for Biotechnology, University of Bergen, Bergen, Norway
| | - Bernhard Schmierer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markku Varjosalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emma Haapaniemi
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
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15
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Zhao S, Wei C, Tang H, Ding H, Han B, Chen S, Song X, Gu Q, Zhang Y, Liu W, Wang J. Elevated DNA Polymerase Delta 1 Expression Correlates With Tumor Progression and Immunosuppressive Tumor Microenvironment in Hepatocellular Carcinoma. Front Oncol 2021; 11:736363. [PMID: 34868924 PMCID: PMC8632622 DOI: 10.3389/fonc.2021.736363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/26/2021] [Indexed: 12/31/2022] Open
Abstract
Background and Objective Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and the DNA polymerase delta (POLD) family is significantly related to cancer prognosis. This study aimed to explore the significance of the POLD family in HCC via the DNA damage repair (DDR) pathway. Methods Data mining was conducted using bioinformatics methods. RNA sequencing and clinicopathological data were collected from The Cancer Genome Atlas, GTEx database and the Gumz Renal cohort. Statistical analyses were also performed in cancer samples (n>12,000) and the Affiliated Hospital of Youjiang Medical University for Nationalities (AHYMUN, n=107) cohort. Results The POLD family (POLD1-4) was identified as the most important functional component of the DDR pathway. Based on the analysis of independent cohorts, we found significantly elevated POLD expression in HCC compared with normal tissues. Second, we investigated the prognostic implication of elevated POLD1 expression in HCC and pan-cancers, revealing that increased POLD1 levels were correlated to worse prognoses for HCC patients. Additionally, we identified 11 hub proteins interacting closely with POLD proteins in base excision repair, protein-DNA complex and mismatch repair signaling pathways. Moreover, POLD1 mutation functioned as an independent biomarker to predict the benefit of targeted treatment. Importantly, POLD1 expression was associated with immune checkpoint molecules, including CD274, CD80, CD86, CTLA4, PDCD1 and TCGIT, and facilitated an immune-excluded tumor microenvironment. Additionally, we confirmed that elevated POLD1 expression was closely correlated with the aggressive progression and poor prognosis of HCC in the real-world AHYMUN cohort. Conclusion We identified a significant association between elevated POLD1 expression and poor patient survival and immune-excluded tumor microenvironment of HCC. Together, these findings indicate that POLD1 provides a valuable biomarker to guide the molecular diagnosis and development of novel targeted therapeutic strategies for HCC patients.
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Affiliation(s)
- Shuai Zhao
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cuicui Wei
- Department of Outpatient, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Haijia Tang
- Department of Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Han Ding
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Han
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuxian Chen
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoling Song
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiang Gu
- Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, China
| | - Yichi Zhang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wangrui Liu
- Department of Outpatient, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.,Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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16
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Schulz D, Piontek G, Zissler UM, Multhoff G, Wirth M, Pickhard A. MEK1/2 regulates APOBEC3B and polymerase iota-induced mutagenesis in head and neck cancer cells. Am J Cancer Res 2021; 11:5581-5590. [PMID: 34873481 PMCID: PMC8640808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023] Open
Abstract
Resistance to chemotherapy provides a major challenge in treatment of metastatic cancer. Prolonged exposure to almost any drug regimen leads to the formation of resistant subclones in almost all advanced solid tumors. Tumor heterogeneity because of intrinsic genetic instability is seen as one of the major contributing factors. In this work, we present evidence that genetic instability measured by mutation frequency is induced by treatment with the EGFR inhibitor afatinib or cisplatin in head and neck squamous cancer cells. We find that APOBEC3B and polymerase iota are upregulated, and inhibition of MEK1/2 by U0126 leads to downregulation on the protein level. Costimulation of afatnib and cisplatin with U0126 leads to a significantly lower mutation frequency. These findings may represent a molecular mechanism for dynamically controlling genetic instability during chemotherapy in head and neck squamous cell carcinoma (HNSCC) cancer cells.
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Affiliation(s)
- Dominik Schulz
- Department of Internal Medicine II, Klinikum Rechts der IsarIsmaninger Straße 22, Munich 81675, Germany
| | - Guido Piontek
- Institute of Pathology, Ludwig Maximilians University of MunichMunich 81377, Germany
| | - Ulrich M Zissler
- Center of Allergy & Environment (ZAUM), German Research Center for Environmental Health, Member of The German Center for Lung Research (DZL), Helmholtz Center Munich, Technical University of Munich (TUM)Biedersteiner Street 29, Munich 80333, Germany
| | - Gabriele Multhoff
- Department of Radiotherapy, Technical University of MunichIsmaninger Straße 22, Munich 80333, Germany
| | - Markus Wirth
- Department of Head and Neck Surgery, Klinikum Rechts der IsarIsmaninger Straße 22, Munich 81675, Germany
| | - Anja Pickhard
- Department of Head and Neck Surgery, Klinikum Rechts der IsarIsmaninger Straße 22, Munich 81675, Germany
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17
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Shimada K, Tsai-Pflugfelder M, Vijeh Motlagh ND, Delgoshaie N, Fuchs J, Gut H, Gasser SM. The stabilized Pol31-Pol3 interface counteracts Pol32 ablation with differential effects on repair. Life Sci Alliance 2021; 4:4/9/e202101138. [PMID: 34226278 PMCID: PMC8321694 DOI: 10.26508/lsa.202101138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/24/2022] Open
Abstract
DNA polymerase δ, which contains the catalytic subunit, Pol3, Pol31, and Pol32, contributes both to DNA replication and repair. The deletion of pol31 is lethal, and compromising the Pol3-Pol31 interaction domains confers hypersensitivity to cold, hydroxyurea (HU), and methyl methanesulfonate, phenocopying pol32Δ. We have identified alanine-substitutions in pol31 that suppress these deficiencies in pol32Δ cells. We characterize two mutants, pol31-T415A and pol31-W417A, which map to a solvent-exposed loop that mediates Pol31-Pol3 and Pol31-Rev3 interactions. The pol31-T415A substitution compromises binding to the Pol3 CysB domain, whereas Pol31-W417A improves it. Importantly, loss of Pol32, such as pol31-T415A, leads to reduced Pol3 and Pol31 protein levels, which are restored by pol31-W417A. The mutations have differential effects on recovery from acute HU, break-induced replication and trans-lesion synthesis repair pathways. Unlike trans-lesion synthesis and growth on HU, the loss of break-induced replication in pol32Δ cells is not restored by pol31-W417A, highlighting pathway-specific roles for Pol32 in fork-related repair. Intriguingly, CHIP analyses of replication forks on HU showed that pol32Δ and pol31-T415A indirectly destabilize DNA pol α and pol ε at stalled forks.
