1
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Hill BR, Ozgencil M, Buckley-Benbow L, Skingsley SLP, Tomlinson D, Eizmendi CO, Agnarelli A, Bellelli R. Loss of POLE3-POLE4 unleashes replicative gap accumulation upon treatment with PARP inhibitors. Cell Rep 2024; 43:114205. [PMID: 38753485 DOI: 10.1016/j.celrep.2024.114205] [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: 12/01/2023] [Revised: 04/06/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
The advent of PARP inhibitors (PARPis) has profoundly changed the treatment landscape of BRCA1/BRCA2-mutated cancers. Despite this, the development of resistance to these compounds has become a major challenge. Hence, a detailed understanding of the mechanisms underlying PARPi sensitivity is crucially needed. Here, we show that loss of the POLE3-POLE4 subunits of DNA polymerase epsilon (Polε) strongly sensitizes cancer cells to PARPis in a Polε level-independent manner. Loss of POLE3-POLE4 is not associated with defective RAD51 foci formation, excluding a major defect in homologous recombination. On the contrary, treatment with PARPis triggers replicative gap accumulation in POLE3-POLE4 knockout (KO) cells in a PRIMPOL-dependent manner. In addition to this, the loss of POLE3-POLE4 further sensitizes BRCA1-silenced cells to PARPis. Importantly, the knockdown of 53BP1 does not rescue PARPi sensitivity in POLE3-POLE4 KO cells, bypassing a common PARPi resistance mechanism and outlining a potential strategy to sensitize cancer cells to PARPis.
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Affiliation(s)
- Bethany Rebekah Hill
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Meryem Ozgencil
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Lauryn Buckley-Benbow
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Sophie Louise Pamela Skingsley
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Danielle Tomlinson
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Carmen Ortueta Eizmendi
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Alessandro Agnarelli
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Roberto Bellelli
- Centre for Cancer Cell & Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK.
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2
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Schreuder A, Wendel TJ, Dorresteijn CGV, Noordermeer SM. (Single-stranded DNA) gaps in understanding BRCAness. Trends Genet 2024:S0168-9525(24)00100-8. [PMID: 38789375 DOI: 10.1016/j.tig.2024.04.013] [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: 02/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
The tumour-suppressive roles of BRCA1 and 2 have been attributed to three seemingly distinct functions - homologous recombination, replication fork protection, and single-stranded (ss)DNA gap suppression - and their relative importance is under debate. In this review, we examine the origin and resolution of ssDNA gaps and discuss the recent advances in understanding the role of BRCA1/2 in gap suppression. There are ample data showing that gap accumulation in BRCA1/2-deficient cells is linked to genomic instability and chemosensitivity. However, it remains unclear whether there is a causative role and the function of BRCA1/2 in gap suppression cannot unambiguously be dissected from their other functions. We therefore conclude that the three functions of BRCA1 and 2 are closely intertwined and not mutually exclusive.
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Affiliation(s)
- Anne Schreuder
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Tiemen J Wendel
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Carlo G V Dorresteijn
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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3
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Batenburg NL, Sowa DJ, Walker JR, Andres SN, Zhu XD. CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells. Nucleic Acids Res 2024; 52:5067-5087. [PMID: 38416570 PMCID: PMC11109976 DOI: 10.1093/nar/gkae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024] Open
Abstract
CSB (Cockayne syndrome group B) and SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent, regulator of chromatin, subfamily A-like 1) are DNA translocases that belong to the SNF2 helicase family. They both are enriched at stalled replication forks. While SMARCAL1 is recruited by RPA32 to stalled forks, little is known about whether RPA32 also regulates CSB's association with stalled forks. Here, we report that CSB directly interacts with RPA, at least in part via a RPA32C-interacting motif within the N-terminal region of CSB. Modeling of the CSB-RPA32C interaction suggests that CSB binds the RPA32C surface previously shown to be important for binding of UNG2 and SMARCAL1. We show that this interaction is necessary for promoting fork slowing and fork degradation in BRCA2-deficient cells but dispensable for mediating restart of stalled forks. CSB competes with SMARCAL1 for RPA32 at stalled forks and acts non-redundantly with SMARCAL1 to restrain fork progression in response to mild replication stress. In contrast to CSB stimulated restart of stalled forks, SMARCAL1 inhibits restart of stalled forks in BRCA2-deficient cells, likely by suppressing BIR-mediated repair of collapsed forks. Loss of CSB leads to re-sensitization of SMARCAL1-depleted BRCA2-deficient cells to chemodrugs, underscoring a role of CSB in targeted cancer therapy.
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Affiliation(s)
- Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Dana J Sowa
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sara N Andres
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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4
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Zaino AM, Dash RC, James SJ, MacGilvary N, Crompton A, McPherson KS, Stanzione M, Korzhnev DM, Dyson NJ, Chatterjee N, Cantor SB, Hadden MK. Lead compound profiling for small molecule inhibitors of the REV1-CT/RIR Translesion synthesis Protein-Protein interaction. Bioorg Med Chem 2024; 106:117755. [PMID: 38749343 DOI: 10.1016/j.bmc.2024.117755] [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] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Translesion synthesis (TLS) is a cellular mechanism through which actively replicating cells recruit specialized, low-fidelity DNA polymerases to damaged DNA to allow for replication past these lesions. REV1 is one of these TLS DNA polymerases that functions primarily as a scaffolding protein to organize the TLS heteroprotein complex and ensure replication occurs in the presence of DNA lesions. The C-Terminal domain of REV1 (REV1-CT) forms many protein-protein interactions (PPIs) with other TLS polymerases, making it essential for TLS function and a promising drug target for anti-cancer drug development. We utilized several lead identification strategies to identify various small molecules capable of disrupting the PPI between REV1-CT and the REV1 Interacting Regions (RIR) present in several other TLS polymerases. These lead compounds were profiled in several in vitro potency and PK assays to identify two scaffolds (1 and 6) as the most promising for further development. Both 1 and 6 synergized with cisplatin in a REV1-dependent fashion and demonstrated promising in vivo PK and toxicity profiles.
