251
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Gali H, Mason-Osann E, Flynn RL. Direct Visualization of DNA Replication at Telomeres Using DNA Fiber Combing Combined with Telomere FISH. Methods Mol Biol 2019; 1999:319-325. [PMID: 31127588 DOI: 10.1007/978-1-4939-9500-4_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The ability to analyze individual DNA fibers undergoing active DNA synthesis has emerged as a powerful technique in the field of DNA replication. Much of the initial analysis has focused on replication throughout the genome. However, more recent advancements in this technique have allowed for the visualization of replication patterns at distinct loci or regions within the genome. This type of locus-specific resolution will greatly enhance our understanding of the dynamics of DNA replication in regions that provide a challenge to the replication machinery. Here, we describe a protocol that will allow for the visualization of DNA replication through one of the most structurally complex regions in the human genome, the telomeric DNA.
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Affiliation(s)
- Himabindu Gali
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Emily Mason-Osann
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Rachel Litman Flynn
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA.
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252
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Tsao WC, Eckert KA. Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress. Int J Mol Sci 2018; 19:ijms19103255. [PMID: 30347795 PMCID: PMC6214091 DOI: 10.3390/ijms19103255] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
Incomplete and low-fidelity genome duplication contribute to genomic instability and cancer development. Difficult-to-Replicate Sequences, or DiToRS, are natural impediments in the genome that require specialized DNA polymerases and repair pathways to complete and maintain faithful DNA synthesis. DiToRS include non B-DNA secondary structures formed by repetitive sequences, for example within chromosomal fragile sites and telomeres, which inhibit DNA replication under endogenous stress conditions. Oncogene activation alters DNA replication dynamics and creates oncogenic replication stress, resulting in persistent activation of the DNA damage and replication stress responses, cell cycle arrest, and cell death. The response to oncogenic replication stress is highly complex and must be tightly regulated to prevent mutations and tumorigenesis. In this review, we summarize types of known DiToRS and the experimental evidence supporting replication inhibition, with a focus on the specialized DNA polymerases utilized to cope with these obstacles. In addition, we discuss different causes of oncogenic replication stress and its impact on DiToRS stability. We highlight recent findings regarding the regulation of DNA polymerases during oncogenic replication stress and the implications for cancer development.
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Affiliation(s)
- Wei-Chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
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253
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Brosnan-Cashman JA, Yuan M, Graham MK, Rizzo AJ, Myers KM, Davis C, Zhang R, Esopi DM, Raabe EH, Eberhart CG, Heaphy CM, Meeker AK. ATRX loss induces multiple hallmarks of the alternative lengthening of telomeres (ALT) phenotype in human glioma cell lines in a cell line-specific manner. PLoS One 2018; 13:e0204159. [PMID: 30226859 PMCID: PMC6143253 DOI: 10.1371/journal.pone.0204159] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/03/2018] [Indexed: 12/05/2022] Open
Abstract
Cancers must maintain their telomeres at lengths sufficient for cell survival. In several cancer subtypes, a recombination-like mechanism termed alternative lengthening of telomeres (ALT), is frequently used for telomere length maintenance. Cancers utilizing ALT often have lost functional ATRX, a chromatin remodeling protein, through mutation or deletion, thereby strongly implicating ATRX as an ALT suppressor. Herein, we have generated functional ATRX knockouts in four telomerase-positive, ALT-negative human glioma cell lines: MOG-G-UVW, SF188, U-251 and UW479. After loss of ATRX, two of the four cell lines (U-251 and UW479) show multiple characteristics of ALT-positive cells, including ultrabright telomeric DNA foci, ALT-associated PML bodies, and c-circles. However, telomerase activity and overall telomere length heterogeneity are unaffected after ATRX loss, regardless of cellular context. The two cell lines that showed ALT hallmarks after complete ATRX loss also did so upon ATRX depletion via shRNA-mediated knockdown. These results suggest that other genomic or epigenetic events, in addition to ATRX loss, are necessary for the induction of ALT in human cancer.
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Affiliation(s)
| | - Ming Yuan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mindy K. Graham
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Anthony J. Rizzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Kaylar M. Myers
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Christine Davis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Rebecca Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David M. Esopi
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Eric H. Raabe
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Pediatric Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Charles G. Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Christopher M. Heaphy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Alan K. Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
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254
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Brosnan-Cashman JA, Graham MK, Heaphy CM. Genetic alterations associated with ALTered telomeres. Oncotarget 2018; 9:33739-33740. [PMID: 30333904 PMCID: PMC6173459 DOI: 10.18632/oncotarget.26111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Jacqueline A Brosnan-Cashman
- Christopher M. Heaphy: Departments of Pathology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mindy K Graham
- Christopher M. Heaphy: Departments of Pathology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher M Heaphy
- Christopher M. Heaphy: Departments of Pathology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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255
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Mason-Osann E, Dai A, Floro J, Lock YJ, Reiss M, Gali H, Matschulat A, Labadorf A, Flynn RL. Identification of a novel gene fusion in ALT positive osteosarcoma. Oncotarget 2018; 9:32868-32880. [PMID: 30214690 PMCID: PMC6132345 DOI: 10.18632/oncotarget.26029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/15/2018] [Indexed: 01/13/2023] Open
Abstract
The Alternative Lengthening of Telomeres (ALT) pathway stimulates telomere elongation and prevents cellular senescence in approximately 60% of osteosarcoma. While the precise mechanism underlying activation of the ALT pathway is unclear, mutations in the chromatin remodeling protein ATRX, histone chaperone DAXX, and the histone variant H3.3 correlate with ALT status. ATRX and DAXX facilitate deposition of the histone variant H3.3 within heterochromatic regions suggesting that loss of ATRX, DAXX, and/or H3.3 lead to defects in the stability of telomeric heterochromatin. Genetic mutations in ATRX, DAXX, and H3.3 have been detected in ALT positive cancers, however, a subset of ALT samples show loss of ATRX or DAXX protein expression or localization without evidence of genetic alterations suggesting additional uncharacterized defects in ATRX/DAXX/H3.3 function. Here, using Next Generation Sequencing we identified a novel gene fusion event between DAXX and the kinesin motor protein, KIFC3, leading to the translation of a chimeric DAXX-KIFC3 fusion protein. Moreover, we demonstrate that the fusion of KIFC3 to DAXX causes defects in DAXX function likely promoting ALT activity. These data highlight a potentially unrecognized mechanism of DAXX inactivation in ALT positive osteosarcoma and provide rationale for thorough and comprehensive analyses of ATRX/DAXX/H3.3 proteins in ALT positive cancers.
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Affiliation(s)
- Emily Mason-Osann
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anqi Dai
- BU Bioinformatics Hub, Boston University, Boston, MA 02118, USA
| | - Jess Floro
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ying Jie Lock
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Matthew Reiss
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Himabindu Gali
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adeline Matschulat
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam Labadorf
- BU Bioinformatics Hub, Boston University, Boston, MA 02118, USA
| | - Rachel Litman Flynn
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
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256
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Abstract
Flaws in the DNA replication process have emerged as a leading driver of genome instability in human diseases. Alteration to replication fork progression is a defining feature of replication stress and the consequent failure to maintain fork integrity and complete genome duplication within a single round of S-phase compromises genetic integrity. This includes increased mutation rates, small and large scale genomic rearrangement and deleterious consequences for the subsequent mitosis that result in the transmission of additional DNA damage to the daughter cells. Therefore, preserving fork integrity and replication competence is an important aspect of how cells respond to replication stress and avoid genetic change. Homologous recombination is a pivotal pathway in the maintenance of genome integrity in the face of replication stress. Here we review our recent understanding of the mechanisms by which homologous recombination acts to protect, restart and repair replication forks. We discuss the dynamics of these genetically distinct functions and their contribution to faithful mitoticsegregation.
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257
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Liu H, Xie Y, Zhang Z, Mao P, Liu J, Ma W, Zhao Y. Telomeric Recombination Induced by DNA Damage Results in Telomere Extension and Length Heterogeneity. Neoplasia 2018; 20:905-916. [PMID: 30118998 PMCID: PMC6097467 DOI: 10.1016/j.neo.2018.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022] Open
Abstract
About 15% of human cancers counteract telomere loss by alternative lengthening of telomeres (ALT), which is attributed to homologous recombination (HR)–mediated events. But how telomeric HR leads to length elongation is poorly understood. Here, we explore telomere clustering and telomeric HR induced by double-stranded breaks (DSBs). We show that telomere clustering could occur at G1 and S phase of cell cycle and that three types of telomeric HR occur based on the manner of telomeric DNA exchange: equivalent telomeric sister chromatin exchange (T-SCE), inequivalent T-SCE, and No-SCE. While inequivalent T-SCE increases telomere length heterogeneity with no net gain of telomere length, No-SCE, which is presumably induced by interchromatid HR and/or break-induced replication, results in telomere elongation. Accordingly, cells subjected to long-term telomeric DSBs display increased heterogeneity of length and longer telomeres. We also demonstrate that DSBs-induced telomere elongation is telomerase independent. Moreover, telomeric recombination induced by DSBs is associated with formation of ALT-associated PML body and C-circle. Thus, DNA damage triggers recombination mediated elongation, leading to the induction of multiple ALT phenotypes.
