1
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Liu Z, Jiang H, Lee SY, Kong N, Chan YW. FANCM promotes PARP inhibitor resistance by minimizing ssDNA gap formation and counteracting resection inhibition. Cell Rep 2024; 43:114464. [PMID: 38985669 DOI: 10.1016/j.celrep.2024.114464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/22/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024] Open
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPis) exhibit remarkable anticancer activity in tumors with homologous recombination (HR) gene mutations. However, the role of other DNA repair proteins in PARPi-induced lethality remains elusive. Here, we reveal that FANCM promotes PARPi resistance independent of the core Fanconi anemia (FA) complex. FANCM-depleted cells retain HR proficiency, acting independently of BRCA1 in response to PARPis. FANCM depletion leads to increased DNA damage in the second S phase after PARPi exposure, driven by elevated single-strand DNA (ssDNA) gap formation behind replication forks in the first S phase. These gaps arise from both 53BP1- and primase and DNA directed polymerase (PRIMPOL)-dependent mechanisms. Notably, FANCM-depleted cells also exhibit reduced resection of collapsed forks, while 53BP1 deletion restores resection and mitigates PARPi sensitivity. Our results suggest that FANCM counteracts 53BP1 to repair PARPi-induced DNA damage. Furthermore, FANCM depletion leads to increased chromatin bridges and micronuclei formation after PARPi treatment, elucidating the mechanism underlying extensive cell death in FANCM-depleted cells.
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Affiliation(s)
- Zeyuan Liu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Huadong Jiang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Sze Yuen Lee
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Nannan Kong
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ying Wai Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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2
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Bennett LG, Vernon EG, Thanendran V, Jones CM, Gamble A, Staples CJ. MRNIP limits ssDNA gaps during replication stress. Nucleic Acids Res 2024:gkae546. [PMID: 38917325 DOI: 10.1093/nar/gkae546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Replication repriming by the specialized primase-polymerase PRIMPOL ensures the continuity of DNA synthesis during replication stress. PRIMPOL activity generates residual post-replicative single-stranded nascent DNA gaps, which are linked with mutagenesis and chemosensitivity in BRCA1/2-deficient models, and which are suppressed by replication fork reversal mediated by the DNA translocases SMARCAL1 and ZRANB3. Here, we report that the MRE11 regulator MRNIP limits the prevalence of PRIMPOL and MRE11-dependent ssDNA gaps in cells in which fork reversal is perturbed either by treatment with the PARP inhibitor Olaparib, or by depletion of SMARCAL1 or ZRANB3. MRNIP-deficient cells are sensitive to PARP inhibition and accumulate PRIMPOL-dependent DNA damage, supportive of a pro-survival role for MRNIP linked to the regulation of gap prevalence. In MRNIP-deficient cells, post-replicative gap filling is driven in S-phase by UBC13-mediated template switching involving REV1 and the TLS polymerase Pol-ζ. Our findings represent the first report of modulation of post-replicative ssDNA gap dynamics by a direct MRE11 regulator.
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Affiliation(s)
- Laura G Bennett
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Ellen G Vernon
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Vithursha Thanendran
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Caryl M Jones
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Amelia Gamble
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Christopher J Staples
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
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3
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García-Rodríguez N, Domínguez-García I, Domínguez-Pérez MD, Huertas P. EXO1 and DNA2-mediated ssDNA gap expansion is essential for ATR activation and to maintain viability in BRCA1-deficient cells. Nucleic Acids Res 2024; 52:6376-6391. [PMID: 38721777 PMCID: PMC11194085 DOI: 10.1093/nar/gkae317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/25/2024] [Accepted: 05/02/2024] [Indexed: 06/25/2024] Open
Abstract
DNA replication faces challenges from DNA lesions originated from endogenous or exogenous sources of stress, leading to the accumulation of single-stranded DNA (ssDNA) that triggers the activation of the ATR checkpoint response. To complete genome replication in the presence of damaged DNA, cells employ DNA damage tolerance mechanisms that operate not only at stalled replication forks but also at ssDNA gaps originated by repriming of DNA synthesis downstream of lesions. Here, we demonstrate that human cells accumulate post-replicative ssDNA gaps following replicative stress induction. These gaps, initiated by PrimPol repriming and expanded by the long-range resection factors EXO1 and DNA2, constitute the principal origin of the ssDNA signal responsible for ATR activation upon replication stress, in contrast to stalled forks. Strikingly, the loss of EXO1 or DNA2 results in synthetic lethality when combined with BRCA1 deficiency, but not BRCA2. This phenomenon aligns with the observation that BRCA1 alone contributes to the expansion of ssDNA gaps. Remarkably, BRCA1-deficient cells become addicted to the overexpression of EXO1, DNA2 or BLM. This dependence on long-range resection unveils a new vulnerability of BRCA1-mutant tumors, shedding light on potential therapeutic targets for these cancers.
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Affiliation(s)
- Néstor García-Rodríguez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Iria Domínguez-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - María del Carmen Domínguez-Pérez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
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4
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Fingerman DF, O'Leary DR, Hansen AR, Tran T, Harris BR, DeWeerd RA, Hayer KE, Fan J, Chen E, Tennakoon M, Meroni A, Szeto JH, Devenport J, LaVigne D, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. EMBO J 2024:10.1038/s44318-024-00137-x. [PMID: 38886582 DOI: 10.1038/s44318-024-00137-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
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Affiliation(s)
- Dylan F Fingerman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Thi Tran
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Brooke R Harris
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiayi Fan
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Emily Chen
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- School of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Mithila Tennakoon
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alice Meroni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Julia H Szeto
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jessica Devenport
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Danielle LaVigne
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Weitzman
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ophir Shalem
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeffrey Bednarski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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5
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Saxena S, Nabel CS, Seay TW, Patel PS, Kawale AS, Crosby CR, Tigro H, Oh E, Vander Heiden MG, Hata AN, Suo Z, Zou L. Unprocessed genomic uracil as a source of DNA replication stress in cancer cells. Mol Cell 2024; 84:2036-2052.e7. [PMID: 38688279 PMCID: PMC11162326 DOI: 10.1016/j.molcel.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024]
Abstract
Alterations of bases in DNA constitute a major source of genomic instability. It is believed that base alterations trigger base excision repair (BER), generating DNA repair intermediates interfering with DNA replication. Here, we show that genomic uracil, a common type of base alteration, induces DNA replication stress (RS) without being processed by BER. In the absence of uracil DNA glycosylase (UNG), genomic uracil accumulates to high levels, DNA replication forks slow down, and PrimPol-mediated repriming is enhanced, generating single-stranded gaps in nascent DNA. ATR inhibition in UNG-deficient cells blocks the repair of uracil-induced gaps, increasing replication fork collapse and cell death. Notably, a subset of cancer cells upregulates UNG2 to suppress genomic uracil and limit RS, and these cancer cells are hypersensitive to co-treatment with ATR inhibitors and drugs increasing genomic uracil. These results reveal unprocessed genomic uracil as an unexpected source of RS and a targetable vulnerability of cancer cells.
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Affiliation(s)
- Sneha Saxena
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Christopher S Nabel
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Turner W Seay
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Parasvi S Patel
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Ajinkya S Kawale
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Caroline R Crosby
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helene Tigro
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Eugene Oh
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Aaron N Hata
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zucai Suo
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Lee Zou
- Mass General Cancer Center, Harvard Medical School, Charlestown, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
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6
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Boldinova EO, Baranovskiy AG, Filina YV, Miftakhova RR, Shamsutdinova YF, Tahirov TH, Makarova AV. PrimPol Variant V102A with Altered Primase and Polymerase Activities. J Mol Biol 2024; 436:168542. [PMID: 38492718 DOI: 10.1016/j.jmb.2024.168542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
PrimPol is a human DNA primase-polymerase which restarts DNA synthesis beyond DNA lesions and non-B DNA structures blocking replication. Disfunction of PrimPol in cells leads to slowing of DNA replication rates in mitochondria and nucleus, accumulation of chromosome aberrations, cell cycle delay, and elevated sensitivity to DNA-damaging agents. A defective PrimPol has been suggested to be associated with the development of ophthalmic diseases, elevated mitochondrial toxicity of antiviral drugs and increased cell resistance to chemotherapy. Here, we describe a rare missense PrimPol variant V102A with altered biochemical properties identified in patients suffering from ovarian and cervical cancer. The Val102 to Ala substitution dramatically reduced both the primase and DNA polymerase activities of PrimPol as well as specifically decreased its ability to incorporate ribonucleotides. Structural analysis indicates that the V102A substitution can destabilize the hydrophobic pocket adjacent to the active site, affecting dNTP binding and catalysis.