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Affiliation(s)
- Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | | | - Neda Delgoshaie
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jeannette Fuchs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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18
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Abstract
Unlike bacteria, mammalian cells need to complete DNA replication before segregating their chromosomes for the maintenance of genome integrity. Thus, cells have evolved efficient pathways to restore stalled and/or collapsed replication forks during S-phase, and when necessary, also to delay cell cycle progression to ensure replication completion. However, strong evidence shows that cells can proceed to mitosis with incompletely replicated DNA when under mild replication stress (RS) conditions. Consequently, the incompletely replicated genomic gaps form, predominantly at common fragile site regions, where the converging fork-like DNA structures accumulate. These branched structures pose a severe threat to the faithful disjunction of chromosomes as they physically interlink the partially duplicated sister chromatids. In this review, we provide an overview discussing how cells respond and deal with the under-replicated DNA structures that escape from the S/G2 surveillance system. We also focus on recent research of a mitotic break-induced replication pathway (also known as mitotic DNA repair synthesis), which has been proposed to operate during prophase in an attempt to finish DNA synthesis at the under-replicated genomic regions. Finally, we discuss recent data on how mild RS may cause chromosome instability and mutations that accelerate cancer genome evolution.
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Affiliation(s)
- Camelia Mocanu
- Chromosome Dynamics and Stability Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 7BG, UK
| | - Kok-Lung Chan
- Chromosome Dynamics and Stability Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 7BG, UK
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19
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Palmieri G, Rozzo CM, Colombino M, Casula M, Sini MC, Manca A, Pisano M, Doneddu V, Paliogiannis P, Cossu A. Are Molecular Alterations Linked to Genetic Instability Worth to Be Included as Biomarkers for Directing or Excluding Melanoma Patients to Immunotherapy? Front Oncol 2021; 11:666624. [PMID: 34026645 PMCID: PMC8132875 DOI: 10.3389/fonc.2021.666624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
The improvement of the immunotherapeutic potential in most human cancers, including melanoma, requires the identification of increasingly detailed molecular features underlying the tumor immune responsiveness and acting as disease-associated biomarkers. In recent past years, the complexity of the immune landscape in cancer tissues is being steadily unveiled with a progressive better understanding of the plethora of actors playing in such a scenario, resulting in histopathology diversification, distinct molecular subtypes, and biological heterogeneity. Actually, it is widely recognized that the intracellular patterns of alterations in driver genes and loci may also concur to interfere with the homeostasis of the tumor microenvironment components, deeply affecting the immune response against the tumor. Among others, the different events linked to genetic instability—aneuploidy/somatic copy number alteration (SCNA) or microsatellite instability (MSI)—may exhibit opposite behaviors in terms of immune exclusion or responsiveness. In this review, we focused on both prevalence and impact of such different types of genetic instability in melanoma in order to evaluate whether their use as biomarkers in an integrated analysis of the molecular profile of such a malignancy may allow defining any potential predictive value for response/resistance to immunotherapy.
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Affiliation(s)
- Giuseppe Palmieri
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Carla Maria Rozzo
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Milena Casula
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Maria Cristina Sini
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Antonella Manca
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Marina Pisano
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Valentina Doneddu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
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20
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Fuchs J, Cheblal A, Gasser SM. Underappreciated Roles of DNA Polymerase δ in Replication Stress Survival. Trends Genet 2021; 37:476-487. [PMID: 33608117 DOI: 10.1016/j.tig.2020.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/06/2023]
Abstract
Recent structural analysis of Fe-S centers in replication proteins and insights into the structure and function of DNA polymerase δ (DNA Pol δ) subunits have shed light on the key role played by this polymerase at replication forks under stress. The sequencing of cancer genomes reveals multiple point mutations that compromise the activity of POLD1, the DNA Pol δ catalytic subunit, whereas the loci encoding the accessory subunits POLD2 and POLD3 are amplified in a very high proportion of human tumors. Consistently, DNA Pol δ is key for the survival of replication stress and is involved in multiple long-patch repair pathways. Synthetic lethality arises from compromising the function and availability of the noncatalytic subunits of DNA Pol δ under conditions of replication stress, opening the door to novel therapies.
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Affiliation(s)
- Jeannette Fuchs
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Anais Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Sciences, University of Basel, Klingelbergstrasse 90, CH-4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Sciences, University of Basel, Klingelbergstrasse 90, CH-4056 Basel, Switzerland.