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Affiliation(s)
- Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, P. R. China
| | - Yujie Xie
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, P. R. China
| | - Zepeng Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, P. R. China
| | - Pingsu Mao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, P. R. China
| | - Jingfan Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, P. R. China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, P. R. China.
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258
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Krupa P, Wales DJ, Sieradzan AK. Computational Studies of the Mechanical Stability for Single-Strand Break DNA. J Phys Chem B 2018; 122:8166-8173. [DOI: 10.1021/acs.jpcb.8b05417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - David J. Wales
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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259
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Upregulation of dNTP Levels After Telomerase Inactivation Influences Telomerase-Independent Telomere Maintenance Pathway Choice in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:2551-2558. [PMID: 29848621 PMCID: PMC6071591 DOI: 10.1534/g3.118.200280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In 10–15% of cancers, telomere length is maintained by a telomerase-independent, recombination-mediated pathway called alternative lengthening of telomeres (ALT). ALT mechanisms were first seen, and have been best studied, in telomerase-null Saccharomyces cerevisiae cells called “survivors”. There are two main types of survivors. Type I survivors amplify Y′ subtelomeric elements while type II survivors, similar to the majority of human ALT cells, amplify the terminal telomeric repeats. Both types of survivors require Rad52, a key homologous recombination protein, and Pol32, a non-essential subunit of DNA polymerase δ. A number of additional proteins have been reported to be important for either type I or type II survivor formation, but it is still unclear how these two pathways maintain telomeres. In this study, we performed a genome-wide screen to identify novel genes that are important for the formation of type II ALT-like survivors. We identified 23 genes that disrupt type II survivor formation when deleted. 17 of these genes had not been previously reported to do so. Several of these genes (DUN1, CCR4, and MOT2) are known to be involved in the regulation of dNTP levels. We find that dNTP levels are elevated early after telomerase inactivation and that this increase favors the formation of type II survivors.
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260
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Pasero P, Vindigni A. Nucleases Acting at Stalled Forks: How to Reboot the Replication Program with a Few Shortcuts. Annu Rev Genet 2018; 51:477-499. [PMID: 29178820 DOI: 10.1146/annurev-genet-120116-024745] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In a lifetime, a human being synthesizes approximately 2×1016 meters of DNA, a distance that corresponds to 130,000 times the distance between the Earth and the Sun. This daunting task is executed by thousands of replication forks, which progress along the chromosomes and frequently stall when they encounter DNA lesions, unusual DNA structures, RNA polymerases, or tightly-bound protein complexes. To complete DNA synthesis before the onset of mitosis, eukaryotic cells have evolved complex mechanisms to process and restart arrested forks through the coordinated action of multiple nucleases, topoisomerases, and helicases. In this review, we discuss recent advances in understanding the role and regulation of nucleases acting at stalled forks with a focus on the nucleolytic degradation of nascent DNA, a process commonly referred to as fork resection. We also discuss the effects of deregulated fork resection on genomic instability and on the unscheduled activation of the interferon response under replication stress conditions.
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Affiliation(s)
- Philippe Pasero
- Institute of Human Genetics, CNRS UMR9002, University of Montpellier, 34396 Montpellier, France;
| | - Alessandro Vindigni
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA;
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261
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Juhász S, Elbakry A, Mathes A, Löbrich M. ATRX Promotes DNA Repair Synthesis and Sister Chromatid Exchange during Homologous Recombination. Mol Cell 2018; 71:11-24.e7. [PMID: 29937341 DOI: 10.1016/j.molcel.2018.05.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/20/2018] [Accepted: 05/10/2018] [Indexed: 01/15/2023]
Abstract
ATRX is a chromatin remodeler that, together with its chaperone DAXX, deposits the histone variant H3.3 in pericentromeric and telomeric regions. Notably, ATRX is frequently mutated in tumors that maintain telomere length by a specific form of homologous recombination (HR). Surprisingly, in this context, we demonstrate that ATRX-deficient cells exhibit a defect in repairing exogenously induced DNA double-strand breaks (DSBs) by HR. ATRX operates downstream of the Rad51 removal step and interacts with PCNA and RFC-1, which are collectively required for DNA repair synthesis during HR. ATRX depletion abolishes DNA repair synthesis and prevents the formation of sister chromatid exchanges at exogenously induced DSBs. DAXX- and H3.3-depleted cells exhibit identical HR defects as ATRX-depleted cells, and both ATRX and DAXX function to deposit H3.3 during DNA repair synthesis. This suggests that ATRX facilitates the chromatin reconstitution required for extended DNA repair synthesis and sister chromatid exchange during HR.
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Affiliation(s)
- Szilvia Juhász
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Amira Elbakry
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Arthur Mathes
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany.
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262
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Joyce BT, Zheng Y, Nannini D, Zhang Z, Liu L, Gao T, Kocherginsky M, Murphy R, Yang H, Achenbach CJ, Roberts LR, Hoxha M, Shen J, Vokonas P, Schwartz J, Baccarelli A, Hou L. DNA Methylation of Telomere-Related Genes and Cancer Risk. Cancer Prev Res (Phila) 2018; 11:511-522. [PMID: 29895583 DOI: 10.1158/1940-6207.capr-17-0413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/03/2018] [Accepted: 05/22/2018] [Indexed: 01/09/2023]
Abstract
Researchers hypothesized that telomere shortening facilitates carcinogenesis. Previous studies found inconsistent associations between blood leukocyte telomere length (LTL) and cancer. Epigenetic reprogramming of telomere maintenance mechanisms may help explain this inconsistency. We examined associations between DNA methylation in telomere-related genes (TRG) and cancer. We analyzed 475 participants providing 889 samples 1 to 3 times (median follow-up, 10.1 years) from 1999 to 2013 in the Normative Aging Study. All participants were cancer-free at each visit and blood leukocytes profiled using the Illumina 450K array. Of 121 participants who developed cancer, 34 had prostate cancer, 10 melanoma, 34 unknown skin malignancies, and 43 another cancer. We examined 2,651 CpGs from 80 TRGs and applied a combination of Cox and mixed models to identify CpGs prospectively associated with cancer (at FDR < 0.05). We also explored trajectories of DNA methylation, logistic regression stratified by time to diagnosis/censoring, and cross-sectional models of LTL at first blood draw. We identified 30 CpGs on 23 TRGs whose methylation was positively associated with cancer incidence (β = 1.0-6.93) and one protective CpG in MAD1L1 (β = -0.65), of which 87% were located in TRG promoters. Methylation trajectories of 21 CpGs increased in cancer cases relative to controls; at 4 to 8 years prediagnosis/censoring, 17 CpGs were positively associated with cancer. Three CpGs were cross-sectionally associated with LTL. TRG methylation may be a mechanism through which LTL dynamics reflect cancer risk. Future research should confirm these findings and explore potential mechanisms underlying these findings, including telomere maintenance and DNA repair dysfunction. Cancer Prev Res; 11(8); 511-22. ©2018 AACR.
