1
|
Ramirez-Otero MA, Costanzo V. "Bridging the DNA divide": Understanding the interplay between replication- gaps and homologous recombination proteins RAD51 and BRCA1/2. DNA Repair (Amst) 2024; 141:103738. [PMID: 39084178 DOI: 10.1016/j.dnarep.2024.103738] [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: 03/31/2024] [Revised: 06/24/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
A key but often neglected component of genomic instability is the emergence of single-stranded DNA (ssDNA) gaps during DNA replication in the absence of functional homologous recombination (HR) proteins, such as RAD51 and BRCA1/2. Research in prokaryotes has shed light on the dual role of RAD51's bacterial ortholog, RecA, in HR and the protection of replication forks, emphasizing its essential role in preventing the formation of ssDNA gaps, which is vital for cellular viability. This phenomenon was corroborated in eukaryotic cells deficient in HR, where the formation of ssDNA gaps within newly synthesized DNA and their subsequent processing by the MRE11 nuclease were observed. Without functional HR proteins, cells employ alternative ssDNA gap-filling mechanisms to ensure survival, though this compensatory response can compromise genomic stability. A notable example is the involvement of the translesion synthesis (TLS) polymerase POLζ, along with the repair protein POLθ, in the suppression of replicative ssDNA gaps. Persistent ssDNA gaps may result in replication fork collapse, chromosomal anomalies, and cell death, which contribute to cancer progression and resistance to therapy. Elucidating the processes that avert ssDNA gaps and safeguard replication forks is critical for enhancing cancer treatment approaches by exploiting the vulnerabilities of cancer cells in these pathways.
Collapse
Affiliation(s)
| | - Vincenzo Costanzo
- IFOM ETS - The AIRC Institute of Molecular Oncology, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy.
| |
Collapse
|
2
|
Bennett L, Vernon E, Thanendran V, Jones C, Gamble A, Staples C. MRNIP limits ssDNA gaps during replication stress. Nucleic Acids Res 2024; 52:8320-8331. [PMID: 38917325 PMCID: PMC11317133 DOI: 10.1093/nar/gkae546] [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: 12/18/2023] [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.
Collapse
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
| |
Collapse
|
3
|
Silva JPL, Donaires FS, Gutierrez-Rodrigues F, Martins DJ, Carvalho VS, Santana BA, Cunha RLG, Kajigaya S, Menck CFM, Young NS, Kjeldsen E, Calado RT. RecQ helicase expression in patients with telomeropathies. Mol Biol Rep 2024; 51:754. [PMID: 38874681 DOI: 10.1007/s11033-024-09678-0] [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: 02/28/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Telomeropathies are a group of inherited disorders caused by germline pathogenic variants in genes involved in telomere maintenance, resulting in excessive telomere attrition that affects several tissues, including hematopoiesis. RecQ and RTEL1 helicases contribute to telomere maintenance by unwinding telomeric structures such as G-quadruplexes (G4), preventing replication defects. Germline RTEL1 variants also are etiologic in telomeropathies. METHODS AND RESULTS Here we investigated the expression of RecQ (RECQL1, BLM, WRN, RECQL4, and RECQL5) and RTEL1 helicase genes in peripheral blood mononuclear cells (PBMCs) from human telomeropathy patients. The mRNA expression levels of all RecQ helicases, but not RTEL1, were significantly downregulated in patients' primary cells. Reduced RecQ expression was not attributable to cell proliferative exhaustion, as RecQ helicases were not attenuated in T cells exhausted in vitro. An additional fifteen genes involved in DNA damage repair and RecQ functional partners also were downregulated in the telomeropathy cells. CONCLUSION These findings indicate that the expression of RecQ helicases and functional partners involved in DNA repair is downregulated in PBMCs of telomeropathy patients.
Collapse
Affiliation(s)
- João Paulo L Silva
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 - 7 o andar, sala 743 - HCRP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Flávia S Donaires
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 - 7 o andar, sala 743 - HCRP, Ribeirão Preto, SP, 14049-900, Brazil
| | | | - Davi J Martins
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vinicius S Carvalho
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 - 7 o andar, sala 743 - HCRP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Barbara A Santana
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 - 7 o andar, sala 743 - HCRP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Renato L G Cunha
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 - 7 o andar, sala 743 - HCRP, Ribeirão Preto, SP, 14049-900, Brazil
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eigil Kjeldsen
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Rodrigo T Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes, 3900 - 7 o andar, sala 743 - HCRP, Ribeirão Preto, SP, 14049-900, Brazil.
| |
Collapse
|
4
|
Ribeiro D, Latancia M, de Souza I, Ariwoola AB, Mendes D, Rocha CRR, Lengert A, Menck C. Temozolomide resistance mechanisms: unveiling the role of translesion DNA polymerase kappa in glioblastoma spheroids in vitro. Biosci Rep 2024; 44:BSR20230667. [PMID: 38717250 PMCID: PMC11139666 DOI: 10.1042/bsr20230667] [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: 12/11/2023] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Temozolomide (TMZ) is the leading therapeutic agent for combating Glioblastoma Multiforme (GBM). Nonetheless, the persistence of chemotherapy-resistant GBM cells remains an ongoing challenge, attributed to various factors, including the translesion synthesis (TLS) mechanism. TLS enables tumor cells to endure genomic damage by utilizing specialized DNA polymerases to bypass DNA lesions. Specifically, TLS polymerase Kappa (Polκ) has been implicated in facilitating DNA damage tolerance against TMZ-induced damage, contributing to a worse prognosis in GBM patients. To better understand the roles of Polκ in TMZ resistance, we conducted a comprehensive assessment of the cytotoxic, antiproliferative, antimetastatic, and genotoxic effects of TMZ on GBM (U251MG) wild-type (WTE) and TLS Polκ knockout (KO) cells, cultivated as three-dimensional (3D) tumor spheroids in vitro. Initial results revealed that TMZ: (i) induces reductions in GBM spheroid diameter (10-200 µM); (ii) demonstrates significant cytotoxicity (25-200 μM); (iii) exerts antiproliferative effects (≤25 μM) and promotes cell cycle arrest (G2/M phase) in Polκ KO spheroids when compared with WTE counterparts. Furthermore, Polκ KO spheroids exhibit elevated levels of cell death (Caspase 3/7) and display greater genotoxicity (53BP1) than WTE following TMZ exposure. Concerning antimetastatic effects, TMZ impedes invadopodia (3D invasion) more effectively in Polκ KO than in WTE spheroids. Collectively, the results suggest that TLS Polκ plays a vital role in the survival, cell death, genotoxicity, and metastatic potential of GBM spheroids in vitro when subjected to TMZ treatment. While the precise mechanisms underpinning this resistance remain elusive, TLS Polκ emerges as a potential therapeutic target for GBM patients.
Collapse
Affiliation(s)
- Diego Luis Ribeiro
- Departament of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Marcela Teatin Latancia
- Departament of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Izadora de Souza
- Department of Clinical and Experimental Oncology, Federal University of São Paulo, São Paulo, São Paulo, Brazil
| | - Abu-Bakr Adetayo Ariwoola
- Departament of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Clinical and Experimental Oncology, Federal University of São Paulo, São Paulo, São Paulo, Brazil
| | - Davi Mendes
- Departament of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - André Van Helvoort Lengert
- Department of Biophysics, Paulista School of Medicine, Federal University of São Paulo, São Paulo, São Paulo, Brazil
| | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Georgieva D, Wang N, Taglialatela A, Jerabek S, Reczek CR, Lim PX, Sung J, Du Q, Horiguchi M, Jasin M, Ciccia A, Baer R, Egli D. BRCA1 and 53BP1 regulate reprogramming efficiency by mediating DNA repair pathway choice at replication-associated double-strand breaks. Cell Rep 2024; 43:114006. [PMID: 38554279 PMCID: PMC11272184 DOI: 10.1016/j.celrep.2024.114006] [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: 02/26/2023] [Revised: 11/26/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
Reprogramming to pluripotency is associated with DNA damage and requires the functions of the BRCA1 tumor suppressor. Here, we leverage separation-of-function mutations in BRCA1/2 as well as the physical and/or genetic interactions between BRCA1 and its associated repair proteins to ascertain the relevance of homology-directed repair (HDR), stalled fork protection (SFP), and replication gap suppression (RGS) in somatic cell reprogramming. Surprisingly, loss of SFP and RGS is inconsequential for the transition to pluripotency. In contrast, cells deficient in HDR, but proficient in SFP and RGS, reprogram with reduced efficiency. Conversely, the restoration of HDR function through inactivation of 53bp1 rescues reprogramming in Brca1-deficient cells, and 53bp1 loss leads to elevated HDR and enhanced reprogramming in mouse and human cells. These results demonstrate that somatic cell reprogramming is especially dependent on repair of replication-associated double-strand breaks (DSBs) by the HDR activity of BRCA1 and BRCA2 and can be improved in the absence of 53BP1.