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21
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Polymerase δ promotes chromosomal rearrangements and imprecise double-strand break repair. Proc Natl Acad Sci U S A 2020; 117:27566-27577. [PMID: 33077594 DOI: 10.1073/pnas.2014176117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent studies have implicated DNA polymerases θ (Pol θ) and β (Pol β) as mediators of alternative nonhomologous end-joining (Alt-NHEJ) events, including chromosomal translocations. Here we identify subunits of the replicative DNA polymerase δ (Pol δ) as promoters of Alt-NHEJ that results in more extensive intrachromosomal mutations at a single double-strand break (DSB) and more frequent translocations between two DSBs. Depletion of the Pol δ accessory subunit POLD2 destabilizes the complex, resulting in degradation of both POLD1 and POLD3 in human cells. POLD2 depletion markedly reduces the frequency of translocations with sequence modifications but does not affect the frequency of translocations with exact joins. Using separation-of-function mutants, we show that both the DNA synthesis and exonuclease activities of the POLD1 subunit contribute to translocations. As described in yeast and unlike Pol θ, Pol δ also promotes homology-directed repair. Codepletion of POLD2 with 53BP1 nearly eliminates translocations. POLD1 and POLD2 each colocalize with phosphorylated H2AX at ionizing radiation-induced DSBs but not with 53BP1. Codepletion of POLD2 with either ligase 3 (LIG3) or ligase 4 (LIG4) does not further reduce translocation frequency compared to POLD2 depletion alone. Together, these data support a model in which Pol δ promotes Alt-NHEJ in human cells at DSBs, including translocations.
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22
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Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability. Cell Rep 2020; 28:1551-1563.e7. [PMID: 31390568 PMCID: PMC6693559 DOI: 10.1016/j.celrep.2019.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/18/2019] [Accepted: 07/01/2019] [Indexed: 01/19/2023] Open
Abstract
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here, we show that human THO interacts with MFAP1 (microfibrillar-associated protein 1), a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent on either transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381 cause similar transcription-independent genome instability, supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses. MFAP1 depletion affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
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23
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Björkman A, Johansen SL, Lin L, Schertzer M, Kanellis DC, Katsori AM, Christensen ST, Luo Y, Andersen JS, Elsässer SJ, Londono-Vallejo A, Bartek J, Schou KB. Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution. Genes Dev 2020; 34:1065-1074. [PMID: 32561545 PMCID: PMC7397856 DOI: 10.1101/gad.330050.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
In this study from Björkman et al., the authors sought to understand how RTEL1 helicase preserves genomic stability during replication. They demonstrate that RTEL1 and the Polδ subunit Poldip3 form a complex and are mutually dependent in chromatin binding after replication stress, and loss of RTEL1 and Poldip3 leads to marked R-loop accumulation that is confined to sites of active replication, thus highlighting a previously unknown role of RTEL1 and Poldip3 in R-loop suppression at genomic regions where transcription and replication intersect. RTEL1 helicase is a component of DNA repair and telomere maintenance machineries. While RTEL1's role in DNA replication is emerging, how RTEL1 preserves genomic stability during replication remains elusive. Here we used a range of proteomic, biochemical, cell, and molecular biology and gene editing approaches to provide further insights into potential role(s) of RTEL1 in DNA replication and genome integrity maintenance. Our results from complementary human cell culture models established that RTEL1 and the Polδ subunit Poldip3 form a complex and are/function mutually dependent in chromatin binding after replication stress. Loss of RTEL1 and Poldip3 leads to marked R-loop accumulation that is confined to sites of active replication, enhances endogenous replication stress, and fuels ensuing genomic instability. The impact of depleting RTEL1 and Poldip3 is epistatic, consistent with our proposed concept of these two proteins operating in a shared pathway involved in DNA replication control under stress conditions. Overall, our data highlight a previously unsuspected role of RTEL1 and Poldip3 in R-loop suppression at genomic regions where transcription and replication intersect, with implications for human diseases including cancer.
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Affiliation(s)
- Andrea Björkman
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Solna 171 77, Sweden
| | - Søren L Johansen
- Department of Cell Biology and Physiology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8200, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Mike Schertzer
- 3UMR 3244 (Telomere and Cancer Laboratory), Centre National de la Recherche Scientifique, Institut Curie, PSL Research University, Sorbonne Universités, Paris 75005, France
| | - Dimitris C Kanellis
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Solna 171 77, Sweden
| | - Anna-Maria Katsori
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Solna 171 77, Sweden
| | - Søren T Christensen
- Department of Cell Biology and Physiology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus 8200, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Simon J Elsässer
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Solna 171 77, Sweden
| | - Arturo Londono-Vallejo
- 3UMR 3244 (Telomere and Cancer Laboratory), Centre National de la Recherche Scientifique, Institut Curie, PSL Research University, Sorbonne Universités, Paris 75005, France
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Solna 171 77, Sweden.,Danish Cancer Society Research Centre, DK-2100 Copenhagen, Denmark
| | - Kenneth B Schou
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Solna 171 77, Sweden
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24
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Bader AS, Hawley BR, Wilczynska A, Bushell M. The roles of RNA in DNA double-strand break repair. Br J Cancer 2020; 122:613-623. [PMID: 31894141 PMCID: PMC7054366 DOI: 10.1038/s41416-019-0624-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/12/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022] Open
Abstract
Effective DNA repair is essential for cell survival: a failure to correctly repair damage leads to the accumulation of mutations and is the driving force for carcinogenesis. Multiple pathways have evolved to protect against both intrinsic and extrinsic genotoxic events, and recent developments have highlighted an unforeseen critical role for RNA in ensuring genome stability. It is currently unclear exactly how RNA molecules participate in the repair pathways, although many models have been proposed and it is possible that RNA acts in diverse ways to facilitate DNA repair. A number of well-documented DNA repair factors have been described to have RNA-binding capacities and, moreover, screens investigating DNA-damage repair mechanisms have identified RNA-binding proteins as a major group of novel factors involved in DNA repair. In this review, we integrate some of these datasets to identify commonalities that might highlight novel and interesting factors for future investigations. This emerging role for RNA opens up a new dimension in the field of DNA repair; we discuss its impact on our current understanding of DNA repair processes and consider how it might influence cancer progression.
