1
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Lee J, Lee J, Sohn EJ, Taglialatela A, O’Sullivan RJ, Ciccia A, Min J. Extrachromosomal telomere DNA derived from excessive strand displacements. Proc Natl Acad Sci U S A 2024; 121:e2318438121. [PMID: 38696464 PMCID: PMC11087782 DOI: 10.1073/pnas.2318438121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism mediated by break-induced replication, evident in approximately 15% of human cancers. A characteristic feature of ALT cancers is the presence of C-circles, circular single-stranded telomeric DNAs composed of C-rich sequences. Despite the fact that extrachromosomal C-rich single-stranded DNAs (ssDNAs), including C-circles, are unique to ALT cells, their generation process remains undefined. Here, we introduce a method to detect single-stranded telomeric DNA, called 4SET (Strand-Specific Southern-blot for Single-stranded Extrachromosomal Telomeres) assay. Utilizing 4SET, we are able to capture C-rich single-stranded DNAs that are near 200 to 1500 nucleotides in size. Both linear C-rich ssDNAs and C-circles are abundant in the fractions of cytoplasm and nucleoplasm, which supports the idea that linear and circular C-rich ssDNAs are generated concurrently. We also found that C-rich ssDNAs originate during Okazaki fragment processing during lagging strand DNA synthesis. The generation of C-rich ssDNA requires CST-PP (CTC1/STN1/TEN1-PRIMASE-Polymerase alpha) complex-mediated priming of the C-strand DNA synthesis and subsequent excessive strand displacement of the C-rich strand mediated by the DNA Polymerase delta and the BLM helicase. Our work proposes a model for the generation of C-rich ssDNAs and C-circles during ALT-mediated telomere elongation.
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Affiliation(s)
- Junyeop Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
| | - Jina Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
| | - Eric J. Sohn
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
| | - Roderick J. O’Sullivan
- Department of Pharmacology and Chemical Biology, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA15213
| | - Alberto Ciccia
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
| | - Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY10032
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2
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Wondisford AR, Lee J, Lu R, Schuller M, Groslambert J, Bhargava R, Schamus-Haynes S, Cespedes LC, Opresko PL, Pickett HA, Min J, Ahel I, O'Sullivan RJ. Deregulated DNA ADP-ribosylation impairs telomere replication. Nat Struct Mol Biol 2024; 31:791-800. [PMID: 38714889 PMCID: PMC11102865 DOI: 10.1038/s41594-024-01279-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/18/2024] [Indexed: 05/21/2024]
Abstract
The recognition that DNA can be ADP ribosylated provides an unexpected regulatory level of how ADP-ribosylation contributes to genome stability, epigenetics and immunity. Yet, it remains unknown whether DNA ADP-ribosylation (DNA-ADPr) promotes genome stability and how it is regulated. Here, we show that telomeres are subject to DNA-ADPr catalyzed by PARP1 and removed by TARG1. Mechanistically, we show that DNA-ADPr is coupled to lagging telomere DNA strand synthesis, forming at single-stranded DNA present at unligated Okazaki fragments and on the 3' single-stranded telomere overhang. Persistent DNA-linked ADPr, due to TARG1 deficiency, eventually leads to telomere shortening. Furthermore, using the bacterial DNA ADP-ribosyl-transferase toxin to modify DNA at telomeres directly, we demonstrate that unhydrolyzed DNA-linked ADP-ribose compromises telomere replication and telomere integrity. Thus, by identifying telomeres as chromosomal targets of PARP1 and TARG1-regulated DNA-ADPr, whose deregulation compromises telomere replication and integrity, our study highlights and establishes the critical importance of controlling DNA-ADPr turnover for sustained genome stability.
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Affiliation(s)
- Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junyeop Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra Schamus-Haynes
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leyneir C Cespedes
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Patricia L Opresko
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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3
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Muoio D, Laspata N, Dannenberg RL, Curry C, Darkoa-Larbi S, Hedglin M, Uttam S, Fouquerel E. PARP2 promotes Break Induced Replication-mediated telomere fragility in response to replication stress. Nat Commun 2024; 15:2857. [PMID: 38565848 PMCID: PMC10987537 DOI: 10.1038/s41467-024-47222-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
PARP2 is a DNA-dependent ADP-ribosyl transferase (ARTs) enzyme with Poly(ADP-ribosyl)ation activity that is triggered by DNA breaks. It plays a role in the Base Excision Repair pathway, where it has overlapping functions with PARP1. However, additional roles for PARP2 have emerged in the response of cells to replication stress. In this study, we demonstrate that PARP2 promotes replication stress-induced telomere fragility and prevents telomere loss following chronic induction of oxidative DNA lesions and BLM helicase depletion. Telomere fragility results from the activity of the break-induced replication pathway (BIR). During this process, PARP2 promotes DNA end resection, strand invasion and BIR-dependent mitotic DNA synthesis by orchestrating POLD3 recruitment and activity. Our study has identified a role for PARP2 in the response to replication stress. This finding may lead to the development of therapeutic approaches that target DNA-dependent ART enzymes, particularly in cancer cells with high levels of replication stress.
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Affiliation(s)
- Daniela Muoio
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA
| | - Natalie Laspata
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University park, State College, PA, 16802, USA
| | - Caroline Curry
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Simone Darkoa-Larbi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233S. 10th street, Philadelphia, PA, 19107, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University park, State College, PA, 16802, USA
| | - Shikhar Uttam
- Department of Computational and Systems Biology, UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, 15213, USA.
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4
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Yang SF, Nelson CB, Wells JK, Fernando M, Lu R, Allen JAM, Malloy L, Lamm N, Murphy VJ, Mackay JP, Deans AJ, Cesare AJ, Sobinoff AP, Pickett HA. ZNF827 is a single-stranded DNA binding protein that regulates the ATR-CHK1 DNA damage response pathway. Nat Commun 2024; 15:2210. [PMID: 38472229 PMCID: PMC10933417 DOI: 10.1038/s41467-024-46578-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
The ATR-CHK1 DNA damage response pathway becomes activated by the exposure of RPA-coated single-stranded DNA (ssDNA) that forms as an intermediate during DNA damage and repair, and as a part of the replication stress response. Here, we identify ZNF827 as a component of the ATR-CHK1 kinase pathway. We demonstrate that ZNF827 is a ssDNA binding protein that associates with RPA through concurrent binding to ssDNA intermediates. These interactions are dependent on two clusters of C2H2 zinc finger motifs within ZNF827. We find that ZNF827 accumulates at stalled forks and DNA damage sites, where it activates ATR and promotes the engagement of homologous recombination-mediated DNA repair. Additionally, we demonstrate that ZNF827 depletion inhibits replication initiation and sensitizes cancer cells to the topoisomerase inhibitor topotecan, revealing ZNF827 as a therapeutic target within the DNA damage response pathway.
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Affiliation(s)
- Sile F Yang
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Jadon K Wells
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Madushan Fernando
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Lisa Malloy
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Noa Lamm
- Nuclear Dynamics Group, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia.
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5
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Thosar SA, Barnes RP, Detwiler A, Bhargava R, Wondisford A, O'Sullivan RJ, Opresko PL. Oxidative guanine base damage plays a dual role in regulating productive ALT-associated homology-directed repair. Cell Rep 2024; 43:113656. [PMID: 38194346 PMCID: PMC10851105 DOI: 10.1016/j.celrep.2023.113656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Cancer cells maintain telomeres by upregulating telomerase or alternative lengthening of telomeres (ALT) via homology-directed repair at telomeric DNA breaks. 8-Oxoguanine (8oxoG) is a highly prevalent endogenous DNA lesion in telomeric sequences, altering telomere structure and telomerase activity, but its impact on ALT is unclear. Here, we demonstrate that targeted 8oxoG formation at telomeres stimulates ALT activity and homologous recombination specifically in ALT cancer cells. Mechanistically, an acute 8oxoG induction increases replication stress, as evidenced by increased telomere fragility and ATR kinase activation at ALT telomeres. Furthermore, ALT cells are more sensitive to chronic telomeric 8oxoG damage than telomerase-positive cancer cells, consistent with increased 8oxoG-induced replication stress. However, telomeric 8oxoG production in G2 phase, when ALT telomere elongation occurs, impairs telomeric DNA synthesis. Our study demonstrates that a common oxidative base lesion has a dual role in regulating ALT depending on when the damage arises in the cell cycle.
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Affiliation(s)
- Sanjana A Thosar
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ryan P Barnes
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ariana Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Ragini Bhargava
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Wondisford
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roderick J O'Sullivan
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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6
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Lu R, Nelson CB, Rogers S, Cesare AJ, Sobinoff AP, Pickett HA. Distinct modes of telomere synthesis and extension contribute to Alternative Lengthening of Telomeres. iScience 2024; 27:108655. [PMID: 38213617 PMCID: PMC10783591 DOI: 10.1016/j.isci.2023.108655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/13/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024] Open
Abstract
Alternative lengthening of telomeres (ALT) is a homology-directed repair mechanism that becomes activated in a subset of cancers to maintain telomere length. One of the defining features of ALT cells is the prevalence of extrachromosomal telomeric repeat (ECTR) DNA. Here, we identify that ALT cells engage in two modes of telomere synthesis. Non-productive telomere synthesis occurs during the G2 phase of the cell cycle and is characterized by newly synthesized internal telomeric regions that are not retained in the subsequent G1, coinciding with an induction of ECTR DNA. Productive telomere synthesis occurs specifically during the transition from G2 to mitosis and is defined as the extension of the telomere termini. While many proteins associated with break-induced telomere synthesis function in both non-productive and productive telomere synthesis, POLH specifically promotes productive telomere lengthening and suppresses non-productive telomere synthesis. These findings delineate the mechanism and cell cycle regulation of ALT-mediated telomere synthesis and extension.