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Affiliation(s)
- Elizaveta O Boldinova
- National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Vavilova 34 / 5, 119334 Moscow, Russia
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yulia V Filina
- "Translational Oncology" Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Regina R Miftakhova
- "Translational Oncology" Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Yana F Shamsutdinova
- Chemotherapy Department №1, Republican Clinical Oncology Dispensary of the Ministry of Health of the Republic of Tatarstan Named After Prof. M.Z. Sigal, Sibirskiy trakt 29, 420029 Kazan, Russia
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Alena V Makarova
- National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Vavilova 34 / 5, 119334 Moscow, Russia.
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7
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Castaño BA, Schorer S, Guo Y, Calzetta NL, Gottifredi V, Wiesmüller L, Biber S. The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage. Nucleic Acids Res 2024; 52:3740-3760. [PMID: 38321962 PMCID: PMC11039994 DOI: 10.1093/nar/gkae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 02/08/2024] Open
Abstract
It is well-established that, through canonical functions in transcription and DNA repair, the tumor suppressor p53 plays a central role in safeguarding cells from the consequences of DNA damage. Recent data retrieved in tumor and stem cells demonstrated that p53 also carries out non-canonical functions when interacting with the translesion synthesis (TLS) polymerase iota (POLι) at DNA replication forks. This protein complex triggers a DNA damage tolerance (DDT) mechanism controlling the DNA replication rate. Given that the levels of p53 trigger non-binary rheostat-like functions in response to stress or during differentiation, we explore the relevance of the p53 levels for its DDT functions at the fork. We show that subtle changes in p53 levels modulate the contribution of some DDT factors including POLι, POLη, POLζ, REV1, PCNA, PRIMPOL, HLTF and ZRANB3 to the DNA replication rate. Our results suggest that the levels of p53 are central to coordinate the balance between DDT pathways including (i) fork-deceleration by the ZRANB3-mediated fork reversal factor, (ii) POLι-p53-mediated fork-slowing, (iii) POLι- and POLη-mediated TLS and (iv) PRIMPOL-mediated fork-acceleration. Collectively, our study reveals the relevance of p53 protein levels for the DDT pathway choice in replicating cells.
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Affiliation(s)
- Bryan A Castaño
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Sabrina Schorer
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Yitian Guo
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | | | | | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
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8
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Sang PB, Jaiswal RK, Lyu X, Chai W. Human CST complex restricts excessive PrimPol repriming upon UV induced replication stress by suppressing p21. Nucleic Acids Res 2024; 52:3778-3793. [PMID: 38348929 DOI: 10.1093/nar/gkae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 04/25/2024] Open
Abstract
DNA replication stress, caused by various endogenous and exogenous agents, halt or stall DNA replication progression. Cells have developed diverse mechanisms to tolerate and overcome replication stress, enabling them to continue replication. One effective strategy to overcome stalled replication involves skipping the DNA lesion using a specialized polymerase known as PrimPol, which reinitiates DNA synthesis downstream of the damage. However, the mechanism regulating PrimPol repriming is largely unclear. In this study, we observe that knockdown of STN1 or CTC1, components of the CTC1/STN1/TEN1 complex, leads to enhanced replication progression following UV exposure. We find that such increased replication is dependent on PrimPol, and PrimPol recruitment to stalled forks increases upon CST depletion. Moreover, we find that p21 is upregulated in STN1-depleted cells in a p53-independent manner, and p21 depletion restores normal replication rates caused by STN1 deficiency. We identify that p21 interacts with PrimPol, and STN1 depletion stimulates p21-PrimPol interaction and facilitates PrimPol recruitment to stalled forks. Our findings reveal a previously undescribed interplay between CST, PrimPol and p21 in promoting repriming in response to stalled replication, and shed light on the regulation of PrimPol repriming at stalled forks.
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Affiliation(s)
- Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Rishi K Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Xinxing Lyu
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
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9
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Pale LM, Khatib JB, Nicolae CM, Moldovan GL. CRISPR knockout genome-wide screens identify the HELQ-RAD52 axis in regulating the repair of cisplatin-induced single stranded DNA gaps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589988. [PMID: 38659927 PMCID: PMC11042333 DOI: 10.1101/2024.04.17.589988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Treatment with genotoxic agents, such as platinum compounds, is still the mainstay therapeutical approach for the majority of cancers. Our understanding of the mechanisms of action of these drugs is however imperfect, and continuously evolving. Recent advances in the field highlighted single stranded DNA (ssDNA) gap accumulation as a potential determinant underlying cisplatin chemosensitivity, at least in some genetic backgrounds, such as BRCA mutations. Cisplatin-induced ssDNA gaps form upon the arrest of replication forks at sites of cisplatin adducts, and restart of DNA synthesis downstream of the lesion through repriming catalyzed by the PRIMPOL enzyme. Here, we show that PRIMPOL overexpression in otherwise wildtype cells results in accumulation of cisplatin-induced ssDNA gaps without sensitizing cells to cisplatin, suggesting that ssDNA gap accumulation does not confer cisplatin sensitivity in BRCA-proficient cells. To understand how ssDNA gaps may cause cellular sensitivity, we employed CRISPR-mediated genome-wide genetic screening to identify factors which enable the cytotoxicity of cisplatin-induced ssDNA gaps. We found that the helicase HELQ specifically suppresses cisplatin sensitivity in PRIMPOL-overexpressing cells, and this is associated with reduced ssDNA accumulation. We moreover identify RAD52 as a mediator of this pathway, and show that RAD52 promotes ssDNA gap accumulation through a BRCA-mediated mechanism. Our work identified the HELQ-RAD52-BRCA axis as a regulator of ssDNA gap processing, shedding light on the mechanisms of cisplatin sensitization in cancer therapy.
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Affiliation(s)
- Lindsey M. Pale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Jude B. Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M. Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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10
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O'Leary DR, Hansen AR, Fingerman DF, Tran T, Harris BR, Hayer KE, Fan J, Chen E, Tennakoon M, DeWeerd RA, Meroni A, Szeto JH, Weitzman MD, Shalem O, Bednarski J, Vindigni A, Zhao X, Green AM. The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.28.568952. [PMID: 38077016 PMCID: PMC10705431 DOI: 10.1101/2023.11.28.568952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
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11
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Nusawardhana A, Pale LM, Nicolae CM, Moldovan GL. USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress. Nucleic Acids Res 2024; 52:2340-2354. [PMID: 38180818 PMCID: PMC10954467 DOI: 10.1093/nar/gkad1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
DNA replication stress-induced fork arrest represents a significant threat to genomic integrity. One major mechanism of replication restart involves repriming downstream of the arrested fork by PRIMPOL, leaving behind a single-stranded DNA (ssDNA) gap. Accumulation of nascent strand ssDNA gaps has emerged as a possible determinant of the cellular hypersensitivity to genotoxic agents in certain genetic backgrounds such as BRCA deficiency, but how gaps are converted into cytotoxic structures is still unclear. Here, we investigate the processing of PRIMPOL-dependent ssDNA gaps upon replication stress induced by hydroxyurea and cisplatin. We show that gaps generated in PRIMPOL-overexpressing cells are expanded in the 3'-5' direction by the MRE11 exonuclease, and in the 5'-3' direction by the EXO1 exonuclease. This bidirectional exonucleolytic gap expansion ultimately promotes their conversion into DSBs. We moreover identify the de-ubiquitinating enzyme USP1 as a critical regulator of PRIMPOL-generated ssDNA gaps. USP1 promotes gap accumulation during S-phase, and their expansion by the MRE11 and EXO1 nucleases. This activity of USP1 is linked to its role in de-ubiquitinating PCNA, suggesting that PCNA ubiquitination prevents gap accumulation during replication. Finally, we show that USP1 depletion suppresses DSB formation in PRIMPOL-overexpressing cells, highlighting an unexpected role for USP1 in promoting genomic instability under these conditions.
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Affiliation(s)
- Alexandra Nusawardhana
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Lindsey M Pale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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12
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nat Commun 2024; 15:1943. [PMID: 38431617 PMCID: PMC10908796 DOI: 10.1038/s41467-024-45947-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas J Blobel
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics, The Rockefeller University, New York, NY, 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA.