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Affiliation(s)
- Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | | | - Martin Bushell
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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25
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Xu Q, Hu C, Zhu Y, Wang K, Lal B, Li L, Tang J, Wei S, Huang G, Xia S, Lv S, Laterra J, Jiang Y, Li Y. ShRNA-based POLD2 expression knockdown sensitizes glioblastoma to DNA-Damaging therapeutics. Cancer Lett 2020; 482:126-135. [PMID: 31954770 DOI: 10.1016/j.canlet.2020.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 10/25/2022]
Abstract
Glioblastoma (GBM) has limited therapeutic options. DNA repair mechanisms contribute GBM cells to escape therapies and re-establish tumor growth. Multiple studies have shown that POLD2 plays a critical role in DNA replication, DNA repair and genomic stability. We demonstrate for the first time that POLD2 is highly expressed in human glioma specimens and that expression correlates with poor patient survival. siRNA or shRNA POLD2 inhibited GBM cell proliferation, cell cycle progression, invasiveness, sensitized GBM cells to chemo/radiation-induced cell death and reversed the cytoprotective effects of EGFR signaling. Conversely, forced POLD2 expression was found to induce GBM cell proliferation, colony formation, invasiveness and chemo/radiation resistance. POLD2 expression associated with stem-like cell subsets (CD133+ and SSEA-1+ cells) and positively correlated with Sox2 expression in clinical specimens. Its expression was induced by Sox2 and inhibited by the forced differentiation of GBM neurospheres. shRNA-POLD2 modestly inhibited GBM neurosphere-derived orthotopic xenografts growth, when combined with radiation, dramatically inhibited xenograft growth in a cooperative fashion. These novel findings identify POLD2 as a new potential therapeutic target for enhancing GBM response to current standard of care therapeutics.
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Affiliation(s)
- Qingfu Xu
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, 510623, PR China; Department of Neurosurgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, PR China; Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Chengchen Hu
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Yan Zhu
- Department of Ultrasonography, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, 510623, PR China; Department of Obstetrics and Gynecology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, PR China
| | - Kimberly Wang
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Bachuchu Lal
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Lichao Li
- Department of Neurosurgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, 730000, PR China
| | - Junhai Tang
- Department of Neurosurgery, Third Military Medical University, Chongqing, 400037, PR China
| | - Shuang Wei
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Guohao Huang
- Department of Neurosurgery, Third Military Medical University, Chongqing, 400037, PR China
| | - Shuli Xia
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Shengqing Lv
- Department of Neurosurgery, Third Military Medical University, Chongqing, 400037, PR China
| | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA; Department of Oncology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA; Department of Neuroscience, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Yugang Jiang
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, PR China
| | - Yunqing Li
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD, 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA.
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26
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Porreca RM, Herrera-Moyano E, Skourti E, Law PP, Gonzalez Franco R, Montoya A, Faull P, Kramer H, Vannier JB. TRF1 averts chromatin remodelling, recombination and replication dependent-break induced replication at mouse telomeres. eLife 2020; 9:49817. [PMID: 31934863 PMCID: PMC6986873 DOI: 10.7554/elife.49817] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/11/2020] [Indexed: 12/29/2022] Open
Abstract
Telomeres are a significant challenge to DNA replication and are prone to replication stress and telomere fragility. The shelterin component TRF1 facilitates telomere replication but the molecular mechanism remains uncertain. By interrogating the proteomic composition of telomeres, we show that mouse telomeres lacking TRF1 undergo protein composition reorganisation associated with the recruitment of DNA damage response and chromatin remodellers. Surprisingly, mTRF1 suppresses the accumulation of promyelocytic leukemia (PML) protein, BRCA1 and the SMC5/6 complex at telomeres, which is associated with increased Homologous Recombination (HR) and TERRA transcription. We uncovered a previously unappreciated role for mTRF1 in the suppression of telomere recombination, dependent on SMC5 and also POLD3 dependent Break Induced Replication at telomeres. We propose that TRF1 facilitates S-phase telomeric DNA synthesis to prevent illegitimate mitotic DNA recombination and chromatin rearrangement.
