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Fiesco-Roa MÓ, García-de Teresa B, Leal-Anaya P, van ‘t Hek R, Wegman-Ostrosky T, Frías S, Rodríguez A. Fanconi anemia and dyskeratosis congenita/telomere biology disorders: Two inherited bone marrow failure syndromes with genomic instability. Front Oncol 2022; 12:949435. [PMID: 36091172 PMCID: PMC9453478 DOI: 10.3389/fonc.2022.949435] [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: 05/20/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a complex and heterogeneous group of genetic diseases. To date, at least 13 IBMFS have been characterized. Their pathophysiology is associated with germline pathogenic variants in genes that affect hematopoiesis. A couple of these diseases also have genomic instability, Fanconi anemia due to DNA damage repair deficiency and dyskeratosis congenita/telomere biology disorders as a result of an alteration in telomere maintenance. Patients can have extramedullary manifestations, including cancer and functional or structural physical abnormalities. Furthermore, the phenotypic spectrum varies from cryptic features to patients with significantly evident manifestations. These diseases require a high index of suspicion and should be considered in any patient with abnormal hematopoiesis, even if extramedullary manifestations are not evident. This review describes the disrupted cellular processes that lead to the affected maintenance of the genome structure, contrasting the dysmorphological and oncological phenotypes of Fanconi anemia and dyskeratosis congenita/telomere biology disorders. Through a dysmorphological analysis, we describe the phenotypic features that allow to make the differential diagnosis and the early identification of patients, even before the onset of hematological or oncological manifestations. From the oncological perspective, we analyzed the spectrum and risks of cancers in patients and carriers.
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Affiliation(s)
- Moisés Ó. Fiesco-Roa
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, Mexico
- Maestría y Doctorado en Ciencias Médicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, Mexico
| | | | - Paula Leal-Anaya
- Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de México, Mexico
| | - Renée van ‘t Hek
- Facultad de Medicina, Universidad Nacional Autoínoma de Meíxico (UNAM), Ciudad Universitaria, Ciudad de México, Mexico
| | - Talia Wegman-Ostrosky
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Sara Frías
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- *Correspondence: Alfredo Rodríguez, ; Sara Frías,
| | - Alfredo Rodríguez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Unidad de Genética de la Nutrición, Instituto Nacional de Pediatría, Ciudad de México, Mexico
- *Correspondence: Alfredo Rodríguez, ; Sara Frías,
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2
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [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: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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3
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Hussain SS, Majumdar R, Moore GM, Narang H, Buechelmaier E, Bazil MJ, Ravindran PT, Leeman J, Li Y, Jalan M, Anderson KS, Farina A, Soni R, Mohibullah N, Hamzic E, Rong-Mullins X, Sifuentes C, Damerla RR, Viale A, Powell SN, Higginson D. Measuring nonhomologous end-joining, homologous recombination and alternative end-joining simultaneously at an endogenous locus in any transfectable human cell. Nucleic Acids Res 2021; 49:e74. [PMID: 33877327 PMCID: PMC8287935 DOI: 10.1093/nar/gkab262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
Double strand break (DSB) repair primarily occurs through 3 pathways: non-homologous end-joining (NHEJ), alternative end-joining (Alt-EJ), and homologous recombination (HR). Typical methods to measure pathway usage include integrated cassette reporter assays or visualization of DNA damage induced nuclear foci. It is now well understood that repair of Cas9-induced breaks also involves NHEJ, Alt-EJ, and HR pathways, providing a new format to measure pathway usage. Here, we have developed a simple Cas9-based system with validated repair outcomes that accurately represent each pathway and then converted it to a droplet digital PCR (ddPCR) readout, thus obviating the need for Next Generation Sequencing and bioinformatic analysis with the goal to make Cas9-based system accessible to more laboratories. The assay system has reproduced several important insights. First, absence of the key Alt-EJ factor Pol θ only abrogates ∼50% of total Alt-EJ. Second, single-strand templated repair (SSTR) requires BRCA1 and MRE11 activity, but not BRCA2, establishing that SSTR commonly used in genome editing is not conventional HR. Third, BRCA1 promotes Alt-EJ usage at two-ended DSBs in contrast to BRCA2. This assay can be used in any system, which permits Cas9 delivery and, importantly, allows rapid genotype-to-phenotype correlation in isogenic cell line pairs.