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13
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Muñoz S, Blanco-Romero E, González-Acosta D, Rodriguez-Acebes S, Megías D, Lopes M, Méndez J. RAD51 restricts DNA over-replication from re-activated origins. EMBO J 2024; 43:1043-1064. [PMID: 38360996 PMCID: PMC10942984 DOI: 10.1038/s44318-024-00038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
Eukaryotic cells rely on several mechanisms to ensure that the genome is duplicated precisely once in each cell division cycle, preventing DNA over-replication and genomic instability. Most of these mechanisms limit the activity of origin licensing proteins to prevent the reactivation of origins that have already been used. Here, we have investigated whether additional controls restrict the extension of re-replicated DNA in the event of origin re-activation. In a genetic screening in cells forced to re-activate origins, we found that re-replication is limited by RAD51 and enhanced by FBH1, a RAD51 antagonist. In the presence of chromatin-bound RAD51, forks stemming from re-fired origins are slowed down, leading to frequent events of fork reversal. Eventual re-initiation of DNA synthesis mediated by PRIMPOL creates ssDNA gaps that facilitate the partial elimination of re-duplicated DNA by MRE11 exonuclease. In the absence of RAD51, these controls are abrogated and re-replication forks progress much longer than in normal conditions. Our study uncovers a safeguard mechanism to protect genome stability in the event of origin reactivation.
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Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Elena Blanco-Romero
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Daniel González-Acosta
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Advanced Optical Microscopy Unit, Central Core Facilities, Instituto de Salud Carlos III, Madrid, Spain
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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14
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Lim PX, Zaman M, Feng W, Jasin M. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair. Mol Cell 2024; 84:447-462.e10. [PMID: 38244544 PMCID: PMC11188060 DOI: 10.1016/j.molcel.2023.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/10/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
Tumor suppressor BRCA2 functions in homology-directed repair (HDR), the protection of stalled replication forks, and the suppression of replicative gaps, but their relative contributions to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for fork protection and gap suppression but not HDR. In mice, the loss of fork protection/gap suppression does not compromise genome stability or shorten tumor latency. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection/gap suppression defects are also observed in Brca2 heterozygous cells, likely due to reduced RAD51 stabilization at stalled forks/gaps. Gaps arise from PRIMPOL activity, which is associated with 5-hydroxymethyl-2'-deoxyuridine sensitivity due to the formation of SMUG1-generated abasic sites and is exacerbated by poly(ADP-ribose) polymerase (PARP) inhibition. However, HDR proficiency has the major role in mitigating sensitivity to chemotherapeutics, including PARP inhibitors.
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Affiliation(s)
- Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mahdia Zaman
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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15
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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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16
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Kawale AS, Ran X, Patel PS, Saxena S, Lawrence MS, Zou L. APOBEC3A induces DNA gaps through PRIMPOL and confers gap-associated therapeutic vulnerability. SCIENCE ADVANCES 2024; 10:eadk2771. [PMID: 38241374 PMCID: PMC10798555 DOI: 10.1126/sciadv.adk2771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Mutation signatures associated with apolipoprotein B mRNA editing catalytic polypeptide-like 3A/B (APOBEC3A/B) cytidine deaminases are prevalent across cancers, implying their roles as mutagenic drivers during tumorigenesis and tumor evolution. APOBEC3A (A3A) expression induces DNA replication stress and increases the cellular dependency on the ataxia telangiectasia and Rad3-related (ATR) kinase for survival. Nonetheless, how A3A induces DNA replication stress remains unclear. We show that A3A induces replication stress without slowing replication forks. We find that A3A induces single-stranded DNA (ssDNA) gaps through PrimPol-mediated repriming. A3A-induced ssDNA gaps are repaired by multiple pathways involving ATR, RAD51, and translesion synthesis. Both ATR inhibition and trapping of poly(ADP-ribose) polymerase (PARP) on DNA by PARP inhibitor impair the repair of A3A-induced gaps, preferentially killing A3A-expressing cells. When used in combination, PARP and ATR inhibitors selectively kill A3A-expressing cells synergistically in a manner dependent on PrimPol-generated gaps. Thus, A3A-induced replication stress arises from PrimPol-generated ssDNA gaps, which confer a therapeutic vulnerability to gap-targeted DNA repair inhibitors.
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Affiliation(s)
- Ajinkya S. Kawale
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Xiaojuan Ran
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Parasvi S. Patel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Michael S. Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
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17
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Fütterer A, Rodriguez-Acebes S, Méndez J, Gutiérrez J, Martínez-A C. PARP1, DIDO3, and DHX9 Proteins Mutually Interact in Mouse Fibroblasts, with Effects on DNA Replication Dynamics, Senescence, and Oncogenic Transformation. Cells 2024; 13:159. [PMID: 38247850 PMCID: PMC10814579 DOI: 10.3390/cells13020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
The regulated formation and resolution of R-loops is a natural process in physiological gene expression. Defects in R-loop metabolism can lead to DNA replication stress, which is associated with a variety of diseases and, ultimately, with cancer. The proteins PARP1, DIDO3, and DHX9 are important players in R-loop regulation. We previously described the interaction between DIDO3 and DHX9. Here, we show that, in mouse embryonic fibroblasts, the three proteins are physically linked and dependent on PARP1 activity. The C-terminal truncation of DIDO3 leads to the impairment of this interaction; concomitantly, the cells show increased replication stress and senescence. DIDO3 truncation also renders the cells partially resistant to in vitro oncogenic transformation, an effect that can be reversed by immortalization. We propose that PARP1, DIDO3, and DHX9 proteins form a ternary complex that regulates R-loop metabolism, preventing DNA replication stress and subsequent senescence.
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Affiliation(s)
- Agnes Fütterer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain;
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (S.R.-A.); (J.M.)
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (S.R.-A.); (J.M.)
| | - Julio Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain;
| | - Carlos Martínez-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain;
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18
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Carrasco B, Torres R, Moreno-del Álamo M, Ramos C, Ayora S, Alonso JC. Processing of stalled replication forks in Bacillus subtilis. FEMS Microbiol Rev 2024; 48:fuad065. [PMID: 38052445 PMCID: PMC10804225 DOI: 10.1093/femsre/fuad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023] Open
Abstract
Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent model system for studying the pathways required to cope with replication stress to preserve genomic stability. This review focuses on the genetics, single molecule choreography, and biochemical properties of the proteins that act to circumvent the replicative arrest allowing the resumption of DNA synthesis. The RecA recombinase, its mediators (RecO, RecR, and RadA/Sms) and modulators (RecF, RecX, RarA, RecU, RecD2, and PcrA), repair licensing (DisA), fork remodelers (RuvAB, RecG, RecD2, RadA/Sms, and PriA), Holliday junction resolvase (RecU), nucleases (RnhC and DinG), and translesion synthesis DNA polymerases (PolY1 and PolY2) are key functions required to overcome a replication stress, provided that the fork does not collapse.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - María Moreno-del Álamo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
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19
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Mellor C, Nassar J, Šviković S, Sale J. PRIMPOL ensures robust handoff between on-the-fly and post-replicative DNA lesion bypass. Nucleic Acids Res 2024; 52:243-258. [PMID: 37971291 PMCID: PMC10783524 DOI: 10.1093/nar/gkad1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
The primase/polymerase PRIMPOL restarts DNA synthesis when replication is arrested by template impediments. However, we do not have a comprehensive view of how PRIMPOL-dependent repriming integrates with the main pathways of damage tolerance, REV1-dependent 'on-the-fly' lesion bypass at the fork and PCNA ubiquitination-dependent post-replicative gap filling. Guided by genome-wide CRISPR/Cas9 screens to survey the genetic interactions of PRIMPOL in a non-transformed and p53-proficient human cell line, we find that PRIMPOL is needed for cell survival following loss of the Y-family polymerases REV1 and POLη in a lesion-dependent manner, while it plays a broader role in promoting survival of cells lacking PCNA K164-dependent post-replicative gap filling. Thus, while REV1- and PCNA K164R-bypass provide two layers of protection to ensure effective damage tolerance, PRIMPOL is required to maximise the effectiveness of the interaction between them. We propose this is through the restriction of post-replicative gap length provided by PRIMPOL-dependent repriming.