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Affiliation(s)
- Robert Lu
- Telomere Length Regulation Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Christopher B. Nelson
- Telomere Length Regulation Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Samuel Rogers
- Genome Integrity Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Anthony J. Cesare
- Genome Integrity Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Alexander P. Sobinoff
- Telomere Length Regulation 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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7
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Menck CFM, Galhardo RS, Quinet A. The accurate bypass of pyrimidine dimers by DNA polymerase eta contributes to ultraviolet-induced mutagenesis. Mutat Res 2024; 828:111840. [PMID: 37984186 DOI: 10.1016/j.mrfmmm.2023.111840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023]
Abstract
Human xeroderma pigmentosum variant (XP-V) patients are mutated in the POLH gene, responsible for encoding the translesion synthesis (TLS) DNA polymerase eta (Pol eta). These patients suffer from a high frequency of skin tumors. Despite several decades of research, studies on Pol eta still offer an intriguing paradox: How does this error-prone polymerase suppress mutations? This review examines recent evidence suggesting that cyclobutane pyrimidine dimers (CPDs) are instructional for Pol eta. Consequently, it can accurately replicate these lesions, and the mutagenic effects induced by UV radiation stem from the deamination of C-containing CPDs. In this model, the deamination of C (forming a U) within CPDs leads to the correct insertion of an A opposite to the deaminated C (or U)-containing dimers. This intricate process results in C>T transitions, which represent the most prevalent mutations detected in skin cancers. Finally, the delayed replication in XP-V cells amplifies the process of C-deamination in CPDs and increases the burden of C>T mutations prevalent in XP-V tumors through the activity of backup TLS polymerases.
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Affiliation(s)
- C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil.
| | - R S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - A Quinet
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
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8
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Clement TVM, van der Smagt C, Wuite GJL. Probing Mitotic Chromosome Mechanics Using Optical Tweezers. Methods Mol Biol 2024; 2694:91-107. [PMID: 37824001 DOI: 10.1007/978-1-0716-3377-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
During mitosis, cells compact their DNA into rodlike shapes, four orders of magnitude shorter than the DNA backbone contour length. We describe an experimental protocol to isolate and study these intricate mitotic chromosomes using optical tweezers. We touch upon the technical details of the required optical tweezers and microfluidics setup, including advanced force calibration procedures to accurately measure the high forces the chromosomes withstand. The procedure used to isolate mitotic chromosomes, including biotinylation of the telomeric ends to facilitate trapping them in optical tweezers, is described in detail. Finally, we provide a protocol for carrying out optical tweezers experiments on the isolated mitotic chromosomes.
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Affiliation(s)
- Tinka V M Clement
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Constantijn van der Smagt
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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9
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Loe TK, Lazzerini Denchi E, Tricola GM, Azeroglu B. ALTercations at telomeres: stress, recombination and extrachromosomal affairs. Biochem Soc Trans 2023; 51:1935-1946. [PMID: 37767563 DOI: 10.1042/bst20230265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Approximately 15% of human cancers depend on the alternative lengthening of telomeres (ALT) pathway to maintain telomeres and proliferate. Telomeres that are elongated using ALT display unique features raising the exciting prospect of tailored cancer therapies. ALT-mediated telomere elongation shares several features with recombination-based DNA repair. Strikingly, cells that use the ALT pathway display abnormal levels of replication stress at telomeres and accumulate abundant extrachromosomal telomeric DNA. In this review, we examine recent findings that shed light on the ALT mechanisms and the strategies currently available to suppress this telomere elongation mechanism.
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Affiliation(s)
- Taylor K Loe
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, U.S.A
| | - Eros Lazzerini Denchi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Gianna M Tricola
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Benura Azeroglu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
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10
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Paniagua I, Jacobs JJL. Freedom to err: The expanding cellular functions of translesion DNA polymerases. Mol Cell 2023; 83:3608-3621. [PMID: 37625405 DOI: 10.1016/j.molcel.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 08/27/2023]
Abstract
Translesion synthesis (TLS) DNA polymerases were originally described as error-prone enzymes involved in the bypass of DNA lesions. However, extensive research over the past few decades has revealed that these enzymes play pivotal roles not only in lesion bypass, but also in a myriad of other cellular processes. Such processes include DNA replication, DNA repair, epigenetics, immune signaling, and even viral infection. This review discusses the wide range of functions exhibited by TLS polymerases, including their underlying biochemical mechanisms and associated mutagenicity. Given their multitasking ability to alleviate replication stress, TLS polymerases represent a cellular dependency and a critical vulnerability of cancer cells. Hence, this review also highlights current and emerging strategies for targeting TLS polymerases in cancer therapy.
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Affiliation(s)
- Inés Paniagua
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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11
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Rose AM, Goncalves T, Cunniffe S, Geiller HEB, Kent T, Shepherd S, Ratnaweera M, O’Sullivan R, Gibbons R, Clynes D. Induction of the alternative lengthening of telomeres pathway by trapping of proteins on DNA. Nucleic Acids Res 2023; 51:6509-6527. [PMID: 36940725 PMCID: PMC10359465 DOI: 10.1093/nar/gkad150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/23/2023] Open
Abstract
Telomere maintenance is a hallmark of malignant cells and allows cancers to divide indefinitely. In some cancers, this is achieved through the alternative lengthening of telomeres (ALT) pathway. Whilst loss of ATRX is a near universal feature of ALT-cancers, it is insufficient in isolation. As such, other cellular events must be necessary - but the exact nature of the secondary events has remained elusive. Here, we report that trapping of proteins (such as TOP1, TOP2A and PARP1) on DNA leads to ALT induction in cells lacking ATRX. We demonstrate that protein-trapping chemotherapeutic agents, such as etoposide, camptothecin and talazoparib, induce ALT markers specifically in ATRX-null cells. Further, we show that treatment with G4-stabilising drugs cause an increase in trapped TOP2A levels which leads to ALT induction in ATRX-null cells. This process is MUS81-endonuclease and break-induced replication dependent, suggesting that protein trapping leads to replication fork stalling, with these forks being aberrantly processed in the absence of ATRX. Finally, we show ALT-positive cells harbour a higher load of genome-wide trapped proteins, such as TOP1, and knockdown of TOP1 reduced ALT activity. Taken together, these findings suggest that protein trapping is a fundamental driving force behind ALT-biology in ATRX-deficient malignancies.
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Affiliation(s)
- Anna M Rose
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Tomas Goncalves
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Siobhan Cunniffe
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Thomas Kent
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sam Shepherd
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Roderick J O’Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - David Clynes
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
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12
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Zhang T, Rawal Y, Jiang H, Kwon Y, Sung P, Greenberg RA. Break-induced replication orchestrates resection-dependent template switching. Nature 2023; 619:201-208. [PMID: 37316655 PMCID: PMC10937050 DOI: 10.1038/s41586-023-06177-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 05/05/2023] [Indexed: 06/16/2023]
Abstract
Break-induced telomere synthesis (BITS) is a RAD51-independent form of break-induced replication that contributes to alternative lengthening of telomeres1,2. This homology-directed repair mechanism utilizes a minimal replisome comprising proliferating cell nuclear antigen (PCNA) and DNA polymerase-δ to execute conservative DNA repair synthesis over many kilobases. How this long-tract homologous recombination repair synthesis responds to complex secondary DNA structures that elicit replication stress remains unclear3-5. Moreover, whether the break-induced replisome orchestrates additional DNA repair events to ensure processivity is also unclear. Here we combine synchronous double-strand break induction with proteomics of isolated chromatin segments (PICh) to capture the telomeric DNA damage response proteome during BITS1,6. This approach revealed a replication stress-dominated response, highlighted by repair synthesis-driven DNA damage tolerance signalling through RAD18-dependent PCNA ubiquitination. Furthermore, the SNM1A nuclease was identified as the major effector of ubiquitinated PCNA-dependent DNA damage tolerance. SNM1A recognizes the ubiquitin-modified break-induced replisome at damaged telomeres, and this directs its nuclease activity to promote resection. These findings show that break-induced replication orchestrates resection-dependent lesion bypass, with SNM1A nuclease activity serving as a critical effector of ubiquitinated PCNA-directed recombination in mammalian cells.
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Affiliation(s)
- Tianpeng Zhang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yashpal Rawal
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Haoyang Jiang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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13
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Li F, Wang Y, Hwang I, Jang JY, Xu L, Deng Z, Yu EY, Cai Y, Wu C, Han Z, Huang YH, Huang X, Zhang L, Yao J, Lue NF, Lieberman PM, Ying H, Paik J, Zheng H. Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance. Nat Commun 2023; 14:1756. [PMID: 36991019 PMCID: PMC10060224 DOI: 10.1038/s41467-023-37480-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Telomere length maintenance is essential for cellular immortalization and tumorigenesis. 5% - 10% of human cancers rely on a recombination-based mechanism termed alternative lengthening of telomeres (ALT) to sustain their replicative immortality, yet there are currently no targeted therapies. Through CRISPR/Cas9-based genetic screens in an ALT-immortalized isogenic cellular model, here we identify histone lysine demethylase KDM2A as a molecular vulnerability selectively for cells contingent on ALT-dependent telomere maintenance. Mechanistically, we demonstrate that KDM2A is required for dissolution of the ALT-specific telomere clusters following recombination-directed telomere DNA synthesis. We show that KDM2A promotes de-clustering of ALT multitelomeres through facilitating isopeptidase SENP6-mediated SUMO deconjugation at telomeres. Inactivation of KDM2A or SENP6 impairs post-recombination telomere de-SUMOylation and thus dissolution of ALT telomere clusters, leading to gross chromosome missegregation and mitotic cell death. These findings together establish KDM2A as a selective molecular vulnerability and a promising drug target for ALT-dependent cancers.
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Affiliation(s)
- Fei Li
- Department of Neurosurgery, Southwest Hospital, Chongqing, 400038, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Yizhe Wang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Inah Hwang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Ja-Young Jang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Libo Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Zhong Deng
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Eun Young Yu
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Yiming Cai
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Caizhi Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Zhenbo Han
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yu-Han Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Xiangao Huang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Ling Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Neal F Lue
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | | | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Hongwu Zheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
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14
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Chakraborty A, Tapryal N, Islam A, Sarker AH, Manohar K, Mitra J, Hegde ML, Hazra T. Human DNA polymerase η promotes RNA-templated error-free repair of DNA double-strand breaks. J Biol Chem 2023; 299:102991. [PMID: 36758800 PMCID: PMC10011834 DOI: 10.1016/j.jbc.2023.102991] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
A growing body of evidence indicates that RNA plays a critical role in orchestrating DNA double-strand break repair (DSBR). Recently, we showed that homologous nascent RNA can be used as a template for error-free repair of double-strand breaks (DSBs) in the transcribed genome and to restore the missing sequence at the break site via the transcription-coupled classical nonhomologous end-joining (TC-NHEJ) pathway. TC-NHEJ is a complex multistep process in which a reverse transcriptase (RT) is essential for synthesizing the DNA strand from template RNA. However, the identity of the RT involved in the TC-NHEJ pathway remained unknown. Here, we report that DNA polymerase eta (Pol η), known to possess RT activity, plays a critical role in TC-NHEJ. We found that Pol η forms a multiprotein complex with RNAP II and other TC-NHEJ factors, while also associating with nascent RNA. Moreover, purified Pol η, along with DSBR proteins PNKP, XRCC4, and Ligase IV can fully repair RNA templated 3'-phosphate-containing gapped DNA substrate. In addition, we demonstrate here that Pol η deficiency leads to accumulation of R-loops and persistent strand breaks in the transcribed genes. Finally, we determined that, in Pol η depleted but not in control cells, TC-NHEJ-mediated repair was severely abrogated when a reporter plasmid containing a DSB with several nucleotide deletion within the E. coli lacZ gene was introduced for repair in lacZ-expressing mammalian cells. Thus, our data strongly suggest that RT activity of Pol η is required in error-free DSBR.