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Affiliation(s)
- Suleman S Hussain
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rahul Majumdar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Grace M Moore
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Himanshi Narang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erika S Buechelmaier
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medicine, Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Maximilian J Bazil
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Jonathan E Leeman
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02189, USA
| | - Yi Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manisha Jalan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kyrie S Anderson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Farina
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rekha Soni
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neeman Mohibullah
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edin Hamzic
- Biocomputix, Sarajevo, 71000, Bosnia and Herzegovina
| | - Xiaoqing Rong-Mullins
- Department of Biostatistics, The Ohio State University College of Public Health, Columbus, OH 43210, USA
| | | | - Rama R Damerla
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Integrated Genomics Operations, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel S Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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4
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Tatin X, Muggiolu G, Sauvaigo S, Breton J. Evaluation of DNA double-strand break repair capacity in human cells: Critical overview of current functional methods. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108388. [PMID: 34893153 DOI: 10.1016/j.mrrev.2021.108388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/05/2023]
Abstract
DNA double-strand breaks (DSBs) are highly deleterious lesions, responsible for mutagenesis, chromosomal translocation or cell death. DSB repair (DSBR) is therefore a critical part of the DNA damage response (DDR) to restore molecular and genomic integrity. In humans, this process is achieved through different pathways with various outcomes. The balance between DSB repair activities varies depending on cell types, tissues or individuals. Over the years, several methods have been developed to study variations in DSBR capacity. Here, we mainly focus on functional techniques, which provide dynamic information regarding global DSB repair proficiency or the activity of specific pathways. These methods rely on two kinds of approaches. Indirect techniques, such as pulse field gel electrophoresis (PFGE), the comet assay and immunofluorescence (IF), measure DSB repair capacity by quantifying the time-dependent decrease in DSB levels after exposure to a DNA-damaging agent. On the other hand, cell-free assays and reporter-based methods directly track the repair of an artificial DNA substrate. Each approach has intrinsic advantages and limitations and despite considerable efforts, there is currently no ideal method to quantify DSBR capacity. All techniques provide different information and can be regarded as complementary, but some studies report conflicting results. Parameters such as the type of biological material, the required equipment or the cost of analysis may also limit available options. Improving currently available methods measuring DSBR capacity would be a major step forward and we present direct applications in mechanistic studies, drug development, human biomonitoring and personalized medicine, where DSBR analysis may improve the identification of patients eligible for chemo- and radiotherapy.
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Affiliation(s)
- Xavier Tatin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France; LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | | | - Sylvie Sauvaigo
- LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Jean Breton
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France.
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5
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Mozaffari NL, Pagliarulo F, Sartori AA. Human CtIP: A 'double agent' in DNA repair and tumorigenesis. Semin Cell Dev Biol 2020; 113:47-56. [PMID: 32950401 DOI: 10.1016/j.semcdb.2020.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Human CtIP was originally identified as an interactor of the retinoblastoma protein and BRCA1, two bona fide tumour suppressors frequently mutated in cancer. CtIP is renowned for its role in the resection of DNA double-strand breaks (DSBs) during homologous recombination, a largely error-free DNA repair pathway crucial in maintaining genome integrity. However, CtIP-dependent DNA end resection is equally accountable for alternative end-joining, a mutagenic DSB repair mechanism implicated in oncogenic chromosomal translocations. In addition, CtIP contributes to transcriptional regulation of G1/S transition, DNA damage checkpoint signalling, and replication fork protection pathways. In this review, we present a perspective on the current state of knowledge regarding the tumour-suppressive and oncogenic properties of CtIP and provide an overview of their relevance for cancer development, progression, and therapy.
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Affiliation(s)
- Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Fabio Pagliarulo
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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6
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Gerovska D, Larrinaga G, Solano-Iturri JD, Márquez J, García Gallastegi P, Khatib AM, Poschmann G, Stühler K, Armesto M, Lawrie CH, Badiola I, Araúzo-Bravo MJ. An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer. Cancers (Basel) 2020; 12:E2380. [PMID: 32842712 PMCID: PMC7565528 DOI: 10.3390/cancers12092380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 12/26/2022] Open
Abstract
(1) Background & Aims: The roles of different cells in the tumor microenvironment (TME) are critical to the metastatic process. The phenotypic transformation of the liver cells is one of the most important stages of the hepatic metastasis progression of colorectal cancer (CRC). Our aim was to identify the major molecules (i.e., genes, miRNAs and proteins) involved in this process. (2) Methods: We isolated and performed whole-genome analysis of gene, miRNA, and protein expression in three types of liver cells (Ito cells, Kupffer cells, and liver sinusoidal endothelial cells) from the TME of a murine model of CRC liver metastasis. We selected the statistically significant differentially expressed molecules using the Student's t-test with Benjamini-Hochberg correction and performed functional statistically-significant enrichment analysis of differentially expressed molecules with hypergeometric distribution using the curated collection of molecular signatures, MSigDB. To build a gene-miRNA-protein network centered in Brca1, we developed a software package (miRDiana) that collects miRNA targets from the union of the TargetScan, MicroCosm, mirTarBase, and miRWalk databases. This was used to search for miRNAs targeting Brca1. We validated the most relevant miRNAs with real-time quantitative PCR. To investigate BRCA1 protein expression, we built tissue microarrays (TMAs) from hepatic metastases of 34 CRC patients. (3) Results: Using integrated omics analyses, we observed that the Brca1 gene is among the twenty transcripts simultaneously up-regulated in all three types of TME liver cells during metastasis. Further analysis revealed that Brca1 is the last BRCA1-associated genome surveillance complex (BASC) gene activated in the TME. We confirmed this finding in human reanalyzing transcriptomics datasets from 184 patients from non-tumor colorectal tissue, primary colorectal tumor and colorectal liver metastasis of the GEO database. We found that the most probable sequence of cell activation during metastasis is Endothelial→Ito→Kupffer. Immunohistochemical analysis of human liver metastases showed the BRCA1 protein was co-localized in Ito, Kupffer, and endothelial cells in 81.8% of early or synchronous metastases. However, in the greater part of the metachronous liver metastases, this protein was not expressed in any of these TME cells. (4) Conclusions: These results suggest a possible role of the co-expression of BRCA1 in Ito, Kupffer, and sinusoidal endothelial cells in the early occurrence of CRC liver metastases, and point to BRCA1 as a potential TME biomarker.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine Group, Biodonostia Health Research Institute, Calle Doctor Beguiristain s/n, 20014 San Sebastián, Spain;
- Computational Biomedicine Data Analysis Platform, Biodonostia Health Research Institute, Calle Doctor Beguiristain s/n, 20014 San Sebastián, Spain
| | - Gorka Larrinaga
- Department of Nursing I, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain;
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain
- BioCruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain;
| | - Jon Danel Solano-Iturri
- BioCruces Health Research Institute, 48903 Barakaldo, Bizkaia, Spain;
- Department of Anatomic Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), 48903 Barakaldo, Bizkaia, Spain
| | - Joana Márquez
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.M.); (P.G.G.)