Collapse
Affiliation(s)
- Daniela Georgieva
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Angelo Taglialatela
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Stepan Jerabek
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 160 00 Praha 6, Czech Republic
| | - Colleen R Reczek
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julie Sung
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Qian Du
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michiko Horiguchi
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alberto Ciccia
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
7
|
Meroni A, Wells SE, Fonseca C, Ray Chaudhuri A, Caldecott KW, Vindigni A. DNA combing versus DNA spreading and the separation of sister chromatids. J Cell Biol 2024; 223:e202305082. [PMID: 38315097 PMCID: PMC10840220 DOI: 10.1083/jcb.202305082] [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: 05/19/2023] [Revised: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
DNA combing and DNA spreading are two central approaches for studying DNA replication fork dynamics genome-wide at single-molecule resolution by distributing labeled genomic DNA on coverslips or slides for immunodetection. Perturbations in DNA replication fork dynamics can differentially affect either leading or lagging strand synthesis, for example, in instances where replication is blocked by a lesion or obstacle on only one of the two strands. Thus, we sought to investigate whether the DNA combing and/or spreading approaches are suitable for resolving adjacent sister chromatids during DNA replication, thereby enabling the detection of DNA replication dynamics within individual nascent strands. To this end, we developed a thymidine labeling scheme that discriminates between these two possibilities. Our data suggests that DNA combing resolves sister chromatids, allowing the detection of strand-specific alterations, whereas DNA spreading typically does not. These findings have important implications when interpreting DNA replication dynamics from data obtained by these two commonly used techniques.
Collapse
Affiliation(s)
- Alice Meroni
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Sophie E. Wells
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer Brighton, UK
| | - Carmen Fonseca
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Keith W. Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer Brighton, UK
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Menck CFM, Galhardo RS, Quinet A. The accurate bypass of pyrimidine dimers by DNA polymerase eta contributes to ultraviolet-induced mutagenesis. Mutat Res 2024; 828:111840. [PMID: 37984186 DOI: 10.1016/j.mrfmmm.2023.111840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023]
Abstract
Human xeroderma pigmentosum variant (XP-V) patients are mutated in the POLH gene, responsible for encoding the translesion synthesis (TLS) DNA polymerase eta (Pol eta). These patients suffer from a high frequency of skin tumors. Despite several decades of research, studies on Pol eta still offer an intriguing paradox: How does this error-prone polymerase suppress mutations? This review examines recent evidence suggesting that cyclobutane pyrimidine dimers (CPDs) are instructional for Pol eta. Consequently, it can accurately replicate these lesions, and the mutagenic effects induced by UV radiation stem from the deamination of C-containing CPDs. In this model, the deamination of C (forming a U) within CPDs leads to the correct insertion of an A opposite to the deaminated C (or U)-containing dimers. This intricate process results in C>T transitions, which represent the most prevalent mutations detected in skin cancers. Finally, the delayed replication in XP-V cells amplifies the process of C-deamination in CPDs and increases the burden of C>T mutations prevalent in XP-V tumors through the activity of backup TLS polymerases.
Collapse
Affiliation(s)
- C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil.
| | - R S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - A Quinet
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
| |
Collapse
|
10
|
Martins DJ, Singh JK, Jahjah T, Vessoni AT, Leandro GDS, Silva MM, Biard DSF, Quinet A, Menck CFM. Polymerase iota plays a key role during translesion synthesis of UV-induced lesions in the absence of polymerase eta. Photochem Photobiol 2024; 100:4-18. [PMID: 37926965 DOI: 10.1111/php.13879] [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: 06/22/2023] [Revised: 09/29/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023]
Abstract
Xeroderma pigmentosum (XP) variant cells are deficient in the translesion synthesis (TLS) DNA polymerase Polη (eta). This protein contributes to DNA damage tolerance, bypassing unrepaired UV photoproducts and allowing S-phase progression with minimal delay. In the absence of Polη, backup polymerases perform TLS of UV lesions. However, which polymerase plays this role in human cells remains an open question. Here, we investigated the potential role of Polι (iota) in bypassing ultraviolet (UV) induced photoproducts in the absence of Polη, using NER-deficient (XP-C) cells knocked down for Polι and/or Polη genes. Our results indicate that cells lacking either Polι or Polη have increased sensitivity to UVC radiation. The lack of both TLS polymerases led to increased cell death and defects in proliferation and migration. Loss of both polymerases induces a significant replication fork arrest and G1/S-phase blockage, compared to the lack of Polη alone. In conclusion, we propose that Polι acts as a bona fide backup for Polη in the TLS of UV-photoproducts.
Collapse
Affiliation(s)
- Davi Jardim Martins
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Jenny Kaur Singh
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
| | - Tiya Jahjah
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
| | - Alexandre Teixeira Vessoni
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
- Sanofi R&D, Vitry-sur-Seine, France
| | - Giovana da Silva Leandro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Matheus Molina Silva
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Denis Serge François Biard
- Université Paris-Saclay, Institut de Biologie François Jacob, Service d'étude des prions et maladies atypiques, iRCM/IBJF, Fontenay-aux-Roses, France
| | - Annabel Quinet
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, Fontenay-aux-Roses, France
| | | |
Collapse
|
11
|
Ronson GE, Starowicz K, Anthony EJ, Piberger AL, Clarke LC, Garvin AJ, Beggs AD, Whalley CM, Edmonds MJ, Beesley JFJ, Morris JR. Mechanisms of synthetic lethality between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta targeting. Nat Commun 2023; 14:7834. [PMID: 38030626 PMCID: PMC10687250 DOI: 10.1038/s41467-023-43677-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
A synthetic lethal relationship exists between disruption of polymerase theta (Polθ), and loss of either 53BP1 or homologous recombination (HR) proteins, including BRCA1; however, the mechanistic basis of these observations are unclear. Here we reveal two distinct mechanisms of Polθ synthetic lethality, identifying dual influences of 1) whether Polθ is lost or inhibited, and 2) the underlying susceptible genotype. Firstly, we find that the sensitivity of BRCA1/2- and 53BP1-deficient cells to Polθ loss, and 53BP1-deficient cells to Polθ inhibition (ART558) requires RAD52, and appropriate reduction of RAD52 can ameliorate these phenotypes. We show that in the absence of Polθ, RAD52 accumulations suppress ssDNA gap-filling in G2/M and encourage MRE11 nuclease accumulation. In contrast, the survival of BRCA1-deficient cells treated with Polθ inhibitor are not restored by RAD52 suppression, and ssDNA gap-filling is prevented by the chemically inhibited polymerase itself. These data define an additional role for Polθ, reveal the mechanism underlying synthetic lethality between 53BP1, BRCA1/2 and Polθ loss, and indicate genotype-dependent Polθ inhibitor mechanisms.
Collapse
Affiliation(s)
- George E Ronson
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Adthera Bio, Lyndon House, 62 Hagley Road, Birmingham, B16 8PE, UK
| | - Elizabeth J Anthony
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann Liza Piberger
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucy C Clarke
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women's Hospital, Mindelsohn Way, Birmingham, B15 2TG, UK
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University of Leeds, Leeds, UK
| | - Andrew D Beggs
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Celina M Whalley
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Matthew J Edmonds
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Certara Insight, Danebrook Court, Oxford Office Village, Kidlington, Oxfordshire, OX5 1LQ, UK
| | - James F J Beesley
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Kang Z, Fu P, Ma H, Li T, Lu K, Liu J, Ginjala V, Romanienko P, Feng Z, Guan M, Ganesan S, Xia B. Distinct functions of EHMT1 and EHMT2 in cancer chemotherapy and immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560719. [PMID: 37873068 PMCID: PMC10592889 DOI: 10.1101/2023.10.03.560719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
EHTM1 (GLP) and EHMT2 (G9a) are closely related protein lysine methyltransferases often thought to function together as a heterodimer to methylate histone H3 and non-histone substrates in diverse cellular processes including transcriptional regulation, genome methylation, and DNA repair. Here we show that EHMT1/2 inhibitors cause ATM-mediated slowdown of replication fork progression, accumulation of single-stranded replication gaps, emergence of cytosolic DNA, and increased expression of STING. EHMT1/2 inhibition strongly potentiates the efficacy of alkylating chemotherapy and anti-PD-1 immunotherapy in mouse models of tripe negative breast cancer. The effects on DNA replication and alkylating agent sensitivity are largely caused by the loss of EHMT1-mediated methylation of LIG1, whereas the elevated STING expression and remarkable response to immunotherapy appear mainly elicited by the loss of EHMT2 activity. Depletion of UHRF1, a protein known to be associated with EHMT1/2 and LIG1, also induces STING expression, and depletion of either EHMT2 or UHRF1 leads to demethylation of specific CpG sites in the STING1 promoter, suggestive of a distinct EHMT2-UHRF1 axis that regulates DNA methylation and gene transcription. These results highlight distinct functions of the two EHMT paralogs and provide enlightening paradigms and corresponding molecular basis for combination therapies involving alkylating agents and immune checkpoint inhibitors.