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Affiliation(s)
- Rosa Maria Porreca
- Telomere Replication and Stability group, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Emilia Herrera-Moyano
- Telomere Replication and Stability group, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Eleni Skourti
- Telomere Replication and Stability group, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pui Pik Law
- Telomere Replication and Stability group, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Roser Gonzalez Franco
- Telomere Replication and Stability group, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom
| | - Peter Faull
- Biological Mass Spectrometry and Proteomics, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom.,The Francis Crick Institute, Proteomics Mass Spectrometry Science and Technology Platform, London, United Kingdom
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom
| | - Jean-Baptiste Vannier
- Telomere Replication and Stability group, Medical Research Council - London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
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27
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Al-Shaheri FN, Al-Shami KM, Gamal EH, Mahasneh AA, Ayoub NM. Association of DNA repair gene polymorphisms with colorectal cancer risk and treatment outcomes. Exp Mol Pathol 2019; 113:104364. [PMID: 31881200 DOI: 10.1016/j.yexmp.2019.104364] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the third most common carcinoma worldwide. Despite the progress in screening and treatment, CRC remains a leading cause of cancer-related mortality. Alterations to normal nucleic acid processing may drive neoplastic transformation of colorectal epithelium. DNA repair machinery performs an essential function in the protection of genome by reducing the number of genetic polymorphisms/variations that may drive carcinogenicity. Four essential DNA repair systems are known which include nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), and double-strand break repair (DSBR). Polymorphisms of DNA repair genes have been shown to influence the risk of cancer development as well as outcomes of treatment. Several studies demonstrated the association between genetic polymorphism of DNA repair genes and increased risk of CRC in different populations. In this review, we have summarized the impact of DNA repair gene polymorphisms on risk of CRC development and treatment outcomes. Advancements of the current understanding for the impact of DNA repair gene polymorphisms on the risk and treatment of CRC may support diagnostic and predictive roles in patients with CRC.
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Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), ImNeuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, University of Heidelberg, ImNeuenheimer Feld 672, 69120 Heidelberg, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Kamal M Al-Shami
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 720 South Donahue Drive, Auburn, Alabama 36849, United States of America; Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Eshrak H Gamal
- Department of Oncology, Collage of Medicine, Bonn University, Germany; Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan.
| | - Amjad A Mahasneh
- Department of Applied Biological Sciences, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Nehad M Ayoub
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan.
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28
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Zhang J, Hou D, Annis J, Sargolzaeiaval F, Appelbaum J, Takahashi E, Martin GM, Herr A, Oshima J. Inactivating Mutations in Exonuclease and Polymerase Domains in DNA Polymerase Delta Alter Sensitivities to Inhibitors of dNTP Synthesis. DNA Cell Biol 2019; 39:50-56. [PMID: 31750734 DOI: 10.1089/dna.2019.5125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
POLD1 encodes the catalytic subunit of DNA polymerase delta (Polδ), the major lagging strand polymerase, which also participates in DNA repair. Mutations affecting the exonuclease domain increase the risk of various cancers, while mutations that change the polymerase active site cause a progeroid syndrome called mandibular hypoplasia, deafness, progeroid features, and lipodystrophy (MDPL) syndrome. We generated a set of catalytic subunit of human telomerase (hTERT)-immortalized human fibroblasts expressing wild-type or mutant POLD1 using the retroviral LXSN vector system. In the resulting cell lines, expression of endogenous POLD1 was suppressed in favor of the recombinant POLD1. The siRNA screening of DNA damage-related genes revealed that fibroblasts expressing D316H and S605del POLD1 were more sensitive to knockdowns of ribonuclease reductase (RNR) components, RRM1 and RRM2 in the presence of hydroxyurea (HU), an RNR inhibitor. On the contrary, SAMHD1 siRNA, which increases the concentration of dNTPs, increased growth of wild type, D316H, and S605del POLD1 fibroblasts. Hypersensitivity to dNTP synthesis inhibition in POLD1 mutant lines was confirmed using gemcitabine. Our finding is consistent with the notion that reduced dNTP concentration negatively affects the cell growth of hTERT fibroblasts expressing exonuclease and polymerase mutant POLD1.
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Affiliation(s)
- Jiaming Zhang
- Department of Pathology, University of Washington, Seattle, Washington
| | - Deyin Hou
- Department of Pathology, University of Washington, Seattle, Washington
| | - James Annis
- Quellos High-Throughput Screening Core, Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington
| | | | - Julia Appelbaum
- Department of Pathology, University of Washington, Seattle, Washington
| | - Eishi Takahashi
- Department of Dermatology, National Hospital Organization Tochigi Medical Center, Tochigi, Japan
| | - George M Martin
- Department of Pathology, University of Washington, Seattle, Washington
| | - Alan Herr
- Department of Pathology, University of Washington, Seattle, Washington
| | - Junko Oshima
- Department of Pathology, University of Washington, Seattle, Washington
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29
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Combined immunodeficiency caused by a loss-of-function mutation in DNA polymerase delta 1. J Allergy Clin Immunol 2019; 145:391-401.e8. [PMID: 31629014 DOI: 10.1016/j.jaci.2019.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/11/2019] [Accepted: 10/04/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND Mutations affecting DNA polymerases have been implicated in genomic instability and cancer development, but the mechanisms by which they can affect the immune system remain largely unexplored. OBJECTIVE We sought to establish the role of DNA polymerase δ1 catalytic subunit (POLD1) as the cause of a primary immunodeficiency in an extended kindred. METHODS We performed whole-exome and targeted gene sequencing, lymphocyte characterization, molecular and functional analyses of the DNA polymerase δ (Polδ) complex, and T- and B-cell antigen receptor repertoire analysis. RESULTS We identified a missense mutation (c. 3178C>T; p.R1060C) in POLD1 in 3 related subjects who presented with recurrent, especially herpetic, infections and T-cell lymphopenia with impaired T-cell but not B-cell proliferation. The mutation destabilizes the Polδ complex, leading to ineffective recruitment of replication factor C to initiate DNA replication. Molecular dynamics simulation revealed that the R1060C mutation disrupts the intramolecular interaction between the POLD1 CysB motif and the catalytic domain and also between POLD1 and the Polδ subunit POLD2. The patients exhibited decreased numbers of naive CD4 and especially CD8 T cells in favor of effector memory subpopulations. This skewing was associated with oligoclonality and restricted T-cell receptor β-chain V-J pairing in CD8+ but not CD4+ T cells, suggesting that POLD1R1060C differentially affects peripheral CD8+ T-cell expansion and possibly thymic selection. CONCLUSION These results identify gene defects in POLD1 as a novel cause of T-cell immunodeficiency.