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Affiliation(s)
- Brian T Joyce
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Yinan Zheng
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Drew Nannini
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Zhou Zhang
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, Missouri
| | - Tao Gao
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Masha Kocherginsky
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Robert Murphy
- Center for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Hushan Yang
- Division of Population Science, Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Chad J Achenbach
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mirjam Hoxha
- Molecular Epidemiology and Environmental Epigenetics Laboratory, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Jincheng Shen
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, Utah
| | - Pantel Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Boston, Massachusetts.,Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Joel Schwartz
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Andrea Baccarelli
- Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, New York
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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263
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Bell WR, Meeker AK, Rizzo A, Rajpara S, Rosenthal IM, Flores Bellver M, Aparicio Domingo S, Zhong X, Barber JR, Joshu CE, Canto-Soler MV, Eberhart CG, Heaphy CM. A unique telomere DNA expansion phenotype in human retinal rod photoreceptors associated with aging and disease. Brain Pathol 2018; 29:45-52. [PMID: 29668072 DOI: 10.1111/bpa.12618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/11/2018] [Indexed: 01/06/2023] Open
Abstract
We have identified a discrete, focal telomere DNA expansion phenotype in the photoreceptor cell layer of normal, non-neoplastic human retinas. This phenotype is similar to that observed in a subset of human cancers, including a large fraction of tumors of the central nervous system, which maintain their telomeres via the non-telomerase-mediated alternative lengthening of telomeres (ALT) mechanism. We observed that these large, ultra-bright telomere DNA foci are restricted to the rod photoreceptors and are not observed in other cell types. Additionally, focus-positive rod cells are dispersed homogeneously throughout the posterior retinal photoreceptor cell layer and appear to be human-specific. We examined 108 normal human retinas obtained at autopsy from a wide range of ages. These large, ultra-bright telomere DNA foci were not observed in infants before 6 months of age; however, the prevalence of focus-positive rod cells dramatically increased throughout life. To investigate associations between this phenotype and retinal pathology, we assessed adult glaucoma (N = 29) and diabetic retinopathy (N = 38) cases. Focus-positive rod cells were prominent in these diseases. When compared to the normal group, after adjusting for age, logistic regression modeling revealed significantly increased odds of falling in the high category of focus-positive rod cells for glaucoma and diabetic retinopathy. In summary, we have identified a dramatic telomere alteration associated with aging and diseases affecting the retina.
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Affiliation(s)
- W Robert Bell
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alan K Meeker
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Anthony Rizzo
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sumit Rajpara
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ian M Rosenthal
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Miguel Flores Bellver
- Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Xiufeng Zhong
- Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - John R Barber
- Departments of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Corinne E Joshu
- Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - M Valeria Canto-Soler
- Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Charles G Eberhart
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher M Heaphy
- Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD.,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
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264
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Kramara J, Osia B, Malkova A. Break-Induced Replication: The Where, The Why, and The How. Trends Genet 2018; 34:518-531. [PMID: 29735283 DOI: 10.1016/j.tig.2018.04.002] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 02/27/2018] [Accepted: 04/05/2018] [Indexed: 01/07/2023]
Abstract
Break-induced replication (BIR) is a pathway that repairs one-ended double-strand breaks (DSBs). For decades, yeast model systems offered the only opportunities to study eukaryotic BIR. These studies described an unusual mode of BIR synthesis that is carried out by a migrating bubble and shows conservative inheritance of newly synthesized DNA, leading to genomic instabilities like those associated with cancer in humans. Yet, evidence of BIR functioning in mammals or during repair of other DNA breaks has been missing. Recent studies have uncovered multiple examples of BIR working in replication restart and repair of eroded telomeres in yeast and mammals, as well as some unexpected findings, including the RAD51 independence of BIR. Strong interest remains in determining the variations in molecular mechanisms that drive and regulate BIR in different genetic backgrounds, across organisms, and particularly in the context of human disease.
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Affiliation(s)
- J Kramara
- These authors contributed equally to this work
| | - B Osia
- These authors contributed equally to this work
| | - A Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
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265
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Gaspar TB, Sá A, Lopes JM, Sobrinho-Simões M, Soares P, Vinagre J. Telomere Maintenance Mechanisms in Cancer. Genes (Basel) 2018; 9:E241. [PMID: 29751586 PMCID: PMC5977181 DOI: 10.3390/genes9050241] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/12/2022] Open
Abstract
Tumour cells can adopt telomere maintenance mechanisms (TMMs) to avoid telomere shortening, an inevitable process due to successive cell divisions. In most tumour cells, telomere length (TL) is maintained by reactivation of telomerase, while a small part acquires immortality through the telomerase-independent alternative lengthening of telomeres (ALT) mechanism. In the last years, a great amount of data was generated, and different TMMs were reported and explained in detail, benefiting from genome-scale studies of major importance. In this review, we address seven different TMMs in tumour cells: mutations of the TERT promoter (TERTp), amplification of the genes TERT and TERC, polymorphic variants of the TERT gene and of its promoter, rearrangements of the TERT gene, epigenetic changes, ALT, and non-defined TMM (NDTMM). We gathered information from over fifty thousand patients reported in 288 papers in the last years. This wide data collection enabled us to portray, by organ/system and histotypes, the prevalence of TERTp mutations, TERT and TERC amplifications, and ALT in human tumours. Based on this information, we discuss the putative future clinical impact of the aforementioned mechanisms on the malignant transformation process in different setups, and provide insights for screening, prognosis, and patient management stratification.
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Affiliation(s)
- Tiago Bordeira Gaspar
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal.
| | - Ana Sá
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal.
| | - José Manuel Lopes
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
- Department of Pathology and Oncology, Centro Hospitalar São João, 4200-139 Porto, Portugal.
| | - Manuel Sobrinho-Simões
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
- Department of Pathology and Oncology, Centro Hospitalar São João, 4200-139 Porto, Portugal.
| | - Paula Soares
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal.
| | - João Vinagre
- Cancer Signaling and Metabolism Group, Institute for Research and Innovation in Health Sciences (i3S), University of Porto, 4200-135 Porto, Portugal.
- Cancer Signaling and Metabolism Group, Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal.
- Medical Faculty of University of Porto (FMUP), 4200-139 Porto, Portugal.
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266
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Dagg RA, Pickett HA, Neumann AA, Napier CE, Henson JD, Teber ET, Arthur JW, Reynolds CP, Murray J, Haber M, Sobinoff AP, Lau LMS, Reddel RR. Extensive Proliferation of Human Cancer Cells with Ever-Shorter Telomeres. Cell Rep 2018. [PMID: 28636942 DOI: 10.1016/j.celrep.2017.05.087] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Acquisition of replicative immortality is currently regarded as essential for malignant transformation. This is achieved by activating a telomere lengthening mechanism (TLM), either telomerase or alternative lengthening of telomeres, to counter normal telomere attrition. However, a substantial proportion of some cancer types, including glioblastomas, liposarcomas, retinoblastomas, and osteosarcomas, are reportedly TLM-negative. As serial samples of human tumors cannot usually be obtained to monitor telomere length changes, it has previously been impossible to determine whether tumors are truly TLM-deficient, there is a previously unrecognized TLM, or the assay results are false-negative. Here, we show that a subset of high-risk neuroblastomas (with ∼50% 5-year mortality) lacked significant TLM activity. Cancer cells derived from these highly aggressive tumors initially had long telomeres and proliferated for >200 population doublings with ever-shorter telomeres. This indicates that prevention of telomere shortening is not always required for oncogenesis, which has implications for inhibiting TLMs for cancer therapy.
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Affiliation(s)
- Rebecca A Dagg
- Children's Cancer Research Unit, The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Axel A Neumann
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jeremy D Henson
- Cancer Cell Immortality Group, Adult Cancer Program, Prince of Wales Clinical School, University of New South Wales, Randwick, NSW 2052, Australia
| | - Erdahl T Teber
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - C Patrick Reynolds
- Cancer Center, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Cell Biology and Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pediatrics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Jayne Murray
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Australia, Randwick, NSW 2031, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Australia, Randwick, NSW 2031, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Loretta M S Lau
- Children's Cancer Research Unit, The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia; Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.
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267
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Mason JMO, McEachern MJ. Chromosome ends as adaptive beginnings: the potential role of dysfunctional telomeres in subtelomeric evolvability. Curr Genet 2018; 64:997-1000. [PMID: 29589105 DOI: 10.1007/s00294-018-0822-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
Abstract
Telomeres serve as protective caps that help the cell differentiate between the naturally occurring ends of chromosomes and double-stranded breaks. When telomere capping function becomes compromised, chromosome ends are subjected to elevated rates of chromosome alterations. These effects can be particularly dramatic in the telomere-adjacent subtelomeric region. While the catastrophic impact of severe telomere dysfunction on genome stability has been well documented, the adaptive telomere failure hypothesis considers an alternative role telomere dysfunction may play in adaptive evolution. This hypothesis suggests that low levels of telomere failure, induced by certain environmental stresses, can lead to elevated subtelomeric recombination. Mutational loss, duplication, or modification of subtelomeric contingency genes could ultimately facilitate adaptation by generating novel mutants better able to survive environmental stress. In this perspective, we discuss recent work that examined mild telomere dysfunction and its role in altering the adaptive potential of subtelomeric genes.
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Affiliation(s)
- Jennifer M O Mason
- Department of Genetics, University of Georgia, Athens, GA, 30605, USA. .,Q2 Solutions, Morrisville, NC, 27560, USA.