Collapse
Affiliation(s)
- Zhihua Kang
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Pan Fu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Clinical Microbiology Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Hui Ma
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Li
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kevin Lu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Juan Liu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Vasudeva Ginjala
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | | | - Zhaohui Feng
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Bing Xia
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Lead contact
| |
Collapse
|
14
|
Corradi C, Vilar JB, Buzatto VC, de Souza TA, Castro LP, Munford V, De Vecchi R, Galante PAF, Orpinelli F, Miller TLA, Buzzo JL, Sotto MN, Saldiva P, de Oliveira JW, Chaibub SCW, Sarasin A, Menck CFM. Mutational signatures and increased retrotransposon insertions in xeroderma pigmentosum variant skin tumors. Carcinogenesis 2023; 44:511-524. [PMID: 37195263 DOI: 10.1093/carcin/bgad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/06/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023] Open
Abstract
Xeroderma pigmentosum variant (XP-V) is an autosomal recessive disease with an increased risk of developing cutaneous neoplasms in sunlight-exposed regions. These cells are deficient in the translesion synthesis (TLS) DNA polymerase eta, responsible for bypassing different types of DNA lesions. From the exome sequencing of 11 skin tumors of a genetic XP-V patients' cluster, classical mutational signatures related to sunlight exposure, such as C>T transitions targeted to pyrimidine dimers, were identified. However, basal cell carcinomas also showed distinct C>A mutation spectra reflecting a mutational signature possibly related to sunlight-induced oxidative stress. Moreover, four samples carry different mutational signatures, with C>A mutations associated with tobacco chewing or smoking usage. Thus, XP-V patients should be warned of the risk of these habits. Surprisingly, higher levels of retrotransposon somatic insertions were also detected when the tumors were compared with non-XP skin tumors, revealing other possible causes for XP-V tumors and novel functions for the TLS polymerase eta in suppressing retrotransposition. Finally, the expected high mutation burden found in most of these tumors renders these XP patients good candidates for checkpoint blockade immunotherapy.
Collapse
Affiliation(s)
- Camila Corradi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Juliana B Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Vanessa C Buzatto
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Tiago A de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
- Tau GC Bioinformatics, Cotia, SP 06711-020, Brazil
| | - Ligia P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | | | - Pedro A F Galante
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Fernanda Orpinelli
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Thiago L A Miller
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP 05508-000, Brazil
| | - José L Buzzo
- Molecular Oncology Center, Bioinformatics Laboratory, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil
| | - Mirian N Sotto
- Medical School, University of Sao Paulo, Sao Paulo, SP 01246-903, Brazil
| | - Paulo Saldiva
- Medical School, University of Sao Paulo, Sao Paulo, SP 01246-903, Brazil
| | - Jocelânio W de Oliveira
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP 05508-090, Brazil
| | | | - Alain Sarasin
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Meroni A, Wells SE, Fonseca C, Ray Chaudhuri A, Caldecott KW, Vindigni A. DNA Combing versus DNA Spreading and the Separation of Sister Chromatids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539129. [PMID: 37205507 PMCID: PMC10187196 DOI: 10.1101/2023.05.02.539129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
DNA combing and DNA spreading are two central approaches for studying DNA replication fork dynamics genome-wide at single-molecule resolution by distributing labeled genomic DNA on coverslips or slides for immunodetection. Perturbations in DNA replication fork dynamics can differentially affect either leading or lagging strand synthesis, for example in instances where replication is blocked by a lesion or obstacle on only one of the two strands. Thus, we sought to investigate whether the DNA combing and/or spreading approaches are suitable for resolving adjacent sister chromatids during DNA replication, thereby enabling the detection of DNA replication dynamics within individual nascent strands. To this end, we developed a thymidine labeling scheme that discriminates between these two possibilities. Our data suggests that DNA combing resolves single chromatids, allowing the detection of strand-specific alterations, whereas DNA spreading does not. These findings have important implications when interpreting DNA replication dynamics from data obtained by these two commonly used techniques.
Collapse
|
19
|
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.
Collapse
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
| | | |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Benureau Y, Pouvelle C, Dupaigne P, Baconnais S, Moreira Tavares E, Mazón G, Despras E, Le Cam E, Kannouche P. Changes in the architecture and abundance of replication intermediates delineate the chronology of DNA damage tolerance pathways at UV-stalled replication forks in human cells. Nucleic Acids Res 2022; 50:9909-9929. [PMID: 36107774 PMCID: PMC9508826 DOI: 10.1093/nar/gkac746] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022] Open
Abstract
DNA lesions in S phase threaten genome stability. The DNA damage tolerance (DDT) pathways overcome these obstacles and allow completion of DNA synthesis by the use of specialised translesion (TLS) DNA polymerases or through recombination-related processes. However, how these mechanisms coordinate with each other and with bulk replication remains elusive. To address these issues, we monitored the variation of replication intermediate architecture in response to ultraviolet irradiation using transmission electron microscopy. We show that the TLS polymerase η, able to accurately bypass the major UV lesion and mutated in the skin cancer-prone xeroderma pigmentosum variant (XPV) syndrome, acts at the replication fork to resolve uncoupling and prevent post-replicative gap accumulation. Repriming occurs as a compensatory mechanism when this on-the-fly mechanism cannot operate, and is therefore predominant in XPV cells. Interestingly, our data support a recombination-independent function of RAD51 at the replication fork to sustain repriming. Finally, we provide evidence for the post-replicative commitment of recombination in gap repair and for pioneering observations of in vivo recombination intermediates. Altogether, we propose a chronology of UV damage tolerance in human cells that highlights the key role of polη in shaping this response and ensuring the continuity of DNA synthesis.
Collapse
Affiliation(s)
- Yann Benureau
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Caroline Pouvelle
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
| | - Pauline Dupaigne
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Sonia Baconnais
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Eliana Moreira Tavares
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Gerard Mazón
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Emmanuelle Despras
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
| | - Eric Le Cam
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Patricia L Kannouche
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
| |
Collapse
|
22
|
Volk LB, Cooper KL, Jiang T, Paffett ML, Hudson LG. Impacts of arsenic on Rad18 and translesion synthesis. Toxicol Appl Pharmacol 2022; 454:116230. [PMID: 36087615 PMCID: PMC10144522 DOI: 10.1016/j.taap.2022.116230] [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: 06/30/2022] [Revised: 08/27/2022] [Accepted: 09/02/2022] [Indexed: 10/31/2022]
Abstract
Arsenite interferes with DNA repair protein function resulting in the retention of UV-induced DNA damage. Accumulated DNA damage promotes replication stress which is bypassed by DNA damage tolerance pathways such as translesion synthesis (TLS). Rad18 is an essential factor in initiating TLS through PCNA monoubiquitination and contains two functionally and structurally distinct zinc fingers that are potential targets for arsenite binding. Arsenite treatment displaced zinc from endogenous Rad18 protein and mass spectrometry analysis revealed arsenite binding to both the Rad18 RING finger and UBZ domains. Consequently, arsenite inhibited Rad18 RING finger dependent PCNA monoubiquitination and polymerase eta recruitment to DNA damage in UV exposed keratinocytes, both of which enhance the bypass of cyclobutane pyrimidine dimers during replication. Further analysis demonstrated multiple effects of arsenite, including the reduction in nuclear localization and UV-induced chromatin recruitment of Rad18 and its binding partner Rad6, which may also negatively impact TLS initiation. Arsenite and Rad18 knockdown in UV exposed keratinocytes significantly increased markers of replication stress and DNA strand breaks to a similar degree, suggesting arsenite mediates its effects through Rad18. Comet assay analysis confirmed an increase in both UV-induced single-stranded DNA and DNA double-strand breaks in arsenite treated keratinocytes compared to UV alone. Altogether, this study supports a mechanism by which arsenite inhibits TLS through the altered activity and regulation of Rad18. Arsenite elevated the levels of UV-induced replication stress and consequently, single-stranded DNA gaps and DNA double-strand breaks. These potentially mutagenic outcomes support a role for TLS in the cocarcinogenicity of arsenite.
Collapse
Affiliation(s)
- L B Volk
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, USA.
| | - K L Cooper
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, USA.
| | - T Jiang
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, USA.
| | - M L Paffett
- Fluorescence Microscopy and Cell Imaging Shared Resource, University of New Mexico Comprehensive Cancer Center, 2325 Camino de Salud, Albuquerque, NM 87131, USA.
| | - L G Hudson
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, USA.
| |
Collapse
|
23
|
Shibata M, Keyamura K, Shioiri T, Noda S, Akanuma G, Hishida T. Diploid-associated adaptation to chronic low-dose UV irradiation requires homologous recombination in Saccharomyces cerevisiae. Genetics 2022; 222:iyac115. [PMID: 35946552 PMCID: PMC9434230 DOI: 10.1093/genetics/iyac115] [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: 04/14/2022] [Accepted: 07/25/2022] [Indexed: 11/14/2022] Open
Abstract
Ultraviolet-induced DNA lesions impede DNA replication and transcription and are therefore a potential source of genome instability. Here, we performed serial transfer experiments on nucleotide excision repair-deficient (rad14Δ) yeast cells in the presence of chronic low-dose ultraviolet irradiation, focusing on the mechanisms underlying adaptive responses to chronic low-dose ultraviolet irradiation. Our results show that the entire haploid rad14Δ population rapidly becomes diploid during chronic low-dose ultraviolet exposure, and the evolved diploid rad14Δ cells were more chronic low-dose ultraviolet-resistant than haploid cells. Strikingly, single-stranded DNA, but not pyrimidine dimer, accumulation is associated with diploid-dependent fitness in response to chronic low-dose ultraviolet stress, suggesting that efficient repair of single-stranded DNA tracts is beneficial for chronic low-dose ultraviolet tolerance. Consistent with this hypothesis, homologous recombination is essential for the rapid evolutionary adaptation of diploidy, and rad14Δ cells lacking Rad51 recombinase, a key player in homologous recombination, exhibited abnormal cell morphology characterized by multiple RPA-yellow fluorescent protein foci after chronic low-dose ultraviolet exposure. Furthermore, interhomolog recombination is increased in chronic low-dose ultraviolet-exposed rad14Δ diploids, which causes frequent loss of heterozygosity. Thus, our results highlight the importance of homologous recombination in the survival and genomic stability of cells with unrepaired lesions.