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Affiliation(s)
- Angela M Zaino
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA
| | - Stephy J James
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA
| | - Nathan MacGilvary
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew Crompton
- University of Vermont Cancer Center and Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Kerry S McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Marcello Stanzione
- Massachusetts General Hospital Cancer Center, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Nimrat Chatterjee
- University of Vermont Cancer Center and Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Sharon B Cantor
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA.
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5
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Uhrig ME, Sharma N, Maxwell P, Selemenakis P, Mazin AV, Wiese C. Disparate requirements for RAD54L in replication fork reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550704. [PMID: 37546955 PMCID: PMC10402051 DOI: 10.1101/2023.07.26.550704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
RAD54L is a DNA motor protein with multiple roles in homologous recombination DNA repair (HR). In vitro , RAD54L was shown to also catalyze the reversal and restoration of model replication forks. In cells, however, little is known about how RAD54L may regulate the dynamics of DNA replication. Here, we show that RAD54L restrains the progression of replication forks and functions as a fork remodeler in human cells. Analogous to HLTF, SMARCAL1, and FBH1, and consistent with a role in fork reversal, RAD54L decelerates fork progression in response to replication stress and suppresses the formation of replication-associated ssDNA gaps. Interestingly, loss of RAD54L prevents nascent strand DNA degradation in both BRCA1/2- and 53BP1-deficient cells, suggesting that RAD54L functions in both pathways of RAD51-mediated replication fork reversal. In the HLTF/SMARCAL1 pathway, RAD54L is critical, but its ability to catalyze branch migration is dispensable, indicative of its function downstream of HLTF/SMARCAL1. Conversely, in the FBH1 pathway, branch migration activity of RAD54L is essential, and FBH1 engagement is dependent on its concerted action with RAD54L. Collectively, our results reveal disparate requirements for RAD54L in two distinct RAD51-mediated fork reversal pathways, positing its potential as a future therapeutic target.
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6
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Rajpurohit YS, Sharma DK, Lal M, Soni I. A perspective on tumor radiation resistance following high-LET radiation treatment. J Cancer Res Clin Oncol 2024; 150:226. [PMID: 38696003 PMCID: PMC11065934 DOI: 10.1007/s00432-024-05757-8] [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: 02/24/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
High-linear energy transfer (LET) radiation is a promising alternative to conventional low-LET radiation for therapeutic gain against cancer owing to its ability to induce complex and clustered DNA lesions. However, the development of radiation resistance poses a significant barrier. The potential molecular mechanisms that could confer resistance development are translesion synthesis (TLS), replication gap suppression (RGS) mechanisms, autophagy, epithelial-mesenchymal transition (EMT) activation, release of exosomes, and epigenetic changes. This article will discuss various types of complex clustered DNA damage, their repair mechanisms, mutagenic potential, and the development of radiation resistance strategies. Furthermore, it highlights the importance of careful consideration and patient selection when employing high-LET radiotherapy in clinical settings.
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Affiliation(s)
- Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India.
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India.
| | - Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Mitu Lal
- Molecular Biology Division, Bhabha Atomic Research Centre, 2-46-S, Modular Lab, A-Block, Mumbai, 400085, India
| | - Ishu Soni
- Homi Bhabha National Institute, DAE- Deemed University, Mumbai, 400094, India
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7
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Castaño BA, Schorer S, Guo Y, Calzetta NL, Gottifredi V, Wiesmüller L, Biber S. The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage. Nucleic Acids Res 2024; 52:3740-3760. [PMID: 38321962 PMCID: PMC11039994 DOI: 10.1093/nar/gkae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 02/08/2024] Open
Abstract
It is well-established that, through canonical functions in transcription and DNA repair, the tumor suppressor p53 plays a central role in safeguarding cells from the consequences of DNA damage. Recent data retrieved in tumor and stem cells demonstrated that p53 also carries out non-canonical functions when interacting with the translesion synthesis (TLS) polymerase iota (POLι) at DNA replication forks. This protein complex triggers a DNA damage tolerance (DDT) mechanism controlling the DNA replication rate. Given that the levels of p53 trigger non-binary rheostat-like functions in response to stress or during differentiation, we explore the relevance of the p53 levels for its DDT functions at the fork. We show that subtle changes in p53 levels modulate the contribution of some DDT factors including POLι, POLη, POLζ, REV1, PCNA, PRIMPOL, HLTF and ZRANB3 to the DNA replication rate. Our results suggest that the levels of p53 are central to coordinate the balance between DDT pathways including (i) fork-deceleration by the ZRANB3-mediated fork reversal factor, (ii) POLι-p53-mediated fork-slowing, (iii) POLι- and POLη-mediated TLS and (iv) PRIMPOL-mediated fork-acceleration. Collectively, our study reveals the relevance of p53 protein levels for the DDT pathway choice in replicating cells.