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268
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Özer Ö, Bhowmick R, Liu Y, Hickson ID. Human cancer cells utilize mitotic DNA synthesis to resist replication stress at telomeres regardless of their telomere maintenance mechanism. Oncotarget 2018; 9:15836-15846. [PMID: 29662610 PMCID: PMC5882301 DOI: 10.18632/oncotarget.24745] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/25/2018] [Indexed: 12/17/2022] Open
Abstract
Telomeres resemble common fragile sites (CFSs) in that they are difficult-to-replicate and exhibit fragility in mitosis in response to DNA replication stress. At CFSs, this fragility is associated with a delay in the completion of DNA replication until early mitosis, whereupon cells are proposed to switch to a RAD52-dependent form of break-induced replication. Here, we show that this mitotic DNA synthesis (MiDAS) is also a feature of human telomeres. Telomeric MiDAS is not restricted to those telomeres displaying overt fragility, and is a feature of a wide range of cell lines irrespective of whether their telomeres are maintained by telomerase or by the alternative lengthening of telomeres (ALT) mechanism. MiDAS at telomeres requires RAD52, and is mechanistically similar to CFS-associated MiDAS, with the notable exception that telomeric MiDAS does not require the MUS81-EME1 endonuclease. We propose a model whereby replication stress initiates a RAD52-dependent form of break-induced replication that bypasses a requirement for MUS81-EME1 to complete DNA synthesis in mitosis.
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Affiliation(s)
- Özgün Özer
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
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269
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Lue NF. Evolving Linear Chromosomes and Telomeres: A C-Strand-Centric View. Trends Biochem Sci 2018; 43:314-326. [PMID: 29550242 DOI: 10.1016/j.tibs.2018.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/15/2018] [Accepted: 02/15/2018] [Indexed: 02/08/2023]
Abstract
Recent studies have resulted in deeper understanding of a variety of telomere maintenance mechanisms as well as plausible models of telomere evolution. Often overlooked in the discussion of telomere regulation and evolution is the synthesis of the DNA strand that bears the 5'-end (i.e., the C-strand). Herein, I describe a scenario for telomere evolution that more explicitly accounts for the evolution of the C-strand synthesis machinery. In this model, CTC1-STN1-TEN1 (CST), the G-strand-binding complex that regulates primase-Pol α-mediated C-strand synthesis, emerges as a pivotal player and evolutionary link. Itself arising from RPA, CST not only coordinates telomere synthesis, but also gives rise to the POT1-TPP1 complex, which became part of shelterin and regulates telomerase in G-strand elongation.
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Affiliation(s)
- Neal F Lue
- Department of Microbiology and Immunology, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
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270
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Misino S, Bonetti D, Luke-Glaser S, Luke B. Increased TERRA levels and RNase H sensitivity are conserved hallmarks of post-senescent survivors in budding yeast. Differentiation 2018; 100:37-45. [DOI: 10.1016/j.diff.2018.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/08/2018] [Accepted: 02/14/2018] [Indexed: 01/17/2023]
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271
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Cleal K, Norris K, Baird D. Telomere Length Dynamics and the Evolution of Cancer Genome Architecture. Int J Mol Sci 2018; 19:E482. [PMID: 29415479 PMCID: PMC5855704 DOI: 10.3390/ijms19020482] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 02/06/2023] Open
Abstract
Telomeres are progressively eroded during repeated rounds of cell division due to the end replication problem but also undergo additional more substantial stochastic shortening events. In most cases, shortened telomeres induce a cell-cycle arrest or trigger apoptosis, although for those cells that bypass such signals during tumour progression, a critical length threshold is reached at which telomere dysfunction may ensue. Dysfunction of the telomere nucleoprotein complex can expose free chromosome ends to the DNA double-strand break (DSB) repair machinery, leading to telomere fusion with both telomeric and non-telomeric loci. The consequences of telomere fusions in promoting genome instability have long been appreciated through the breakage-fusion-bridge (BFB) cycle mechanism, although recent studies using high-throughput sequencing technologies have uncovered evidence of involvement in a wider spectrum of genomic rearrangements including chromothripsis. A critical step in cancer progression is the transition of a clone to immortality, through the stabilisation of the telomere repeat array. This can be achieved via the reactivation of telomerase, or the induction of the alternative lengthening of telomeres (ALT) pathway. Whilst telomere dysfunction may promote genome instability and tumour progression, by limiting the replicative potential of a cell and enforcing senescence, telomere shortening can act as a tumour suppressor mechanism. However, the burden of senescent cells has also been implicated as a driver of ageing and age-related pathology, and in the promotion of cancer through inflammatory signalling. Considering the critical role of telomere length in governing cancer biology, we review questions related to the prognostic value of studying the dynamics of telomere shortening and fusion, and discuss mechanisms and consequences of telomere-induced genome rearrangements.
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Affiliation(s)
- Kez Cleal
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
| | - Kevin Norris
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
| | - Duncan Baird
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
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272
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Abstract
Break-induced replication (BIR) is an important mechanism aimed to repair one-ended double-strand DNA breaks. BIR is initiated by invasion of a broken DNA end into a homologous template followed by DNA synthesis that can proceed for hundreds of kilobases to the end of the chromosome. Unlike S-phase replication, BIR is carried out by a migrating DNA bubble and is associated with conservative inheritance of newly synthesized DNA. The unusual mode of DNA synthesis during BIR leads to an increased level of genetic instabilities including increased mutagenesis and chromosomal rearrangements. Here, we describe our experimental system in yeast Saccharomyces cerevisiae where BIR is initiated by a site-specific DNA break and where the repair involves two copies of chromosome III. This system allows investigation of BIR using genetic and molecular biology approaches, and can be used for characterization of the BIR mechanism, roles of individual proteins in BIR, and for the analysis of genetic instabilities associated with BIR.
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Affiliation(s)
| | | | - Liping Liu
- University of Iowa, Iowa City, IA, United States
| | - Anna Malkova
- University of Iowa, Iowa City, IA, United States.
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273
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Verma P, Dilley RL, Gyparaki MT, Greenberg RA. Direct Quantitative Monitoring of Homology-Directed DNA Repair of Damaged Telomeres. Methods Enzymol 2018; 600:107-134. [PMID: 29458755 DOI: 10.1016/bs.mie.2017.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Homology-directed DNA repair (HDR) is an evolutionary conserved mechanism that is required for genome integrity and organismal fitness across species. While a myriad of different factors and mechanisms are able to execute HDR, all forms necessitate common steps of DNA damage recognition, homology search and capture, and assembly of a DNA polymerase complex to conduct templated DNA synthesis. The central question of what determines HDR mechanism utilization in mammalian cells has been limited by an inability to directly monitor the DNA damage response and products of repair as they arise from a defined genomic lesion. In this chapter, we describe several methodologies to delineate major steps of HDR during alternative lengthening of telomeres in human cells. This includes procedures to visualize interchromosomal telomere homology searches in real time and quantitatively detect HDR synthesis of nascent telomeres emanating from synchronous activation of telomere DNA double-strand breaks. We highlight the critical details of these methods and their applicability to monitoring HDR at telomeres in a broad variety of mammalian cell types.
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Affiliation(s)
- Priyanka Verma
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Robert L Dilley
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Melina T Gyparaki
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Roger A Greenberg
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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274
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Fann LY, Chen Y, Chu DC, Weng SJ, Chu HC, Wu ATH, Lee JF, Ali AAA, Chen TC, Huang HS, Ma KH. Identification and preclinical evaluation of the small molecule, NSC745887, for treating glioblastomas via suppressing DcR3-associated signaling pathways. Oncotarget 2017; 9:11922-11937. [PMID: 29552282 PMCID: PMC5844718 DOI: 10.18632/oncotarget.23714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/11/2017] [Indexed: 11/25/2022] Open
Abstract
The small-molecule naphtha [2,3-f]quinoxaline-7,12-dione (NSC745887) can effectively inhibit the proliferation of various cancers by trapping DNA-topoisomerase cleavage. The aim of this study was to elucidate cellular responses of NSC745887 in human glioblastoma multiforme (GBM, U118MG and U87MG cells) and investigate the underlying molecular mechanisms. NSC745887 reduced the cell survival rate and increased the sub-G1 population in dose- and time-dependent manners in GBM cells. Moreover, NSC745887 increased expression of γH2AX and caused DNA fragmentation leading to DNA damage. Furthermore, Annexin V/propidium iodide and Br-dTP staining showed the apoptotic effect of NSC745887 in GBM cells. DNA repair proteins of ataxia-telangiectasia mutated (ATM), ATM and Rad3-related, and decoy receptor 3 also decreased with NSC745887 treatment. In addition, NSC745887 caused apoptosis by the caspase-8/9-caspase-3-poly(ADP-ribose) polymerase cascade. An in vivo study indicated that NSC745887 suppressed the [18F]-FDG-specific uptake value in brain tumors. Histological staining also indicated a decrease in Ki-67 and increases in γH2AX and cleaved caspase-3 in the brain tumor area. These data provide preclinical evidence for NSC745887 as a potential new small molecule drug for managing glioblastomas.