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Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joelle Nassar
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Saša Šviković
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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20
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Spegg V, Altmeyer M. Genome maintenance meets mechanobiology. Chromosoma 2024; 133:15-36. [PMID: 37581649 PMCID: PMC10904543 DOI: 10.1007/s00412-023-00807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023]
Abstract
Genome stability is key for healthy cells in healthy organisms, and deregulated maintenance of genome integrity is a hallmark of aging and of age-associated diseases including cancer and neurodegeneration. To maintain a stable genome, genome surveillance and repair pathways are closely intertwined with cell cycle regulation and with DNA transactions that occur during transcription and DNA replication. Coordination of these processes across different time and length scales involves dynamic changes of chromatin topology, clustering of fragile genomic regions and repair factors into nuclear repair centers, mobilization of the nuclear cytoskeleton, and activation of cell cycle checkpoints. Here, we provide a general overview of cell cycle regulation and of the processes involved in genome duplication in human cells, followed by an introduction to replication stress and to the cellular responses elicited by perturbed DNA synthesis. We discuss fragile genomic regions that experience high levels of replication stress, with a particular focus on telomere fragility caused by replication stress at the ends of linear chromosomes. Using alternative lengthening of telomeres (ALT) in cancer cells and ALT-associated PML bodies (APBs) as examples of replication stress-associated clustered DNA damage, we discuss compartmentalization of DNA repair reactions and the role of protein properties implicated in phase separation. Finally, we highlight emerging connections between DNA repair and mechanobiology and discuss how biomolecular condensates, components of the nuclear cytoskeleton, and interfaces between membrane-bound organelles and membraneless macromolecular condensates may cooperate to coordinate genome maintenance in space and time.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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21
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González-Acosta D, Lopes M. DNA replication and replication stress response in the context of nuclear architecture. Chromosoma 2024; 133:57-75. [PMID: 38055079 PMCID: PMC10904558 DOI: 10.1007/s00412-023-00813-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
The DNA replication process needs to be coordinated with other DNA metabolism transactions and must eventually extend to the full genome, regardless of chromatin status, gene expression, secondary structures and DNA lesions. Completeness and accuracy of DNA replication are crucial to maintain genome integrity, limiting transformation in normal cells and offering targeting opportunities for proliferating cancer cells. DNA replication is thus tightly coordinated with chromatin dynamics and 3D genome architecture, and we are only beginning to understand the underlying molecular mechanisms. While much has recently been discovered on how DNA replication initiation is organised and modulated in different genomic regions and nuclear territories-the so-called "DNA replication program"-we know much less on how the elongation of ongoing replication forks and particularly the response to replication obstacles is affected by the local nuclear organisation. Also, it is still elusive how specific components of nuclear architecture participate in the replication stress response. Here, we review known mechanisms and factors orchestrating replication initiation, and replication fork progression upon stress, focusing on recent evidence linking genome organisation and nuclear architecture with the cellular responses to replication interference, and highlighting open questions and future challenges to explore this exciting new avenue of research.
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Affiliation(s)
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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22
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Khatib JB, Nicolae CM, Moldovan GL. Role of Translesion DNA Synthesis in the Metabolism of Replication-associated Nascent Strand Gaps. J Mol Biol 2024; 436:168275. [PMID: 37714300 PMCID: PMC10842951 DOI: 10.1016/j.jmb.2023.168275] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Translesion DNA synthesis (TLS) is a DNA damage tolerance pathway utilized by cells to overcome lesions encountered throughout DNA replication. During replication stress, cancer cells show increased dependency on TLS proteins for cellular survival and chemoresistance. TLS proteins have been described to be involved in various DNA repair pathways. One of the major emerging roles of TLS is single-stranded DNA (ssDNA) gap-filling, primarily after the repriming activity of PrimPol upon encountering a lesion. Conversely, suppression of ssDNA gap accumulation by TLS is considered to represent a mechanism for cancer cells to evade the toxicity of chemotherapeutic agents, specifically in BRCA-deficient cells. Thus, TLS inhibition is emerging as a potential treatment regimen for DNA repair-deficient tumors.
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Affiliation(s)
- Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA. https://twitter.com/JudeBKhatib
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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23
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Velázquez-Ruiz C, Blanco L, Martínez-Jiménez MI. 3'dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol. Int J Mol Sci 2023; 25:51. [PMID: 38203225 PMCID: PMC10778844 DOI: 10.3390/ijms25010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
PrimPol is a DNA primase/polymerase from the Archaeo-Eukaryotic Primase (AEP) superfamily that enables the progression of stalled replication forks by synthesizing DNA primers ahead of blocking lesions or abnormal structures in the ssDNA template. PrimPol's active site is formed by three AEP-conserved motifs: A, B and C. Motifs A and C of human PrimPol (HsPrimPol) harbor the catalytic residues (Asp114, Glu116, Asp280) acting as metal ligands, whereas motif B includes highly conserved residues (Lys165, Ser167 and His169), which are postulated to stabilize 3' incoming deoxynucleotides (dNTPs). Additionally, other putative nucleotide ligands are situated close to motif C: Lys297, almost invariant in the whole AEP superfamily, and Lys300, specifically conserved in eukaryotic PrimPols. Here, we demonstrate that His169 is absolutely essential for 3'dNTP binding and, hence, for both primase and polymerase activities of HsPrimPol, whereas Ser167 and Lys297 are crucial for the dimer synthesis initiation step during priming, but dispensable for subsequent dNTP incorporation on growing primers. Conversely, the elimination of Lys165 does not affect the overall primase function; however, it is required for damage avoidance via primer-template realignments. Finally, Lys300 is identified as an extra anchor residue to stabilize the 3' incoming dNTP. Collectively, these results demonstrate that individual ligands modulate the stabilization of 3' incoming dNTPs to optimize DNA primer synthesis efficiency during initiation and primer maturation.
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Affiliation(s)
| | - Luis Blanco
- Centro de Biología Molecular Severo Ochoa, (CSIC-UAM), c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain;
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24
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Bainbridge LJ, Zabrady K, Doherty AJ. Coordination of Primer Initiation Within the Catalytic Domain of Human PrimPol. J Mol Biol 2023; 435:168338. [PMID: 37923120 DOI: 10.1016/j.jmb.2023.168338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
To facilitate the eukaryotic repriming pathway of DNA damage tolerance, PrimPol synthesises de novo oligonucleotide primers downstream of polymerase-stalling obstacles. These primers enable replicative polymerases to resume synthesis and ensure the timely completion of DNA replication. Initiating synthesis de novo requires the coordination of single-stranded DNA, initiating nucleotides, and metal ions within PrimPol's active site to catalyze the formation of the first phosphodiester bond. Here we examine the interactions between human PrimPol's catalytic domain, nucleotides, and DNA template during each of the various catalytic steps to determine the 'choreography' of primer synthesis, where substrates bind in an ordered manner. Our findings show that the ability of PrimPol to conduct de novo primer synthesis is underpinned by a network of stabilising interactions between the enzyme, template, and nucleotides, as we previously observed for related primase CRISPR-Associated Prim-Pol (CAPP). Together, these findings establish a detailed model for the initiation of DNA synthesis by human PrimPol, which appears highly conserved.
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Affiliation(s)
- Lewis J Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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25
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Palumbieri MD, Merigliano C, González-Acosta D, Kuster D, Krietsch J, Stoy H, von Känel T, Ulferts S, Welter B, Frey J, Doerdelmann C, Sanchi A, Grosse R, Chiolo I, Lopes M. Nuclear actin polymerization rapidly mediates replication fork remodeling upon stress by limiting PrimPol activity. Nat Commun 2023; 14:7819. [PMID: 38016948 PMCID: PMC10684888 DOI: 10.1038/s41467-023-43183-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase and observed their rapid extension in number and length upon genotoxic treatments, frequently taking contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork remodeling is linked to deregulated chromatin loading of PrimPol, which promotes unrestrained and discontinuous DNA synthesis and limits the recruitment of RAD51 and SMARCAL1 to nascent DNA. Moreover, defective nuclear actin polymerization upon mild replication interference induces chromosomal instability in a PRIMPOL-dependent manner. Hence, by limiting PrimPol activity, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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Affiliation(s)
| | - Chiara Merigliano
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | | | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Department of Cellular and Molecular Medicine, Copenhagen University, Copenhagen, Denmark
| | - Thomas von Känel
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Svenja Ulferts
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Welter
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Joël Frey
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Cyril Doerdelmann
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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26
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Duardo RC, Guerra F, Pepe S, Capranico G. Non-B DNA structures as a booster of genome instability. Biochimie 2023; 214:176-192. [PMID: 37429410 DOI: 10.1016/j.biochi.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Non-canonical secondary structures (NCSs) are alternative nucleic acid structures that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on the sequence. The majority of these structures form in the context of physiological processes, such as transcription-associated R-loops, G4s, as well as hairpins and slipped-strand DNA, whose formation can be dependent on DNA replication. It is therefore not surprising that NCSs play important roles in the regulation of key biological processes. In the last years, increasing published data have supported their biological role thanks to genome-wide studies and the development of bioinformatic prediction tools. Data have also highlighted the pathological role of these secondary structures. Indeed, the alteration or stabilization of NCSs can cause the impairment of transcription and DNA replication, modification in chromatin structure and DNA damage. These events lead to a wide range of recombination events, deletions, mutations and chromosomal aberrations, well-known hallmarks of genome instability which are strongly associated with human diseases. In this review, we summarize molecular processes through which NCSs trigger genome instability, with a focus on G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform and multi-stranded structures known as triplexes.