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Affiliation(s)
- Bryan A Castaño
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Sabrina Schorer
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Yitian Guo
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | | | | | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
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8
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Sang PB, Jaiswal RK, Lyu X, Chai W. Human CST complex restricts excessive PrimPol repriming upon UV induced replication stress by suppressing p21. Nucleic Acids Res 2024; 52:3778-3793. [PMID: 38348929 DOI: 10.1093/nar/gkae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 04/25/2024] Open
Abstract
DNA replication stress, caused by various endogenous and exogenous agents, halt or stall DNA replication progression. Cells have developed diverse mechanisms to tolerate and overcome replication stress, enabling them to continue replication. One effective strategy to overcome stalled replication involves skipping the DNA lesion using a specialized polymerase known as PrimPol, which reinitiates DNA synthesis downstream of the damage. However, the mechanism regulating PrimPol repriming is largely unclear. In this study, we observe that knockdown of STN1 or CTC1, components of the CTC1/STN1/TEN1 complex, leads to enhanced replication progression following UV exposure. We find that such increased replication is dependent on PrimPol, and PrimPol recruitment to stalled forks increases upon CST depletion. Moreover, we find that p21 is upregulated in STN1-depleted cells in a p53-independent manner, and p21 depletion restores normal replication rates caused by STN1 deficiency. We identify that p21 interacts with PrimPol, and STN1 depletion stimulates p21-PrimPol interaction and facilitates PrimPol recruitment to stalled forks. Our findings reveal a previously undescribed interplay between CST, PrimPol and p21 in promoting repriming in response to stalled replication, and shed light on the regulation of PrimPol repriming at stalled forks.
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Affiliation(s)
- Pau Biak Sang
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Rishi K Jaiswal
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Xinxing Lyu
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
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9
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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.
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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
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10
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Leuzzi G, Vasciaveo A, Taglialatela A, Chen X, Firestone TM, Hickman AR, Mao W, Thakar T, Vaitsiankova A, Huang JW, Cuella-Martin R, Hayward SB, Kesner JS, Ghasemzadeh A, Nambiar TS, Ho P, Rialdi A, Hebrard M, Li Y, Gao J, Gopinath S, Adeleke OA, Venters BJ, Drake CG, Baer R, Izar B, Guccione E, Keogh MC, Guerois R, Sun L, Lu C, Califano A, Ciccia A. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell 2024; 187:861-881.e32. [PMID: 38301646 PMCID: PMC10980358 DOI: 10.1016/j.cell.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 07/23/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 limits endogenous DNA damage, thereby suppressing cGAS-STING-dependent signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a PD-L1 transcriptional regulatory element, thereby promoting PD-L1 expression in cancer cells. SMARCAL1 loss hinders the ability of tumor cells to induce PD-L1 in response to genomic instability, enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a promising target for cancer immunotherapy.
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Affiliation(s)
- Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alessandro Vasciaveo
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | | | - Wendy Mao
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tanay Thakar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alina Vaitsiankova
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jordan S Kesner
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ali Ghasemzadeh
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander Rialdi
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxime Hebrard
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jinmei Gao
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | | | - Charles G Drake
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lu Sun
- EpiCypher Inc., Durham, NC 27709, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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11
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Lim PX, Zaman M, Feng W, Jasin M. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair. Mol Cell 2024; 84:447-462.e10. [PMID: 38244544 DOI: 10.1016/j.molcel.2023.12.025] [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: 04/07/2023] [Revised: 10/10/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
Tumor suppressor BRCA2 functions in homology-directed repair (HDR), the protection of stalled replication forks, and the suppression of replicative gaps, but their relative contributions to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for fork protection and gap suppression but not HDR. In mice, the loss of fork protection/gap suppression does not compromise genome stability or shorten tumor latency. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection/gap suppression defects are also observed in Brca2 heterozygous cells, likely due to reduced RAD51 stabilization at stalled forks/gaps. Gaps arise from PRIMPOL activity, which is associated with 5-hydroxymethyl-2'-deoxyuridine sensitivity due to the formation of SMUG1-generated abasic sites and is exacerbated by poly(ADP-ribose) polymerase (PARP) inhibition. However, HDR proficiency has the major role in mitigating sensitivity to chemotherapeutics, including PARP inhibitors.
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Affiliation(s)
- Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mahdia Zaman
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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12
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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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13
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Kawale AS, Ran X, Patel PS, Saxena S, Lawrence MS, Zou L. APOBEC3A induces DNA gaps through PRIMPOL and confers gap-associated therapeutic vulnerability. SCIENCE ADVANCES 2024; 10:eadk2771. [PMID: 38241374 PMCID: PMC10798555 DOI: 10.1126/sciadv.adk2771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Mutation signatures associated with apolipoprotein B mRNA editing catalytic polypeptide-like 3A/B (APOBEC3A/B) cytidine deaminases are prevalent across cancers, implying their roles as mutagenic drivers during tumorigenesis and tumor evolution. APOBEC3A (A3A) expression induces DNA replication stress and increases the cellular dependency on the ataxia telangiectasia and Rad3-related (ATR) kinase for survival. Nonetheless, how A3A induces DNA replication stress remains unclear. We show that A3A induces replication stress without slowing replication forks. We find that A3A induces single-stranded DNA (ssDNA) gaps through PrimPol-mediated repriming. A3A-induced ssDNA gaps are repaired by multiple pathways involving ATR, RAD51, and translesion synthesis. Both ATR inhibition and trapping of poly(ADP-ribose) polymerase (PARP) on DNA by PARP inhibitor impair the repair of A3A-induced gaps, preferentially killing A3A-expressing cells. When used in combination, PARP and ATR inhibitors selectively kill A3A-expressing cells synergistically in a manner dependent on PrimPol-generated gaps. Thus, A3A-induced replication stress arises from PrimPol-generated ssDNA gaps, which confer a therapeutic vulnerability to gap-targeted DNA repair inhibitors.