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30
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Wells JP, White J, Stirling PC. R Loops and Their Composite Cancer Connections. Trends Cancer 2019; 5:619-631. [DOI: 10.1016/j.trecan.2019.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022]
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31
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Chang EYC, Tsai S, Aristizabal MJ, Wells JP, Coulombe Y, Busatto FF, Chan YA, Kumar A, Dan Zhu Y, Wang AYH, Fournier LA, Hieter P, Kobor MS, Masson JY, Stirling PC. MRE11-RAD50-NBS1 promotes Fanconi Anemia R-loop suppression at transcription-replication conflicts. Nat Commun 2019; 10:4265. [PMID: 31537797 PMCID: PMC6753070 DOI: 10.1038/s41467-019-12271-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
Ectopic R-loop accumulation causes DNA replication stress and genome instability. To avoid these outcomes, cells possess a range of anti-R-loop mechanisms, including RNaseH that degrades the RNA moiety in R-loops. To comprehensively identify anti-R-loop mechanisms, we performed a genome-wide trigenic interaction screen in yeast lacking RNH1 and RNH201. We identified >100 genes critical for fitness in the absence of RNaseH, which were enriched for DNA replication fork maintenance factors including the MRE11-RAD50-NBS1 (MRN) complex. While MRN has been shown to promote R-loops at DNA double-strand breaks, we show that it suppresses R-loops and associated DNA damage at transcription-replication conflicts. This occurs through a non-nucleolytic function of MRE11 that is important for R-loop suppression by the Fanconi Anemia pathway. This work establishes a novel role for MRE11-RAD50-NBS1 in directing tolerance mechanisms at transcription-replication conflicts.
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Affiliation(s)
| | - Shuhe Tsai
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - James P Wells
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yan Coulombe
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Franciele F Busatto
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Yujia A Chan
- The Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Arun Kumar
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yi Dan Zhu
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | | | | | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - Jean-Yves Masson
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada.
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32
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Newton R, Wernisch L. A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes. PLoS One 2019; 14:e0213221. [PMID: 31335867 PMCID: PMC6650054 DOI: 10.1371/journal.pone.0213221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
The copy numbers of genes in cancer samples are often highly disrupted and form a natural amplification/deletion experiment encompassing multiple genes. Matched array comparative genomics and transcriptomics datasets from such samples can be used to predict inter-chromosomal gene regulatory relationships. Previously we published the database METAMATCHED, comprising the results from such an analysis of a large number of publically available cancer datasets. Here we investigate genes in the database which are unusual in that their copy number exhibits consistent heterogeneous disruption in a high proportion of the cancer datasets. We assess the potential relevance of these genes to the pathology of the cancer samples, in light of their predicted regulatory relationships and enriched biological pathways. A network-based method was used to identify enriched pathways from the genes’ inferred targets. The analysis predicts both known and new regulator-target interactions and pathway memberships. We examine examples in detail, in particular the gene POGZ, which is disrupted in many of the cancer datasets and has an unusually large number of predicted targets, from which the network analysis predicts membership of cancer related pathways. The results suggest close involvement in known cancer pathways of genes exhibiting consistent heterogeneous copy number disruption. Further experimental work would clarify their relevance to tumor biology. The results of the analysis presented in the database METAMATCHED, and included here as an R archive file, constitute a large number of predicted regulatory relationships and pathway memberships which we anticipate will be useful in informing such experiments.
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Affiliation(s)
- Richard Newton
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
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Ji J, Tang X, Hu W, Maggert KA, Rong YS. The processivity factor Pol32 mediates nuclear localization of DNA polymerase delta and prevents chromosomal fragile site formation in Drosophila development. PLoS Genet 2019; 15:e1008169. [PMID: 31100062 PMCID: PMC6542543 DOI: 10.1371/journal.pgen.1008169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/30/2019] [Accepted: 04/30/2019] [Indexed: 12/29/2022] Open
Abstract
The Pol32 protein is one of the universal subunits of DNA polymerase δ (Pol δ), which is responsible for genome replication in eukaryotic cells. Although the role of Pol32 in DNA repair has been well-characterized, its exact function in genome replication remains obscure as studies in single cell systems have not established an essential role for Pol32 in the process. Here we characterize Pol32 in the context of Drosophila melanogaster development. In the rapidly dividing embryonic cells, loss of Pol32 halts genome replication as it specifically disrupts Pol δ localization to the nucleus. This function of Pol32 in facilitating the nuclear import of Pol δ would be similar to that of accessory subunits of DNA polymerases from mammalian Herpes viruses. In post-embryonic cells, loss of Pol32 reveals mitotic fragile sites in the Drosophila genome, a defect more consistent with Pol32’s role as a polymerase processivity factor. Interestingly, these fragile sites do not favor repetitive sequences in heterochromatin, with the rDNA locus being a striking exception. Our study uncovers a possibly universal function for DNA polymerase ancillary factors and establishes a powerful system for the study of chromosomal fragile sites in a non-mammalian organism. Cancer etiological studies suggest that the majority of pathological mutations occurred under near normal DNA replication conditions, emphasizing the importance of understanding replication regulation under non-lethal conditions. To gain such a better understanding, we investigated the function of Pol32, a conserved ancillary subunit of the essential DNA polymerase Delta complex, through the development of the fruit fly Drosophila. We uncovered a previously unappreciated function of Pol32 in regulating the nuclear import of the polymerase complex, and this function is developmentally regulated. By utilizing mutations in pol32 and other replication factors, we have started to define basic features of Chromosome Fragile Sites (CFS) in Drosophila somatic cells. CFS is a major source of genome instability associated with replication stresses, and has been an important topic of cancer biology. We discovered that CFS formation does not favor genomic regions with repetitive sequences except the highly transcribed locus encoding ribosomal RNA. Our work lays the groundwork for future studies using Drosophila as an alternative system to uncover the most fundamental features of CFS.