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Affiliation(s)
- Renée C Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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27
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Gromova AS, Boldinova EO, Kim DV, Chuprov-Netochin RN, Leonov SV, Pustovalova MV, Zharkov DO, Makarova AV. Response of PRIMPOL-Knockout Human Lung Adenocarcinoma A549 Cells to Genotoxic Stress. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1933-1943. [PMID: 38105210 DOI: 10.1134/s0006297923110214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/08/2023] [Accepted: 09/15/2023] [Indexed: 12/19/2023]
Abstract
Human DNA primase/polymerase PrimPol synthesizes DNA primers de novo after replication fork stalling at the sites of DNA damage, thus contributing to the DNA damage tolerance. The role of PrimPol in response to the different types of DNA damage is poorly understood. We knocked out the PRIMPOL gene in the lung carcinoma A549 cell line and characterized the response of the obtained cells to the DNA damage caused by hydrogen peroxide, methyl methanesulfonate (MMS), cisplatin, bleomycin, and ionizing radiation. The PRIMPOL knockout reduced the number of proliferating cells and cells in the G2 phase after treatment with MMS and caused a more pronounced delay of the S phase in the cisplatin-treated cells. Ionizing radiation at a dose of 10 Gy significantly increased the content of apoptotic cells among the PRIMPOL-deficient cells, while the proportion of cells undergoing necroptosis increased in both parental and knockout cells at any radiation dose. The viability of PRIMPOL-deficient cells upon the hydrogen peroxide-induced oxidative stress increased compared to the control cells, as determined by the methyl tetrazolium (MTT) assay. The obtained data indicate the involvement of PRIMPOL in the modulation of adaptive cell response to various types of genotoxic stress.
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Affiliation(s)
- Anastasia S Gromova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Elizaveta O Boldinova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Daria V Kim
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Roman N Chuprov-Netochin
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Sergey V Leonov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
- Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Margarita V Pustovalova
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, Kurchatov Institute National Research Center, Moscow, 123182, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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28
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Zabrady K, Li AWH, Doherty AJ. Mechanism of primer synthesis by Primase-Polymerases. Curr Opin Struct Biol 2023; 82:102652. [PMID: 37459807 DOI: 10.1016/j.sbi.2023.102652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 09/16/2023]
Abstract
Members of the primase-polymerase (Prim-Pol) superfamily are found in all domains of life and play diverse roles in genome stability, including primer synthesis during DNA replication, lesion repair and damage tolerance. This review focuses primarily on Prim-Pol members capable of de novo primer synthesis that have experimentally derived structural models available. We discuss the mechanism of DNA primer synthesis initiation by Prim-Pol catalytic domains, based on recent structural and functional studies. We also describe a general model for primer initiation that also includes the ancillary domains/subunits, which stimulate the initiation of primer synthesis.
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Affiliation(s)
- Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK. https://twitter.com/@KZabrady
| | - Arthur W H Li
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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29
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Gyüre Z, Póti Á, Németh E, Szikriszt B, Lózsa R, Krawczyk M, Richardson AL, Szüts D. Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase ζ and PRIMPOL. Cell Rep 2023; 42:112887. [PMID: 37498746 DOI: 10.1016/j.celrep.2023.112887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL-/- cells. Small deletions in short repeats appear in REV1-/-PCNAK164R/K164R double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1-/- and REV3L-/- mutants, and chromosomal instability is detectable in REV1-/-PRIMPOL-/- cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.
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Affiliation(s)
- Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, 1085 Budapest, Hungary; Turbine Simulated Cell Technologies, 1027 Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Michał Krawczyk
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; National Laboratory for Drug Research and Development, 1117 Budapest, Hungary.
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30
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Igarashi T, Mazevet M, Yasuhara T, Yano K, Mochizuki A, Nishino M, Yoshida T, Yoshida Y, Takamatsu N, Yoshimi A, Shiraishi K, Horinouchi H, Kohno T, Hamamoto R, Adachi J, Zou L, Shiotani B. An ATR-PrimPol pathway confers tolerance to oncogenic KRAS-induced and heterochromatin-associated replication stress. Nat Commun 2023; 14:4991. [PMID: 37591859 PMCID: PMC10435487 DOI: 10.1038/s41467-023-40578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
Activation of the KRAS oncogene is a source of replication stress, but how this stress is generated and how it is tolerated by cancer cells remain poorly understood. Here we show that induction of KRASG12V expression in untransformed cells triggers H3K27me3 and HP1-associated chromatin compaction in an RNA transcription dependent manner, resulting in replication fork slowing and cell death. Furthermore, elevated ATR expression is necessary and sufficient for tolerance of KRASG12V-induced replication stress to expand replication stress-tolerant cells (RSTCs). PrimPol is phosphorylated at Ser255, a potential Chk1 substrate site, under KRASG12V-induced replication stress and promotes repriming to maintain fork progression and cell survival in an ATR/Chk1-dependent manner. However, ssDNA gaps are generated at heterochromatin by PrimPol-dependent repriming, leading to genomic instability. These results reveal a role of ATR-PrimPol in enabling precancerous cells to survive KRAS-induced replication stress and expand clonally with accumulation of genomic instability.
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Affiliation(s)
- Taichi Igarashi
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Biosciences, School of Science, Kitasato University, Minami-ku, Sagamihara-city, Kanagawa, 252-0373, Japan
| | - Marianne Mazevet
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takaaki Yasuhara
- Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kimiyoshi Yano
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akifumi Mochizuki
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Makoto Nishino
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, 104-0045, Japan
| | - Nobuhiko Takamatsu
- Department of Biosciences, School of Science, Kitasato University, Minami-ku, Sagamihara-city, Kanagawa, 252-0373, Japan
| | - Akihide Yoshimi
- Department of Biosciences, School of Science, Kitasato University, Minami-ku, Sagamihara-city, Kanagawa, 252-0373, Japan
- Division of Cancer RNA Research, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hidehito Horinouchi
- Department of Thoracic Oncology, National Cancer Center Hospital, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery, Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki-city, Osaka, 567-0085, Japan
| | - 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, 02115, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27708, USA
| | - Bunsyo Shiotani
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo, 104-0045, Japan.
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31
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Boldinova EO, Baranovskiy AG, Gagarinskaya DI, Manukyan A, Makarova A, Tahirov T. The role of catalytic and regulatory domains of human PrimPol in DNA binding and synthesis. Nucleic Acids Res 2023; 51:7541-7551. [PMID: 37326028 PMCID: PMC10415149 DOI: 10.1093/nar/gkad507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/28/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Human PrimPol possesses DNA primase and DNA polymerase activities and restarts stalled replication forks protecting cells against DNA damage in nuclei and mitochondria. The zinc-binding motif (ZnFn) of the C-terminal domain (CTD) of PrimPol is required for DNA primase activity but the mechanism is not clear. In this work, we biochemically demonstrate that PrimPol initiates de novo DNA synthesis in cis-orientation, when the N-terminal catalytic domain (NTD) and the CTD of the same molecule cooperate for substrates binding and catalysis. The modeling studies revealed that PrimPol uses a similar mode of initiating NTP coordination as the human primase. The ZnFn motif residue Arg417 is required for binding the 5'-triphosphate group that stabilizes the PrimPol complex with a DNA template-primer. We found that the NTD alone is able to initiate DNA synthesis, and the CTD stimulates the primase activity of NTD. The regulatory role of the RPA-binding motif in the modulation of PrimPol binding to DNA is also demonstrated.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Diana I Gagarinskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Anna A Manukyan
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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32
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Boldinova EO, Makarova AV. Regulation of Human DNA Primase-Polymerase PrimPol. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1139-1155. [PMID: 37758313 DOI: 10.1134/s0006297923080084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 10/03/2023]
Abstract
Transmission of genetic information depends on successful completion of DNA replication. Genomic DNA is subjected to damage on a daily basis. DNA lesions create obstacles for DNA polymerases and can lead to the replication blockage, formation of DNA breaks, cell cycle arrest, and apoptosis. Cells have evolutionary adapted to DNA damage by developing mechanisms allowing elimination of lesions prior to DNA replication (DNA repair) and helping to bypass lesions during DNA synthesis (DNA damage tolerance). The second group of mechanisms includes the restart of DNA synthesis at the sites of DNA damage by DNA primase-polymerase PrimPol. Human PrimPol was described in 2013. The properties and functions of this enzyme have been extensively studied in recent years, but very little is known about the regulation of PrimPol and association between the enzyme dysfunction and diseases. In this review, we described the mechanisms of human PrimPol regulation in the context of DNA replication, discussed in detail interactions of PrimPol with other proteins, and proposed possible pathways for the regulation of human PrimPol activity. The article also addresses the association of PrimPol dysfunction with human diseases.