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Affiliation(s)
- Li-Yun Fann
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, ROC.,Department of Nursing and Department of Neurosurgery, Taipei City Hospital, Taipei, Taiwan, ROC.,Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, ROC
| | - Ying Chen
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, ROC.,Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Da-Chen Chu
- Department of Nursing and Department of Neurosurgery, Taipei City Hospital, Taipei, Taiwan, ROC
| | - Shao-Ju Weng
- Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Heng-Cheng Chu
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, ROC
| | - Alexander T H Wu
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, ROC
| | - Jiann-Fong Lee
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, ROC
| | - Ahmed Atef Ahmed Ali
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, ROC
| | - Tsung-Chih Chen
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, ROC
| | - Hsu-Shan Huang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, ROC.,Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan, ROC.,Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, ROC
| | - Kuo-Hsing Ma
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, ROC.,Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan, ROC
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275
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Quinet A, Lemaçon D, Vindigni A. Replication Fork Reversal: Players and Guardians. Mol Cell 2017; 68:830-833. [PMID: 29220651 DOI: 10.1016/j.molcel.2017.11.022] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/07/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
Replication fork reversal is a rapidly emerging and remarkably frequent mechanism of fork stabilization in response to genotoxic insults. Here, we summarize recent findings that uncover key molecular determinants for reversed fork formation and describe how the homologous recombination factors BRCA1, BRCA2, and RAD51 protect these structures from extended nucleolytic degradation.
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Affiliation(s)
- Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Delphine Lemaçon
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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276
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Pompili L, Leonetti C, Biroccio A, Salvati E. Diagnosis and treatment of ALT tumors: is Trabectedin a new therapeutic option? JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:189. [PMID: 29273061 PMCID: PMC5741932 DOI: 10.1186/s13046-017-0657-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/01/2017] [Indexed: 12/22/2022]
Abstract
Telomeres are specialized nucleoprotein structures responsible for protecting chromosome ends in order to prevent the loss of genomic information. Telomere maintenance is required for achieving immortality by neoplastic cells. While most cancer cells rely on telomerase re-activation for linear chromosome maintenance and sustained proliferation, a significant population of cancers (10-15%) employs telomerase-independent strategies, collectively referred to as Alternative Lengthening of Telomeres (ALT). ALT mechanisms involve different types of homology-directed telomere recombination and synthesis. These processes are facilitated by loss of the ATRX or DAXX chromatin-remodeling factors and by abnormalities of the telomere nucleoprotein architecture. Although the functional consequences of telomerase and ALT up-regulation are similar in that they both prevent overall telomere shortening in tumors, these telomere maintenance mechanisms (TMMs) differ in several aspects which may account for their differential prognostic significance and response to therapy in various tumor types. Therefore, reliable methods for detecting telomerase activity and ALT are likely to become an important pre-requisite for the use of treatments targeting one or other of these mechanisms. However, the question whether ALT presence can confer sensitivity to rationally designed anti-cancer therapies is still open. Here we review the latest discoveries in terms of mechanisms of ALT activation and maintenance in human tumors, methods for ALT identification in cell lines and human tissues and biomarkers validation. Then, original results on sensitivity to rational based pre-clinical and clinical anti-tumor drugs in ALT vs hTERT positive cells will be presented.
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Affiliation(s)
- Luca Pompili
- UOSD SAFU, Regina Elena National Cancer Institute, Rome, Italy.,University of Tuscia, Viterbo, Italy
| | - Carlo Leonetti
- UOSD SAFU, Regina Elena National Cancer Institute, Rome, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Via Elio Chianesi, 53 -, 00144, Rome, Italy
| | - Erica Salvati
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Via Elio Chianesi, 53 -, 00144, Rome, Italy.
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277
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Chen C, Sang H, Ding P, Sun Y, Mura M, Hu Y, Kantorovich LN, Besenbacher F, Yu M. Xanthine Quartets on Au(111). J Am Chem Soc 2017; 140:54-57. [DOI: 10.1021/jacs.7b10444] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Chong Chen
- School of Chemistry & Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
- iNANO
and Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark
| | - Hongqian Sang
- Institute
for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Pengcheng Ding
- Condensed
Matter Science and Technology Institute, Harbin Institute of Technology, Harbin 150001, China
| | - Ye Sun
- Condensed
Matter Science and Technology Institute, Harbin Institute of Technology, Harbin 150001, China
| | - Manuela Mura
- School
of Mathematics and Physics, University of Lincoln, Brayford Pool LN6 7TS, United Kingdom
| | - Ying Hu
- School
of
Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Lev N. Kantorovich
- Department
of Physics, King’s College London, The Strand, London WC2R
2LS, United Kingdom
| | - Flemming Besenbacher
- iNANO
and Department of Physics and Astronomy, Aarhus University, Aarhus 8000, Denmark
| | - Miao Yu
- School of Chemistry & Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
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278
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Tardat M, Déjardin J. Telomere chromatin establishment and its maintenance during mammalian development. Chromosoma 2017; 127:3-18. [PMID: 29250704 PMCID: PMC5818603 DOI: 10.1007/s00412-017-0656-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Telomeres are specialized structures that evolved to protect the end of linear chromosomes from the action of the cell DNA damage machinery. They are composed of tandem arrays of repeated DNA sequences with a specific heterochromatic organization. The length of telomeric repeats is dynamically regulated and can be affected by changes in the telomere chromatin structure. When telomeres are not properly controlled, the resulting chromosomal alterations can induce genomic instability and ultimately the development of human diseases, such as cancer. Therefore, proper establishment, regulation, and maintenance of the telomere chromatin structure are required for cell homeostasis. Here, we review the current knowledge on telomeric chromatin dynamics during cell division and early development in mammals, and how its proper regulation safeguards genome stability.
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Affiliation(s)
- Mathieu Tardat
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Jérôme Déjardin
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
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279
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Sobinoff AP, Pickett HA. Alternative Lengthening of Telomeres: DNA Repair Pathways Converge. Trends Genet 2017; 33:921-932. [DOI: 10.1016/j.tig.2017.09.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 08/30/2017] [Accepted: 09/08/2017] [Indexed: 02/08/2023]
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280
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McFarlane RJ, Wakeman JA. Meiosis-like Functions in Oncogenesis: A New View of Cancer. Cancer Res 2017; 77:5712-5716. [PMID: 29061671 DOI: 10.1158/0008-5472.can-17-1535] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/03/2017] [Accepted: 08/16/2017] [Indexed: 11/16/2022]
Abstract
Cancer cells have many abnormal characteristics enabling tumors to grow, spread, and avoid immunologic and therapeutic destruction. Central to this is the innate ability of populations of cancer cells to rapidly evolve. One feature of many cancers is that they activate genes that are normally associated with distinct developmental states, including germ cell-specific genes. This has historically led to the proposal that tumors take on embryonal characteristics, the so called embryonal theory of cancer. However, one group of germline genes, not directly associated with embryonic somatic tissue genesis, is the one that encodes the specific factors to drive the unique reductional chromosome segregation of meiosis I, which also results in chromosomal exchanges. Here, we propose that meiosis I-specific modulators of reductional segregation can contribute to oncogenic chromosome dynamics and that the embryonal theory for cancer cell growth/proliferation is overly simplistic, as meiotic factors are not a feature of most embryonic tissue development. We postulate that some meiotic chromosome-regulatory functions contribute to a soma-to-germline model for cancer, in which activation of germline (including meiosis) functions drive oncogenesis, and we extend this to propose that meiotic factors could be powerful sources of targets for therapeutics and biomonitoring in oncology. Cancer Res; 77(21); 5712-6. ©2017 AACR.