| | - Patricia García Gallastegi
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.M.); (P.G.G.)
| | - Abdel-Majid Khatib
- University of Bordeaux, Allée Geoffroy St Hilaire, 33615 Pessac, France; INSERM, LAMC, UMR 1029, Allée Geoffroy St Hilaire, 33615 Pessac, France;
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (G.P.); (K.S.)
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (G.P.); (K.S.)
- Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - María Armesto
- Molecular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastián, Spain; (M.A.); (C.H.L.)
| | - Charles H. Lawrie
- Molecular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastián, Spain; (M.A.); (C.H.L.)
- Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
- IKERBASQUE, Basque Foundation for Science, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
| | - Iker Badiola
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.M.); (P.G.G.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine Group, Biodonostia Health Research Institute, Calle Doctor Beguiristain s/n, 20014 San Sebastián, Spain;
- Computational Biomedicine Data Analysis Platform, Biodonostia Health Research Institute, Calle Doctor Beguiristain s/n, 20014 San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- CIBER of Frailty and Healthy Aging (CIBERfes), 28029 Madrid, Spain
- Computational Biology and Bioinformatics Group, Max Planck Institute for Molecular Biomedicine, Röntgenstr. 20, 48149 Münster, Germany
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Eckelmann BJ, Bacolla A, Wang H, Ye Z, Guerrero EN, Jiang W, El-Zein R, Hegde ML, Tomkinson AE, Tainer JA, Mitra S. XRCC1 promotes replication restart, nascent fork degradation and mutagenic DNA repair in BRCA2-deficient cells. NAR Cancer 2020; 2:zcaa013. [PMID: 32776008 PMCID: PMC7397735 DOI: 10.1093/narcan/zcaa013] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/30/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Homologous recombination/end joining (HR/HEJ)-deficient cancers with BRCA mutations utilize alternative DNA double-strand break repair pathways, particularly alternative non-homologous end joining or microhomology-mediated end joining (alt-EJ/MMEJ) during S and G2 cell cycle phases. Depletion of alt-EJ factors, including XRCC1, PARP1 and POLQ, is synthetically lethal with BRCA2 deficiency; yet, XRCC1 roles in HR-deficient cancers and replication stress are enigmatic. Here, we show that after replication stress, XRCC1 forms an active repair complex with POLQ and MRE11 that supports alt-EJ activity in vitro. BRCA2 limits XRCC1 recruitment and repair complex formation to suppress alt-EJ at stalled forks. Without BRCA2 fork protection, XRCC1 enables cells to complete DNA replication at the expense of increased genome instability by promoting MRE11-dependent fork resection and restart. High XRCC1 and MRE11 gene expression negatively impacts Kaplan–Meier survival curves and hazard ratios for HR-deficient breast cancer patients in The Cancer Genome Atlas. The additive effects of depleting both BRCA2 and XRCC1 indicate distinct pathways for replication restart. Our collective data show that XRCC1-mediated processing contributes to replication fork degradation, replication restart and chromosome aberrations in BRCA2-deficient cells, uncovering new roles of XRCC1 and microhomology-mediated repair mechanisms in HR-deficient cancers, with implications for chemotherapeutic strategies targeting POLQ and PARP activities.
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Affiliation(s)
- Bradley J Eckelmann
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zu Ye
- Departments of Cancer Biology and Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erika N Guerrero
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Wei Jiang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518036, China
| | - Randa El-Zein
- Department of Radiology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics & Microbiology, and the University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John A Tainer
- Departments of Cancer Biology and Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
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8
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Nera B, Huang HS, Hendrickson EA, Xu L. Both the classical and alternative non-homologous end joining pathways contribute to the fusion of drastically shortened telomeres induced by TRF2 overexpression. Cell Cycle 2019; 18:880-888. [PMID: 30907229 DOI: 10.1080/15384101.2019.1598724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The double-stranded telomeric binding protein TRF2 is expressed in many human cancers at elevated levels. Moreover, experimental overexpression of TRF2 in human cells causes replication stalling in telomeric tracts, which leads to drastic telomere shortening and fusion of deprotected chromosome ends. To understand which end joining pathway is involved in mediating these chromosome fusions, we overexpressed TRF2 in human HCT116 cell lines that were deficient for the DNA Ligase 4 (Lig4)-dependent classical non-homologous end joining (C-NHEJ) or the DNA Ligase 3 (Lig3)-dependent alternative non-homologous end joining (A-NHEJ) pathway. Surprisingly, abrogation of either Lig4 or nuclear Lig3 significantly reduced inter-chromosomal fusion of drastically shortened telomeres, suggesting that both the C-NHEJ and A-NHEJ pathways are involved in mediating this type of fusion. Fusion between deprotected sister chromatids, however, only required the Lig3-dependent A-NHEJ pathway. Interestingly, a previous study reported similar end joining pathway requirements for the fusion of critically shortened telomeres during a telomere attrition-based cellular crisis. We speculate that, as in cellular crisis, the same repair pathway(s) may drive clonal and genomic evolution in human cancers containing elevated TRF2 levels.