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Affiliation(s)
- Elizaveta O Boldinova
- Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alena V Makarova
- Kurchatov Institute National Research Centre, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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33
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Bainbridge L, Zabrady K, Doherty A. Primase-polymerases: how to make a primer from scratch. Biosci Rep 2023; 43:BSR20221986. [PMID: 37358261 PMCID: PMC10345425 DOI: 10.1042/bsr20221986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 06/27/2023] Open
Abstract
To pass on genetic information to the next generation, cells must faithfully replicate their genomes to provide copies for each daughter cell. To synthesise these duplicates, cells employ specialised enzymes called DNA polymerases, which rapidly and accurately replicate nucleic acid polymers. However, most polymerases lack the ability to directly initiate DNA synthesis and required specialised replicases called primases to make short polynucleotide primers, from which they then extend. Replicative primases (eukaryotes and archaea) belong to a functionally diverse enzyme superfamily known as Primase-Polymerases (Prim-Pols), with orthologues present throughout all domains of life. Characterised by a conserved catalytic Prim-Pol domain, these enzymes have evolved various roles in DNA metabolism, including DNA replication, repair, and damage tolerance. Many of these biological roles are fundamentally underpinned by the ability of Prim-Pols to generate primers de novo. This review examines our current understanding of the catalytic mechanisms utilised by Prim-Pols to initiate primer synthesis.
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Affiliation(s)
- Lewis J. Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
| | - Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
| | - Aidan J. Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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35
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Zerbib A, Simon I. Characterization of Unidirectional Replication Forks in the Mouse Genome. Int J Mol Sci 2023; 24:9611. [PMID: 37298562 PMCID: PMC10253849 DOI: 10.3390/ijms24119611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
Origins of replication are genomic regions in which replication initiates in a bidirectional manner. Recently, a new methodology (origin-derived single-stranded DNA sequencing; ori-SSDS) was developed that allows the detection of replication initiation in a strand-specific manner. Reanalysis of the strand-specific data revealed that 18-33% of the peaks are non-symmetrical, suggesting a single direction of replication. Analysis of replication fork direction data revealed that these are origins of replication in which the replication is paused in one of the directions, probably due to the existence of a replication fork barrier. Analysis of the unidirectional origins revealed a preference of G4 quadruplexes for the blocked leading strand. Taken together, our analysis identified hundreds of genomic locations in which the replication initiates only in one direction, and suggests that G4 quadruplexes may serve as replication fork barriers in such places.
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Affiliation(s)
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel;
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36
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Yurchenko AA, Rajabi F, Braz-Petta T, Fassihi H, Lehmann A, Nishigori C, Wang J, Padioleau I, Gunbin K, Panunzi L, Morice-Picard F, Laplante P, Robert C, Kannouche PL, Menck CFM, Sarasin A, Nikolaev SI. Genomic mutation landscape of skin cancers from DNA repair-deficient xeroderma pigmentosum patients. Nat Commun 2023; 14:2561. [PMID: 37142601 PMCID: PMC10160032 DOI: 10.1038/s41467-023-38311-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Xeroderma pigmentosum (XP) is a genetic disorder caused by mutations in genes of the Nucleotide Excision Repair (NER) pathway (groups A-G) or in Translesion Synthesis DNA polymerase η (V). XP is associated with an increased skin cancer risk, reaching, for some groups, several thousand-fold compared to the general population. Here, we analyze 38 skin cancer genomes from five XP groups. We find that the activity of NER determines heterogeneity of the mutation rates across skin cancer genomes and that transcription-coupled NER extends beyond the gene boundaries reducing the intergenic mutation rate. Mutational profile in XP-V tumors and experiments with POLH knockout cell line reveal the role of polymerase η in the error-free bypass of (i) rare TpG and TpA DNA lesions, (ii) 3' nucleotides in pyrimidine dimers, and (iii) TpT photodimers. Our study unravels the genetic basis of skin cancer risk in XP and provides insights into the mechanisms reducing UV-induced mutagenesis in the general population.
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Affiliation(s)
- Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Fatemeh Rajabi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Tirzah Braz-Petta
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, s/n, Natal, 59078-970, Brazil
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, Department of Photodermatology, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London, SE1 7EH, UK
| | - Alan Lehmann
- National Xeroderma Pigmentosum Service, Department of Photodermatology, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London, SE1 7EH, UK
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Jinxin Wang
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Ismael Padioleau
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Konstantin Gunbin
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Leonardo Panunzi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | | | - Pierre Laplante
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
- Department of Medical Oncology, Gustave Roussy and Paris-Saclay University, Villejuif, France
| | - Patricia L Kannouche
- CNRS UMR9019 Genome Integrity and Cancers, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Alain Sarasin
- CNRS UMR9019 Genome Integrity and Cancers, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Sergey I Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France.
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Mansilla SF, Bertolin AP, Venerus Arbilla S, Castaño BA, Jahjah T, Singh JK, Siri SO, Castro MV, de la Vega MB, Quinet A, Wiesmüller L, Gottifredi V. Polymerase iota (Pol ι) prevents PrimPol-mediated nascent DNA synthesis and chromosome instability. SCIENCE ADVANCES 2023; 9:eade7997. [PMID: 37058556 PMCID: PMC10104471 DOI: 10.1126/sciadv.ade7997] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Recent studies have described a DNA damage tolerance pathway choice that involves a competition between PrimPol-mediated repriming and fork reversal. Screening different translesion DNA synthesis (TLS) polymerases by the use of tools for their depletion, we identified a unique role of Pol ι in regulating such a pathway choice. Pol ι deficiency unleashes PrimPol-dependent repriming, which accelerates DNA replication in a pathway that is epistatic with ZRANB3 knockdown. In Pol ι-depleted cells, the excess participation of PrimPol in nascent DNA elongation reduces replication stress signals, but thereby also checkpoint activation in S phase, triggering chromosome instability in M phase. This TLS-independent function of Pol ι requires its PCNA-interacting but not its polymerase domain. Our findings unravel an unanticipated role of Pol ι in protecting the genome stability of cells from detrimental changes in DNA replication dynamics caused by PrimPol.
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Affiliation(s)
| | - Agostina P. Bertolin
- Fundación Instituto Leloir, CONICET, 1405 Buenos Aires, Argentina
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Bryan A. Castaño
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany
| | - Tiya Jahjah
- 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
| | - Jenny K. Singh
- 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
| | | | | | | | - Annabel 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
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany
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Lim PX, Zaman M, Jasin M. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536470. [PMID: 37090587 PMCID: PMC10120702 DOI: 10.1101/2023.04.11.536470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Highlights Gap suppression requires BRCA2 C-terminal RAD51 binding in mouse and human cells Brca2 heterozygosity in mice results in fork protection and gap suppression defects Gap suppression mitigates sensitivity to hmdU, but only when HDR is unperturbedHDR deficiency is the primary driver of chemotherapeutic sensitivity. eTOC blurb Lim et al . report that gap suppression as well as fork protection require BRCA2 stabilization of RAD51 filaments in human and mouse cells but have minimal impact on genome integrity, oncogenesis, and drug resistance. BRCA2 suppression of PRIMPOL-mediated replication gaps confers resistance to the nucleotide hmdU, incorporation of which leads to cytotoxic abasic sites.This effect is diminished when HDR is abrogated. Summary Tumor suppressor BRCA2 functions in homology-directed repair (HDR), protection of stalled replication forks, and suppression of replicative gaps. The relative contributions of these pathways to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for both fork protection and gap suppression, but not HDR. Loss of fork protection and gap suppression do not compromise genome instability or shorten tumor latency in mice or cause replication stress in human mammary cells. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection and gap suppression defects are also observed in Brca2 heterozygous mouse cells, likely due to reduced RAD51 stabilization at stalled forks and gaps. Gaps arise from PRIMPOL activity, which is associated with sensitivity to 5-hydroxymethyl-2’-deoxyuridine due to the formation of abasic sites by SMUG1 glycosylase and is exacerbated by poly(ADP-ribose) polymerase inhibition. However, HDR deficiency ultimately modulates sensitivity to chemotherapeutics, including PARP inhibitors.