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Affiliation(s)
- Ajinkya S. Kawale
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Xiaojuan Ran
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Parasvi S. Patel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Michael S. Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
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14
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Mellor C, Nassar J, Šviković S, Sale J. PRIMPOL ensures robust handoff between on-the-fly and post-replicative DNA lesion bypass. Nucleic Acids Res 2024; 52:243-258. [PMID: 37971291 PMCID: PMC10783524 DOI: 10.1093/nar/gkad1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
The primase/polymerase PRIMPOL restarts DNA synthesis when replication is arrested by template impediments. However, we do not have a comprehensive view of how PRIMPOL-dependent repriming integrates with the main pathways of damage tolerance, REV1-dependent 'on-the-fly' lesion bypass at the fork and PCNA ubiquitination-dependent post-replicative gap filling. Guided by genome-wide CRISPR/Cas9 screens to survey the genetic interactions of PRIMPOL in a non-transformed and p53-proficient human cell line, we find that PRIMPOL is needed for cell survival following loss of the Y-family polymerases REV1 and POLη in a lesion-dependent manner, while it plays a broader role in promoting survival of cells lacking PCNA K164-dependent post-replicative gap filling. Thus, while REV1- and PCNA K164R-bypass provide two layers of protection to ensure effective damage tolerance, PRIMPOL is required to maximise the effectiveness of the interaction between them. We propose this is through the restriction of post-replicative gap length provided by PRIMPOL-dependent repriming.
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Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joelle Nassar
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Saša Šviković
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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15
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Spegg V, Altmeyer M. Genome maintenance meets mechanobiology. Chromosoma 2024; 133:15-36. [PMID: 37581649 PMCID: PMC10904543 DOI: 10.1007/s00412-023-00807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023]
Abstract
Genome stability is key for healthy cells in healthy organisms, and deregulated maintenance of genome integrity is a hallmark of aging and of age-associated diseases including cancer and neurodegeneration. To maintain a stable genome, genome surveillance and repair pathways are closely intertwined with cell cycle regulation and with DNA transactions that occur during transcription and DNA replication. Coordination of these processes across different time and length scales involves dynamic changes of chromatin topology, clustering of fragile genomic regions and repair factors into nuclear repair centers, mobilization of the nuclear cytoskeleton, and activation of cell cycle checkpoints. Here, we provide a general overview of cell cycle regulation and of the processes involved in genome duplication in human cells, followed by an introduction to replication stress and to the cellular responses elicited by perturbed DNA synthesis. We discuss fragile genomic regions that experience high levels of replication stress, with a particular focus on telomere fragility caused by replication stress at the ends of linear chromosomes. Using alternative lengthening of telomeres (ALT) in cancer cells and ALT-associated PML bodies (APBs) as examples of replication stress-associated clustered DNA damage, we discuss compartmentalization of DNA repair reactions and the role of protein properties implicated in phase separation. Finally, we highlight emerging connections between DNA repair and mechanobiology and discuss how biomolecular condensates, components of the nuclear cytoskeleton, and interfaces between membrane-bound organelles and membraneless macromolecular condensates may cooperate to coordinate genome maintenance in space and time.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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16
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González-Acosta D, Lopes M. DNA replication and replication stress response in the context of nuclear architecture. Chromosoma 2024; 133:57-75. [PMID: 38055079 PMCID: PMC10904558 DOI: 10.1007/s00412-023-00813-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
The DNA replication process needs to be coordinated with other DNA metabolism transactions and must eventually extend to the full genome, regardless of chromatin status, gene expression, secondary structures and DNA lesions. Completeness and accuracy of DNA replication are crucial to maintain genome integrity, limiting transformation in normal cells and offering targeting opportunities for proliferating cancer cells. DNA replication is thus tightly coordinated with chromatin dynamics and 3D genome architecture, and we are only beginning to understand the underlying molecular mechanisms. While much has recently been discovered on how DNA replication initiation is organised and modulated in different genomic regions and nuclear territories-the so-called "DNA replication program"-we know much less on how the elongation of ongoing replication forks and particularly the response to replication obstacles is affected by the local nuclear organisation. Also, it is still elusive how specific components of nuclear architecture participate in the replication stress response. Here, we review known mechanisms and factors orchestrating replication initiation, and replication fork progression upon stress, focusing on recent evidence linking genome organisation and nuclear architecture with the cellular responses to replication interference, and highlighting open questions and future challenges to explore this exciting new avenue of research.
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Affiliation(s)
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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17
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Jennings L, Walters HA, McCraw TJ, Turner JL, Mason JM. FBH1 deficiency sensitizes cells to WEE1 inhibition by promoting mitotic catastrophe. DNA Repair (Amst) 2024; 133:103611. [PMID: 38103522 PMCID: PMC10872337 DOI: 10.1016/j.dnarep.2023.103611] [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: 05/15/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
WEE1 kinase phosphorylates CDK1 and CDK2 to regulate origin firing and mitotic entry. Inhibition of WEE1 has become an attractive target for cancer therapy due to the simultaneous induction of replication stress and inhibition of the G2/M checkpoint. WEE1 inhibition in cancer cells with high levels of replication stress results in induction of replication catastrophe and mitotic catastrophe. To increase potential as a single agent chemotherapeutic, a better understanding of genetic alterations that impact cellular responses to WEE1 inhibition is warranted. Here, we investigate the impact of loss of the helicase, FBH1, on the cellular response to WEE1 inhibition. FBH1-deficient cells have a reduction in ssDNA and double strand break signaling indicating FBH1 is required for induction of replication stress response in cells treated with WEE1 inhibitors. Despite the defect in the replication stress response, FBH1-deficiency sensitizes cells to WEE1 inhibition by increasing mitotic catastrophe. We propose loss of FBH1 is resulting in replication-associated damage that requires the WEE1-dependent G2 checkpoint for repair.
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Affiliation(s)
- Lucy Jennings
- Department of Genetics and Biochemistry, Clemson University, United States
| | | | - Tyler J McCraw
- Department of Genetics and Biochemistry, Clemson University, United States
| | - Joshua L Turner
- Department of Genetics and Biochemistry, Clemson University, United States
| | - Jennifer M Mason
- Department of Genetics and Biochemistry, Clemson University, United States.