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Affiliation(s)
- Anirban Chakraborty
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Nisha Tapryal
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Azharul Islam
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Altaf H Sarker
- Life Sciences Division, Department of Cancer and DNA Damage Responses, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kodavati Manohar
- Department of Neurosurgery, Center for Neuroregeneration, The Houston Methodist Research Institute, Houston, Texas, USA
| | - Joy Mitra
- Department of Neurosurgery, Center for Neuroregeneration, The Houston Methodist Research Institute, Houston, Texas, USA
| | - Muralidhar L Hegde
- Department of Neurosurgery, Center for Neuroregeneration, The Houston Methodist Research Institute, Houston, Texas, USA
| | - Tapas Hazra
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas, USA.
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15
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Li F, Wang Y, Hwang I, Jang JY, Xu L, Deng Z, Yu EY, Cai Y, Wu C, Han Z, Huang YH, Huang X, Zhang L, Yao J, Lue NF, Lieberman PM, Ying H, Paik J, Zheng H. Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance. bioRxiv 2023:2023. [PMID: 36798426 DOI: 10.1101/2023.02.10.528023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Telomere length maintenance is essential for cellular immortalization and tumorigenesis. 5% - 10% of human cancers rely on a recombination-based mechanism termed alternative lengthening of telomeres (ALT) to sustain their replicative immortality, yet there are currently no targeted therapies. Through CRISPR/Cas9-based genetic screens in an ALT-immortalized isogenic cellular model, here we identify histone lysine demethylase KDM2A as a molecular vulnerability selectively for cells contingent on ALT-dependent telomere maintenance. Mechanistically, we demonstrate that KDM2A is required for dissolution of the ALT-specific telomere clusters following homology-directed telomere DNA synthesis. We show that KDM2A promotes de-clustering of ALT multitelomeres through facilitating isopeptidase SENP6-mediated SUMO deconjugation at telomeres. Inactivation of KDM2A or SENP6 impairs post-recombination telomere de-SUMOylation and thus dissolution of ALT telomere clusters, leading to gross chromosome missegregation and mitotic cell death. These findings together establish KDM2A as a selective molecular vulnerability and a promising drug target for ALT-dependent cancers.
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16
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Sun H, Chen G, Guo B, Lv S, Yuan G. Potential clinical treatment prospects behind the molecular mechanism of alternative lengthening of telomeres (ALT). J Cancer 2023; 14:417-433. [PMID: 36860927 PMCID: PMC9969575 DOI: 10.7150/jca.80097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/25/2022] [Indexed: 02/04/2023] Open
Abstract
Normal somatic cells inevitably experience replicative stress and senescence during proliferation. Somatic cell carcinogenesis can be prevented in part by limiting the reproduction of damaged or old cells and removing them from the cell cycle [1, 2]. However, Cancer cells must overcome the issues of replication pressure and senescence as well as preserve telomere length in order to achieve immortality, in contrast to normal somatic cells [1, 2]. Although telomerase accounts for the bulk of telomere lengthening methods in human cancer cells, there is a non-negligible portion of telomere lengthening pathways that depend on alternative lengthening of telomeres (ALT) [3]. For the selection of novel possible therapeutic targets for ALT-related disorders, a thorough understanding of the molecular biology of these diseases is crucial [4]. The roles of ALT, typical ALT tumor cell traits, the pathophysiology and molecular mechanisms of ALT tumor disorders, such as adrenocortical carcinoma (ACC), are all summarized in this work. Additionally, this research compiles as many of its hypothetically viable but unproven treatment targets as it can (ALT-associated PML bodies (APB), etc.). This review is intended to contribute as much as possible to the development of research, while also trying to provide a partial information for prospective investigations on ALT pathways and associated diseases.
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Affiliation(s)
- Haolu Sun
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230011, China
| | - Guijuan Chen
- School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei, 230011, China
| | - Baochang Guo
- Rehabilitation Department of Traditional Chinese Medicine, 969 Hospital of the Joint Support Force of the Chinese People's Liberation Army, Hohhot, 010000, China
| | - Shushu Lv
- Department of Pathology, The First Affiliated Hospital of Huzhou University, Huzhou 313000, China
| | - Guojun Yuan
- School of Environment and Chemical Engineering, Anhui Vocational and Technical College, Hefei, 230011, China
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17
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Barnes RP, Thosar SA, Opresko PL. Telomere Fragility and MiDAS: Managing the Gaps at the End of the Road. Genes (Basel) 2023; 14:genes14020348. [PMID: 36833275 PMCID: PMC9956152 DOI: 10.3390/genes14020348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Telomeres present inherent difficulties to the DNA replication machinery due to their repetitive sequence content, formation of non-B DNA secondary structures, and the presence of the nucleo-protein t-loop. Especially in cancer cells, telomeres are hot spots for replication stress, which can result in a visible phenotype in metaphase cells termed "telomere fragility". A mechanism cells employ to mitigate replication stress, including at telomeres, is DNA synthesis in mitosis (MiDAS). While these phenomena are both observed in mitotic cells, the relationship between them is poorly understood; however, a common link is DNA replication stress. In this review, we will summarize what is known to regulate telomere fragility and telomere MiDAS, paying special attention to the proteins which play a role in these telomere phenotypes.
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Affiliation(s)
- Ryan P. Barnes
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
- Correspondence: (R.P.B.); (P.L.O.)
| | - Sanjana A. Thosar
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Patricia L. Opresko
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Correspondence: (R.P.B.); (P.L.O.)
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18
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He X, Chen X, Wang Y. Mass Spectrometry for Assessing Protein-Nucleic Acid Interactions. Anal Chem 2023; 95:115-127. [PMID: 36625126 PMCID: PMC9869667 DOI: 10.1021/acs.analchem.2c04353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Eckert KA. Nontraditional Roles of DNA Polymerase Eta Support Genome Duplication and Stability. Genes (Basel) 2023; 14:genes14010175. [PMID: 36672916 PMCID: PMC9858799 DOI: 10.3390/genes14010175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
DNA polymerase eta (Pol η) is a Y-family polymerase and the product of the POLH gene. Autosomal recessive inheritance of POLH mutations is the cause of the xeroderma pigmentosum variant, a cancer predisposition syndrome. This review summarizes mounting evidence for expanded Pol η cellular functions in addition to DNA lesion bypass that are critical for maintaining genome stability. In vitro, Pol η displays efficient DNA synthesis through difficult-to-replicate sequences, catalyzes D-loop extensions, and utilizes RNA-DNA hybrid templates. Human Pol η is constitutively present at the replication fork. In response to replication stress, Pol η is upregulated at the transcriptional and protein levels, and post-translational modifications regulate its localization to chromatin. Numerous studies show that Pol η is required for efficient common fragile site replication and stability. Additionally, Pol η can be recruited to stalled replication forks through protein-protein interactions, suggesting a broader role in replication fork recovery. During somatic hypermutations, Pol η is recruited by mismatch repair proteins and is essential for VH gene A:T basepair mutagenesis. Within the global context of repeat-dense genomes, the recruitment of Pol η to perform specialized functions during replication could promote genome stability by interrupting pure repeat arrays with base substitutions. Alternatively, not engaging Pol η in genome duplication is costly, as the absence of Pol η leads to incomplete replication and increased chromosomal instability.
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Affiliation(s)
- Kristin A Eckert
- Gittlen Cancer Research Laboratories, Department of Pathology, Penn State University College of Medicine, 500 University Drive, Hershey, PA 17036, USA
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20
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Rapchak K, Yagobian SD, Moore J, Khattri M, Shuda M. Merkel cell polyomavirus small T antigen is a viral transcription activator that is essential for viral genome maintenance. PLoS Pathog 2022; 18:e1011039. [PMID: 36574443 PMCID: PMC9829177 DOI: 10.1371/journal.ppat.1011039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/09/2023] [Accepted: 12/01/2022] [Indexed: 12/29/2022] Open
Abstract
Merkel cell polyomavirus (MCV) is a small DNA tumor virus that persists in human skin and causes Merkel cell carcinoma (MCC) in immunocompromised individuals. The multi-functional protein MCV small T (sT) activates viral DNA replication by stabilizing large T (LT) and promotes cell transformation through the LT stabilization domain (LTSD). Using MCVΔsT, a mutant MCV clone that ablates sT, we investigated the role of sT in MCV genome maintenance. sT was dispensable for initiation of viral DNA replication, but essential for maintenance of the MCV genome and activation of viral early and late gene expression for progression of the viral lifecycle. Furthermore, in phenotype rescue studies, exogenous sT activated viral DNA replication and mRNA expression in MCVΔsT through the LTSD. While exogenous LT expression, which mimics LT stabilization, increased viral DNA replication, it did not activate viral mRNA expression. After cataloging transcriptional regulator proteins by proximity-based MCV sT-host protein interaction analysis, we validated LTSD-dependent sT interaction with four transcriptional regulators: Cux1, c-Jun, BRD9, and CBP. Functional studies revealed Cux1 and c-Jun as negative regulators, and CBP and BRD9 as positive regulators of MCV transcription. CBP inhibitor A-485 suppressed sT-induced viral gene activation in replicating MCVΔsT and inhibited early gene expression in MCV-integrated MCC cells. These results suggest that sT promotes viral lifecycle progression by activating mRNA expression and capsid protein production through interaction with the transcriptional regulators. This activity is essential for MCV genome maintenance, suggesting a critical role of sT in MCV persistence and MCC carcinogenesis.