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Affiliation(s)
- Jingyun Ji
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaona Tang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wen Hu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Keith A. Maggert
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, United States of America
| | - Yikang S. Rong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail:
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Tumini E, Herrera-Moyano E, San Martín-Alonso M, Barroso S, Galmarini CM, Aguilera A. The Antitumor Drugs Trabectedin and Lurbinectedin Induce Transcription-Dependent Replication Stress and Genome Instability. Mol Cancer Res 2018; 17:773-782. [PMID: 30552231 DOI: 10.1158/1541-7786.mcr-18-0575] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 11/30/2018] [Indexed: 02/07/2023]
Abstract
R-loops are a major source of replication stress, DNA damage, and genome instability, which are major hallmarks of cancer cells. Accordingly, growing evidence suggests that R-loops may also be related to cancer. Here we show that R-loops play an important role in the cellular response to trabectedin (ET743), an anticancer drug from marine origin and its derivative lurbinectedin (PM01183). Trabectedin and lurbinectedin induced RNA-DNA hybrid-dependent DNA damage in HeLa cells, causing replication impairment and genome instability. We also show that high levels of R-loops increase cell sensitivity to trabectedin. In addition, trabectedin led to transcription-dependent FANCD2 foci accumulation, which was suppressed by RNase H1 overexpression. In yeast, trabectedin and lurbinectedin increased the presence of Rad52 foci, a marker of DNA damage, in an R-loop-dependent manner. In addition to providing new insights into the mechanisms of action of these drugs, our study reveals that R-loops could be targeted by anticancer agents. Given the increasing evidence that R-loops occur all over the genome, the ability of lurbinectedin and trabectedin to act on them may contribute to enhance their efficacy, opening the possibility that R-loops might be a feature shared by specific cancers. IMPLICATIONS: The data presented in this study provide the new concept that R-loops are important cellular factors that contribute to trabectedin and lurbinectedin anticancer activity.
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Affiliation(s)
- Emanuela Tumini
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, CSIC-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Emilia Herrera-Moyano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, CSIC-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Marta San Martín-Alonso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, CSIC-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, CSIC-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | | | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, CSIC-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain.
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Microarray-based measurement of microRNA-449c-5p levels in hepatocellular carcinoma and bioinformatic analysis of potential signaling pathways. Pathol Res Pract 2018; 215:68-81. [PMID: 30389318 DOI: 10.1016/j.prp.2018.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/15/2018] [Accepted: 10/17/2018] [Indexed: 12/15/2022]
Abstract
The clinical role and potential molecular mechanisms of microRNA-449c-5p (miR-449c-5p) in hepatocellular carcinoma (HCC) tissues remains unclear. Combining multiple bioinformatic tools, we studied the miR-449c-5p expression levels in HCC tissues and explored possible target genes and related signaling pathways. First, miR-449c-5p expression data from microarrays provided by publicly available sources were mined and analyzed using various meta-analysis methods. Next, genes that were downregulated after miR-449c-5p mimic transfection into HCC cells were identified, and in silico methods were used to predict potential target genes. Several bioinformatic assessments were also performed to evaluate the possible signaling pathways of miR-449c-5p in HCC. Five microarrays were included in the current study, including GSE98269, GSE64632, GSE74618, GSE40744 and GSE57555. The standard mean difference was 0.44 (0.07-0.80), and the area under the curve was 0.68 (0.63-0.72), as assessed by meta-analyses, which consistently indicated the upregulation of miR-449c-5p in HCC tissues. A total of 2244 genes were downregulated after miR-449c-5p mimic transfection into an HCC cell line, while 5217 target genes were predicted by in silico methods. The overlap of these two gene pools led to a final group of 428 potential target genes of miR-449c-5p. These 428 potential target genes were primarily enriched in the homologous recombination pathway, which includes DNA Polymerase Delta 3 (POLD3). Data mining with Oncomine and the Human Protein Atlas showed a decreasing trend in POLD3 mRNA and protein levels in HCC tissue samples. This evidence suggests that miR-449c-5p could play an essential role in HCC through various pathways and that POLD3 could be a potential miR-449c-5p target. However, these in silico findings should be validated with further experiments.