Collapse
Affiliation(s)
- Mana Shibata
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Takuya Shioiri
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Shunsuke Noda
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Genki Akanuma
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| |
Collapse
|
24
|
Saxena S, Zou L. Hallmarks of DNA replication stress. Mol Cell 2022; 82:2298-2314. [PMID: 35714587 DOI: 10.1016/j.molcel.2022.05.004] [Citation(s) in RCA: 111] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/15/2022] [Accepted: 05/04/2022] [Indexed: 12/12/2022]
Abstract
Faithful DNA replication is critical for the maintenance of genomic integrity. Although DNA replication machinery is highly accurate, the process of DNA replication is constantly challenged by DNA damage and other intrinsic and extrinsic stresses throughout the genome. A variety of cellular stresses interfering with DNA replication, which are collectively termed replication stress, pose a threat to genomic stability in both normal and cancer cells. To cope with replication stress and maintain genomic stability, cells have evolved a complex network of cellular responses to alleviate and tolerate replication problems. This review will focus on the major sources of replication stress, the impacts of replication stress in cells, and the assays to detect replication stress, offering an overview of the hallmarks of DNA replication stress.
Collapse
Affiliation(s)
- Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| |
Collapse
|
25
|
Ler AAL, Carty MP. DNA Damage Tolerance Pathways in Human Cells: A Potential Therapeutic Target. Front Oncol 2022; 11:822500. [PMID: 35198436 PMCID: PMC8859465 DOI: 10.3389/fonc.2021.822500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022] Open
Abstract
DNA lesions arising from both exogenous and endogenous sources occur frequently in DNA. During DNA replication, the presence of unrepaired DNA damage in the template can arrest replication fork progression, leading to fork collapse, double-strand break formation, and to genome instability. To facilitate completion of replication and prevent the generation of strand breaks, DNA damage tolerance (DDT) pathways play a key role in allowing replication to proceed in the presence of lesions in the template. The two main DDT pathways are translesion synthesis (TLS), which involves the recruitment of specialized TLS polymerases to the site of replication arrest to bypass lesions, and homology-directed damage tolerance, which includes the template switching and fork reversal pathways. With some exceptions, lesion bypass by TLS polymerases is a source of mutagenesis, potentially contributing to the development of cancer. The capacity of TLS polymerases to bypass replication-blocking lesions induced by anti-cancer drugs such as cisplatin can also contribute to tumor chemoresistance. On the other hand, during homology-directed DDT the nascent sister strand is transiently utilised as a template for replication, allowing for error-free lesion bypass. Given the role of DNA damage tolerance pathways in replication, mutagenesis and chemoresistance, a more complete understanding of these pathways can provide avenues for therapeutic exploitation. A number of small molecule inhibitors of TLS polymerase activity have been identified that show synergy with conventional chemotherapeutic agents in killing cancer cells. In this review, we will summarize the major DDT pathways, explore the relationship between damage tolerance and carcinogenesis, and discuss the potential of targeting TLS polymerases as a therapeutic approach.
Collapse
Affiliation(s)
- Ashlynn Ai Li Ler
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
| | - Michael P. Carty
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
- DNA Damage Response Laboratory, Centre for Chromosome Biology, NUI Galway, Galway, Ireland
- *Correspondence: Michael P. Carty,
| |
Collapse
|
26
|
Genetic and physical interactions between Polη and Rev1 in response to UV-induced DNA damage in mammalian cells. Sci Rep 2021; 11:21364. [PMID: 34725419 PMCID: PMC8560953 DOI: 10.1038/s41598-021-00878-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
In response to UV irradiation, translesion DNA synthesis (TLS) utilizes specialized DNA polymerases to bypass replication-blocking lesions. In a well-established polymerase switch model, Polη is thought to be a preferred TLS polymerase to insert correct nucleotides across from the thymine dimer, and Rev1 plays a scaffold role through physical interaction with Polη and the Rev7 subunit of Polζ for continual DNA synthesis. Defective Polη causes a variant form of xeroderma pigmentosum (XPV), a disease with predisposition to sunlight-induced skin cancer. Previous studies revealed that expression of Rev1 alone is sufficient to confer enhanced UV damage tolerance in mammalian cells, which depends on its physical interaction with Polζ but is independent of Polη, a conclusion that appears to contradict current literature on the critical roles of Polη in TLS. To test a hypothesis that the Rev1 catalytic activity is required to backup Polη in TLS, we found that the Rev1 polymerase-dead mutation is synergistic with either Polη mutation or the Polη-interaction mutation in response to UV-induced DNA damage. On the other hand, functional complementation of polH cells by Polη relies on its physical interaction with Rev1. Hence, our studies reveal critical interactions between Rev1 and Polη in response to UV damage.
Collapse
|
27
|
Kang Z, Fu P, Alcivar AL, Fu H, Redon C, Foo TK, Zuo Y, Ye C, Baxley R, Madireddy A, Buisson R, Bielinsky AK, Zou L, Shen Z, Aladjem MI, Xia B. BRCA2 associates with MCM10 to suppress PRIMPOL-mediated repriming and single-stranded gap formation after DNA damage. Nat Commun 2021; 12:5966. [PMID: 34645815 PMCID: PMC8514439 DOI: 10.1038/s41467-021-26227-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/23/2021] [Indexed: 11/28/2022] Open
Abstract
The BRCA2 tumor suppressor protects genome integrity by promoting homologous recombination-based repair of DNA breaks, stability of stalled DNA replication forks and DNA damage-induced cell cycle checkpoints. BRCA2 deficient cells display the radio-resistant DNA synthesis (RDS) phenotype, however the mechanism has remained elusive. Here we show that cells without BRCA2 are unable to sufficiently restrain DNA replication fork progression after DNA damage, and the underrestrained fork progression is due primarily to Primase-Polymerase (PRIMPOL)-mediated repriming of DNA synthesis downstream of lesions, leaving behind single-stranded DNA gaps. Moreover, we find that BRCA2 associates with the essential DNA replication factor MCM10 and this association suppresses PRIMPOL-mediated repriming and ssDNA gap formation, while having no impact on the stability of stalled replication forks. Our findings establish an important function for BRCA2, provide insights into replication fork control during the DNA damage response, and may have implications in tumor suppression and therapy response. Tumor suppressor BRCA2 is known to stabilize and restart stalled DNA replication forks. Here the authors show that BRCA2 is recruited to the replication fork through its interaction with MCM10 and inhibits Primase-Polymerase-mediated repriming, lesion bypass and single strand DNA gap formation after DNA damage.
Collapse
Affiliation(s)
- Zhihua Kang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Pan Fu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Allen L Alcivar
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Bristol-Myers Squibb Company, Bloomsbury, NJ, 08804, USA
| | - Haiqing Fu
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christophe Redon
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Yamei Zuo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Caiyong Ye
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Ryan Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Remi Buisson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
| |
Collapse
|
28
|
hSSB2 (NABP1) is required for the recruitment of RPA during the cellular response to DNA UV damage. Sci Rep 2021; 11:20256. [PMID: 34642383 PMCID: PMC8511049 DOI: 10.1038/s41598-021-99355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
Maintenance of genomic stability is critical to prevent diseases such as cancer. As such, eukaryotic cells have multiple pathways to efficiently detect, signal and repair DNA damage. One common form of exogenous DNA damage comes from ultraviolet B (UVB) radiation. UVB generates cyclobutane pyrimidine dimers (CPD) that must be rapidly detected and repaired to maintain the genetic code. The nucleotide excision repair (NER) pathway is the main repair system for this type of DNA damage. Here, we determined the role of the human Single-Stranded DNA Binding protein 2, hSSB2, in the response to UVB exposure. We demonstrate that hSSB2 levels increase in vitro and in vivo after UVB irradiation and that hSSB2 rapidly binds to chromatin. Depletion of hSSB2 results in significantly decreased Replication Protein A (RPA32) phosphorylation and impaired RPA32 localisation to the site of UV-induced DNA damage. Delayed recruitment of NER protein Xeroderma Pigmentosum group C (XPC) was also observed, leading to increased cellular sensitivity to UVB. Finally, hSSB2 was shown to have affinity for single-strand DNA containing a single CPD and for duplex DNA with a two-base mismatch mimicking a CPD moiety. Altogether our data demonstrate that hSSB2 is involved in the cellular response to UV exposure.
Collapse
|
29
|
Taglialatela A, Leuzzi G, Sannino V, Cuella-Martin R, Huang JW, Wu-Baer F, Baer R, Costanzo V, Ciccia A. REV1-Polζ maintains the viability of homologous recombination-deficient cancer cells through mutagenic repair of PRIMPOL-dependent ssDNA gaps. Mol Cell 2021; 81:4008-4025.e7. [PMID: 34508659 PMCID: PMC8500949 DOI: 10.1016/j.molcel.2021.08.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 05/29/2021] [Accepted: 08/11/2021] [Indexed: 12/11/2022]
Abstract
BRCA1/2 mutant tumor cells display an elevated mutation burden, the etiology of which remains unclear. Here, we report that these cells accumulate ssDNA gaps and spontaneous mutations during unperturbed DNA replication due to repriming by the DNA primase-polymerase PRIMPOL. Gap accumulation requires the DNA glycosylase SMUG1 and is exacerbated by depletion of the translesion synthesis (TLS) factor RAD18 or inhibition of the error-prone TLS polymerase complex REV1-Polζ by the small molecule JH-RE-06. JH-RE-06 treatment of BRCA1/2-deficient cells results in reduced mutation rates and PRIMPOL- and SMUG1-dependent loss of viability. Through cellular and animal studies, we demonstrate that JH-RE-06 is preferentially toxic toward HR-deficient cancer cells. Furthermore, JH-RE-06 remains effective toward PARP inhibitor (PARPi)-resistant BRCA1 mutant cells and displays additive toxicity with crosslinking agents or PARPi. Collectively, these studies identify a protective and mutagenic role for REV1-Polζ in BRCA1/2 mutant cells and provide the rationale for using REV1-Polζ inhibitors to treat BRCA1/2 mutant tumors.