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Debaugnies M, Rodríguez-Acebes S, Blondeau J, Parent MA, Zocco M, Song Y, de Maertelaer V, Moers V, Latil M, Dubois C, Coulonval K, Impens F, Van Haver D, Dufour S, Uemura A, Sotiropoulou PA, Méndez J, Blanpain C. RHOJ controls EMT-associated resistance to chemotherapy. Nature 2023; 616:168-175. [PMID: 36949199 PMCID: PMC10076223 DOI: 10.1038/s41586-023-05838-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/14/2023] [Indexed: 03/24/2023]
Abstract
The resistance of cancer cells to therapy is responsible for the death of most patients with cancer1. Epithelial-to-mesenchymal transition (EMT) has been associated with resistance to therapy in different cancer cells2,3. However, the mechanisms by which EMT mediates resistance to therapy remain poorly understood. Here, using a mouse model of skin squamous cell carcinoma undergoing spontaneous EMT during tumorigenesis, we found that EMT tumour cells are highly resistant to a wide range of anti-cancer therapies both in vivo and in vitro. Using gain and loss of function studies in vitro and in vivo, we found that RHOJ-a small GTPase that is preferentially expressed in EMT cancer cells-controls resistance to therapy. Using genome-wide transcriptomic and proteomic profiling, we found that RHOJ regulates EMT-associated resistance to chemotherapy by enhancing the response to replicative stress and activating the DNA-damage response, enabling tumour cells to rapidly repair DNA lesions induced by chemotherapy. RHOJ interacts with proteins that regulate nuclear actin, and inhibition of actin polymerization sensitizes EMT tumour cells to chemotherapy-induced cell death in a RHOJ-dependent manner. Together, our study uncovers the role and the mechanisms through which RHOJ acts as a key regulator of EMT-associated resistance to chemotherapy.
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Affiliation(s)
- Maud Debaugnies
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
- CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Jeremy Blondeau
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Marie-Astrid Parent
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Manuel Zocco
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Yura Song
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Viviane de Maertelaer
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Virginie Moers
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Mathilde Latil
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Christine Dubois
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Katia Coulonval
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sara Dufour
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Akiyoshi Uemura
- Department of Retinal Vascular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | | | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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Andrs M, Stoy H, Boleslavska B, Chappidi N, Kanagaraj R, Nascakova Z, Menon S, Rao S, Oravetzova A, Dobrovolna J, Surendranath K, Lopes M, Janscak P. Excessive reactive oxygen species induce transcription-dependent replication stress. Nat Commun 2023; 14:1791. [PMID: 36997515 PMCID: PMC10063555 DOI: 10.1038/s41467-023-37341-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
Elevated levels of reactive oxygen species (ROS) reduce replication fork velocity by causing dissociation of the TIMELESS-TIPIN complex from the replisome. Here, we show that ROS generated by exposure of human cells to the ribonucleotide reductase inhibitor hydroxyurea (HU) promote replication fork reversal in a manner dependent on active transcription and formation of co-transcriptional RNA:DNA hybrids (R-loops). The frequency of R-loop-dependent fork stalling events is also increased after TIMELESS depletion or a partial inhibition of replicative DNA polymerases by aphidicolin, suggesting that this phenomenon is due to a global replication slowdown. In contrast, replication arrest caused by HU-induced depletion of deoxynucleotides does not induce fork reversal but, if allowed to persist, leads to extensive R-loop-independent DNA breakage during S-phase. Our work reveals a link between oxidative stress and transcription-replication interference that causes genomic alterations recurrently found in human cancer.
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Affiliation(s)
- Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Nagaraja Chappidi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Radhakrishnan Kanagaraj
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, London, UK
- School of Life Sciences, University of Bedfordshire, Luton, UK
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, India
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Shruti Menon
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- School of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Satyajeet Rao
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Anna Oravetzova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jana Dobrovolna
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kalpana Surendranath
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, London, UK
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, India
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Pavel Janscak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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Palumbieri MD, Merigliano C, Acosta DG, von Känel T, Welter B, Stoy H, Krietsch J, Ulferts S, Sanchi A, Grosse R, Chiolo I, Lopes M. Replication fork plasticity upon replication stress requires rapid nuclear actin polymerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534097. [PMID: 36993227 PMCID: PMC10055433 DOI: 10.1101/2023.03.24.534097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase, rapidly extending in number and thickness upon genotoxic treatments, and taking frequent contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork plasticity is linked to reduced recruitment of RAD51 and SMARCAL1 to nascent DNA. Conversely, PRIMPOL gains access to replicating chromatin, promoting unrestrained and discontinuous DNA synthesis, which is associated with increased chromosomal instability and decreased cellular resistance to replication stress. Hence, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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42
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley T, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532415. [PMID: 36993543 PMCID: PMC10054921 DOI: 10.1101/2023.03.13.532415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Genetic information is duplicated via the highly regulated process of DNA replication. The machinery coordinating this process, the replisome, encounters many challenges, including replication fork-stalling lesions that threaten the accurate and timely transmission of genetic information. Cells have multiple mechanisms to repair or bypass lesions that would otherwise compromise DNA replication1,2. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2) function to regulate Replication Termination Factor 2 (RTF2) at the stalled replisome, allowing for replication fork stabilization and restart3. Here we show that RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme responsible for removing RNA in the context of RNA-DNA heteroduplexes4-6. We show that during unperturbed DNA replication, RTF2, like RNase H2, is required to maintain normal replication fork speeds. However, persistent RTF2 and RNase H2 at stalled replication forks compromises the replication stress response, preventing efficient replication restart. Such restart is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for regulation of replication-coupled ribonucleotide incorporation during normal replication and the replication stress response that is achieved through RTF2. We also provide evidence for PRIM1 function in direct replication restart following replication stress in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University
| | | | | | | | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Tom Wiley
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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Gospodinov A, Dzhokova S, Petrova M, Ugrinova I. Chromatin regulators in DNA replication and genome stability maintenance during S-phase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:243-280. [PMID: 37061334 DOI: 10.1016/bs.apcsb.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The duplication of genetic information is central to life. The replication of genetic information is strictly controlled to ensure that each piece of genomic DNA is copied only once during a cell cycle. Factors that slow or stop replication forks cause replication stress. Replication stress is a major source of genome instability in cancer cells. Multiple control mechanisms facilitate the unimpeded fork progression, prevent fork collapse and coordinate fork repair. Chromatin alterations, caused by histone post-translational modifications and chromatin remodeling, have critical roles in normal replication and in avoiding replication stress and its consequences. This text reviews the chromatin regulators that ensure DNA replication and the proper response to replication stress. We also briefly touch on exploiting replication stress in therapeutic strategies. As chromatin regulators are frequently mutated in cancer, manipulating their activity could provide many possibilities for personalized treatment.
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Affiliation(s)
- Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Stefka Dzhokova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Petrova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Abstract
High-fidelity DNA replication is critical for the faithful transmission of genetic information to daughter cells. Following genotoxic stress, specialized DNA damage tolerance pathways are activated to ensure replication fork progression. These pathways include translesion DNA synthesis, template switching and repriming. In this Review, we describe how DNA damage tolerance pathways impact genome stability, their connection with tumorigenesis and their effects on cancer therapy response. We discuss recent findings that single-strand DNA gap accumulation impacts chemoresponse and explore a growing body of evidence that suggests that different DNA damage tolerance factors, including translesion synthesis polymerases, template switching proteins and enzymes affecting single-stranded DNA gaps, represent useful cancer targets. We further outline how the consequences of DNA damage tolerance mechanisms could inform the discovery of new biomarkers to refine cancer therapies.