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Affiliation(s)
- Bernadette Nera
- a Department of Microbiology and Molecular Genetics , University of California , Davis , CA , USA
| | - Hui-Shun Huang
- a Department of Microbiology and Molecular Genetics , University of California , Davis , CA , USA
| | - Eric A Hendrickson
- b Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Lifeng Xu
- a Department of Microbiology and Molecular Genetics , University of California , Davis , CA , USA
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9
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Mukherjee S, Sinha D, Bhattacharya S, Srinivasan K, Abdisalaam S, Asaithamby A. Werner Syndrome Protein and DNA Replication. Int J Mol Sci 2018; 19:ijms19113442. [PMID: 30400178 PMCID: PMC6274846 DOI: 10.3390/ijms19113442] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/22/2018] [Accepted: 10/25/2018] [Indexed: 01/07/2023] Open
Abstract
Werner Syndrome (WS) is an autosomal recessive disorder characterized by the premature development of aging features. Individuals with WS also have a greater predisposition to rare cancers that are mesenchymal in origin. Werner Syndrome Protein (WRN), the protein mutated in WS, is unique among RecQ family proteins in that it possesses exonuclease and 3' to 5' helicase activities. WRN forms dynamic sub-complexes with different factors involved in DNA replication, recombination and repair. WRN binding partners either facilitate its DNA metabolic activities or utilize it to execute their specific functions. Furthermore, WRN is phosphorylated by multiple kinases, including Ataxia telangiectasia mutated, Ataxia telangiectasia and Rad3 related, c-Abl, Cyclin-dependent kinase 1 and DNA-dependent protein kinase catalytic subunit, in response to genotoxic stress. These post-translational modifications are critical for WRN to function properly in DNA repair, replication and recombination. Accumulating evidence suggests that WRN plays a crucial role in one or more genome stability maintenance pathways, through which it suppresses cancer and premature aging. Among its many functions, WRN helps in replication fork progression, facilitates the repair of stalled replication forks and DNA double-strand breaks associated with replication forks, and blocks nuclease-mediated excessive processing of replication forks. In this review, we specifically focus on human WRN's contribution to replication fork processing for maintaining genome stability and suppressing premature aging. Understanding WRN's molecular role in timely and faithful DNA replication will further advance our understanding of the pathophysiology of WS.
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Affiliation(s)
- Shibani Mukherjee
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Debapriya Sinha
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Souparno Bhattacharya
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Kalayarasan Srinivasan
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Salim Abdisalaam
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Aroumougame Asaithamby
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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10
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BRCA1 ensures genome integrity by eliminating estrogen-induced pathological topoisomerase II-DNA complexes. Proc Natl Acad Sci U S A 2018; 115:E10642-E10651. [PMID: 30352856 DOI: 10.1073/pnas.1803177115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Women having BRCA1 germ-line mutations develop cancer in breast and ovary, estrogen-regulated tissues, with high penetrance. Binding of estrogens to the estrogen receptor (ER) transiently induces DNA double-strand breaks (DSBs) by topoisomerase II (TOP2) and controls gene transcription. TOP2 resolves catenated DNA by transiently generating DSBs, TOP2-cleavage complexes (TOP2ccs), where TOP2 covalently binds to 5' ends of DSBs. TOP2 frequently fails to complete its catalysis, leading to formation of pathological TOP2ccs. We have previously shown that the endonucleolytic activity of MRE11 plays a key role in removing 5' TOP2 adducts in G1 phase. We show here that BRCA1 promotes MRE11-mediated removal of TOP2 adducts in G1 phase. We disrupted the BRCA1 gene in 53BP1-deficient ER-positive breast cancer and B cells. The loss of BRCA1 caused marked increases of pathological TOP2ccs in G1 phase following exposure to etoposide, which generates pathological TOP2ccs. We conclude that BRCA1 promotes the removal of TOP2 adducts from DSB ends for subsequent nonhomologous end joining. BRCA1-deficient cells showed a decrease in etoposide-induced MRE11 foci in G1 phase, suggesting that BRCA1 repairs pathological TOP2ccs by promoting the recruitment of MRE11 to TOP2cc sites. BRCA1 depletion also leads to the increase of unrepaired DSBs upon estrogen treatment both in vitro in G1-arrested breast cancer cells and in vivo in epithelial cells of mouse mammary glands. BRCA1 thus plays a critical role in removing pathological TOP2ccs induced by estrogens as well as etoposide. We propose that BRCA1 suppresses tumorigenesis by removing estrogen-induced pathological TOP2ccs throughout the cell cycle.