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18
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Khatib JB, Nicolae CM, Moldovan GL. Role of Translesion DNA Synthesis in the Metabolism of Replication-associated Nascent Strand Gaps. J Mol Biol 2024; 436:168275. [PMID: 37714300 PMCID: PMC10842951 DOI: 10.1016/j.jmb.2023.168275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Translesion DNA synthesis (TLS) is a DNA damage tolerance pathway utilized by cells to overcome lesions encountered throughout DNA replication. During replication stress, cancer cells show increased dependency on TLS proteins for cellular survival and chemoresistance. TLS proteins have been described to be involved in various DNA repair pathways. One of the major emerging roles of TLS is single-stranded DNA (ssDNA) gap-filling, primarily after the repriming activity of PrimPol upon encountering a lesion. Conversely, suppression of ssDNA gap accumulation by TLS is considered to represent a mechanism for cancer cells to evade the toxicity of chemotherapeutic agents, specifically in BRCA-deficient cells. Thus, TLS inhibition is emerging as a potential treatment regimen for DNA repair-deficient tumors.
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Affiliation(s)
- Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA. https://twitter.com/JudeBKhatib
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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19
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Nickoloff JA, Jaiswal AS, Sharma N, Williamson EA, Tran MT, Arris D, Yang M, Hromas R. Cellular Responses to Widespread DNA Replication Stress. Int J Mol Sci 2023; 24:16903. [PMID: 38069223 PMCID: PMC10707325 DOI: 10.3390/ijms242316903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Aruna S. Jaiswal
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Elizabeth A. Williamson
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Manh T. Tran
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Dominic Arris
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Ming Yang
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
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20
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Palumbieri MD, Merigliano C, González-Acosta D, Kuster D, Krietsch J, Stoy H, von Känel T, Ulferts S, Welter B, Frey J, Doerdelmann C, Sanchi A, Grosse R, Chiolo I, Lopes M. Nuclear actin polymerization rapidly mediates replication fork remodeling upon stress by limiting PrimPol activity. Nat Commun 2023; 14:7819. [PMID: 38016948 PMCID: PMC10684888 DOI: 10.1038/s41467-023-43183-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase and observed their rapid extension in number and length upon genotoxic treatments, frequently taking contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork remodeling is linked to deregulated chromatin loading of PrimPol, which promotes unrestrained and discontinuous DNA synthesis and limits the recruitment of RAD51 and SMARCAL1 to nascent DNA. Moreover, defective nuclear actin polymerization upon mild replication interference induces chromosomal instability in a PRIMPOL-dependent manner. Hence, by limiting PrimPol activity, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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Affiliation(s)
| | - Chiara Merigliano
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | | | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Department of Cellular and Molecular Medicine, Copenhagen University, Copenhagen, Denmark
| | - Thomas von Känel
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Svenja Ulferts
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Welter
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Joël Frey
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Cyril Doerdelmann
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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21
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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. The Response of the Replication Apparatus to Leading Template Strand Blocks. Cells 2023; 12:2607. [PMID: 37998342 PMCID: PMC10670059 DOI: 10.3390/cells12222607] [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: 10/23/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Duplication of the genome requires the replication apparatus to overcome a variety of impediments, including covalent DNA adducts, the most challenging of which is on the leading template strand. Replisomes consist of two functional units, a helicase to unwind DNA and polymerases to synthesize it. The helicase is a multi-protein complex that encircles the leading template strand and makes the first contact with a leading strand adduct. The size of the channel in the helicase would appear to preclude transit by large adducts such as DNA: protein complexes (DPC). Here we discuss some of the extensively studied pathways that support replication restart after replisome encounters with leading template strand adducts. We also call attention to recent work that highlights the tolerance of the helicase for adducts ostensibly too large to pass through the central channel.
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Affiliation(s)
| | | | | | | | - Michael M. Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (M.A.B.)
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22
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Bai G, Endres T, Kühbacher U, Greer BH, Peacock EM, Crossley MP, Sathirachinda A, Cortez D, Eichman BF, Cimprich KA. HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.563641. [PMID: 37961428 PMCID: PMC10634870 DOI: 10.1101/2023.10.27.563641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
G-quadruplexes (G4s) form throughout the genome and influence important cellular processes, but their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected, dual role for the dsDNA translocase HLTF in G4 metabolism. First, we find that HLTF is enriched at G4s in the human genome and suppresses G4 accumulation throughout the cell cycle using its ATPase activity. This function of HLTF affects telomere maintenance by restricting alternative lengthening of telomeres, a process stimulated by G4s. We also show that HLTF and MSH2, a mismatch repair factor that binds G4s, act in independent pathways to suppress G4s and to promote resistance to G4 stabilization. In a second, distinct role, HLTF restrains DNA synthesis upon G4 stabilization by suppressing PrimPol-dependent repriming. Together, the dual functions of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
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23
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Paniagua I, Jacobs JJL. Freedom to err: The expanding cellular functions of translesion DNA polymerases. Mol Cell 2023; 83:3608-3621. [PMID: 37625405 DOI: 10.1016/j.molcel.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 08/27/2023]
Abstract
Translesion synthesis (TLS) DNA polymerases were originally described as error-prone enzymes involved in the bypass of DNA lesions. However, extensive research over the past few decades has revealed that these enzymes play pivotal roles not only in lesion bypass, but also in a myriad of other cellular processes. Such processes include DNA replication, DNA repair, epigenetics, immune signaling, and even viral infection. This review discusses the wide range of functions exhibited by TLS polymerases, including their underlying biochemical mechanisms and associated mutagenicity. Given their multitasking ability to alleviate replication stress, TLS polymerases represent a cellular dependency and a critical vulnerability of cancer cells. Hence, this review also highlights current and emerging strategies for targeting TLS polymerases in cancer therapy.