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Affiliation(s)
- Ramsay J McFarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom.
| | - Jane A Wakeman
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
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281
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Lemaçon D, Jackson J, Quinet A, Brickner JR, Li S, Yazinski S, You Z, Ira G, Zou L, Mosammaparast N, Vindigni A. MRE11 and EXO1 nucleases degrade reversed forks and elicit MUS81-dependent fork rescue in BRCA2-deficient cells. Nat Commun 2017; 8:860. [PMID: 29038425 PMCID: PMC5643552 DOI: 10.1038/s41467-017-01180-5] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 08/23/2017] [Indexed: 12/31/2022] Open
Abstract
The breast cancer susceptibility proteins BRCA1 and BRCA2 have emerged as key stabilizing factors for the maintenance of replication fork integrity following replication stress. In their absence, stalled replication forks are extensively degraded by the MRE11 nuclease, leading to chemotherapeutic sensitivity. Here we report that BRCA proteins prevent nucleolytic degradation by protecting replication forks that have undergone fork reversal upon drug treatment. The unprotected regressed arms of reversed forks are the entry point for MRE11 in BRCA-deficient cells. The CtIP protein initiates MRE11-dependent degradation, which is extended by the EXO1 nuclease. Next, we show that the initial limited resection of the regressed arms establishes the substrate for MUS81 in BRCA2-deficient cells. In turn, MUS81 cleavage of regressed forks with a ssDNA tail promotes POLD3-dependent fork rescue. We propose that targeting this pathway may represent a new strategy to modulate BRCA2-deficient cancer cell response to chemotherapeutics that cause fork degradation. BRCA proteins have emerged as key stabilizing factors for the maintenance of replication forks following replication stress. Here the authors describe how reversed replication forks are degraded in the absence of BRCA2, and a MUS81 and POLD3-dependent mechanism of rescue following the withdrawal of genotoxic agent.
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Affiliation(s)
- Delphine Lemaçon
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, 63104, USA
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, 63104, USA
| | - Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, 63104, USA
| | - Joshua R Brickner
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, Campus Box 8228, 660S. Euclid Ave., St Louis, MO, 63110, USA
| | - Stephanie Yazinski
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, Campus Box 8228, 660S. Euclid Ave., St Louis, MO, 63110, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02129, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO, 63104, USA.
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282
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Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens. G3-GENES GENOMES GENETICS 2017; 7:3295-3303. [PMID: 28801508 PMCID: PMC5633380 DOI: 10.1534/g3.117.300141] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in Caenorhabditis elegans and in three human cell types, utilizing a set of DNA topology-dependent approaches for enrichment and characterization. The use of parallel biophysical, enzymatic, and informatic approaches provides a comprehensive profiling of eccDNA robust to isolation and analysis methodology. Results in human and nematode systems provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture, in which endogenous genomic DNA circles are present in normal physiological states, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples.
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283
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Alternative Lengthening of Telomeres Mediated by Mitotic DNA Synthesis Engages Break-Induced Replication Processes. Mol Cell Biol 2017; 37:MCB.00226-17. [PMID: 28760773 DOI: 10.1128/mcb.00226-17] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers. By analyzing telomerase-positive cells and their human TERC knockout-derived ALT human cell lines, we show that ALT cells harbor more fragile telomeres representing telomere replication problems. ALT-associated replication defects trigger mitotic DNA synthesis (MiDAS) at telomeres in a RAD52-dependent, but RAD51-independent, manner. Telomeric MiDAS is a conservative DNA synthesis process, potentially mediated by break-induced replication, similar to type II ALT survivors in Saccharomyces cerevisiae Replication stresses induced by ectopic oncogenic expression of cyclin E, G-quadruplexes, or R-loop formation facilitate the ALT pathway and lead to telomere clustering, a hallmark of ALT cancers. The TIMELESS/TIPIN complex suppresses telomere clustering and telomeric MiDAS, whereas the SMC5/6 complex promotes them. In summary, ALT cells exhibit more telomere replication defects that result in persistent DNA damage responses at telomeres, leading to the engagement of telomeric MiDAS (spontaneous mitotic telomere synthesis) that is triggered by DNA replication stress, a potential driver of genomic duplications in cancer.
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284
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Sobinoff AP, Allen JA, Neumann AA, Yang SF, Walsh ME, Henson JD, Reddel RR, Pickett HA. BLM and SLX4 play opposing roles in recombination-dependent replication at human telomeres. EMBO J 2017; 36:2907-2919. [PMID: 28877996 DOI: 10.15252/embj.201796889] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere lengthening pathway that predominates in aggressive tumors of mesenchymal origin; however, the underlying mechanism of telomere synthesis is not fully understood. Here, we show that the BLM-TOP3A-RMI (BTR) dissolvase complex is required for ALT-mediated telomere synthesis. We propose that recombination intermediates formed during strand invasion are processed by the BTR complex, initiating rapid and extensive POLD3-dependent telomere synthesis followed by dissolution, with no overall exchange of telomeric DNA. This process is counteracted by the SLX4-SLX1-ERCC4 complex, which promotes resolution of the recombination intermediate, resulting in telomere exchange in the absence of telomere extension. Our data are consistent with ALT being a conservative DNA replication process, analogous to break-induced replication, which is dependent on BTR and counteracted by SLX4 complex-mediated resolution events.
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Affiliation(s)
- Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Joshua Am Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Axel A Neumann
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Sile F Yang
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Monica E Walsh
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Jeremy D Henson
- Cancer Cell Immortality Group, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
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285
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Wu WJ, Yang W, Tsai MD. How DNA polymerases catalyse replication and repair with contrasting fidelity. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0068] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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286
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Sotiriou SK, Kamileri I, Lugli N, Evangelou K, Da-Ré C, Huber F, Padayachy L, Tardy S, Nicati NL, Barriot S, Ochs F, Lukas C, Lukas J, Gorgoulis VG, Scapozza L, Halazonetis TD. Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks. Mol Cell 2017; 64:1127-1134. [PMID: 27984746 PMCID: PMC5179496 DOI: 10.1016/j.molcel.2016.10.038] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/08/2016] [Accepted: 10/28/2016] [Indexed: 02/01/2023]
Abstract
Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose depletion inhibited G1 to S phase progression when oncogenic cyclin E was overexpressed. RAD52, a gene dispensable for normal development in mice, was among the top hits. In cells in which fork collapse was induced by oncogenes or chemicals, the Rad52 protein localized to DRS foci. Depletion of Rad52 by siRNA or knockout of the gene by CRISPR/Cas9 compromised restart of collapsed forks and led to DNA damage in cells experiencing DRS. Furthermore, in cancer-prone, heterozygous APC mutant mice, homozygous deletion of the Rad52 gene suppressed tumor growth and prolonged lifespan. We therefore propose that mammalian RAD52 facilitates repair of collapsed DNA replication forks in cancer cells. Mammalian RAD52 is involved in the oncogene-induced DNA replication stress response Mammalian RAD52 functions in the repair of collapsed DNA replication forks Rad52 deficiency prolongs the lifespan of Apcmin/+ mice
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Affiliation(s)
- Sotirios K Sotiriou
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Irene Kamileri
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Natalia Lugli
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Konstantinos Evangelou
- Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Caterina Da-Ré
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Florian Huber
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Sebastien Tardy
- School of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, CMU, University of Geneva and University of Lausanne, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Noemie L Nicati
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, CMU, University of Geneva and University of Lausanne, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Samia Barriot
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Fena Ochs
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Claudia Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Vassilis G Gorgoulis
- Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PL, UK; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Leonardo Scapozza
- School of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, CMU, University of Geneva and University of Lausanne, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland.
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287
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Bournique E, Dall'Osto M, Hoffmann JS, Bergoglio V. Role of specialized DNA polymerases in the limitation of replicative stress and DNA damage transmission. Mutat Res 2017; 808:62-73. [PMID: 28843435 DOI: 10.1016/j.mrfmmm.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/31/2023]
Abstract
Replication stress is a strong and early driving force for genomic instability and tumor development. Beside replicative DNA polymerases, an emerging group of specialized DNA polymerases is involved in the technical assistance of the replication machinery in order to prevent replicative stress and its deleterious consequences. During S-phase, altered progression of the replication fork by endogenous or exogenous impediments induces replicative stress, causing cells to reach mitosis with genomic regions not fully duplicated. Recently, specific mechanisms to resolve replication intermediates during mitosis with the aim of limiting DNA damage transmission to daughter cells have been identified. In this review, we detail the two major actions of specialized DNA polymerases that limit DNA damage transmission: the prevention of replicative stress by non-B DNA replication and the recovery of stalled replication forks.
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Affiliation(s)
- Elodie Bournique
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Marina Dall'Osto
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037, Toulouse, France.
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288
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Wang Z, Deng Z, Tutton S, Lieberman PM. The Telomeric Response to Viral Infection. Viruses 2017; 9:v9080218. [PMID: 28792463 PMCID: PMC5580475 DOI: 10.3390/v9080218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/06/2017] [Accepted: 08/06/2017] [Indexed: 12/16/2022] Open
Abstract
The ends of linear genomes, whether viral or cellular, can elicit potent DNA damage and innate immune signals. DNA viruses entering the nucleus share many features with telomeres in their ability to either suppress or co-opt these pathways. Here, we review some of the common mechanisms that viruses and telomeres use to manage the DNA damage and innate immune response pathways. We highlight recent studies on the role of the telomere repeat-containing RNA (TERRA) in response to viral infection. We discuss how TERRA can be activated through a p53-response element embedded in a retrotransposon-like repeat found in human subtelomeres. We consider how TERRA can function as a danger signal when secreted in extracellular vesicles to induce inflammatory cytokines in neighboring cells. These findings suggest that TERRA may be part of the innate immune response to viral infection, and support the hypothesis that telomeres and viruses utilize common mechanisms to maintain genome integrity and regulate innate immunity.