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11
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Harvey A, Mielke N, Grimstead JW, Jones RE, Nguyen T, Mueller M, Baird DM, Hendrickson EA. PARP1 is required for preserving telomeric integrity but is dispensable for A-NHEJ. Oncotarget 2018; 9:34821-34837. [PMID: 30410680 PMCID: PMC6205175 DOI: 10.18632/oncotarget.26201] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/15/2018] [Indexed: 01/07/2023] Open
Abstract
Poly-ADP ribose polymerase 1 (PARP1) is clinically important because of its synthetic lethality with breast cancer allele 1 and 2 mutations, which are causative for inherited breast and ovarian cancers. Biochemically, PARP1 is a single-stranded DNA break repair protein that is needed for preserving genomic integrity. In addition, PARP1 has been implicated in a veritable plethora of additional cellular pathways and thus its precise contribution(s) to human biology has remained obscure. To help address this deficiency, we utilized gene editing to construct genetically-null PARP1 human cancer cells. We found a minor role for PARP1 in an alternative form of DNA double-strand break (DSB) repair, but only when these cells were deficient for the classical form of DSB repair. Despite being proficient for DSB repair, however, cell cycle progression defects and elevated endogenous DNA damage signaling were observed. These deficiencies were instead linked to telomere defects, where PARP1 -/- cells had short telomeres that co-localized with markers of endogenous DNA damage and were compromised in their ability to escape a telomere-driven crisis. Our data suggest that while PARP1 does not participate significantly in DNA DSB repair itself, it does prevent the incidence of telomeric DSBs, which, in turn, can drive genomic instability.
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Affiliation(s)
- Adam Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Nicholas Mielke
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Julia W. Grimstead
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Rhiannon E. Jones
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Thanh Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Matthew Mueller
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Eric A. Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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12
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Hu WL, Jin L, Xu A, Wang YF, Thorne RF, Zhang XD, Wu M. GUARDIN is a p53-responsive long non-coding RNA that is essential for genomic stability. Nat Cell Biol 2018; 20:492-502. [DOI: 10.1038/s41556-018-0066-7] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 02/15/2018] [Indexed: 12/11/2022]
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13
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Reczek CR, Shakya R, Miteva Y, Szabolcs M, Ludwig T, Baer R. The DNA resection protein CtIP promotes mammary tumorigenesis. Oncotarget 2017; 7:32172-83. [PMID: 27058754 PMCID: PMC5078005 DOI: 10.18632/oncotarget.8605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/14/2016] [Indexed: 01/15/2023] Open
Abstract
Many DNA repair factors act to suppress tumor formation by preserving genomic stability. Similarly, the CtIP protein, which interacts with the BRCA1 tumor suppressor, is also thought to have tumor suppression activity. Through its role in DNA end resection, CtIP facilitates DNA double-strand break (DSB) repair by homologous recombination (DSBR-HR) and microhomology-mediated end joining (MMEJ). In addition, however, CtIP has also been implicated in the formation of aberrant chromosomal rearrangements in an MMEJ-dependent manner, an activity that could potentially promote tumor development by increasing genome instability. To clarify whether CtIP acts in vivo to suppress or promote tumorigenesis, we have examined its oncogenic potential in mouse models of human breast cancer. Surprisingly, mice heterozygous for a null Ctip allele did not display an increased susceptibility to tumor formation. Moreover, mammary-specific biallelic CtIP ablation did not elicit breast tumors in a manner reminiscent of BRCA1 loss. Instead, CtIP inactivation dramatically reduced the kinetics of mammary tumorigenesis in mice bearing mammary-specific lesions of the p53 gene. Thus, unlike other repair factors, CtIP is not a tumor suppressor, but has oncogenic properties that can promote tumorigenesis, consistent with its ability to facilitate MMEJ-dependent chromosomal instability. Consequently, inhibition of CtIP-mediated MMEJ may prove effective against tumor types, such as human breast cancer, that display MMEJ-dependent chromosomal rearrangements.
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Affiliation(s)
- Colleen R Reczek
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Reena Shakya
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.,Current address: Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Wexner Medical Center and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Yana Miteva
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthias Szabolcs
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Thomas Ludwig
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.,Current address: Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University Wexner Medical Center and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Richard Baer
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
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14
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Yang L, Sun L, Teng Y, Chen H, Gao Y, Levine AS, Nakajima S, Lan L. Tankyrase1-mediated poly(ADP-ribosyl)ation of TRF1 maintains cell survival after telomeric DNA damage. Nucleic Acids Res 2017; 45:3906-3921. [PMID: 28160604 PMCID: PMC5397190 DOI: 10.1093/nar/gkx083] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
Oxidative DNA damage triggers telomere erosion and cellular senescence. However, how repair is initiated at telomeres is largely unknown. Here, we found unlike PARP1-mediated Poly-ADP-Ribosylation (PARylation) at genomic damage sites, PARylation at telomeres is mainly dependent on tankyrase1 (TNKS1). TNKS1 is recruited to damaged telomeres via its interaction with TRF1, which subsequently facilitates the PARylation of TRF1 after damage. TNKS inhibition abolishes the recruitment of the repair proteins XRCC1 and polymerase β at damaged telomeres, while the PARP1/2 inhibitor only has such an effect at non-telomeric damage sites. The ANK domain of TNKS1 is essential for the telomeric damage response and TRF1 interaction. Mutation of the tankyrase-binding motif (TBM) on TRF1 (13R/18G to AA) disrupts its interaction with TNKS1 concomitant recruitment of TNKS1 and repair proteins after damage. Either TNKS1 inhibition or TBM mutated TRF1 expression markedly sensitizes cells to telomere oxidative damage as well as XRCC1 inhibition. Together, our data reveal a novel role of TNKS1 in facilitating SSBR at damaged telomeres through PARylation of TRF1, thereby protecting genome stability and cell viability.