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Affiliation(s)
- Kyle Rapchak
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Shiva D. Yagobian
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Jackson Moore
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Michelle Khattri
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Masahiro Shuda
- Cancer Virology Program, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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21
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Misino S, Busch A, Wagner CB, Bento F, Luke B. TERRA increases at short telomeres in yeast survivors and regulates survivor associated senescence (SAS). Nucleic Acids Res 2022; 50:12829-12843. [PMID: 36513120 PMCID: PMC9825167 DOI: 10.1093/nar/gkac1125] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
Cancer cells achieve immortality by employing either homology-directed repair (HDR) or the telomerase enzyme to maintain telomeres. ALT (alternative lengthening of telomeres) refers to the subset of cancer cells that employ HDR. Many ALT features are conserved from yeast to human cells, with the yeast equivalent being referred to as survivors. The non-coding RNA TERRA, and its ability to form RNA-DNA hybrids, has been implicated in ALT/survivor maintenance by promoting HDR. It is not understood which telomeres in ALT/survivors engage in HDR, nor is it clear which telomeres upregulate TERRA. Using yeast survivors as a model for ALT, we demonstrate that HDR only occurs at telomeres when they become critically short. Moreover, TERRA levels steadily increase as telomeres shorten and decrease again following HDR-mediated recombination. We observe that survivors undergo cycles of senescence, in a similar manner to non-survivors following telomerase loss, which we refer to as survivor associated senescence (SAS). Similar to 'normal' senescence, we report that RNA-DNA hybrids slow the rate of SAS, likely through the elongation of critically short telomeres, however decreasing the rate of telomere shortening may contribute to this effect. In summary, TERRA RNA-DNA hybrids regulate telomere dysfunction-induced senescence before and after survivor formation.
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Affiliation(s)
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Fabio Bento
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
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22
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Yadav T, Zhang JM, Ouyang J, Leung W, Simoneau A, Zou L. TERRA and RAD51AP1 promote alternative lengthening of telomeres through an R- to D-loop switch. Mol Cell 2022; 82:3985-4000.e4. [PMID: 36265486 PMCID: PMC9637728 DOI: 10.1016/j.molcel.2022.09.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/08/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
Alternative lengthening of telomeres (ALT), a telomerase-independent process maintaining telomeres, is mediated by break-induced replication (BIR). RAD52 promotes ALT by facilitating D-loop formation, but ALT also occurs through a RAD52-independent BIR pathway. Here, we show that the telomere non-coding RNA TERRA forms dynamic telomeric R-loops and contributes to ALT activity in RAD52 knockout cells. TERRA forms R-loops in vitro and at telomeres in a RAD51AP1-dependent manner. The formation of R-loops by TERRA increases G-quadruplexes (G4s) at telomeres. G4 stabilization enhances ALT even when TERRA is depleted, suggesting that G4s act downstream of R-loops to promote BIR. In vitro, the telomeric R-loops assembled by TERRA and RAD51AP1 generate G4s, which persist after R-loop resolution and allow formation of telomeric D-loops without RAD52. Thus, the dynamic telomeric R-loops formed by TERRA and RAD51AP1 enable the RAD52-independent ALT pathway, and G4s orchestrate an R- to D-loop switch at telomeres to stimulate BIR.
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Affiliation(s)
- Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jia-Min Zhang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Wendy Leung
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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23
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Kaminski N, Wondisford AR, Kwon Y, Lynskey ML, Bhargava R, Barroso-González J, García-Expósito L, He B, Xu M, Mellacheruvu D, Watkins SC, Modesti M, Miller KM, Nesvizhskii AI, Zhang H, Sung P, O'Sullivan RJ. RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. Mol Cell 2022; 82:4001-4017.e7. [PMID: 36265488 PMCID: PMC9713952 DOI: 10.1016/j.molcel.2022.09.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/10/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a homology-directed repair (HDR) mechanism of telomere elongation that controls proliferation in subsets of aggressive cancer. Recent studies have revealed that telomere repeat-containing RNA (TERRA) promotes ALT-associated HDR (ALT-HDR). Here, we report that RAD51AP1, a crucial ALT factor, interacts with TERRA and utilizes it to generate D- and R-loop HR intermediates. We also show that RAD51AP1 binds to and might stabilize TERRA-containing R-loops as RAD51AP1 depletion reduces R-loop formation at telomere DNA breaks. Proteomic analyses uncover a role for RAD51AP1-mediated TERRA R-loop homeostasis in a mechanism of chromatin-directed suppression of TERRA and prevention of transcription-replication collisions (TRCs) during ALT-HDR. Intriguingly, we find that both TERRA binding and this non-canonical function of RAD51AP1 require its intrinsic SUMO-SIM regulatory axis. These findings provide insights into the multi-contextual functions of RAD51AP1 within the ALT mechanism and regulation of TERRA.
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Affiliation(s)
- Nicole Kaminski
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Boxue He
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Meng Xu
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Dattatreya Mellacheruvu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm UMR1068, Aix Marseille Université U105, Institut Paoli Calmettes, 27 Boulevard Lei Roure CS30059, 13273 Marseille Cedex 09, France
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Huaiying Zhang
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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Singh M, Zhang S, Perez AM, Lee EYC, Lee MYWT, Zhang D. POLDIP3: At the Crossroad of RNA and DNA Metabolism. Genes (Basel) 2022; 13:1921. [PMID: 36360158 PMCID: PMC9690394 DOI: 10.3390/genes13111921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
POLDIP3 was initially identified as a DNA polymerase delta (Pol δ) interacting protein almost twenty years ago. Intriguingly, it also interacts with proteins involved in a variety of RNA related biological processes, such as transcription, pre-mRNA splicing, mRNA export, and translation. Studies in recent years revealed that POLDIP3 also plays critical roles in disassembling genome wide R-loop formation and activating the DNA damage checkpoint in vivo. Here, we review the functions of POLDIP3 in various RNA and DNA related cellular processes. We then propose a unified model to illustrate how POLDIP3 plays such a versatile role at the crossroad of the RNA and DNA metabolism.
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Affiliation(s)
- Manrose Singh
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Alexis M. Perez
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
| | - Ernest Y. C. Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Marietta Y. W. T. Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Northern Blvd, Old Westbury, NY 11568, USA
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25
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Zhang S, Lee EYC, Lee MYWT, Zhang D. DNA polymerase delta interacting protein 3 facilitates the activation and maintenance of DNA damage checkpoint in response to replication stress. Animal Model Exp Med 2022; 5:461-469. [PMID: 36168146 PMCID: PMC9610138 DOI: 10.1002/ame2.12274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 01/22/2023] Open
Abstract
Background Replication stress response is crucial for the maintenance of a stable genome. POLDIP3 (DNA polymerase delta interacting protein 3) was initially identified as one of the DNA polymerase δ (Pol δ) interacting proteins almost 20 years ago. Using a variety of in vitro biochemical assays, we previously established that POLDIP3 is a key regulator of the enzymatic activity of Pol δ. However, the in vivo function of POLDIP3 in DNA replication and DNA damage response has been elusive. Methods We first generated POLDIP3 knockout (KO) cells using the CRISPR/Cas9 technology. We then investigated its biological functions in vivo using a variety of biochemical and cell biology assays. Results We showed that although the POLDIP3‐KO cells manifest no pronounced defect in global DNA synthesis under nonstress conditions, they are sensitive to a variety of replication fork blockers. Intriguingly, we found that POLDIP3 plays a crucial role in the activation and maintenance of the DNA damage checkpoint in response to exogenous as well as endogenous replication stress. Conclusion Our results indicate that when the DNA replication fork is blocked, POLDIP3 can be recruited to the stalled replication fork and functions to bridge the early DNA damage checkpoint response and the later replication fork repair/restart.
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Affiliation(s)
- Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, New York, USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, New York, USA
| | - Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, New York, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, New York, USA
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26
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Abstract
Cancer cells establish replicative immortality by activating a telomere-maintenance mechanism (TMM), be it telomerase or the alternative lengthening of telomeres (ALT) pathway. Targeting telomere maintenance represents an intriguing opportunity to treat the vast majority of all cancer types. Whilst telomerase inhibitors have historically been heralded as promising anticancer agents, the reality has been more challenging, and there are currently no therapeutic options for cancer types that use ALT despite their aggressive nature and poor prognosis. In this Review, we discuss the mechanistic differences between telomere maintenance by telomerase and ALT, the current methods used to detect each mechanism, the utility of these tests for clinical diagnosis, and recent developments in the therapeutic strategies being employed to target both telomerase and ALT. We present notable developments in repurposing established therapeutic agents and new avenues that are emerging to target cancer types according to which TMM they employ. These opportunities extend beyond inhibition of telomere maintenance, by finding and exploiting inherent weaknesses in the telomeres themselves to trigger rapid cellular effects that lead to cell death.
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Affiliation(s)
- Jixuan Gao
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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27
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de Nonneville A, Salas S, Bertucci F, Sobinoff AP, Adélaïde J, Guille A, Finetti P, Noble JR, Churikov D, Chaffanet M, Lavit E, Pickett HA, Bouvier C, Birnbaum D, Reddel RR, Géli V. TOP3A amplification and ATRX inactivation are mutually exclusive events in pediatric osteosarcomas using ALT. EMBO Mol Med 2022; 14:e15859. [PMID: 35920001 PMCID: PMC9549729 DOI: 10.15252/emmm.202215859] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 02/05/2023] Open
Abstract
In some types of cancer, telomere length is maintained by the alternative lengthening of telomeres (ALT) mechanism. In many ALT cancers, the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene is mutated leading to the conclusion that the ATRX complex represses ALT. Here, we report that most high-grade pediatric osteosarcomas maintain their telomeres by ALT, and that the majority of these ALT tumors are ATRX wild-type (wt) and instead carry an amplified 17p11.2 chromosomal region containing TOP3A. We found that TOP3A was overexpressed in the ALT-positive ATRX-wt tumors consistent with its amplification. We demonstrated the functional significance of these results by showing that TOP3A overexpression in ALT cancer cells countered ATRX-mediated ALT inhibition and that TOP3A knockdown disrupted the ALT phenotype in ATRX-wt cells. Moreover, we report that TOP3A is required for proper BLM localization and promotes ALT DNA synthesis in ALT cell lines. Collectively, our results identify TOP3A as a major ALT player and potential therapeutic target.