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Mijnes J, Veeck J, Gaisa NT, Burghardt E, de Ruijter TC, Gostek S, Dahl E, Pfister D, Schmid SC, Knüchel R, Rose M. Promoter methylation of DNA damage repair (DDR) genes in human tumor entities: RBBP8/ CtIP is almost exclusively methylated in bladder cancer. Clin Epigenetics 2018; 10:15. [PMID: 29445424 PMCID: PMC5802064 DOI: 10.1186/s13148-018-0447-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/22/2018] [Indexed: 01/18/2023] Open
Abstract
Background Genome-wide studies identified pan-cancer genes and shared biological networks affected by epigenetic dysregulation among diverse tumor entities. Here, we systematically screened for hypermethylation of DNA damage repair (DDR) genes in a comprehensive candidate-approach and exemplarily identify and validate candidate DDR genes as targets of epigenetic inactivation unique to bladder cancer (BLCA), which may serve as non-invasive biomarkers. Methods Genome-wide DNA methylation datasets (2755 CpG probes of n = 7819 tumor and n = 659 normal samples) of the TCGA network covering 32 tumor entities were analyzed in silico for 177 DDR genes. Genes of interest were defined as differentially methylated between normal and cancerous tissues proximal to transcription start sites. The lead candidate gene was validated by methylation-specific PCR (MSP) and/or bisulfite-pyrosequencing in different human cell lines (n = 36), in primary BLCA tissues (n = 43), and in voided urine samples (n = 74) of BLCA patients. Urines from healthy donors and patients with urological benign and malignant diseases were included as controls (n = 78). mRNA expression was determined using qRT-PCR in vitro before (n = 5) and after decitabine treatment (n = 2). Protein expression was assessed by immunohistochemistry (n = 42). R 3.2.0. was used for statistical data acquisition and SPSS 21.0 for statistical analysis. Results Overall, 39 DDR genes were hypermethylated in human cancers. Most exclusively and frequently methylated (37%) in primary BLCA was RBBP8, encoding endonuclease CtIP. RBBP8 hypermethylation predicted longer overall survival (OS) and was found in 2/4 bladder cancer cell lines but not in any of 33 cancer cell lines from entities with another origin like prostate. RBBP8 methylation was inversely correlated with RBBP8 mRNA and nuclear protein expression while RBBP8 was re-expressed after in vitro demethylation. RBBP8 methylation was associated with histological grade in primary BLCA and urine samples. RBBP8 methylation was detectable in urine samples of bladder cancer patients achieving a sensitivity of 52%, at 91% specificity. Conclusions RBBP8 was identified as almost exclusively hypermethylated in BLCA. RBBP8/CtIP has a proven role in homologous recombination-mediated DNA double-strand break repair known to sensitize cancer cells for PARP1 inhibitors. Since RBBP8 methylation was detectable in urines, it may be a complementary marker of high specificity in urine for BLCA detection.
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Affiliation(s)
- Jolein Mijnes
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Jürgen Veeck
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,2Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands.,3GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands.,4RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Nadine T Gaisa
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Eduard Burghardt
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Tim C de Ruijter
- 2Division of Medical Oncology, Maastricht University Medical Centre, Maastricht, The Netherlands.,3GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Sonja Gostek
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Edgar Dahl
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,4RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - David Pfister
- 5Department of Urology, RWTH Aachen University, Aachen, Germany.,6Department of Urology, Uro-Oncology, Robot Assisted and Reconstructive Urologic Surgery, University Hospital Cologne, Cologne, Germany
| | - Sebastian C Schmid
- 7Department of Urology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Ruth Knüchel
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Michael Rose
- 1Institute of Pathology, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,4RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
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Chang EYC, Novoa CA, Aristizabal MJ, Coulombe Y, Segovia R, Chaturvedi R, Shen Y, Keong C, Tam AS, Jones SJM, Masson JY, Kobor MS, Stirling PC. RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability. J Cell Biol 2017; 216:3991-4005. [PMID: 29042409 PMCID: PMC5716281 DOI: 10.1083/jcb.201703168] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 01/01/2023] Open
Abstract
Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability.
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Affiliation(s)
| | - Carolina A Novoa
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | | | - Yan Coulombe
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Romulo Segovia
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Richa Chaturvedi
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Yaoqing Shen
- Michael Smith Genome Sciences Centre, Vancouver, Canada
| | - Christelle Keong
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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Szwajczak E, Fijalkowska IJ, Suski C. The CysB motif of Rev3p involved in the formation of the four-subunit DNA polymerase ζ is required for defective-replisome-induced mutagenesis. Mol Microbiol 2017; 106:659-672. [PMID: 28941243 DOI: 10.1111/mmi.13846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2017] [Indexed: 12/16/2022]
Abstract
Eukaryotic DNA replication is performed by high-fidelity multi-subunit replicative B-family DNA polymerases (Pols) α, δ and ɛ. Those complexes are composed of catalytic and accessory subunits and organized in multicomplex machinery: the replisome. The fourth B-family member, DNA polymerase zeta (Pol ζ), is responsible for a large portion of mutagenesis in eukaryotic cells. Two forms of Pol ζ have been identified, a hetero-dimeric (Pol ζ2 ) and a hetero-tetrameric (Pol ζ4 ) ones and recent data have demonstrated that Pol ζ4 is responsible for damage-induced mutagenesis. Here, using yeast Pol ζ mutant defective in the assembly of the Pol ζ four-subunit form, we show in vivo that [4Fe-4S] cluster in Pol ζ catalytic subunit (Rev3p) is also required for spontaneous (wild-type cells) and defective-replisome-induced mutagenesis - DRIM (pol3-Y708A, pol2-1 or psf1-100 cells), when cells are not treated with any external damaging agents.
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Affiliation(s)
- Ewa Szwajczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, 02-106, Poland
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, 02-106, Poland
| | - Catherine Suski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, 02-106, Poland
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