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Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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Franca MM, Condezo YB, Elzaiat M, Felipe-Medina N, Sánchez-Sáez F, Muñoz S, Sainz-Urruela R, Martín-Hervás MR, García-Valiente R, Sánchez-Martín MA, Astudillo A, Mendez J, Llano E, Veitia RA, Mendonca BB, Pendás AM. A truncating variant of RAD51B associated with primary ovarian insufficiency provides insights into its meiotic and somatic functions. Cell Death Differ 2022; 29:2347-2361. [PMID: 35624308 PMCID: PMC9751091 DOI: 10.1038/s41418-022-01021-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/31/2023] Open
Abstract
Primary ovarian insufficiency (POI) causes female infertility by abolishing normal ovarian function. Although its genetic etiology has been extensively investigated, most POI cases remain unexplained. Using whole-exome sequencing, we identified a homozygous variant in RAD51B -(c.92delT) in two sisters with POI. In vitro studies revealed that this variant leads to translation reinitiation at methionine 64. Here, we show that this is a pathogenic hypomorphic variant in a mouse model. Rad51bc.92delT/c.92delT mice exhibited meiotic DNA repair defects due to RAD51 and HSF2BP/BMRE1 accumulation in the chromosome axes leading to a reduction in the number of crossovers. Interestingly, the interaction of RAD51B-c.92delT with RAD51C and with its newly identified interactors RAD51 and HELQ was abrogated or diminished. Repair of mitomycin-C-induced chromosomal aberrations was impaired in RAD51B/Rad51b-c.92delT human and mouse somatic cells in vitro and in explanted mouse bone marrow cells. Accordingly, Rad51b-c.92delT variant reduced replication fork progression of patient-derived lymphoblastoid cell lines and pluripotent reprogramming efficiency of primary mouse embryonic fibroblasts. Finally, Rad51bc.92delT/c.92delT mice displayed increased incidence of pituitary gland hyperplasia. These results provide new mechanistic insights into the role of RAD51B not only in meiosis but in the maintenance of somatic genome stability.
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Affiliation(s)
- Monica M Franca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42 and SELA, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brasil
- Section of Endocrinology Diabetes and Metabolism, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Yazmine B Condezo
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Maëva Elzaiat
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Natalia Felipe-Medina
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Fernando Sánchez-Sáez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Raquel Sainz-Urruela
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - M Rosario Martín-Hervás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Rodrigo García-Valiente
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Manuel A Sánchez-Martín
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Transgenic Facility, Nucleus platform, Universidad de Salamanca, Salamanca, Spain
| | | | - Juan Mendez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Elena Llano
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, Salamanca, Spain
| | - Reiner A Veitia
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France.
- Université Paris-Saclay and Institut François Jacob, Comissariat à l'Energie Atomique, Gif-sur-Yvette, France.
| | - Berenice B Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42 and SELA, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brasil.
| | - Alberto M Pendás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain.
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Verdú C, Pérez-Arnaiz P, Peropadre A, Berenguer J, Mencía M. Deletion of the primase-polymerases encoding gene, located in a mobile element in Thermus thermophilus HB27, leads to loss of function mutation of addAB genes. Front Microbiol 2022; 13:1005862. [DOI: 10.3389/fmicb.2022.1005862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
DNA primase-polymerases (Ppol) have been shown to play active roles in DNA repair and damage tolerance, both in prokaryotes and eukaryotes. The ancestral thermophilic bacterium Thermus thermophilus strain HB27 encodes a Ppol protein among the genes present in mobile element ICETh2, absent in other T. thermophilus strains. Using different strategies we ablated the function of Ppol in HB27 cells, either by knocking out the gene through insertional mutagenesis, markerless deletion or through abolition of its catalytic activity. Whole genome sequencing of this diverse collection of Ppol mutants showed spontaneous loss of function mutation in the helicase-nuclease AddAB in every ppol mutant isolated. Given that AddAB is a major player in recombinational repair in many prokaryotes, with similar activity to the proteobacterial RecBCD complex, we have performed a detailed characterization of the ppol mutants in combination with addAB mutants. The results show that knockout addAB mutants are more sensitive to DNA damage agents than the wild type, and present a dramatic three orders of magnitude increase in natural transformation efficiencies with both plasmid and lineal DNA, whereas ppol mutants show defects in plasmid stability. Interestingly, DNA-integrity comet assays showed that the genome of all the ppol and/or addAB mutants was severely affected by widespread fragmentation, however, this did not translate in neat loss of viability of the strains. All these data support that Ppol appears to keep in balance the activity of AddAB as a part of the DNA housekeeping maintenance in T. thermophilus HB27, thus, playing a key role in its genome stability.
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Boldinova EO, Ghodke PP, Sudhakar S, Mishra VK, Manukyan AA, Miropolskaya N, Pradeepkumar PI, Makarova AV. Translesion Synthesis across the N2-Ethyl-deoxyguanosine Adduct by Human PrimPol. ACS Chem Biol 2022; 17:3238-3250. [PMID: 36318733 DOI: 10.1021/acschembio.2c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Primase-DNA polymerase (PrimPol) is involved in reinitiating DNA synthesis at stalled replication forks. PrimPol also possesses DNA translesion (TLS) activity and bypasses several endogenous nonbulky DNA lesions in vitro. Little is known about the TLS activity of PrimPol across bulky carcinogenic adducts. We analyzed the DNA polymerase activity of human PrimPol on DNA templates with seven N2-dG lesions of different steric bulkiness. In the presence of Mg2+ ions, bulky N2-isobutyl-dG, N2-benzyl-dG, N2-methyl(1-naphthyl)-dG, N2-methyl(9-anthracenyl)-dG, N2-methyl(1-pyrenyl)-dG, and N2-methyl(1,3-dimethoxyanthraquinone)-dG adducts fully blocked PrimPol activity. At the same time, PrimPol incorporated complementary deoxycytidine monophosphate (dCMP) opposite N2-ethyl-dG with moderate efficiency but did not extend DNA beyond the lesion. We also demonstrated that mutation of the Arg288 residue abrogated dCMP incorporation opposite the lesion in the presence of Mn2+ ions. When Mn2+ replaced Mg2+, PrimPol carried out DNA synthesis on all DNA templates with N2-dG adducts in standing start reactions with low efficiency and accuracy, possibly utilizing a lesion "skipping" mechanism. The TLS activity of PrimPol opposite N2-ethyl-dG but not bulkier adducts was stimulated by accessory proteins, polymerase delta-interacting protein 2 (PolDIP2), and replication protein A (RPA). Molecular dynamics studies demonstrated the absence of stable interactions with deoxycytidine triphosphate (dCTP), large reactions, and C1'-C1' distances for the N2-isobutyl-dG and N2-benzyl-dG PrimPol complexes, suggesting that the size of the adduct is a limiting factor for efficient TLS across minor groove adducts by PrimPol.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | - Pratibha P Ghodke
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vipin Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anna A Manukyan
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | - Nataliya Miropolskaya
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
| | | | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Kurchatov sq. 2, Moscow 123182, Russia
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49
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Li T, Tang L, Kou H, Wang F. PRIMPOL competes with RAD51 to resolve G-quadruplex-induced replication stress via its interaction with RPA. Acta Biochim Biophys Sin (Shanghai) 2022; 55:498-507. [PMID: 36647718 PMCID: PMC10160237 DOI: 10.3724/abbs.2022165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
<p indent="0mm">PRIMPOL (primase-polymerase) is a recently discovered DNA primase-polymerase involved in DNA damage tolerance and replication stress response in eukaryotic cells. However, the detailed mechanism of the PRIMPOL response to replication stress remains elusive. Here, we demonstrate that replication-related factors, including replication protein A (RPA), regulate the accumulation of PRIMPOL in subnuclear foci in response to replication stress induced by replication inhibitors. Moreover, PRIMPOL works at G-quadruplexes (G4s) in human cells to resolve the replication stress induced by G4s. The formation of PRIMPOL foci persists throughout the cell cycle. We further demonstrate that PRIMPOL competes with RAD51 to resolve G4-induced replication stress. In conclusion, our results provide novel insight into the mechanism of PRIMPOL in G4s to resolve replication stress and competition between PRIMPOL (repriming)- and RAD51 (fork reversal)-mediated pathways, which indicates a new strategy to improve the tumor response to DNA-damaging chemotherapy by targeting the PRIMPOL pathway.</p>.
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Affiliation(s)
- Tingfang Li
- Department of Genetics, School of Basic Medical Sciences, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical, General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Lu Tang
- Department of Stomatology, Shengjing Hospital, China Medical University, Shenyang 110004, China
| | - Haomeng Kou
- Department of Genetics, School of Basic Medical Sciences, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical, General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Feng Wang
- Department of Genetics, School of Basic Medical Sciences, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical, General Hospital, Tianjin Medical University, Tianjin 300070, China.,School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China
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50
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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