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Affiliation(s)
- Alexandre de Nonneville
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance,Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia,Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Sébastien Salas
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - François Bertucci
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - José Adélaïde
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Arnaud Guille
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Pascal Finetti
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Jane R Noble
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Dimitri Churikov
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
| | - Max Chaffanet
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Elise Lavit
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Corinne Bouvier
- Department of PathologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Roger R Reddel
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
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28
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Feltes BC, Menck CFM. Current state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations. Mutat Res Rev Mutat Res 2022; 790:108436. [PMID: 35952573 DOI: 10.1016/j.mrrev.2022.108436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/29/2022] [Accepted: 07/31/2022] [Indexed: 01/01/2023]
Abstract
POLη, encoded by the POLH gene, is a crucial protein for replicating damaged DNA and the most studied specialized translesion synthesis polymerases. Mutations in POLη are associated with cancer and the human syndrome xeroderma pigmentosum variant, which is characterized by extreme photosensitivity and an increased likelihood of developing skin cancers. The myriad of structural information about POLη is vast, covering dozens of different mutants, numerous crucial residues, domains, and posttranslational modifications that are essential for protein function within cells. Since POLη is key vital enzyme for cell survival, and mutations in this protein are related to aggressive diseases, understanding its structure is crucial for biomedical sciences, primarily due to its similarities with other Y-family polymerases and its potential as a targeted therapy-drug for tumors. This work provides an up-to-date review on structural aspects of the human POLη: from basic knowledge about critical residues and protein domains to its mutant variants, posttranslational modifications, and our current understanding of therapeutic molecules that target POLη. Thus, this review provides lessons about POLη's structure and gathers critical discussions and hypotheses that may contribute to understanding this protein's vital roles within the cells.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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29
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Brenner KA, Nandakumar J. Consequences of telomere replication failure: the other end-replication problem. Trends Biochem Sci 2022; 47:506-517. [PMID: 35440402 PMCID: PMC9106919 DOI: 10.1016/j.tibs.2022.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/28/2022] [Accepted: 03/17/2022] [Indexed: 01/14/2023]
Abstract
Telomeres are chromosome-capping structures that protect ends of the linear genome from DNA damage sensors. However, these structures present obstacles during DNA replication. Incomplete telomere replication accelerates telomere shortening and limits replicative lifespan. Therefore, continued proliferation under conditions of replication stress requires a means of telomere repair, particularly in the absence of telomerase. It was recently revealed that replication stress triggers break-induced replication (BIR) and mitotic DNA synthesis (MiDAS) at mammalian telomeres; however, these mechanisms are error prone and primarily utilized in tumorigenic contexts. In this review article, we discuss the consequences of replication stress at telomeres and how use of available repair pathways contributes to genomic instability. Current research suggests that fragile telomeres are ultimately tumor-suppressive and thus may be better left unrepaired.
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Affiliation(s)
- Kirsten A Brenner
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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30
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Meijering AEC, Sarlós K, Nielsen CF, Witt H, Harju J, Kerklingh E, Haasnoot GH, Bizard AH, Heller I, Broedersz CP, Liu Y, Peterman EJG, Hickson ID, Wuite GJL. Nonlinear mechanics of human mitotic chromosomes. Nature 2022; 605:545-550. [PMID: 35508652 PMCID: PMC9117150 DOI: 10.1038/s41586-022-04666-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/21/2022] [Indexed: 12/26/2022]
Abstract
In preparation for mitotic cell division, the nuclear DNA of human cells is compacted into individualized, X-shaped chromosomes1. This metamorphosis is driven mainly by the combined action of condensins and topoisomerase IIα (TOP2A)2,3, and has been observed using microscopy for over a century. Nevertheless, very little is known about the structural organization of a mitotic chromosome. Here we introduce a workflow to interrogate the organization of human chromosomes based on optical trapping and manipulation. This allows high-resolution force measurements and fluorescence visualization of native metaphase chromosomes to be conducted under tightly controlled experimental conditions. We have used this method to extensively characterize chromosome mechanics and structure. Notably, we find that under increasing mechanical load, chromosomes exhibit nonlinear stiffening behaviour, distinct from that predicted by classical polymer models4. To explain this anomalous stiffening, we introduce a hierarchical worm-like chain model that describes the chromosome as a heterogeneous assembly of nonlinear worm-like chains. Moreover, through inducible degradation of TOP2A5 specifically in mitosis, we provide evidence that TOP2A has a role in the preservation of chromosome compaction. The methods described here open the door to a wide array of investigations into the structure and dynamics of both normal and disease-associated chromosomes.
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Affiliation(s)
- Anna E C Meijering
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian F Nielsen
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Witt
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Janni Harju
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Emma Kerklingh
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Guus H Haasnoot
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anna H Bizard
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Iddo Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Chase P Broedersz
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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31
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Bhargava R, Lynskey ML, O’Sullivan RJ. New twists to the ALTernative endings at telomeres. DNA Repair (Amst) 2022; 115:103342. [DOI: 10.1016/j.dnarep.2022.103342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
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Hou K, Yu Y, Li D, Zhang Y, Zhang K, Tong J, Yang K, Jia S. Alternative Lengthening of Telomeres and Mediated Telomere Synthesis. Cancers (Basel) 2022; 14:cancers14092194. [PMID: 35565323 PMCID: PMC9105334 DOI: 10.3390/cancers14092194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Alternative lengthing of telomere (ALT) is an important mechanism for maintaining telomere length and cell proliferation in telomerase-negative tumor cells. However, the molecular mechanism of ALT is still poorly understood. ALT occurs in a wide range of tumor types and usually associated with a worse clinical consequence. Here, we review the recent findings of ALT mechanisms, which promise ALT could be a valuable drug target for clinical telomerase-negative tumor treatment. Abstract Telomeres are DNA–protein complexes that protect eukaryotic chromosome ends from being erroneously repaired by the DNA damage repair system, and the length of telomeres indicates the replicative potential of the cell. Telomeres shorten during each division of the cell, resulting in telomeric damage and replicative senescence. Tumor cells tend to ensure cell proliferation potential and genomic stability by activating telomere maintenance mechanisms (TMMs) for telomere lengthening. The alternative lengthening of telomeres (ALT) pathway is the most frequently activated TMM in tumors of mesenchymal and neuroepithelial origin, and ALT also frequently occurs during experimental cellular immortalization of mesenchymal cells. ALT is a process that relies on homologous recombination (HR) to elongate telomeres. However, some processes in the ALT mechanism remain poorly understood. Here, we review the most recent understanding of ALT mechanisms and processes, which may help us to better understand how the ALT pathway is activated in cancer cells and determine the potential therapeutic targets in ALT pathway-stabilized tumors.
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Affiliation(s)
- Kailong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China;
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
| | - Yuyang Yu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Duda Li
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Yanduo Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Ke Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Jinkai Tong
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Kunxian Yang
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
- Correspondence: (K.Y.); (S.J.)
| | - Shuting Jia
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- Correspondence: (K.Y.); (S.J.)
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33
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Sakellariou D, Bak ST, Isik E, Barroso SI, Porro A, Aguilera A, Bartek J, Janscak P, Peña-Diaz J. MutSβ regulates G4-associated telomeric R-loops to maintain telomere integrity in ALT cancer cells. Cell Rep 2022; 39:110602. [PMID: 35385755 DOI: 10.1016/j.celrep.2022.110602] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/17/2021] [Accepted: 03/10/2022] [Indexed: 12/24/2022] Open
Abstract
Up to 15% of human cancers maintain their telomeres through a telomerase-independent mechanism, termed "alternative lengthening of telomeres" (ALT) that relies on homologous recombination between telomeric sequences. Emerging evidence suggests that the recombinogenic nature of ALT telomeres results from the formation of RNA:DNA hybrids (R-loops) between telomeric DNA and the long-noncoding telomeric repeat-containing RNA (TERRA). Here, we show that the mismatch repair protein MutSβ, a heterodimer of MSH2 and MSH3 subunits, is enriched at telomeres in ALT cancer cells, where it prevents the accumulation of telomeric G-quadruplex (G4) structures and R-loops. Cells depleted of MSH3 display increased incidence of R-loop-dependent telomere fragility and accumulation of telomeric C-circles. We also demonstrate that purified MutSβ recognizes and destabilizes G4 structures in vitro. These data suggest that MutSβ destabilizes G4 structures in ALT telomeres to regulate TERRA R-loops, which is a prerequisite for maintenance of telomere integrity during ALT.
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Affiliation(s)
- Despoina Sakellariou
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen, Denmark; Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Sara Thornby Bak
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Esin Isik
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zürich, Switzerland
| | - Sonia I Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, University of Seville-CSIC-UPO, Seville, Spain
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zürich, Switzerland
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, University of Seville-CSIC-UPO, Seville, Spain
| | - Jiri Bartek
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, 17177 Stockholm, Sweden; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14300 Prague, Czech Republic
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zürich, Switzerland; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14300 Prague, Czech Republic.
| | - Javier Peña-Diaz
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen, Denmark.
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Xiao D, Wu J, Zhao H, Jiang X, Nie C. RPP25 as a Prognostic-Related Biomarker That Correlates With Tumor Metabolism in Glioblastoma. Front Oncol 2022; 11:714904. [PMID: 35096558 PMCID: PMC8790702 DOI: 10.3389/fonc.2021.714904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
RPP25, a 25 kDa protein subunit of ribonuclease P (RNase P), is a protein-coding gene. Disorders associated with RPP25 include chromosome 15Q24 deletion syndrome and diffuse scleroderma, while systemic sclerosis can be complicated by malignancy. However, the functional role of RPP25 expression in glioblastoma multiforme (GBM) is unclear. In this study, comprehensive bioinformatics analysis was used to evaluate the impact of RPP25 on GBM occurrence and prognosis. Differential analysis of multiple databases showed that RPP25 was commonly highly expressed in multiple cancers but lowly expressed in GBM. Survival prognostic results showed that RPP25 was prognostically relevant in six tumors (CESC, GBM, LAML, LUAD, SKCM, and UVM), but high RPP25 expression was significantly associated with poor patient prognosis except for CESC. Analysis of RPP25 expression in GBM alone revealed that RPP25 was significantly downregulated in GBM compared with normal tissue. Receiver operating characteristic (ROC) combined with Kaplan-Meier (KM) analysis and Cox regression analysis showed that high RPP25 expression was a prognostic risk factor for GBM and had a predictive value for the 1-year, 2-year, and 3-year survival of GBM patients. In addition, the expression of RPP25 was correlated with the level of immune cell infiltration. The gene set enrichment analysis (GSEA) results showed that RPP25 was mainly associated with signalling pathways related to tumor progression and tumor metabolism.