Collapse
Affiliation(s)
- Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Foon Wu-Baer
- Institute for Cancer Genetics, Department of Pathology & Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Baer
- Institute for Cancer Genetics, Department of Pathology & Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM, FIRC Institute for Molecular Oncology, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
30
|
Tirman S, Quinet A, Wood M, Meroni A, Cybulla E, Jackson J, Pegoraro S, Simoneau A, Zou L, Vindigni A. Temporally distinct post-replicative repair mechanisms fill PRIMPOL-dependent ssDNA gaps in human cells. Mol Cell 2021; 81:4026-4040.e8. [PMID: 34624216 PMCID: PMC8555837 DOI: 10.1016/j.molcel.2021.09.013] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/20/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022]
Abstract
PRIMPOL repriming allows DNA replication to skip DNA lesions, leading to ssDNA gaps. These gaps must be filled to preserve genome stability. Using a DNA fiber approach to directly monitor gap filling, we studied the post-replicative mechanisms that fill the ssDNA gaps generated in cisplatin-treated cells upon increased PRIMPOL expression or when replication fork reversal is defective because of SMARCAL1 inactivation or PARP inhibition. We found that a mechanism dependent on the E3 ubiquitin ligase RAD18, PCNA monoubiquitination, and the REV1 and POLζ translesion synthesis polymerases promotes gap filling in G2. The E2-conjugating enzyme UBC13, the RAD51 recombinase, and REV1-POLζ are instead responsible for gap filling in S, suggesting that temporally distinct pathways of gap filling operate throughout the cell cycle. Furthermore, we found that BRCA1 and BRCA2 promote gap filling by limiting MRE11 activity and that simultaneously targeting fork reversal and gap filling enhances chemosensitivity in BRCA-deficient cells.
Collapse
Affiliation(s)
- Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew Wood
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alice Meroni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Silvia Pegoraro
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
31
|
Wu D, Banerjee A, Cai S, Li N, Han C, Bai X, Zhang J, Wang QE. Determination of DNA lesion bypass using a ChIP-based assay. DNA Repair (Amst) 2021; 108:103230. [PMID: 34571449 DOI: 10.1016/j.dnarep.2021.103230] [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: 05/17/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/19/2022]
Abstract
DNA lesion bypass facilitates DNA synthesis across bulky DNA lesions, playing a critical role in DNA damage tolerance and cell survival after DNA damage. Assessing lesion bypass efficiency in the cell is important to better understanding of the mechanism of carcinogenesis and chemoresistance. Here we developed a chromatin immunoprecipitation (ChIP)-based method to measure lesion bypass activity across cisplatin-induced intrastrand crosslinks in cancer cells. DNA lesion bypass enables the replication to continue in the presence of replication blocks. Thus, the successful lesion bypass should result in the coexistence of DNA lesions and the newly synthesized DNA fragment opposite to this lesion. Using ChIP, we precipitated the cisplatin-induced intrastrand crosslinks, and quantitated the precipitated newly synthesized DNA that was labeled with BrdU. We validated this method on ovarian cancer cells with inhibited TLS activity. We then applied this method to show that ovarian cancer stem cells exhibit high lesion bypass activity relative to bulk cancer cells from the same cell line. In conclusion, this novel ChIP-based lesion bypass assay can detect the extent to which cisplatin-induced DNA lesions are bypassed in live cells. Our study may be applied more broadly to the study of other DNA lesions, as specific antibodies to these specific lesions are available.
Collapse
Affiliation(s)
- Dayong Wu
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Ananya Banerjee
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Shurui Cai
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Na Li
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Chunhua Han
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Xuetao Bai
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Junran Zhang
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Qi-En Wang
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
32
|
Quintero-Ruiz N, Corradi C, Moreno NC, de Souza TA, Pereira Castro L, Rocha CRR, Menck CFM. Mutagenicity Profile Induced by UVB Light in Human Xeroderma Pigmentosum Group C Cells †. Photochem Photobiol 2021; 98:713-731. [PMID: 34516658 DOI: 10.1111/php.13516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
Nucleotide excision repair (NER) is one of the main pathways for genome protection against structural DNA damage caused by sunlight, which in turn is extensively related to skin cancer development. The mutation spectra induced by UVB were investigated by whole-exome sequencing of randomly selected clones of NER-proficient and XP-C-deficient human skin fibroblasts. As a model, a cell line unable to recognize and remove lesions (XP-C) was used and compared to the complemented isogenic control (COMP). As expected, a significant increase of mutagenesis was observed in irradiated XP-C cells, mainly C>T transitions, but also CC>TT and C>A base substitutions. Remarkably, the C>T mutations occur mainly at the second base of dipyrimidine sites in pyrimidine-rich sequence contexts, with 5'TC sequence the most mutated. Although T>N mutations were also significantly increased, they were not directly related to pyrimidine dimers. Moreover, the large-scale study of a single UVB irradiation on XP-C cells allowed recovering the typical mutation spectrum found in human skin cancer tumors. Eventually, the data may be used for comparison with the mutational profiles of skin tumors obtained from XP-C patients and may help to understand the mutational process in nonaffected individuals.
Collapse
Affiliation(s)
- Nathalia Quintero-Ruiz
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Camila Corradi
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Natália Cestari Moreno
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago Antonio de Souza
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Tau GC Bioinformatics, São Paulo, Brazil
| | - Ligia Pereira Castro
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Clarissa Ribeiro Reily Rocha
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Drug resistance and mutagenesis Laboratory, Departmento de Oncologia Clínica e Experimental, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos Frederico Martins Menck
- Laboratorio de reparo de DNA, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
33
|
Cong K, Peng M, Kousholt AN, Lee WTC, Lee S, Nayak S, Krais J, VanderVere-Carozza PS, Pawelczak KS, Calvo J, Panzarino NJ, Turchi JJ, Johnson N, Jonkers J, Rothenberg E, Cantor SB. Replication gaps are a key determinant of PARP inhibitor synthetic lethality with BRCA deficiency. Mol Cell 2021; 81:3128-3144.e7. [PMID: 34216544 PMCID: PMC9089372 DOI: 10.1016/j.molcel.2021.06.011] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/19/2021] [Accepted: 06/09/2021] [Indexed: 01/04/2023]
Abstract
Mutations in BRCA1 or BRCA2 (BRCA) is synthetic lethal with poly(ADP-ribose) polymerase inhibitors (PARPi). Lethality is thought to derive from DNA double-stranded breaks (DSBs) necessitating BRCA function in homologous recombination (HR) and/or fork protection (FP). Here, we report instead that toxicity derives from replication gaps. BRCA1- or FANCJ-deficient cells, with common repair defects but distinct PARPi responses, reveal gaps as a distinguishing factor. We further uncouple HR, FP, and fork speed from PARPi response. Instead, gaps characterize BRCA-deficient cells, are diminished upon resistance, restored upon resensitization, and, when exposed, augment PARPi toxicity. Unchallenged BRCA1-deficient cells have elevated poly(ADP-ribose) and chromatin-associated PARP1, but aberrantly low XRCC1 consistent with defects in backup Okazaki fragment processing (OFP). 53BP1 loss resuscitates OFP by restoring XRCC1-LIG3 that suppresses the sensitivity of BRCA1-deficient cells to drugs targeting OFP or generating gaps. We highlight gaps as a determinant of PARPi toxicity changing the paradigm for synthetic lethal interactions.
Collapse
Affiliation(s)
- Ke Cong
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Min Peng
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Arne Nedergaard Kousholt
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Wei Ting C Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Silviana Lee
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sumeet Nayak
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - John Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | | | - Jennifer Calvo
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas J Panzarino
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - John J Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA; NERx Biosciences, 212 W. 10th St., Suite A480, Indianapolis, IN 46202, USA
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Sharon B Cantor
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
34
|
Quinet A, Tirman S, Cybulla E, Meroni A, Vindigni A. To skip or not to skip: choosing repriming to tolerate DNA damage. Mol Cell 2021; 81:649-658. [PMID: 33515486 PMCID: PMC7935405 DOI: 10.1016/j.molcel.2021.01.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
Accurate DNA replication is constantly threatened by DNA lesions arising from endogenous and exogenous sources. Specialized DNA replication stress response pathways ensure replication fork progression in the presence of DNA lesions with minimal delay in fork elongation. These pathways broadly include translesion DNA synthesis, template switching, and replication fork repriming. Here, we discuss recent advances toward our understanding of the mechanisms that regulate the fine-tuned balance between these different replication stress response pathways. We also discuss the molecular pathways required to fill single-stranded DNA gaps that accumulate throughout the genome after repriming and the biological consequences of using repriming instead of other DNA damage tolerance pathways on genome integrity and cell fitness.