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Affiliation(s)
- Lu Yang
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Luxi Sun
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Yaqun Teng
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Hao Chen
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Ying Gao
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Arthur S Levine
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Satoshi Nakajima
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Li Lan
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
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15
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Sinha S, Li F, Villarreal D, Shim JH, Yoon S, Myung K, Shim EY, Lee SE. Microhomology-mediated end joining induces hypermutagenesis at breakpoint junctions. PLoS Genet 2017; 13:e1006714. [PMID: 28419093 PMCID: PMC5413072 DOI: 10.1371/journal.pgen.1006714] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 05/02/2017] [Accepted: 03/24/2017] [Indexed: 01/12/2023] Open
Abstract
Microhomology (MH) flanking a DNA double-strand break (DSB) drives chromosomal rearrangements but its role in mutagenesis has not yet been analyzed. Here we determined the mutation frequency of a URA3 reporter gene placed at multiple locations distal to a DSB, which is flanked by different sizes (15-, 18-, or 203-bp) of direct repeat sequences for efficient repair in budding yeast. Induction of a DSB accumulates mutations in the reporter gene situated up to 14-kb distal to the 15-bp MH, but more modestly to those carrying 18- and 203-bp or no homology. Increased mutagenesis in MH-mediated end joining (MMEJ) appears coupled to its slower repair kinetics and the extensive resection occurring at flanking DNA. Chromosomal translocations via MMEJ also elevate mutagenesis of the flanking DNA sequences 7.1 kb distal to the breakpoint junction as compared to those without MH. The results suggest that MMEJ could destabilize genomes by triggering structural alterations and increasing mutation burden. Recurrent chromosome translocations juxtapose chromosomal fragments and alter expression of tumor suppressors or oncogenes at or near breakpoint junctions to develop distinct types of leukemias and childhood sarcomas. The prevalence of 2–20 bp of imperfect overlapping sequences (a.k.a. microhomology [MH]) at the breakpoint junctions suggests the type of repair events joining two chromosomal fragments and the formation of oncogenic chromosomal translocations. In this study, we discovered that MH-mediated end joining (MMEJ) operates with kinetics markedly slower than other repair options. The slower kinetics leads to extensive resection and drives hypermutagenesis at sequences flanking the break site. We also found that MH-mediated chromosomal translocations accumulate mutations at sequences up to several kilobases distal to the breakpoint junction as compared to those without MH. Our results revealed that MH contributes to genetic instability by facilitating chromosomal translocations and increasing mutational load at the sequences flanking the breakpoints.
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Affiliation(s)
- Supriya Sinha
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Fuyang Li
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Diana Villarreal
- Children's Hospital of San Antonio, Baylor College of Medicine, San Antonio, TX, United States of America
| | - Jae Hoon Shim
- Korea Institute of Radiological & Medical Sciences (KIRAMS), 75 Nowon-ro, Nowon-gu, Seoul, Republic of Korea
| | - Suhyeon Yoon
- Department of Biological Science, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44818, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44818, Republic of Korea
- Department of Biological Science, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44818, Republic of Korea
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- * E-mail:
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16
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Zhang J, Shim G, de Toledo SM, Azzam EI. The Translationally Controlled Tumor Protein and the Cellular Response to Ionizing Radiation-Induced DNA Damage. Results Probl Cell Differ 2017; 64:227-253. [DOI: 10.1007/978-3-319-67591-6_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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17
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Shamanna RA, Lu H, de Freitas JK, Tian J, Croteau DL, Bohr VA. WRN regulates pathway choice between classical and alternative non-homologous end joining. Nat Commun 2016; 7:13785. [PMID: 27922005 PMCID: PMC5150655 DOI: 10.1038/ncomms13785] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 11/01/2016] [Indexed: 11/20/2022] Open
Abstract
Werner syndrome (WS) is an accelerated ageing disorder with genomic instability caused by WRN protein deficiency. Many features seen in WS can be explained by the diverse functions of WRN in DNA metabolism. However, the origin of the large genomic deletions and telomere fusions are not yet understood. Here, we report that WRN regulates the pathway choice between classical (c)- and alternative (alt)-nonhomologous end joining (NHEJ) during DNA double-strand break (DSB) repair. It promotes c-NHEJ via helicase and exonuclease activities and inhibits alt-NHEJ using non-enzymatic functions. When WRN is recruited to the DSBs it suppresses the recruitment of MRE11 and CtIP, and protects the DSBs from 5′ end resection. Moreover, knockdown of Wrn, alone or in combination with Trf2 in mouse embryonic fibroblasts results in increased telomere fusions, which were ablated by Ctip knockdown. We show that WRN regulates alt-NHEJ and shields DSBs from MRE11/CtIP-mediated resection to prevent large deletions and telomere fusions. Werner Syndrome is an accelerated aging disorder marked by genome instability, large deletions and telomere fusions, hallmarks of aberrant DNA repair. Here the authors report a role for the WRN helicase in regulating the choice between classical and alternative non-homologous end-joning.