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Affiliation(s)
- Inés Paniagua
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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24
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Gökbuget D, Lenshoek K, Boileau RM, Bayerl J, Huang H, Wiita AP, Laird DJ, Blelloch R. Transcriptional repression upon S phase entry protects genome integrity in pluripotent cells. Nat Struct Mol Biol 2023; 30:1561-1570. [PMID: 37696959 DOI: 10.1038/s41594-023-01092-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/07/2023] [Indexed: 09/13/2023]
Abstract
Coincident transcription and DNA replication causes replication stress and genome instability. Rapidly dividing mouse pluripotent stem cells are highly transcriptionally active and experience elevated replication stress, yet paradoxically maintain genome integrity. Here, we study FOXD3, a transcriptional repressor enriched in pluripotent stem cells, and show that its repression of transcription upon S phase entry is critical to minimizing replication stress and preserving genome integrity. Acutely deleting Foxd3 leads to immediate replication stress, G2/M phase arrest, genome instability and p53-dependent apoptosis. FOXD3 binds near highly transcribed genes during S phase entry, and its loss increases the expression of these genes. Transient inhibition of RNA polymerase II in S phase reduces observed replication stress and cell cycle defects. Loss of FOXD3-interacting histone deacetylases induces replication stress, while transient inhibition of histone acetylation opposes it. These results show how a transcriptional repressor can play a central role in maintaining genome integrity through the transient inhibition of transcription during S phase, enabling faithful DNA replication.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Kayla Lenshoek
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan M Boileau
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Bayerl
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, San Francisco, CA, USA
| | - Hector Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Arun P Wiita
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Diana J Laird
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, San Francisco, CA, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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25
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Hawks AL, Bergmann A, McCraw TJ, Mason JM. UBC13-mediated template switching promotes replication stress resistance in FBH1-deficient cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556280. [PMID: 37732269 PMCID: PMC10508767 DOI: 10.1101/2023.09.04.556280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The proper resolution of DNA damage during replication is essential for genome stability. FBH1, a UvrD, helicase plays crucial roles in the DNA damage response. FBH1 promotes double strand break formation and signaling in response to prolonged replication stress to initiate apoptosis. Human FBH1 regulates RAD51 to inhibit homologous recombination. A previous study suggested that mis-regulation of RAD51 may contribute to replication stress resistance in FBH1-deficient cells, but the underlying mechanism remains unknown. Here, we provide direct evidence that RAD51 promotes replication stress resistance in FBH1-deficient cells. We demonstrate inhibition of RAD51 using the small molecule, B02, partially rescues double strand break signaling in FBH1-deficient cells. We show that inhibition of only the strand exchange activity of RAD51 rescues double strand break signaling in FBH1 knockout cells. Finally, we show that depletion of UBC13, a E2 protein that promotes RAD51-dependent template switching, rescues double strand break formation and signaling sensitizing FBH1-deficient cells to replication stress. Our results suggest FBH1 regulates template switching to promote replication stress sensitivity.
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Affiliation(s)
- Alexandra L. Hawks
- Department of Genetics and Biochemistry, Clemson University, Clemson University
| | - Amy Bergmann
- Department of Genetics and Biochemistry, Clemson University, Clemson University
| | - Tyler J. McCraw
- Department of Genetics and Biochemistry, Clemson University, Clemson University
| | - Jennifer M. Mason
- Department of Genetics and Biochemistry, Clemson University, Clemson University
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26
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Martinez-Marin D, Helmer RA, Kaur G, Washburn RL, Martinez-Zaguilan R, Sennone SR, Dufour JM, Chilton BS. Helicase-like transcription factor (HLTF)-deleted CDX/TME model of colorectal cancer increased transcription of oxidative phosphorylation genes and diverted glycolysis to boost S-glutathionylation in lymphatic intravascular metastatic niches. PLoS One 2023; 18:e0291023. [PMID: 37682902 PMCID: PMC10490896 DOI: 10.1371/journal.pone.0291023] [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: 06/20/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Helicase-like transcription factor (HLTF) also known as SMARCA3, protects genome integrity. A tumor suppressor, HLTF is expressed in tumor cells but not in the tumor microenvironment (TME) in early-stage colorectal cancer (CRC). With disease progression, there is high concordance between epigenetic silencing of HLTF in CRC cells and negligible HLTF expression in the TME. We developed a cell line-derived xenograft (CDX) model and show for the first time that HLTF-deletion in cancer cells and the TME results in metabolic reprogramming that mitigates oxidative stress in lymphatic intravascular metastatic niches. The two metabolic pathways that derive energy from glucose-glycolysis and oxidative phosphorylation (OXPHOS)-are variously utilized by cancer cells depending upon the TME. HIF-1α, a master regulator of glycolysis, was eliminated from a role in reprogramming metabolism to satisfy CDX energetic requirements by RNAseq and spatial transcriptomics. Variability in the gut microbiome, with a putative role in altered metabolism, was also eliminated. HLTF-deleted cancer cells recovered from DNA damage at a transcriptomic level induction of DNA repair and OXPHOS genes linked to an amoeboid-associated phenotype at the tumor border (confocal microscopy). HLTF-deleted cancer and endothelial cells of lymphatic (PDPN) intravascular niches in the TME shared a site-specific protein S-glutathionylation signature (2D DIGE, MALDI-TOF/TOF mass spectrometry) for three glycolytic enzymes (PGK1 Cys379/380, PGAM1 Cys55, ENOA1 Cys119) that diverted glycolysis in support of continued glutathione biosynthesis. The collective absence of HLTF/Hltf from tumor and TME achieved redox homeostasis throughout the CDX and promoted metastasis.