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Affiliation(s)
- Zhuo Wang
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Zhong Deng
- The Wistar Institute, Philadelphia, PA 19104, USA.
| | - Steve Tutton
- The Wistar Institute, Philadelphia, PA 19104, USA.
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289
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Min J, Wright WE, Shay JW. Alternative lengthening of telomeres can be maintained by preferential elongation of lagging strands. Nucleic Acids Res 2017; 45:2615-2628. [PMID: 28082393 PMCID: PMC5389697 DOI: 10.1093/nar/gkw1295] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/04/2017] [Indexed: 11/14/2022] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase independent telomere maintenance mechanism that occurs in ∼15% of cancers. The potential mechanism of ALT is homology-directed telomere synthesis, but molecular mechanisms of how ALT maintains telomere length in human cancer is poorly understood. Here, we generated TERC (telomerase RNA) gene knockouts in telomerase positive cell lines that resulted in long-term surviving clones acquiring the ALT pathway but at a very low frequency. By comparing these ALT cells with parental telomerase positive cells, we observed that ALT cells possess excessively long telomeric overhangs derived from telomere elongation processes that mostly occur during S phase. ALT cells exhibited preferential elongation of the telomeric lagging strands, whereas telomerase positive cells exhibited similar elongation between leading and lagging strands. We propose that the ALT pathway preferentially occurs at telomeric lagging strands leading to heterogeneous telomere lengths observed in most ALT cancers.
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Affiliation(s)
- Jaewon Min
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9039, USA
| | - Woodring E Wright
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9039, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9039, USA
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290
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Abstract
In this review, we discuss how two evolutionarily conserved pathways at the interface of DNA replication and repair, template switching and break-induced replication, lead to the deleterious large-scale expansion of trinucleotide DNA repeats that cause numerous hereditary diseases. We highlight that these pathways, which originated in prokaryotes, may be subsequently hijacked to maintain long DNA microsatellites in eukaryotes. We suggest that the negative mutagenic outcomes of these pathways, exemplified by repeat expansion diseases, are likely outweighed by their positive role in maintaining functional repetitive regions of the genome such as telomeres and centromeres.
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Affiliation(s)
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
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291
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Dershem R, Chu X, Wood GC, Benotti P, Still CD, Rolston DD. Changes in telomere length 3-5 years after gastric bypass surgery. Int J Obes (Lond) 2017; 41:1718-1720. [PMID: 28676678 PMCID: PMC5675791 DOI: 10.1038/ijo.2017.156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/11/2017] [Accepted: 06/25/2017] [Indexed: 11/16/2022]
Abstract
Increased inflammation and oxidative stress associated with obesity can accelerate aging. Telomere length (TL) has the capacity to serve as an aging indicator at the cellular level. Obesity has a known association with shorter TL. This study evaluated TL of immune cells in a population of obese individuals who underwent gastric bypass surgery. Pre and post-operative DNA samples were available for 50 subjects who had gastric bypass surgery. DNA was analyzed via quantitative polymerase chain reaction (q-PCR) to determine TL. Changes in TL were evaluated by comparing TL at baseline to TL at 3-5 years post gastric bypass surgery. Sixty percent of the individuals in the study observed an increase in TL. Significant lengthening was observed for those with the shortest baseline TL (p=0.0011), but not for those with intermediate baseline TL (p=0.411) or longest baseline TL (p=0.207). Change in TL was negatively correlated with age and triglycerides but not correlated with weight loss induced by bariatric surgery. This study confirms that TL lengthening is observed post bariatric surgery and is the first to detect TL lengthening 3-5 years after surgery.
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Affiliation(s)
- R Dershem
- Geisinger Obesity Research Institute, Geisinger Clinic, Danville, PA, USA.,Weis Center for Research, Geisinger Clinic, Danville, PA, USA
| | - X Chu
- Geisinger Obesity Research Institute, Geisinger Clinic, Danville, PA, USA
| | - G C Wood
- Geisinger Obesity Research Institute, Geisinger Clinic, Danville, PA, USA
| | - P Benotti
- Geisinger Obesity Research Institute, Geisinger Clinic, Danville, PA, USA
| | - C D Still
- Geisinger Obesity Research Institute, Geisinger Clinic, Danville, PA, USA
| | - D D Rolston
- Department of Internal Medicine, Geisinger Clinic, Danville, PA, USA
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292
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VandenBussche CJ, Allison DB, Graham MK, Charu V, Lennon AM, Wolfgang CL, Hruban RH, Heaphy CM. Alternative lengthening of telomeres and ATRX/DAXX loss can be reliably detected in FNAs of pancreatic neuroendocrine tumors. Cancer 2017; 125:544-551. [PMID: 28371511 PMCID: PMC5511056 DOI: 10.1002/cncy.21857] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 11/11/2022]
Abstract
BACKGROUND Pancreatic neuroendocrine tumors (PanNETs) frequently use the alternative lengthening of telomeres (ALT) pathway for telomere maintenance. ALT is strongly correlated with α thalassemia-mental retardation, X linked (ATRX), and death domain-associated protein 6 (DAXX) alterations and a poor prognosis in patients with primary PanNET. Because fine-needle aspiration (FNA) is a noninvasive way to sample tumors, the authors evaluated whether they could accurately detect ALT and loss of ATRX/DAXX in a primary PanNET cohort of FNAs. METHODS All preoperative FNA cytology cases (2005-2016) with adequate remnant FNA cell block material were assessed for ALT by telomere-specific fluorescence in situ hybridization and for ATRX and DAXX protein expression by immunohistochemistry. For 21 patients who underwent tumor resection, the resected specimen also was assessed to determine the concordance between the FNA and surgical specimens. RESULTS In the primary PanNET cohort of 65 FNAs, ALT was detected in 15 specimens (23%). Although all ATRX-negative and DAXX-negative tumors were ALT-positive, 3 of 14 (21%) ALT-positive tumors did not exhibit nuclear loss of either ATRX or DAXX. The ALT-positive tumors were associated with larger radiographic size (4.9 vs 2.4 cm, on average; P < .05) and higher grade (P < .05). Overall, there was 100% concordance in ALT status and ATRX/DAXX immunohistochemistry results between the FNA and surgical specimens. CONCLUSIONS Both ALT and loss of ATRX/DAXX can be accurately performed on FNA specimens with adequate material. Because ALT is a fundamental mechanism of pathogenesis, the ability to determine ALT in small biospecimens has implications for the design of clinical trials. Cancer Cytopathol 2017;125:544-51. © 2017 American Cancer Society.
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Affiliation(s)
- Christopher J. VandenBussche
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Derek B. Allison
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mindy K. Graham
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vivek Charu
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anne Marie Lennon
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Gastroenterology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher L. Wolfgang
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Ralph H. Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Christopher M. Heaphy
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
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293
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Lugli N, Sotiriou SK, Halazonetis TD. The role of SMARCAL1 in replication fork stability and telomere maintenance. DNA Repair (Amst) 2017. [PMID: 28623093 DOI: 10.1016/j.dnarep.2017.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SMARCAL1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1), also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage. Mutations in this gene are the cause of Schimke immune-osseous dysplasia (SIOD), an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions. In this review, we summarize the main roles of SMARCAL1 in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress.
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Affiliation(s)
- Natalia Lugli
- Department of Molecular Biology, University of Geneva, Switzerland
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294
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Abstract
Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease. One important DNA repair mechanism to maintain genomic integrity is recombination. Though early studies dismissed recombination as a mechanism driving repeat expansion and instability, recent results indicate that mitotic recombination is a key pathway operating within repetitive DNA. The action is two-fold: first, it is an important mechanism to repair nicks, gaps, breaks, or stalled forks to prevent chromosome fragility and protect cell health; second, recombination can cause repeat expansions or contractions, which can be deleterious. In this review, we summarize recent developments that illuminate the role of recombination in maintaining genome stability at DNA repeats.