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Affiliation(s)
- Dongdong Xiao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingnan Wu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongyang Zhao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuansheng Nie
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Armendáriz-castillo I, Hidalgo-fernández K, Pérez-villa A, García-cárdenas JM, López-cortés A, Guerrero S. Identification of Key Proteins from the Alternative Lengthening of Telomeres-Associated Promyelocytic Leukemia Nuclear Bodies Pathway. Biology 2022; 11:185. [PMID: 35205052 PMCID: PMC8868596 DOI: 10.3390/biology11020185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/26/2022]
Abstract
Simple Summary The alternative lengthening of telomeres is a telomere maintenance mechanism used by some cancer types to elongate their telomeres without the aid of telomerase. This mechanism contributes to the proliferation and immortality of cancer cells. One of the hallmarks of this mechanism is the interaction with promyelocytic leukemia nuclear bodies, which are suspected to be the key places where telomere extension occurs. Despite the discovery of some mechanisms, elements, key genes, and proteins from the pathway, the alternative lengthening of telomeres mechanism is still poorly understood, and it is highly associated with a poor prognosis. In this study, we combined multiomics approaches with genomic, transcriptomic, and proteomic analyses of 71 genes/proteins related to promyelocytic leukemia nuclear bodies in more than 10,000 cancer samples from The Cancer Genome Atlas Consortium. As a result, 13 key proteins were proposed as candidates for future experimental studies that will validate these proteins as therapeutic markers, which will improve the understanding and treatment of these type of cancers. Abstract Alternative lengthening of telomeres-associated promyelocytic leukemia nuclear bodies (APBs) are a hallmark of telomere maintenance. In the last few years, APBs have been described as the main place where telomeric extension occurs in ALT-positive cancer cell lines. A different set of proteins have been associated with APBs function, however, the molecular mechanisms behind their assembly, colocalization, and clustering of telomeres, among others, remain unclear. To improve the understanding of APBs in the ALT pathway, we integrated multiomics analyses to evaluate genomic, transcriptomic and proteomic alterations, and functional interactions of 71 APBs-related genes/proteins in 32 Pan-Cancer Atlas studies from The Cancer Genome Atlas Consortium (TCGA). As a result, we identified 13 key proteins which showed distinctive mutations, interactions, and functional enrichment patterns across all the cancer types and proposed this set of proteins as candidates for future ex vivo and in vivo analyses that will validate these proteins to improve the understanding of the ALT pathway, fill the current research gap about APBs function and their role in ALT, and be considered as potential therapeutic targets for the diagnosis and treatment of ALT-positive cancers in the future.
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Barroso-González J, García-Expósito L, Galaviz P, Lynskey ML, Allen JAM, Hoang S, Watkins SC, Pickett HA, O'Sullivan RJ. Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell Rep 2021; 37:110088. [PMID: 34879271 PMCID: PMC8724847 DOI: 10.1016/j.celrep.2021.110088] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 01/02/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in ~15% of cancer subtypes. Current models indicate that ALT is mediated by homology-directed repair mechanisms. By disrupting MSH6 gene expression, we show that the deficiency of MutSα (MSH2/MSH6) DNA mismatch repair complex causes striking telomere hyperextension. Mechanistically, we show MutSα is specifically recruited to telomeres in ALT cells by associating with the proliferating-cell nuclear antigen (PCNA) subunit of the ALT telomere replisome. We also provide evidence that MutSα counteracts Bloom (BLM) helicase, which adopts a crucial role in stabilizing hyper-extended telomeres and maintaining the survival of MutSα-deficient ALT cancer cells. Lastly, we propose a model in which MutSα deficiency impairs heteroduplex rejection, leading to premature initiation of telomere DNA synthesis that coincides with an accumulation of telomere variant repeats (TVRs). These findings provide evidence that the MutSα DNA mismatch repair complex acts to restrain unwarranted ALT. Barroso-Gonzalez et al. show that the mismatch repair complex MutSα restricts the alternative lengthening of telomeres (ALT) pathway in cancer cells. MutSα has an anti-recombination function and limits recombination between heteroduplex sequences at telomeres, in part by counteracting the Bloom helicase (BLM).
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Pablo Galaviz
- Bioinformatics Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - SongMy Hoang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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Scott WA, Dhanji EZ, Dyakov BJA, Dreseris ES, Asa JS, Grange LJ, Mirceta M, Pearson CE, Stewart GS, Gingras AC, Campos EI. ATRX proximal protein associations boast roles beyond histone deposition. PLoS Genet 2021; 17:e1009909. [PMID: 34780483 DOI: 10.1371/journal.pgen.1009909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/29/2021] [Accepted: 10/23/2021] [Indexed: 12/31/2022] Open
Abstract
The ATRX ATP-dependent chromatin remodelling/helicase protein associates with the DAXX histone chaperone to deposit histone H3.3 over repetitive DNA regions. Because ATRX-protein interactions impart functions, such as histone deposition, we used proximity-dependent biotinylation (BioID) to identify proximal associations for ATRX. The proteomic screen captured known interactors, such as DAXX, NBS1, and PML, but also identified a range of new associating proteins. To gauge the scope of their roles, we examined three novel ATRX-associating proteins that likely differed in function, and for which little data were available. We found CCDC71 to associate with ATRX, but also HP1 and NAP1, suggesting a role in chromatin maintenance. Contrastingly, FAM207A associated with proteins involved in ribosome biosynthesis and localized to the nucleolus. ATRX proximal associations with the SLF2 DNA damage response factor help inhibit telomere exchanges. We further screened for the proteomic changes at telomeres when ATRX, SLF2, or both proteins were deleted. The loss caused important changes in the abundance of chromatin remodelling, DNA replication, and DNA repair factors at telomeres. Interestingly, several of these have previously been implicated in alternative lengthening of telomeres. Altogether, this study expands the repertoire of ATRX-associating proteins and functions. ATRX is a protein that is needed to keep repetitive DNA regions organized. It does so in part by binding the DAXX histone chaperone to deposit histone proteins on DNA and assemble structures known as nucleosomes. While important, ATRX has additional functions that remain understudied. To better understand its various biological roles, we first identified the other proteins that are found in its proximity. ATRX-associating proteins were implicated in a range of functions, in addition to histone deposition. Our results suggest that ATRX-associating proteins likely help compact DNA after it is assembled into nucleosomes, and also promote its stability. We then examined the effect of ATRX on telomeres (repetitive DNA regions at the end of chromosomes). ATRX and at least one of its associating proteins suppressed spurious DNA exchanges at telomeres. To understand why, we then identified proteomic changes that occur at telomeres when ATRX was deleted. Loss of ATRX altered the enrichment of a surprising number of proteins at telomeres, including several DNA damage response and chromatin remodelling proteins.
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Teng FY, Jiang ZZ, Guo M, Tan XZ, Chen F, Xi XG, Xu Y. G-quadruplex DNA: a novel target for drug design. Cell Mol Life Sci 2021; 78:6557-6583. [PMID: 34459951 PMCID: PMC11072987 DOI: 10.1007/s00018-021-03921-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
G-quadruplex (G4) DNA is a type of quadruple helix structure formed by a continuous guanine-rich DNA sequence. Emerging evidence in recent years authenticated that G4 DNA structures exist both in cell-free and cellular systems, and function in different diseases, especially in various cancers, aging, neurological diseases, and have been considered novel promising targets for drug design. In this review, we summarize the detection method and the structure of G4, highlighting some non-canonical G4 DNA structures, such as G4 with a bulge, a vacancy, or a hairpin. Subsequently, the functions of G4 DNA in physiological processes are discussed, especially their regulation of DNA replication, transcription of disease-related genes (c-MYC, BCL-2, KRAS, c-KIT et al.), telomere maintenance, and epigenetic regulation. Typical G4 ligands that target promoters and telomeres for drug design are also reviewed, including ellipticine derivatives, quinoxaline analogs, telomestatin analogs, berberine derivatives, and CX-5461, which is currently in advanced phase I/II clinical trials for patients with hematologic cancer and BRCA1/2-deficient tumors. Furthermore, since the long-term stable existence of G4 DNA structures could result in genomic instability, we summarized the G4 unfolding mechanisms emerged recently by multiple G4-specific DNA helicases, such as Pif1, RecQ family helicases, FANCJ, and DHX36. This review aims to present a general overview of the field of G-quadruplex DNA that has progressed in recent years and provides potential strategies for drug design and disease treatment.
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Affiliation(s)
- Fang-Yuan Teng
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zong-Zhe Jiang
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiao-Zhen Tan
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Feng Chen
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61, Avenue du Président Wilson, 94235, Cachan, France.
| | - Yong Xu
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
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Glousker G, Lingner J. Challenging endings: How telomeres prevent fragility. Bioessays 2021; 43:e2100157. [PMID: 34436787 DOI: 10.1002/bies.202100157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022]
Abstract
It has become apparent that difficulties to replicate telomeres concern not only the very ends of eukaryotic chromosomes. The challenges already start when the replication fork enters the telomeric repeats. The obstacles encountered consist mainly of noncanonical nucleic acid structures that interfere with replication if not resolved. Replication stress at telomeres promotes the formation of so-called fragile telomeres displaying an abnormal appearance in metaphase chromosomes though their exact molecular nature remains to be elucidated. A substantial number of factors is required to counteract fragility. In this review we promote the hypothesis that telomere fragility is not caused directly by an initial insult during replication but it results as a secondary consequence of DNA repair of damaged replication forks by the homologous DNA recombination machinery. Incomplete DNA synthesis at repair sites or partial chromatin condensation may become apparent as telomere fragility. Fragility and DNA repair during telomere replication emerges as a common phenomenon which exacerbates in multiple disease conditions.