Collapse
Affiliation(s)
- Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alice Meroni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
35
|
Tirman S, Cybulla E, Quinet A, Meroni A, Vindigni A. PRIMPOL ready, set, reprime! Crit Rev Biochem Mol Biol 2021; 56:17-30. [PMID: 33179522 PMCID: PMC7906090 DOI: 10.1080/10409238.2020.1841089] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
DNA replication forks are constantly challenged by DNA lesions induced by endogenous and exogenous sources. DNA damage tolerance mechanisms ensure that DNA replication continues with minimal effects on replication fork elongation either by using specialized DNA polymerases, which have the ability to replicate through the damaged template, or by skipping the damaged DNA, leaving it to be repaired after replication. These mechanisms are evolutionarily conserved in bacteria, yeast, and higher eukaryotes, and are paramount to ensure timely and faithful duplication of the genome. The Primase and DNA-directed Polymerase (PRIMPOL) is a recently discovered enzyme that possesses both primase and polymerase activities. PRIMPOL is emerging as a key player in DNA damage tolerance, particularly in vertebrate and human cells. Here, we review our current understanding of the function of PRIMPOL in DNA damage tolerance by focusing on the structural aspects that define its dual enzymatic activity, as well as on the mechanisms that control its chromatin recruitment and expression levels. We also focus on the latest findings on the mitochondrial and nuclear functions of PRIMPOL and on the impact of loss of these functions on genome stability and cell survival. Defining the function of PRIMPOL in DNA damage tolerance is becoming increasingly important in the context of human disease. In particular, we discuss recent evidence pointing at the PRIMPOL pathway as a novel molecular target to improve cancer cell response to DNA-damaging chemotherapy and as a predictive parameter to stratify patients in personalized cancer therapy.
Collapse
Affiliation(s)
- Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Alice Meroni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis MO, 63110, USA
| |
Collapse
|
36
|
Nayak S, Calvo JA, Cantor SB. Targeting translesion synthesis (TLS) to expose replication gaps, a unique cancer vulnerability. Expert Opin Ther Targets 2021; 25:27-36. [PMID: 33416413 PMCID: PMC7837368 DOI: 10.1080/14728222.2021.1864321] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/11/2020] [Indexed: 02/09/2023]
Abstract
Introduction: Translesion synthesis (TLS) is a DNA damage tolerance (DDT) mechanism that employs error-prone polymerases to bypass replication blocking DNA lesions, contributing to a gain in mutagenesis and chemo-resistance. However, recent findings illustrate an emerging role for TLS in replication gap suppression (RGS), distinct from its role in post-replication gap filling. Here, TLS protects cells from replication stress (RS)-induced toxic single-stranded DNA (ssDNA) gaps that accumulate in the wake of active replication. Intriguingly, TLS-mediated RGS is specifically observed in several cancer cell lines and contributes to their survival. Thus, targeting TLS has the potential to uniquely eradicate tumors without harming non-cancer tissues. Areas Covered: This review provides an innovative perspective on the role of TLS beyond its canonical function of lesion bypass or post-replicative gap filling. We provide a comprehensive analysis that underscores the emerging role of TLS as a cancer adaptation necessary to overcome the replication stress response (RSR), an anti-cancer barrier. Expert Opinion: TLS RGS is critical for tumorigenesis and is a new hallmark of cancer. Although the exact mechanism and extent of TLS dependency in cancer is still emerging, TLS inhibitors have shown promise as an anti-cancer therapy in selectively targeting this unique cancer vulnerability.
Collapse
Affiliation(s)
- Sumeet Nayak
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School , Worcester, MA USA
| | - Jennifer A Calvo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School , Worcester, MA USA
| | - Sharon B Cantor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School , Worcester, MA USA
| |
Collapse
|
37
|
Conti BA, Smogorzewska A. Mechanisms of direct replication restart at stressed replisomes. DNA Repair (Amst) 2020; 95:102947. [PMID: 32853827 PMCID: PMC7669714 DOI: 10.1016/j.dnarep.2020.102947] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/09/2023]
Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA.
| |
Collapse
|
38
|
Bai G, Kermi C, Stoy H, Schiltz CJ, Bacal J, Zaino AM, Hadden MK, Eichman BF, Lopes M, Cimprich KA. HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis. Mol Cell 2020; 78:1237-1251.e7. [PMID: 32442397 PMCID: PMC7305998 DOI: 10.1016/j.molcel.2020.04.031] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023]
Abstract
DNA replication stress can stall replication forks, leading to genome instability. DNA damage tolerance pathways assist fork progression, promoting replication fork reversal, translesion DNA synthesis (TLS), and repriming. In the absence of the fork remodeler HLTF, forks fail to slow following replication stress, but underlying mechanisms and cellular consequences remain elusive. Here, we demonstrate that HLTF-deficient cells fail to undergo fork reversal in vivo and rely on the primase-polymerase PRIMPOL for repriming, unrestrained replication, and S phase progression upon limiting nucleotide levels. By contrast, in an HLTF-HIRAN mutant, unrestrained replication relies on the TLS protein REV1. Importantly, HLTF-deficient cells also exhibit reduced double-strand break (DSB) formation and increased survival upon replication stress. Our findings suggest that HLTF promotes fork remodeling, preventing other mechanisms of replication stress tolerance in cancer cells. This remarkable plasticity of the replication fork may determine the outcome of replication stress in terms of genome integrity, tumorigenesis, and response to chemotherapy.
Collapse
Affiliation(s)
- Gongshi Bai
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Chames Kermi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Carl J Schiltz
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Julien Bacal
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Angela M Zaino
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06029-3092, USA
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
| |
Collapse
|
39
|
The 6-4 photoproduct is the trigger of UV-induced replication blockage and ATR activation. Proc Natl Acad Sci U S A 2020; 117:12806-12816. [PMID: 32444488 DOI: 10.1073/pnas.1917196117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The most prevalent human carcinogen is sunlight-associated ultraviolet (UV), a physiologic dose of which generates thousands of DNA lesions per cell, mostly of two types: cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). It has not been possible, in living cells, to precisely characterize the respective contributions of these two lesion types to the signals that regulate cell cycle progression, DNA replication, and cell survival. Here we coupled multiparameter flow cytometry with lesion-specific photolyases that eliminate either CPDs or 6-4PPs and determined their respective contributions to DNA damage responses. Strikingly, only 6-4PP lesions activated the ATR-Chk1 DNA damage response pathway. Mechanistically, 6-4PPs, but not CPDs, impeded DNA replication across the genome as revealed by microfluidic-assisted replication track analysis. Furthermore, single-stranded DNA accumulated preferentially at 6-4PPs during DNA replication, indicating selective and prolonged replication blockage at 6-4PPs. These findings suggest that 6-4PPs, although eightfold fewer in number than CPDs, are the trigger for UV-induced DNA damage responses.
Collapse
|
40
|
Federico MB, Siri SO, Calzetta NL, Paviolo NS, de la Vega MB, Martino J, Campana MC, Wiesmüller L, Gottifredi V. Unscheduled MRE11 activity triggers cell death but not chromosome instability in polymerase eta-depleted cells subjected to UV irradiation. Oncogene 2020; 39:3952-3964. [PMID: 32203168 DOI: 10.1038/s41388-020-1265-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/17/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
The elimination of DNA polymerase eta (pol η) causes discontinuous DNA elongation and fork stalling in UV-irradiated cells. Such alterations in DNA replication are followed by S-phase arrest, DNA double-strand break (DSB) accumulation, and cell death. However, their molecular triggers and the relative timing of these events have not been fully elucidated. Here, we report that DSBs accumulate relatively early after UV irradiation in pol η-depleted cells. Despite the availability of repair pathways, DSBs persist and chromosome instability (CIN) is not detectable. Later on cells with pan-nuclear γH2AX and massive exposure of template single-stranded DNA (ssDNA), which indicate severe replication stress, accumulate and such events are followed by cell death. Reinforcing the causal link between the accumulation of pan-nuclear ssDNA/γH2AX signals and cell death, downregulation of RPA increased both replication stress and the cell death of pol η-deficient cells. Remarkably, DSBs, pan-nuclear ssDNA/γH2AX, S-phase arrest, and cell death are all attenuated by MRE11 nuclease knockdown. Such results suggest that unscheduled MRE11-dependent activities at replicating DNA selectively trigger cell death, but not CIN. Together these results show that pol η-depletion promotes a type of cell death that may be attractive as a therapeutic tool because of the lack of CIN.