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Affiliation(s)
- Raghavendra A Shamanna
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, Maryland 21224, USA
| | - Huiming Lu
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, Maryland 21224, USA
| | - Jessica K de Freitas
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, Maryland 21224, USA
| | - Jane Tian
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, Maryland 21224, USA
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, Maryland 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, Biomedical Research Center, 251 Bayview Boulevard, National Institute on Aging, NIH, Baltimore, Maryland 21224, USA
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18
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Differences in the recruitment of DNA repair proteins at subtelomeric and interstitial I-SceI endonuclease-induced DNA double-strand breaks. DNA Repair (Amst) 2016; 49:1-8. [PMID: 27842255 DOI: 10.1016/j.dnarep.2016.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/21/2016] [Accepted: 10/26/2016] [Indexed: 12/28/2022]
Abstract
Telomeres are nucleoprotein structures that are required to protect chromosome ends. Dysfunctional telomeres are recognized as DNA double-strand breaks (DSBs), and elicit the activation of a DNA damage response (DDR). We have previously reported that DSBs near telomeres are poorly repaired, resulting in a high frequency of large deletions and gross chromosome rearrangements (GCRs). Our previous genetic studies have demonstrated that this sensitivity of telomeric regions to DSBs is a result of excessive processing. In the current study, we have further investigated the sensitivity of telomeric regions to DSBs through the analysis of repair proteins associated with DSBs at interstitial and telomeric sites. Following the inducible expression of I-SceI endonuclease, chromatin immunoprecipitation (ChIP) and real-time quantitative PCR were used to compare the recruitment of repair proteins at I-SceI-induced DSBs at interstitial and subtelomeric sites. We observed that proteins that are specifically associated with processing of DSBs during homologous recombination repair, RAD51, BRCA1, and CtIP, are present at a much greater abundance at subtelomeric DSBs. In contrast, Ku70, which is specifically involved in classical nonhomologous end joining, showed no difference at interstitial and subtelomeric DSBs. Importantly, ATM was lower in abundance at subtelomeric DSBs, while ATR was in greater abundance at subtelomeric DSBs, consistent with the accumulation of processed DSBs near telomeres, since processing is accompanied by a transition from ATM to ATR binding. Combined, our results suggest that excessive processing is responsible for the increased frequency of large deletions and GCRs at DSBs near telomeres.
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19
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Kargaran PK, Yasaei H, Anjomani-Virmouni S, Mangiapane G, Slijepcevic P. Analysis of alternative lengthening of telomere markers in BRCA1 defective cells. Genes Chromosomes Cancer 2016; 55:864-76. [PMID: 27295426 PMCID: PMC5113789 DOI: 10.1002/gcc.22386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/03/2016] [Accepted: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
Telomeres are specialized structures responsible for the chromosome end protection. Previous studies have revealed that defective BRCA1 may lead to elevated telomere fusions and accelerated telomere shortening. In addition, BRCA1 associates with promyelocytic leukemia (PML) bodies in alternative lengthening of telomeres (ALTs) positive cells. We report here elevated recombination rates at telomeres in cells from human BRCA1 mutation carriers and in mouse embryonic stem cells lacking both copies of functional Brca1. An increased recombination rate at telomeres is one of the signs of ALT. To investigate this possibility further we employed the C-circle assay that identifies ALT unequivocally. Our results revealed elevated levels of ALT activity in Brca1 defective mouse cells. Similar results were obtained when the same cells were assayed for the presence of another ALT marker, namely the frequency of PML bodies. These results suggest that BRCA1 may act as a repressor of ALT. © 2016 The Authors Genes, Chromosomes & Cancer Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Parisa K Kargaran
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Hemad Yasaei
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Sara Anjomani-Virmouni
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Giovanna Mangiapane
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Predrag Slijepcevic
- Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK.
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20
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Saha J, Davis AJ. Unsolved mystery: the role of BRCA1 in DNA end-joining. JOURNAL OF RADIATION RESEARCH 2016; 57 Suppl 1:i18-i24. [PMID: 27170701 PMCID: PMC4990114 DOI: 10.1093/jrr/rrw032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/11/2016] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Heritable mutations in the tumor suppressor gene BRCA1 increase a woman's lifetime risk of developing breast and ovarian cancer. BRCA1's tumor suppressor function is directly linked to its myriad of functions in the cellular response to DNA double-strand breaks (DSBs). BRCA1 interacts with an extensive array of DNA damage responsive proteins and plays important roles in DSB repair, mediated by the homologous recombination pathway, and in the activation of cell cycle checkpoints. However, the role of BRCA1 in the other two DSB repair pathways, classical non-homologous end-joining (C-NHEJ) and alternative NHEJ (A-NHEJ), remains unclear. In this review, we will discuss the current literature on BRCA1's potential role(s) in modulating both C-NHEJ and A-NHEJ. We also present a model showing that BRCA1 contributes to genomic maintenance by promoting precise DNA repair across all cell cycle phases via the direct modulation of DNA end-joining.