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Affiliation(s)
- Galina Glousker
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Joachim Lingner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
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40
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Hoffmann JS. The Heritability of Replication Problems. Cells 2021; 10:cells10061464. [PMID: 34207969 PMCID: PMC8230577 DOI: 10.3390/cells10061464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/23/2022] Open
Abstract
The major challenge of DNA replication is to provide daughter cells with intact and fully duplicated genetic material. However, various endogenous or environmental factors can slow down or stall DNA replication forks; these replication problems are known to fuel genomic instability and associated pathology, including cancer progression. Whereas the mechanisms emphasizing the source and the cellular responses of replicative problems have attracted much consideration over the past decade, the propagation through mitosis of genome modification and its heritability in daughter cells when the stress is not strong enough to provoke a checkpoint response in G2/M was much less documented. Some recent studies addressing whether low replication stress could impact the DNA replication program of the next generation of cells made the remarkable discovery that DNA damage can indeed be transmitted to daughter cells and can be processed in the subsequent S-phase, and that the replication timing program at a subset of chromosomal domains can also be impacted in the next generation of cells. Such a progression of replication problems into mitosis and daughter cells may appear counter-intuitive, but it could offer considerable advantages by alerting the next generation of cells of potentially risky loci and offering the possibility of an adaptive mechanism to anticipate a reiteration of problems, notably for cancer cells in the context of resistance to therapy.
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Affiliation(s)
- Jean-Sébastien Hoffmann
- Laboratoire de Pathologie, Laboratoire d'Excellence Toulouse Cancer, CHU Toulouse, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, CEDEX, 31059 Toulouse, France
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Tsao WC, Buj R, Aird KM, Sidorova JM, Eckert KA. Overexpression of oncogenic H-Ras in hTERT-immortalized and SV40-transformed human cells targets replicative and specialized DNA polymerases for depletion. PLoS One 2021; 16:e0251188. [PMID: 33961649 PMCID: PMC8104423 DOI: 10.1371/journal.pone.0251188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022] Open
Abstract
DNA polymerases play essential functions in replication fork progression and genome maintenance. DNA lesions and drug-induced replication stress result in up-regulation and re-localization of specialized DNA polymerases η and κ. Although oncogene activation significantly alters DNA replication dynamics, causing replication stress and genome instability, little is known about DNA polymerase expression and regulation in response to oncogene activation. Here, we investigated the consequences of mutant H-RASG12V overexpression on the regulation of DNA polymerases in h-TERT immortalized and SV40-transformed human cells. Focusing on DNA polymerases associated with the replication fork, we demonstrate that DNA polymerases are depleted in a temporal manner in response to H-RASG12V overexpression. The polymerases targeted for depletion, as cells display markers of senescence, include the Pol α catalytic subunit (POLA1), Pol δ catalytic and p68 subunits (POLD1 and POLD3), Pol η, and Pol κ. Both transcriptional and post-transcriptional mechanisms mediate this response. Pol η (POLH) depletion is sufficient to induce a senescence-like growth arrest in human foreskin fibroblast BJ5a cells, and is associated with decreased Pol α expression. Using an SV-40 transformed cell model, we observed cell cycle checkpoint signaling differences in cells with H-RasG12V-induced polymerase depletion, as compared to Pol η-deficient cells. Our findings contribute to our understanding of cellular events following oncogene activation and cellular transformation.
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Affiliation(s)
- Wei-chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Raquel Buj
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Katherine M. Aird
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
- Penn State Cancer Institute, Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Julia M. Sidorova
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kristin A. Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
- Penn State Cancer Institute, Pennsylvania State University, Hershey, Pennsylvania, United States of America
- * E-mail:
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Maiorano D, El Etri J, Franchet C, Hoffmann JS. Translesion Synthesis or Repair by Specialized DNA Polymerases Limits Excessive Genomic Instability upon Replication Stress. Int J Mol Sci 2021; 22:3924. [PMID: 33920223 PMCID: PMC8069355 DOI: 10.3390/ijms22083924] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
DNA can experience "replication stress", an important source of genome instability, induced by various external or endogenous impediments that slow down or stall DNA synthesis. While genome instability is largely documented to favor both tumor formation and heterogeneity, as well as drug resistance, conversely, excessive instability appears to suppress tumorigenesis and is associated with improved prognosis. These findings support the view that karyotypic diversity, necessary to adapt to selective pressures, may be limited in tumors so as to reduce the risk of excessive instability. This review aims to highlight the contribution of specialized DNA polymerases in limiting extreme genetic instability by allowing DNA replication to occur even in the presence of DNA damage, to either avoid broken forks or favor their repair after collapse. These mechanisms and their key regulators Rad18 and Polθ not only offer diversity and evolutionary advantage by increasing mutagenic events, but also provide cancer cells with a way to escape anti-cancer therapies that target replication forks.
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Affiliation(s)
- Domenico Maiorano
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Jana El Etri
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, 34396 Montpellier, France; (D.M.); (J.E.E.)
| | - Camille Franchet
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire D’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
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Mentegari E, Bertoletti F, Kissova M, Zucca E, Galli S, Tagliavini G, Garbelli A, Maffia A, Bione S, Ferrari E, d’Adda di Fagagna F, Francia S, Sabbioneda S, Chen LY, Lingner J, Bergoglio V, Hoffmann JS, Hübscher U, Crespan E, Maga G. A Role for Human DNA Polymerase λ in Alternative Lengthening of Telomeres. Int J Mol Sci 2021; 22:ijms22052365. [PMID: 33673424 PMCID: PMC7956399 DOI: 10.3390/ijms22052365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Telomerase negative cancer cell types use the Alternative Lengthening of Telomeres (ALT) pathway to elongate telomeres ends. Here, we show that silencing human DNA polymerase (Pol λ) in ALT cells represses ALT activity and induces telomeric stress. In addition, replication stress in the absence of Pol λ, strongly affects the survival of ALT cells. In vitro, Pol λ can promote annealing of even a single G-rich telomeric repeat to its complementary strand and use it to prime DNA synthesis. The noncoding telomeric repeat containing RNA TERRA and replication protein A negatively regulate this activity, while the Protection of Telomeres protein 1 (POT1)/TPP1 heterodimer stimulates Pol λ. Pol λ associates with telomeres and colocalizes with TPP1 in cells. In summary, our data suggest a role of Pol λ in the maintenance of telomeres by the ALT mechanism.
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Affiliation(s)
- Elisa Mentegari
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Federica Bertoletti
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Miroslava Kissova
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elisa Zucca
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Galli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Giulia Tagliavini
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Antonio Maffia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Silvia Bione
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Fabrizio d’Adda di Fagagna
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- IFOM-The FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Sofia Francia
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
| | - Liuh-Yow Chen
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Frontiers in Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, CH-1015 Lausanne, Switzerland; (L.-Y.C.); (J.L.)
| | - Valerie Bergoglio
- UMR1037 INSERM, Cancer Research Center of Toulouse, 2 Avenue Curien, 31037 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, 31059 Toulouse, France;
| | - Ulrich Hübscher
- Department of Molecular Mechanisms of Disease, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; (E.F.); (U.H.)
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, via Abbiategrasso 207, 27100 Pavia, Italy; (E.M.); (F.B.); (M.K.); (E.Z.); (S.G.); (G.T.); (A.G.); (A.M.); (S.B.); (F.d.d.F.); (S.F.); (S.S.)
- Correspondence: (E.C.); (G.M.)
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Raghunandan M, Geelen D, Majerova E, Decottignies A. NHP2 downregulation counteracts hTR-mediated activation of the DNA damage response at ALT telomeres. EMBO J 2021; 40:e106336. [PMID: 33595114 DOI: 10.15252/embj.2020106336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/09/2022] Open
Abstract
About 10% of cancer cells employ the "alternative lengthening of telomeres" (ALT) pathway instead of re-activating the hTERT subunit of human telomerase. The hTR RNA subunit is also abnormally silenced in some ALT+ cells not expressing hTERT, suggesting a possible negative non-canonical impact of hTR on ALT. Indeed, we show that ectopically expressed hTR reduces phosphorylation of ssDNA-binding protein RPA (p-RPAS33 ) at ALT telomeres by promoting the hnRNPA1- and DNA-PK-dependent depletion of RPA. The resulting defective ATR checkpoint signaling at telomeres impairs recruitment of the homologous recombination protein, RAD51. This induces ALT telomere fragility, increases POLD3-dependent C-circle production, and promotes the recruitment of the DNA damage marker 53BP1. In ALT+ cells that naturally retain hTR expression, NHP2 H/ACA ribonucleoprotein levels are downregulated, likely in order to restrain DNA damage response (DDR) activation at telomeres through reduced 53BP1 recruitment. This unexpected role of NHP2 is independent from hTR's non-canonical function in modulating telomeric p-RPAS33 . Collectively, our study shines new light on the interference between telomerase- and ALT-dependent pathways and unravels a crucial role for hTR and NHP2 in DDR regulation at ALT telomeres.
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Affiliation(s)
- Maya Raghunandan
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université catholique de Louvain, Brussels, Belgium
| | - Dan Geelen
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université catholique de Louvain, Brussels, Belgium
| | - Eva Majerova
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université catholique de Louvain, Brussels, Belgium
| | - Anabelle Decottignies
- Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Faculty of Pharmacy and Biomedical Sciences, Université catholique de Louvain, Brussels, Belgium
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45
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Shen M, Young A, Autexier C. PCNA, a focus on replication stress and the alternative lengthening of telomeres pathway. DNA Repair (Amst) 2021; 100:103055. [PMID: 33581499 DOI: 10.1016/j.dnarep.2021.103055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of telomeres, which are specialized stretches of DNA found at the ends of linear chromosomes, is a crucial step for the immortalization of cancer cells. Approximately 10-15 % of cancer cells use a homologous recombination-based mechanism known as the Alternative Lengthening of Telomeres (ALT) pathway to maintain their telomeres. Telomeres in general pose a challenge to DNA replication owing to their repetitive nature and potential for forming secondary structures. Telomeres in ALT+ cells especially are subject to elevated levels of replication stress compared to telomeres that are maintained by the enzyme telomerase, in part due to the incorporation of telomeric variant repeats at ALT+ telomeres, their on average longer lengths, and their modified chromatin states. Many DNA metabolic strategies exist to counter replication stress and to protect stalled replication forks. The role of proliferating cell nuclear antigen (PCNA) as a platform for recruiting protein partners that participate in several of these DNA replication and repair pathways has been well-documented. We propose that many of these pathways may be active at ALT+ telomeres, either to facilitate DNA replication, to manage replication stress, or during telomere extension. Here, we summarize recent evidence detailing the role of PCNA in pathways including DNA secondary structure resolution, DNA damage bypass, replication fork restart, and DNA damage synthesis. We propose that an examination of PCNA and its post-translational modifications (PTMs) may offer a unique lens by which we might gain insight into the DNA metabolic landscape that is distinctively present at ALT+ telomeres.