Collapse
Affiliation(s)
- María Belén Federico
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina
| | - Sebastián Omar Siri
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina
| | - Nicolás Luis Calzetta
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina
| | - Natalia Soledad Paviolo
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina
| | - María Belén de la Vega
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina
| | - Julieta Martino
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina
| | - María Carolina Campana
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, D-89075, Ulm, Germany
| | - Vanesa Gottifredi
- Cell Cycle and Genomic Stability laboratory. Fundación Instituto Leloir. CONICET, Av. Patricias Argentinas 435, 1405, Buenos Aires, Argentina.
| |
Collapse
|
41
|
White PA, Long AS, Johnson GE. Quantitative Interpretation of Genetic Toxicity Dose-Response Data for Risk Assessment and Regulatory Decision-Making: Current Status and Emerging Priorities. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:66-83. [PMID: 31794061 DOI: 10.1002/em.22351] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 11/27/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
The screen-and-bin approach for interpretation of genotoxicity data is predicated on three false assumptions: that genotoxicants are rare, that genotoxicity dose-response functions do not contain a low-dose region mechanistically characterized by zero-order kinetics, and that genotoxicity is not a bona fide toxicological endpoint. Consequently, there is a need to develop and implement quantitative methods to interpret genotoxicity dose-response data for risk assessment and regulatory decision-making. Standardized methods to analyze dose-response data, and determine point-of-departure (PoD) metrics, have been established; the most robust PoD is the benchmark dose (BMD). However, there are no standards for regulatory interpretation of mutagenicity BMDs. Although 5-10% is often used as a critical effect size (CES) for BMD determination, values for genotoxicity endpoints have not been established. The use of BMDs to determine health-based guidance values (HBGVs) requires assessment factors (AFs) to account for interspecies differences and variability in human sensitivity. Default AFs used for other endpoints may not be appropriate for interpretation of in vivo mutagenicity BMDs. Analyses of published dose-response data showing the effects of compensatory pathway deficiency indicate that AFs for sensitivity differences should be in the range of 2-20. Additional analyses indicate that the AF to compensate for short treatment durations should be in the range of 5-15. Future work should use available data to empirically determine endpoint-specific CES values; similarly, to determine AF values for BMD adjustment. Future work should also evaluate the ability to use in vitro dose-response data for risk assessment, and the utility of probabilistic methods for determination of mutagenicity HBGVs. Environ. Mol. Mutagen. 61:66-83, 2020. © 2019 Her Majesty the Queen in Right of Canada.
Collapse
Affiliation(s)
- Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Alexandra S Long
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - George E Johnson
- Swansea University Medical School, Swansea, Wales, United Kingdom
| |
Collapse
|
42
|
Akagi JI, Hashimoto K, Suzuki K, Yokoi M, de Wind N, Iwai S, Ohmori H, Moriya M, Hanaoka F. Effect of sequence context on Polζ-dependent error-prone extension past (6-4) photoproducts. DNA Repair (Amst) 2019; 87:102771. [PMID: 31911268 DOI: 10.1016/j.dnarep.2019.102771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/21/2019] [Accepted: 12/13/2019] [Indexed: 11/30/2022]
Abstract
The (6-4) pyrimidine-pyrimidone photoproduct [(6-4)PP] is a major DNA lesion induced by ultraviolet radiation. (6-4)PP induces complex mutations opposite its downstream bases, in addition to opposite 3' or 5' base, as has been observed through a site-specific translesion DNA synthesis (TLS) assay. The mechanism by which these mutations occur is not well understood. To elucidate the mechanisms underlying mutagenesis induced by (6-4)PP, we performed an intracellular TLS assay using a replicative vector with site-specific T(thymidine)-T (6-4)PP. Rev3-/-p53-/- mouse embryonic fibroblast (MEF) cells (defective in Polζ) were almost completely defective in bypassing T-T (6-4)PP, whereas both Rev1-/- and Polh-/-Poli-/-Polk-/- MEF cells (defective in Polη, Polι, and Polκ) presented bypassing activity comparable to that of wild-type cells, indicating that Y-family TLS polymerases are dispensable for bypassing activity, whereas Polζ plays an essential role, probably at the extension step. Among all cells tested, misincorporation occurred most frequently just beyond the lesion (position +1), indicating that the Polζ-dependent extension step is crucial for (6-4)PP-induced mutagenesis. We then examined the effects of sequence context on T-T (6-4)PP bypass using a series of T-T (6-4)PP templates with different sequences at position +1 or -1 to the lesion, and found that the dependency of T-T (6-4)PP bypass on Polζ is not sequence specific. However, the misincorporation frequency at position +1 differed significantly among these templates. The misincorporation of A at position +1 occurred frequently when a purine base was located at position -1. These results indicate that Polζ-dependent extension plays a major role in inducing base substitutions in (6-4)PP-induced mutagenesis, and its fidelity is affected by sequence context surrounding a lesion.
Collapse
Affiliation(s)
- Jun-Ichi Akagi
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan; Division of Pathology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Keiji Hashimoto
- Laboratory of Chemical Biology, Department of Pharmacological Sciences, State University of New York, Stony Brook, NY, 11794-8651, USA
| | - Kenji Suzuki
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Masayuki Yokoi
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan; Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka, 560-8531, Japan
| | - Haruo Ohmori
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Masaaki Moriya
- Laboratory of Chemical Biology, Department of Pharmacological Sciences, State University of New York, Stony Brook, NY, 11794-8651, USA
| | - Fumio Hanaoka
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Osaka, 565-0871, Japan; National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
| |
Collapse
|
43
|
Paviolo NS, Vega MBDL, Pansa MF, García IA, Calzetta NL, Soria G, Gottifredi V. Persistent double strand break accumulation does not precede cell death in an Olaparib-sensitive BRCA-deficient colorectal cancer cell model. Genet Mol Biol 2019; 43:e20190070. [PMID: 31930278 PMCID: PMC7198003 DOI: 10.1590/1678-4685-gmb-2019-0070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/05/2019] [Indexed: 12/20/2022] Open
Abstract
The poly (adenosine diphosphate (ADP)-ribosyl) polymerase inhibitors (PARPi) selectively kill cancer cells with BRCA1 or BRCA2 (BRCA)-mutations. It has been proposed that cell death induction after PARPi depends on unrepaired double strand breaks (DSBs) that accumulate due to the homologous recombination deficiency of BRCA-mutated cells. Such accumulation of DSBs is inferred mainly from the high levels of DNA damage markers like phosphorylated histone H2AX. Herein, we developed a model of isogenic cell lines to show that depletion of BRCA causes PARPi-triggered cell death, replication stress (phosphorylated-H2AX and 53BP1 foci), and genomic instability. However, persistent DSBs accumulation was not detected under the same experimental conditions. Hence, at least in this cellular model, the trigger for cell death in PARPi-treated BRCA-depleted samples is not the accumulation of unrepaired DSBs. Instead, cell death better correlates with a rapid and aberrant resolution of DSBs by error-prone pathways that leads to severe chromosomic aberrations. Therefore, our results suggest that in PARPi-treated BRCA-deficient cells, chromosome aberrations may dually trigger both genomic instability and cell death.
Collapse
Affiliation(s)
- Natalia Soledad Paviolo
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires. Buenos Aires, Argentina
| | - María Belén de la Vega
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires. Buenos Aires, Argentina
| | - María Florencia Pansa
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET. Córdoba, Argentina.,Departamento de Bioquímica Clínica. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. Córdoba, Argentina
| | - Iris Alejandra García
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET. Córdoba, Argentina.,Departamento de Bioquímica Clínica. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. Córdoba, Argentina
| | - Nicolás Luis Calzetta
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires. Buenos Aires, Argentina
| | - Gastón Soria
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET. Córdoba, Argentina.,Departamento de Bioquímica Clínica. Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. Córdoba, Argentina
| | - Vanesa Gottifredi
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires. Buenos Aires, Argentina
| |
Collapse
|
44
|
Masuda Y, Masutani C. Spatiotemporal regulation of PCNA ubiquitination in damage tolerance pathways. Crit Rev Biochem Mol Biol 2019; 54:418-442. [PMID: 31736364 DOI: 10.1080/10409238.2019.1687420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA is constantly exposed to a wide variety of exogenous and endogenous agents, and most DNA lesions inhibit DNA synthesis. To cope with such problems during replication, cells have molecular mechanisms to resume DNA synthesis in the presence of DNA lesions, which are known as DNA damage tolerance (DDT) pathways. The concept of ubiquitination-mediated regulation of DDT pathways in eukaryotes was established via genetic studies in the yeast Saccharomyces cerevisiae, in which two branches of the DDT pathway are regulated via ubiquitination of proliferating cell nuclear antigen (PCNA): translesion DNA synthesis (TLS) and homology-dependent repair (HDR), which are stimulated by mono- and polyubiquitination of PCNA, respectively. Over the subsequent nearly two decades, significant progress has been made in understanding the mechanisms that regulate DDT pathways in other eukaryotes. Importantly, TLS is intrinsically error-prone because of the miscoding nature of most damaged nucleotides and inaccurate replication of undamaged templates by TLS polymerases (pols), whereas HDR is theoretically error-free because the DNA synthesis is thought to be predominantly performed by pol δ, an accurate replicative DNA pol, using the undamaged sister chromatid as its template. Thus, the regulation of the choice between the TLS and HDR pathways is critical to determine the appropriate biological outcomes caused by DNA damage. In this review, we summarize our current understanding of the species-specific regulatory mechanisms of PCNA ubiquitination and how cells choose between TLS and HDR. We then provide a hypothetical model for the spatiotemporal regulation of DDT pathways in human cells.