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295
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Naderlinger E, Holzmann K. Epigenetic Regulation of Telomere Maintenance for Therapeutic Interventions in Gliomas. Genes (Basel) 2017; 8:E145. [PMID: 28513547 PMCID: PMC5448019 DOI: 10.3390/genes8050145] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 02/07/2023] Open
Abstract
High-grade astrocytoma of WHO grade 4 termed glioblastoma multiforme (GBM) is a common human brain tumor with poor patient outcome. Astrocytoma demonstrates two known telomere maintenance mechanisms (TMMs) based on telomerase activity (TA) and on alternative lengthening of telomeres (ALT). ALT is associated with lower tumor grades and better outcome. In contrast to ALT, regulation of TA in tumors by direct mutation and epigenetic activation of the hTERT promoter is well established. Here, we summarize the genetic background of TMMs in non-malignant cells and in cancer, in addition to clinical and pathological features of gliomas. Furthermore, we present new evidence for epigenetic mechanisms (EMs) involved in regulation of ALT and TA with special emphasis on human diffuse gliomas as potential therapeutic drug targets. We discuss the role of TMM associated telomeric chromatin factors such as DNA and histone modifying enzymes and non-coding RNAs including microRNAs and long telomeric TERRA transcripts.
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Affiliation(s)
- Elisabeth Naderlinger
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, Vienna 1090, Austria.
| | - Klaus Holzmann
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8a, Vienna 1090, Austria.
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296
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Abstract
The phenomenon of gradual telomere shortening has become a paradigm for how we understand the biology of aging and cancer. Cell proliferation is accompanied by cumulative telomere loss, and the aged cell either senesces, dies or transforms toward cancer. This transformation requires the activation of telomere elongation mechanisms in order to restore telomere length such that cell death or senescence programs are not induced. Most of the time, this occurs through telomerase reactivation. In other rare cases, the Alternative lengthening of telomeres (ALT) pathway hijacks DNA recombination-associated mechanisms to hyperextend telomeres, often to more than 50 kb. Why telomere length is restricted and what sets their maximal length has been a long-standing puzzle in cell biology. Two recent studies published in this issue of EMBO Reports [1] and recently in Science [2] sought to address this important question. Both built on omics approaches that identified ZBTB48 as a potential telomere-associated protein and reveal it to be a critical regulator of telomere length homeostasis by the telomere trimming mechanism. These discoveries provide fundamental insights for our understanding of telomere trimming and how it impacts telomere integrity in stem and cancer cells.
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Affiliation(s)
- Laura Garcia-Exposito
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh Cancer Center (UPCI), University of Pittsburgh, Pittsburgh, PA, USA
| | - Roderick J O'Sullivan
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh Cancer Center (UPCI), University of Pittsburgh, Pittsburgh, PA, USA
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297
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Bhowmick R, Hickson ID. The "enemies within": regions of the genome that are inherently difficult to replicate. F1000Res 2017; 6:666. [PMID: 28620461 PMCID: PMC5461909 DOI: 10.12688/f1000research.11024.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 12/23/2022] Open
Abstract
An unusual feature of many eukaryotic genomes is the presence of regions that appear intrinsically difficult to copy during the process of DNA replication. Curiously, the location of these difficult-to-replicate regions is often conserved between species, implying a valuable role in some aspect of genome organization or maintenance. The most prominent class of these regions in mammalian cells is defined as chromosome fragile sites, which acquired their name because of a propensity to form visible gaps/breaks on otherwise-condensed chromosomes in mitosis. This fragility is particularly apparent following perturbation of DNA replication-a phenomenon often referred to as "replication stress". Here, we review recent data on the molecular basis for chromosome fragility and the role of fragile sites in the etiology of cancer. In particular, we highlight how studies on fragile sites have provided unexpected insights into how the DNA repair machinery assists in the completion of DNA replication.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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298
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Natsume T, Nishimura K, Minocherhomji S, Bhowmick R, Hickson ID, Kanemaki MT. Acute inactivation of the replicative helicase in human cells triggers MCM8-9-dependent DNA synthesis. Genes Dev 2017; 31:816-829. [PMID: 28487407 PMCID: PMC5435893 DOI: 10.1101/gad.297663.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/10/2017] [Indexed: 01/15/2023]
Abstract
DNA replication fork progression can be disrupted at difficult to replicate loci in the human genome, which has the potential to challenge chromosome integrity. This replication fork disruption can lead to the dissociation of the replisome and the formation of DNA damage. To model the events stemming from replisome dissociation during DNA replication perturbation, we used a degron-based system for inducible proteolysis of a subunit of the replicative helicase. We show that MCM2-depleted cells activate a DNA damage response pathway and generate replication-associated DNA double-strand breaks (DSBs). Remarkably, these cells maintain some DNA synthesis in the absence of MCM2, and this requires the MCM8-9 complex, a paralog of the MCM2-7 replicative helicase. We show that MCM8-9 functions in a homologous recombination-based pathway downstream from RAD51, which is promoted by DSB induction. This RAD51/MCM8-9 axis is distinct from the recently described RAD52-dependent DNA synthesis pathway that operates in early mitosis at common fragile sites. We propose that stalled replication forks can be restarted in S phase via homologous recombination using MCM8-9 as an alternative replicative helicase.
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Affiliation(s)
- Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Kohei Nishimura
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan
| | - Sheroy Minocherhomji
- Center for Chromosome Stability.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, 2200 Copenhagen N, Denmark
| | - Rahul Bhowmick
- Center for Chromosome Stability.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, 2200 Copenhagen N, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, 2200 Copenhagen N, Denmark
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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299
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Kwon Y, Daley JM, Sung P. Reconstituted System for the Examination of Repair DNA Synthesis in Homologous Recombination. Methods Enzymol 2017. [PMID: 28645374 DOI: 10.1016/bs.mie.2017.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
In homologous recombination (HR), DNA polymerase δ-mediated DNA synthesis occurs within the displacement loop (D-loop) that is made by the recombinase Rad51 in conjunction with accessory factors. We describe in this chapter the reconstitution of the D-loop and repair DNA synthesis reactions using purified Saccharomyces cerevisiae HR (Rad51, RPA, and Rad54) and DNA replication (PCNA, RFC, and DNA polymerase δ) proteins and document the role of the Pif1 helicase in DNA synthesis via a migrating DNA bubble intermediate. These reconstituted systems are particularly valuable for understanding the conserved mechanism of repair DNA synthesis dependent on DNA polymerase δ and its cognate helicase in eukaryotic organisms.
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Affiliation(s)
- Youngho Kwon
- Yale University School of Medicine, New Haven, CT, United States
| | - James M Daley
- Yale University School of Medicine, New Haven, CT, United States
| | - Patrick Sung
- Yale University School of Medicine, New Haven, CT, United States.
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300
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Hou C, Wang F, Liu X, Chang G, Wang F, Geng X. Comprehensive Analysis of Interaction Networks of Telomerase Reverse Transcriptase with Multiple Bioinformatic Approaches: Deep Mining the Potential Functions of Telomere and Telomerase. Rejuvenation Res 2017; 20:320-333. [PMID: 28281877 DOI: 10.1089/rej.2016.1909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Telomerase reverse transcriptase (TERT) is the protein component of telomerase complex. Evidence has accumulated showing that the nontelomeric functions of TERT are independent of telomere elongation. However, the mechanisms governing the interaction between TERT and its target genes are not clearly revealed. The biological functions of TERT are not fully elucidated and have thus far been underestimated. To further explore these functions, we investigated TERT interaction networks using multiple bioinformatic databases, including BioGRID, STRING, DAVID, GeneCards, GeneMANIA, PANTHER, miRWalk, mirTarBase, miRNet, miRDB, and TargetScan. In addition, network diagrams were built using Cytoscape software. As competing endogenous RNAs (ceRNAs) are endogenous transcripts that compete for the binding of microRNAs (miRNAs) by using shared miRNA recognition elements, they are involved in creating widespread regulatory networks. Therefore, the ceRNA regulatory networks of TERT were also investigated in this study. Interestingly, we found that the three genes PABPC1, SLC7A11, and TP53 were present in both TERT interaction networks and ceRNAs target genes. It was predicted that TERT might play nontelomeric roles in the generation or development of some rare diseases, such as Rift Valley fever and dyscalculia. Thus, our data will help to decipher the interaction networks of TERT and reveal the unknown functions of telomerase in cancer and aging-related diseases.
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Affiliation(s)
- Chunyu Hou
- 1 Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin, China .,2 Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital , Tianjin, China
| | - Fei Wang
- 3 Department of Neurology, Tianjin Medical University , Tianjin, China
| | - Xuewen Liu
- 1 Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin, China
| | - Guangming Chang
- 4 Department of Clinical Laboratory, General Hospital, Tianjin Medical University , Tianjin, China
| | - Feng Wang
- 5 Department of Genetics, Tianjin Medical University , Tianjin, China
| | - Xin Geng
- 1 Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin, China .,6 Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University , Tianjin, China .,7 Key Laboratory of Educational Ministry of China, Tianjin Medical University , Tianjin, China
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