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Affiliation(s)
- Michelle Shen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Adrian Young
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada.
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46
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Zhang JM, Genois MM, Ouyang J, Lan L, Zou L. Alternative lengthening of telomeres is a self-perpetuating process in ALT-associated PML bodies. Mol Cell 2021; 81:1027-1042.e4. [PMID: 33453166 DOI: 10.1016/j.molcel.2020.12.030] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/03/2020] [Accepted: 12/15/2020] [Indexed: 01/16/2023]
Abstract
Alternative lengthening of telomeres (ALT) is mediated by break-induced replication (BIR), but how BIR is regulated at telomeres is poorly understood. Here, we show that telomeric BIR is a self-perpetuating process. By tethering PML-IV to telomeres, we induced telomere clustering in ALT-associated PML bodies (APBs) and a POLD3-dependent ATR response at telomeres, showing that BIR generates replication stress. Ablation of BLM helicase activity in APBs abolishes telomere synthesis but causes multiple chromosome bridges between telomeres, revealing a function of BLM in processing inter-telomere BIR intermediates. Interestingly, the accumulation of BLM in APBs requires its own helicase activity and POLD3, suggesting that BIR triggers a feedforward loop to further recruit BLM. Enhancing BIR induces PIAS4-mediated TRF2 SUMOylation, and PIAS4 loss deprives APBs of repair proteins and compromises ALT telomere synthesis. Thus, a BLM-driven and PIAS4-mediated feedforward loop operates in APBs to perpetuate BIR, providing a critical mechanism to extend ALT telomeres.
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47
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Codd V, Wang Q, Allara E, Musicha C, Kaptoge S, Stoma S, Jiang T, Hamby SE, Braund PS, Bountziouka V, Budgeon CA, Denniff M, Swinfield C, Papakonstantinou M, Sheth S, Nanus DE, Warner SC, Wang M, Khera AV, Eales J, Ouwehand WH, Thompson JR, Di Angelantonio E, Wood AM, Butterworth AS, Danesh JN, Nelson CP, Samani NJ. Polygenic basis and biomedical consequences of telomere length variation. Nat Genet 2021; 53:1425-1433. [PMID: 34611362 PMCID: PMC8492471 DOI: 10.1038/s41588-021-00944-6] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023]
Abstract
Telomeres, the end fragments of chromosomes, play key roles in cellular proliferation and senescence. Here we characterize the genetic architecture of naturally occurring variation in leukocyte telomere length (LTL) and identify causal links between LTL and biomedical phenotypes in 472,174 well-characterized UK Biobank participants. We identified 197 independent sentinel variants associated with LTL at 138 genomic loci (108 new). Genetically determined differences in LTL were associated with multiple biological traits, ranging from height to bone marrow function, as well as several diseases spanning neoplastic, vascular and inflammatory pathologies. Finally, we estimated that, at the age of 40 years, people with an LTL >1 s.d. shorter than the population mean had a 2.5-year-lower life expectancy compared with the group with ≥1 s.d. longer LDL. Overall, we furnish new insights into the genetic regulation of LTL, reveal wide-ranging influences of LTL on physiological traits, diseases and longevity, and provide a powerful resource available to the global research community.
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Affiliation(s)
- Veryan Codd
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Qingning Wang
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Elias Allara
- grid.5335.00000000121885934British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Crispin Musicha
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Stephen Kaptoge
- grid.5335.00000000121885934British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Svetlana Stoma
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Tao Jiang
- grid.5335.00000000121885934British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Stephen E. Hamby
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Peter S. Braund
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Vasiliki Bountziouka
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Charley A. Budgeon
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK ,grid.1012.20000 0004 1936 7910School of Population and Global Health, University of Western Australia, Perth, Western Australia Australia
| | - Matthew Denniff
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Chloe Swinfield
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Manolo Papakonstantinou
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Shilpi Sheth
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Dominika E. Nanus
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Sophie C. Warner
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Minxian Wang
- grid.66859.34Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA USA
| | - Amit V. Khera
- grid.66859.34Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA ,grid.32224.350000 0004 0386 9924Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA USA
| | - James Eales
- grid.5379.80000000121662407Division of Cardiovascular Sciences, University of Manchester, Manchester, UK
| | - Willem H. Ouwehand
- grid.5335.00000000121885934British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Haematology, University of Cambridge, Cambridge, UK ,grid.436365.10000 0000 8685 6563NHS Blood and Transplant, Cambridge, UK ,grid.52996.310000 0000 8937 2257University College London Hospitals NHS Foundation Trust, London, UK
| | - John R. Thompson
- grid.9918.90000 0004 1936 8411Department of Health Sciences, University of Leicester, Leicester, UK
| | - Emanuele Di Angelantonio
- grid.5335.00000000121885934British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK ,grid.10306.340000 0004 0606 5382Health Data Research UK Cambridge, Wellcome Sanger Institute, EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge, UK
| | - Angela M. Wood
- grid.5335.00000000121885934British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK ,grid.10306.340000 0004 0606 5382Health Data Research UK Cambridge, Wellcome Sanger Institute, EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge, UK ,grid.499548.d0000 0004 5903 3632The Alan Turing Institute, London, UK
| | - Adam S. Butterworth
- grid.5335.00000000121885934British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK ,grid.10306.340000 0004 0606 5382Health Data Research UK Cambridge, Wellcome Sanger Institute, EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge, UK
| | - John N. Danesh
- grid.5335.00000000121885934British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK ,grid.10306.340000 0004 0606 5382Health Data Research UK Cambridge, Wellcome Sanger Institute, EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge, UK ,grid.10306.340000 0004 0606 5382Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Christopher P. Nelson
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Nilesh J. Samani
- grid.9918.90000 0004 1936 8411Department of Cardiovascular Sciences, University of Leicester, Leicester, UK ,grid.412925.90000 0004 0400 6581NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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48
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Abstract
T-loops are thought to hide telomeres from DNA damage signaling and DSB repair pathways. T-loop formation requires the shelterin component TRF2, which represses ATM signaling and NHEJ. Here we establish that TRF2 alone, in the absence of other shelterin proteins can form t-loops. Mouse and human cells contain two isoforms of TRF2, one of which is uncharacterized. We show that both isoforms protect telomeres and form t-loops. The isoforms are not cell cycle regulated and t-loops are present in G1, S, and G2. Using the DNA wrapping deficient TRF2 Topless mutant, we confirm its inability to form t-loops and repress ATM. However, since the mutant is also defective in repression of NHEJ and telomeric localization, the role of topological changes in telomere protection remains unclear. Finally, we show that Rad51 does not affect t-loop frequencies or telomere protection. Therefore, alternative models for how TRF2 forms t-loops should be explored.
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Affiliation(s)
- Leonid A Timashev
- Laboratory for Cell Biology and Genetics, Rockefeller University , New York, USA
| | - Titia De Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University , New York, USA
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49
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Hoang SM, Kaminski N, Bhargava R, Barroso-González J, Lynskey ML, García-Expósito L, Roncaioli JL, Wondisford AR, Wallace CT, Watkins SC, James DI, Waddell ID, Ogilvie D, Smith KM, da Veiga Leprevost F, Mellacharevu D, Nesvizhskii AI, Li J, Ray-Gallet D, Sobol RW, Almouzni G, O'Sullivan RJ. Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol 2020; 27:1152-1164. [PMID: 33046907 PMCID: PMC7809635 DOI: 10.1038/s41594-020-0512-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Abstract
The synthesis of poly(ADP-ribose) (PAR) reconfigures the local chromatin environment and recruits DNA-repair complexes to damaged chromatin. PAR degradation by poly(ADP-ribose) glycohydrolase (PARG) is essential for progression and completion of DNA repair. Here, we show that inhibition of PARG disrupts homology-directed repair (HDR) mechanisms that underpin alternative lengthening of telomeres (ALT). Proteomic analyses uncover a new role for poly(ADP-ribosyl)ation (PARylation) in regulating the chromatin-assembly factor HIRA in ALT cancer cells. We show that HIRA is enriched at telomeres during the G2 phase and is required for histone H3.3 deposition and telomere DNA synthesis. Depletion of HIRA elicits systemic death of ALT cancer cells that is mitigated by re-expression of ATRX, a protein that is frequently inactivated in ALT tumors. We propose that PARylation enables HIRA to fulfill its essential role in the adaptive response to ATRX deficiency that pervades ALT cancers.
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Affiliation(s)
- Song My Hoang
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicole Kaminski
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle L Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Callen T Wallace
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dominic I James
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Ian D Waddell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Donald Ogilvie
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Kate M Smith
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | | | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jianfeng Li
- Department of Pharmacology and the Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée, Ligue contre le Cancer, Paris, France
| | - Robert W Sobol
- Department of Pharmacology and the Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Genevieve Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée, Ligue contre le Cancer, Paris, France
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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Pinzaru AM, Kareh M, Lamm N, Lazzerini-Denchi E, Cesare AJ, Sfeir A. Replication stress conferred by POT1 dysfunction promotes telomere relocalization to the nuclear pore. Genes Dev 2020; 34:1619-36. [PMID: 33122293 DOI: 10.1101/gad.337287.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/21/2020] [Indexed: 12/31/2022]
Abstract
In this study, Pinzaru et al. set out to uncover the pathways that enable the proliferation of cells expressing cancer-associated POT1 mutations. Using complementary genetic and proteomic approaches, the authors identify a conserved function for the NPC in resolving replication defects at telomere loci. Mutations in the telomere-binding protein POT1 are associated with solid tumors and leukemias. POT1 alterations cause rapid telomere elongation, ATR kinase activation, telomere fragility, and accelerated tumor development. Here, we define the impact of mutant POT1 alleles through complementary genetic and proteomic approaches based on CRISPR interference and biotin-based proximity labeling, respectively. These screens reveal that replication stress is a major vulnerability in cells expressing mutant POT1, which manifests as increased telomere mitotic DNA synthesis at telomeres. Our study also unveils a role for the nuclear pore complex in resolving replication defects at telomeres. Depletion of nuclear pore complex subunits in the context of POT1 dysfunction increases DNA damage signaling, telomere fragility and sister chromatid exchanges. Furthermore, we observed telomere repositioning to the nuclear periphery driven by nuclear F-actin polymerization in cells with POT1 mutations. In conclusion, our study establishes that relocalization of dysfunctional telomeres to the nuclear periphery is critical to preserve telomere repeat integrity.
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