Collapse
Affiliation(s)
- Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
| |
Collapse
|
45
|
Quinet A, Tirman S, Jackson J, Šviković S, Lemaçon D, Carvajal-Maldonado D, González-Acosta D, Vessoni AT, Cybulla E, Wood M, Tavis S, Batista LFZ, Méndez J, Sale JE, Vindigni A. PRIMPOL-Mediated Adaptive Response Suppresses Replication Fork Reversal in BRCA-Deficient Cells. Mol Cell 2019; 77:461-474.e9. [PMID: 31676232 PMCID: PMC7007862 DOI: 10.1016/j.molcel.2019.10.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/29/2019] [Accepted: 10/07/2019] [Indexed: 12/20/2022]
Abstract
Acute treatment with replication-stalling chemotherapeutics causes reversal of replication forks. BRCA proteins protect reversed forks from nucleolytic degradation, and their loss leads to chemosensitivity. Here, we show that fork degradation is no longer detectable in BRCA1-deficient cancer cells exposed to multiple cisplatin doses, mimicking a clinical treatment regimen. This effect depends on increased expression and chromatin loading of PRIMPOL and is regulated by ATR activity. Electron microscopy and single-molecule DNA fiber analyses reveal that PRIMPOL rescues fork degradation by reinitiating DNA synthesis past DNA lesions. PRIMPOL repriming leads to accumulation of ssDNA gaps while suppressing fork reversal. We propose that cells adapt to repeated cisplatin doses by activating PRIMPOL repriming under conditions that would otherwise promote pathological reversed fork degradation. This effect is generalizable to other conditions of impaired fork reversal (e.g., SMARCAL1 loss or PARP inhibition) and suggests a new strategy to modulate cisplatin chemosensitivity by targeting the PRIMPOL pathway. Multiple cisplatin doses suppress reversed fork degradation in BRCA-deficient cells The PRIMPOL adaptive response suppresses fork reversal and leads to ssDNA gaps The ATR kinase regulates the PRIMPOL-mediated adaptive response Impaired fork reversal shifts the balance toward PRIMPOL-mediated repriming
Collapse
Affiliation(s)
- Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Saša Šviković
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Delphine Lemaçon
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Denisse Carvajal-Maldonado
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | | | - Alexandre T Vessoni
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Matthew Wood
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Steven Tavis
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Luis F Z Batista
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juan Méndez
- Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
| |
Collapse
|
46
|
ATR Signaling Uncouples the Role of RAD51 Paralogs in Homologous Recombination and Replication Stress Response. Cell Rep 2019; 29:551-559.e4. [DOI: 10.1016/j.celrep.2019.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/31/2019] [Accepted: 09/04/2019] [Indexed: 01/09/2023] Open
|
47
|
Kelso AA, Lopezcolorado FW, Bhargava R, Stark JM. Distinct roles of RAD52 and POLQ in chromosomal break repair and replication stress response. PLoS Genet 2019; 15:e1008319. [PMID: 31381562 PMCID: PMC6695211 DOI: 10.1371/journal.pgen.1008319] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/15/2019] [Accepted: 07/18/2019] [Indexed: 12/18/2022] Open
Abstract
Disrupting either the DNA annealing factor RAD52 or the A-family DNA polymerase POLQ can cause synthetic lethality with defects in BRCA1 and BRCA2, which are tumor suppressors important for homology-directed repair of DNA double-strand breaks (DSBs), and protection of stalled replication forks. A likely mechanism of this synthetic lethality is that RAD52 and/or POLQ are important for backup pathways for DSB repair and/or replication stress responses. The features of DSB repair events that require RAD52 vs. POLQ, and whether combined disruption of these factors causes distinct effects on genome maintenance, have been unclear. Using human U2OS cells, we generated a cell line with POLQ mutations upstream of the polymerase domain, a RAD52 knockout cell line, and a line with combined disruption of both genes. We also examined RAD52 and POLQ using RNA-interference. We find that combined disruption of RAD52 and POLQ causes at least additive hypersensitivity to cisplatin, and a synthetic reduction in replication fork restart velocity. We also examined the influence of RAD52 and POLQ on several DSB repair events. We find that RAD52 is particularly important for repair using ≥ 50 nt repeat sequences that flank the DSB, and that also involve removal of non-homologous sequences flanking the repeats. In contrast, POLQ is important for repair events using 6 nt (but not ≥ 18 nt) of flanking repeats that are at the edge of the break, as well as oligonucleotide microhomology-templated (i.e., 12-20 nt) repair events requiring nascent DNA synthesis. Finally, these factors show key distinctions with BRCA2, regarding effects on DSB repair events and response to stalled replication forks. These findings indicate that RAD52 and POLQ have distinct roles in genome maintenance, including for specific features of DSB repair events, such that combined disruption of these factors may be effective for genotoxin sensitization and/or synthetic lethal strategies.
Collapse
Affiliation(s)
- Andrew A. Kelso
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Felicia Wednesday Lopezcolorado
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | - Jeremy M. Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| |
Collapse
|
48
|
Masuda Y, Mitsuyuki S, Kanao R, Hishiki A, Hashimoto H, Masutani C. Regulation of HLTF-mediated PCNA polyubiquitination by RFC and PCNA monoubiquitination levels determines choice of damage tolerance pathway. Nucleic Acids Res 2019; 46:11340-11356. [PMID: 30335157 PMCID: PMC6265450 DOI: 10.1093/nar/gky943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/04/2018] [Indexed: 12/16/2022] Open
Abstract
DNA-damage tolerance protects cells via at least two sub-pathways regulated by proliferating cell nuclear antigen (PCNA) ubiquitination in eukaryotes: translesion DNA synthesis (TLS) and template switching (TS), which are stimulated by mono- and polyubiquitination, respectively. However, how cells choose between the two pathways remains unclear. The regulation of ubiquitin ligases catalyzing polyubiquitination, such as helicase-like transcription factor (HLTF), could play a role in the choice of pathway. Here, we demonstrate that the ligase activity of HLTF is stimulated by double-stranded DNA via HIRAN domain-dependent recruitment to stalled primer ends. Replication factor C (RFC) and PCNA located at primer ends, however, suppress en bloc polyubiquitination in the complex, redirecting toward sequential chain elongation. When PCNA in the complex is monoubiquitinated by RAD6-RAD18, the resulting ubiquitin moiety is immediately polyubiquitinated by coexisting HLTF, indicating a coupling reaction between mono- and polyubiquitination. By contrast, when PCNA was monoubiquitinated in the absence of HLTF, it was not polyubiquitinated by subsequently recruited HLTF unless all three-subunits of PCNA were monoubiquitinated, indicating that the uncoupling reaction specifically occurs on three-subunit-monoubiquitinated PCNA. We discuss the physiological relevance of the different modes of the polyubiquitination to the choice of cells between TLS and TS under different conditions.
Collapse
Affiliation(s)
- Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Satoshi Mitsuyuki
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Rie Kanao
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8002, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8002, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| |
Collapse
|
49
|
Suan Lim K, Li H, Roberts EA, Gaudiano EF, Clairmont C, Sambel L, Ponnienselvan K, Liu JC, Yang C, Kozono D, Parmar K, Yusufzai T, Zheng N, D’Andrea AD. USP1 Is Required for Replication Fork Protection in BRCA1-Deficient Tumors. Mol Cell 2018; 72:925-941.e4. [PMID: 30576655 PMCID: PMC6390489 DOI: 10.1016/j.molcel.2018.10.045] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/23/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
Abstract
BRCA1-deficient tumor cells have defects in homologous-recombination repair and replication fork stability, resulting in PARP inhibitor sensitivity. Here, we demonstrate that a deubiquitinase, USP1, is upregulated in tumors with mutations in BRCA1. Knockdown or inhibition of USP1 resulted in replication fork destabilization and decreased viability of BRCA1-deficient cells, revealing a synthetic lethal relationship. USP1 binds to and is stimulated by fork DNA. A truncated form of USP1, lacking its DNA-binding region, was not stimulated by DNA and failed to localize and protect replication forks. Persistence of monoubiquitinated PCNA at the replication fork was the mechanism of cell death in the absence of USP1. Taken together, USP1 exhibits DNA-mediated activation at the replication fork, protects the fork, and promotes survival in BRCA1-deficient cells. Inhibition of USP1 may be a useful treatment for a subset of PARP-inhibitor-resistant BRCA1-deficient tumors with acquired replication fork stabilization.
Collapse
Affiliation(s)
- Kah Suan Lim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Heng Li
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Emma A. Roberts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Emily F. Gaudiano
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Larissa Sambel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Jessica C. Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Chunyu Yang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kalindi Parmar
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA,Howard Hughes Medical Institute, Box 357280, Seattle, WA
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| |
Collapse
|
50
|
Cervical cancer cell lines are sensitive to sub-erythemal UV exposure. Gene 2018; 688:44-53. [PMID: 30517878 DOI: 10.1016/j.gene.2018.11.079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/24/2018] [Indexed: 11/22/2022]
Abstract
High risk human papillomavirus (HPV) infections are the causative agent in virtually every cervical cancer as well as a host of other anogenital and oropharyngeal malignancies. These viruses must activate DNA repair pathways to facilitate their replication, while avoiding the cell cycle arrest and apoptosis that can accompany DNA damage. HPV oncoproteins facilitate each of these goals, but also reduce genome stability. Our data dissect the cytotoxic and cytoprotective characteristics of HPV oncogenes in cervical cancer cells. These data show that while the transformation of keratinocytes by HPV oncogene leaves these cells more sensitive to UV, the oncogenes also protect against UV-induced apoptosis. Cisplatin and UV resistant cervical cancer cell lines were generated and probed for their sensitivity to genotoxic agents. Cervical cancer cells can acquire resistance to one DNA crosslinking agent (UV or cisplatin) without gaining broad tolerance of crosslinked DNA. Further, cisplatin resistance may or may not result in sensitivity to PARP1 inhibition.
Collapse
|