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Affiliation(s)
- Janapriya Saha
- Department of Radiation Oncology, Division of Molecular Radiation Biology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390-9187, USA
| | - Anthony J Davis
- Department of Radiation Oncology, Division of Molecular Radiation Biology, University of Texas Southwestern Medical Center, 2201 Inwood Rd, Dallas, Texas 75390-9187, USA
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21
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Ahrabi S, Sarkar S, Pfister SX, Pirovano G, Higgins GS, Porter ACG, Humphrey TC. A role for human homologous recombination factors in suppressing microhomology-mediated end joining. Nucleic Acids Res 2016; 44:5743-57. [PMID: 27131361 PMCID: PMC4937322 DOI: 10.1093/nar/gkw326] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 04/13/2016] [Accepted: 04/14/2016] [Indexed: 12/22/2022] Open
Abstract
DNA double-strand breaks (DSBs) are toxic lesions, which if improperly repaired can result in cell death or genomic instability. DSB repair is usually facilitated by the classical non-homologous end joining (C-NHEJ), or homologous recombination (HR) pathways. However, a mutagenic alternative NHEJ pathway, microhomology-mediated end joining (MMEJ), can also be deployed. While MMEJ is suppressed by C-NHEJ, the relationship between HR and MMEJ is less clear. Here, we describe a role for HR genes in suppressing MMEJ in human cells. By monitoring DSB mis-repair using a sensitive HPRT assay, we found that depletion of HR proteins, including BRCA2, BRCA1 or RPA, resulted in a distinct mutational signature associated with significant increases in break-induced mutation frequencies, deletion lengths and the annealing of short regions of microhomology (2-6 bp) across the break-site. This signature was dependent on CtIP, MRE11, POLQ and PARP, and thus indicative of MMEJ. In contrast to CtIP or MRE11, depletion of BRCA1 resulted in increased partial resection and MMEJ, thus revealing a functional distinction between these early acting HR factors. Together these findings indicate that HR factors suppress mutagenic MMEJ following DSB resection.
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Affiliation(s)
- Sara Ahrabi
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sovan Sarkar
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sophia X Pfister
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Giacomo Pirovano
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Geoff S Higgins
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Imperial College Faculty of Medicine, London W12 0NN, UK
| | - Timothy C Humphrey
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
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Stop pulling my strings - what telomeres taught us about the DNA damage response. Nat Rev Mol Cell Biol 2016; 17:364-78. [PMID: 27165790 DOI: 10.1038/nrm.2016.43] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mammalian cells have evolved specialized mechanisms to sense and repair double-strand breaks (DSBs) to maintain genomic stability. However, in certain cases, the activity of these pathways can lead to aberrant DNA repair, genomic instability and tumorigenesis. One such case is DNA repair at the natural ends of linear chromosomes, known as telomeres, which can lead to chromosome-end fusions. Here, we review data obtained over the past decade and discuss the mechanisms that protect mammalian chromosome ends from the DNA damage response. We also discuss how telomere research has helped to uncover key steps in DSB repair. Last, we summarize how dysfunctional telomeres and the ensuing genomic instability drive the progression of cancer.
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TRF2-RAP1 is required to protect telomeres from engaging in homologous recombination-mediated deletions and fusions. Nat Commun 2016; 7:10881. [PMID: 26941064 PMCID: PMC4785230 DOI: 10.1038/ncomms10881] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/29/2016] [Indexed: 12/27/2022] Open
Abstract
Repressor/activator protein 1 (RAP1) is a highly conserved telomere-interacting protein. Yeast Rap1 protects telomeres from non-homologous end joining (NHEJ), plays important roles in telomere length control and is involved in transcriptional gene regulation. However, a role for mammalian RAP1 in telomere end protection remains controversial. Here we present evidence that mammalian RAP1 is essential to protect telomere from homology directed repair (HDR) of telomeres. RAP1 cooperates with the basic domain of TRF2 (TRF2B) to repress PARP1 and SLX4 localization to telomeres. Without RAP1 and TRF2B, PARP1 and SLX4 HR factors promote rapid telomere resection, resulting in catastrophic telomere loss and the generation of telomere-free chromosome fusions in both mouse and human cells. The RAP1 Myb domain is required to repress both telomere loss and formation of telomere-free fusions. Our results highlight the importance of the RAP1-TRF2 heterodimer in protecting telomeres from inappropriate processing by the HDR pathway. While yeast Rap1 regulates telomere length and protects telomeres from non-homologous end joining, its role in higher eukaryotes is controversial. Here the authors present evidence that in mammals, RAP1 cooperates with TRF2 to prevent homologous recombination-mediated repair of telomeres.
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DNA repair factor BRCA1 depletion occurs in Alzheimer brains and impairs cognitive function in mice. Nat Commun 2015; 6:8897. [PMID: 26615780 PMCID: PMC4674776 DOI: 10.1038/ncomms9897] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 10/14/2015] [Indexed: 02/08/2023] Open
Abstract
Maintaining DNA integrity is vital for all cells and organisms. Defective DNA repair may contribute to neurological disorders, including Alzheimer's disease (AD). We found reduced levels of BRCA1, but not of other DNA repair factors, in the brains of AD patients and human amyloid precursor protein (hAPP) transgenic mice. Amyloid-β oligomers reduced BRCA1 levels in primary neuronal cultures. In wild-type mice, knocking down neuronal BRCA1 in the dentate gyrus caused increased DNA double-strand breaks, neuronal shrinkage, synaptic plasticity impairments, and learning and memory deficits, but not apoptosis. Low levels of hAPP/Amyloid-β overexpression exacerbated these effects. Physiological neuronal activation increased BRCA1 levels, whereas stimulating predominantly extrasynaptic N-methyl-D-aspartate receptors promoted the proteasomal degradation of BRCA1. We conclude that BRCA1 is regulated by neuronal activity, protects the neuronal genome, and critically supports neuronal integrity and cognitive functions. Pathological accumulation of Aβ depletes neuronal BRCA1, which may contribute to cognitive deficits in AD.
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