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Affiliation(s)
- Dalia Martinez-Marin
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Immunology and Molecular Microbiology, Texas Tech University-Health Sciences Center, Lubbock, Texas, United States of America
| | - Rebecca A. Helmer
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Current address: Garrison Independent School District, Garrison, Texas, United States of America
| | - Gurvinder Kaur
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rachel L. Washburn
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Souad R. Sennone
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Texas Center for Comparative Cancer Research, Texas Tech University School of Veterinary Medicine, Amarillo, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Texas Center for Comparative Cancer Research, Texas Tech University School of Veterinary Medicine, Amarillo, Texas, United States of America
- School of Medicine Cancer Center, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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27
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Rastokina A, Cebrián J, Mozafari N, Mandel NH, Smith CI, Lopes M, Zain R, Mirkin S. Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers. Nucleic Acids Res 2023; 51:8532-8549. [PMID: 37216608 PMCID: PMC10484681 DOI: 10.1093/nar/gkad441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/02/2023] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Friedreich's ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron of the human FXN gene that occur during both intergenerational transmissions and in somatic cells. Here we describe an experimental system to analyze large-scale repeat expansions in cultured human cells. It employs a shuttle plasmid that can replicate from the SV40 origin in human cells or be stably maintained in S. cerevisiae utilizing ARS4-CEN6. It also contains a selectable cassette allowing us to detect repeat expansions that accumulated in human cells upon plasmid transformation into yeast. We indeed observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system to study large-scale repeat expansions in human cells. Further, GAA•TTC repeats stall replication fork progression, while the frequency of repeat expansions appears to depend on proteins implicated in replication fork stalling, reversal, and restart. Locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers, which interfere with triplex formation at GAA•TTC repeats in vitro, prevented the expansion of these repeats in human cells. We hypothesize, therefore, that triplex formation by GAA•TTC repeats stall replication fork progression, ultimately leading to repeat expansions during replication fork restart.
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Affiliation(s)
| | - Jorge Cebrián
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | | | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
- Center for Rare Diseases, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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28
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Kaur G, Helmer RA, Martinez-Marin D, Sennoune SR, Washburn RL, Martinez-Zaguilan R, Dufour JM, Chilton BS. Helicase-like transcription factor (Hltf)-deletion activates Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality. PLoS One 2023; 18:e0286109. [PMID: 37624843 PMCID: PMC10456192 DOI: 10.1371/journal.pone.0286109] [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: 12/05/2022] [Accepted: 05/09/2023] [Indexed: 08/27/2023] Open
Abstract
Epigenetic mechanisms are integral to pancreatic β cell function. Promoter hypermethylation of the helicase like-transcription factor (HLTF) gene-a component of the cellular DNA damage response that contributes to genome stability-has been implicated in age-associated changes in β cells. To study HLTF, we generated global and β cell-specific (β) Hltf knockout (KO) immune competent (IC) and immune deficient (ID) Rag2-/IL2- mice. IC global and β Hltf KO mice were neonatal lethal whereas ID global and β Hltf KO newborn mice had normal survival. This focused our investigation on the effects of Rag2 interruption with common gamma chain interruption on β cell function/survival. Three-way transcriptomic (RNAseq) analyses of whole pancreata from IC and ID newborn β Hltf KO and wild type (Hltf +/+) controls combined with spatially resolved transcriptomic analysis of formalin fixed paraffin embedded tissue, immunohistochemistry and laser scanning confocal microscopy showed DNA damage caused by β Hltf KO in IC mice upregulated the Hmgb1-Rage axis and a gene signature for innate immune cells. Perforin-delivered granzyme A (GzmA) activation of DNase, Nme1, showed damaged nuclear single-stranded DNA (γH2AX immunostaining). This caspase-independent method of cell death was supported by transcriptional downregulation of Serpinc1 gene that encodes a serine protease inhibitor of GzmA. Increased transcriptional availability of complement receptors C3ar1 and C5ar1 likely invited crosstalk with Hmgb1 to amplify inflammation. This study explores the complex dialog between β cells and immune cells during development. It has implications for the initiation of type I diabetes in utero when altered gene expression that compromises genome stability invokes a localized inflammatory response.
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Affiliation(s)
- Gurvinder Kaur
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rebecca A. Helmer
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Dalia Martinez-Marin
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Immunology and Molecular Microbiology, Texas Tech University-Health Sciences Center, Lubbock, Texas, United States of America
| | - Souad R. Sennoune
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rachel L. Washburn
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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29
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Rousseau V, Einig E, Jin C, Horn J, Riebold M, Poth T, Jarboui MA, Flentje M, Popov N. Trim33 masks a non-transcriptional function of E2f4 in replication fork progression. Nat Commun 2023; 14:5143. [PMID: 37612308 PMCID: PMC10447549 DOI: 10.1038/s41467-023-40847-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
Replicative stress promotes genomic instability and tumorigenesis but also presents an effective therapeutic endpoint, rationalizing detailed analysis of pathways that control DNA replication. We show here that the transcription factor E2f4 recruits the DNA helicase Recql to facilitate progression of DNA replication forks upon drug- or oncogene-induced replicative stress. In unperturbed cells, the Trim33 ubiquitin ligase targets E2f4 for degradation, limiting its genomic binding and interactions with Recql. Replicative stress blunts Trim33-dependent ubiquitination of E2f4, which stimulates transient Recql recruitment to chromatin and facilitates recovery of DNA synthesis. In contrast, deletion of Trim33 induces chronic genome-wide recruitment of Recql and strongly accelerates DNA replication under stress, compromising checkpoint signaling and DNA repair. Depletion of Trim33 in Myc-overexpressing cells leads to accumulation of replication-associated DNA damage and delays Myc-driven tumorigenesis. We propose that the Trim33-E2f4-Recql axis controls progression of DNA replication forks along transcriptionally active chromatin to maintain genome integrity.
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Affiliation(s)
- Vanessa Rousseau
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076, Tübingen, Germany
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str 2, 97080, Würzburg, Germany
- Interfaculty Institute for Biochemistry, University Hospital Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany
| | - Elias Einig
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076, Tübingen, Germany
| | - Chao Jin
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076, Tübingen, Germany
| | - Julia Horn
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str 2, 97080, Würzburg, Germany
- Wakenitzmauer 3, 23552, Lübeck, Germany
| | - Mathias Riebold
- Department of Gastroenterology, Gastrointestinal Oncology, Hepatology, Infectiology, and Geriatry, University Hospital Tübingen, Otfried-Müller-Str 12, 72076, Tübingen, Germany
| | - Tanja Poth
- Center for Model System and Comparative Pathology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Mohamed-Ali Jarboui
- Core Facility for Medical Bioanalytics, Proteomics Platform Tübingen (PxP), Institute for Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Str 7, 72076, Tübingen, Germany
| | - Michael Flentje
- Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Str 2, 97080, Würzburg, Germany
| | - Nikita Popov
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Müller-Str 14, 72076, Tübingen, Germany.
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30
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Batenburg NL, Walker JR, Zhu XD. CSB Regulates Pathway Choice in Response to DNA Replication Stress Induced by Camptothecin. Int J Mol Sci 2023; 24:12419. [PMID: 37569794 PMCID: PMC10418903 DOI: 10.3390/ijms241512419] [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: 06/28/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Topoisomerase inhibitor camptothecin (CPT) induces fork stalling and is highly toxic to proliferating cells. However, how cells respond to CPT-induced fork stalling has not been fully characterized. Here, we report that Cockayne syndrome group B (CSB) protein inhibits PRIMPOL-dependent fork repriming in response to a low dose of CPT. At a high concentration of CPT, CSB is required to promote the restart of DNA replication through MUS81-RAD52-POLD3-dependent break-induced replication (BIR). In the absence of CSB, resumption of DNA synthesis at a high concentration of CPT can occur through POLQ-LIG3-, LIG4-, or PRIMPOL-dependent pathways, which are inhibited, respectively, by RAD51, BRCA1, and BRCA2 proteins. POLQ and LIG3 are core components of alternative end joining (Alt-EJ), whereas LIG4 is a core component of nonhomologous end joining (NHEJ). These results suggest that CSB regulates fork restart pathway choice following high-dosage CPT-induced fork stalling, promoting BIR but inhibiting Alt-EJ, NHEJ, and fork repriming. We find that loss of CSB and BRCA2 is a toxic combination to genomic stability and cell survival at a high concentration of CPT, which is likely due to accumulation of ssDNA gaps, underscoring an important role of CSB in regulating the therapy response in cancers lacking functional BRCA2.
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Affiliation(s)
| | | | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (N.L.B.); (J.R.W.)
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31
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Boldinova EO, Makarova AV. Regulation of Human DNA Primase-Polymerase PrimPol. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1139-1155. [PMID: 37758313 DOI: 10.1134/s0006297923080084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 10/03/2023]
Abstract
Transmission of genetic information depends on successful completion of DNA replication. Genomic DNA is subjected to damage on a daily basis. DNA lesions create obstacles for DNA polymerases and can lead to the replication blockage, formation of DNA breaks, cell cycle arrest, and apoptosis. Cells have evolutionary adapted to DNA damage by developing mechanisms allowing elimination of lesions prior to DNA replication (DNA repair) and helping to bypass lesions during DNA synthesis (DNA damage tolerance). The second group of mechanisms includes the restart of DNA synthesis at the sites of DNA damage by DNA primase-polymerase PrimPol. Human PrimPol was described in 2013. The properties and functions of this enzyme have been extensively studied in recent years, but very little is known about the regulation of PrimPol and association between the enzyme dysfunction and diseases. In this review, we described the mechanisms of human PrimPol regulation in the context of DNA replication, discussed in detail interactions of PrimPol with other proteins, and proposed possible pathways for the regulation of human PrimPol activity. The article also addresses the association of PrimPol dysfunction with human diseases.
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Affiliation(s)
- Elizaveta O Boldinova
- Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alena V Makarova
- Kurchatov Institute National Research Centre, Moscow, 123182, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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32
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Beauvois A, Gazon H, Chauhan PS, Jamakhani M, Jacques JR, Thiry M, Dejardin E, Valentin ED, Twizere JC, Péloponèse JM, Njock MS, Yasunaga JI, Matsuoka M, Hamaïdia M, Willems L. The helicase-like transcription factor redirects the autophagic flux and restricts human T cell leukemia virus type 1 infection. Proc Natl Acad Sci U S A 2023; 120:e2216127120. [PMID: 37487091 PMCID: PMC10400947 DOI: 10.1073/pnas.2216127120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/11/2023] [Indexed: 07/26/2023] Open
Abstract
Retroviruses and their host have coevolved in a delicate balance between viral replication and survival of the infected cell. In this equilibrium, restriction factors expressed by infected cells control different steps of retroviral replication such as entry, uncoating, nuclear import, expression, or budding. Here, we describe a mechanism of restriction against human T cell leukemia virus type 1 (HTLV-1) by the helicase-like transcription factor (HLTF). We show that RNA and protein levels of HLTF are reduced in primary T cells of HTLV-1-infected subjects, suggesting a clinical relevance. We further demonstrate that the viral oncogene Tax represses HLTF transcription via the Enhancer of zeste homolog 2 methyltransferase of the Polycomb repressive complex 2. The Tax protein also directly interacts with HLTF and induces its proteasomal degradation. RNA interference and gene transduction in HTLV-1-infected T cells derived from patients indicate that HLTF is a restriction factor. Restoring the normal levels of HLTF expression induces the dispersal of the Golgi apparatus and overproduction of secretory granules. By synergizing with Tax-mediated NF-κB activation, physiologically relevant levels of HLTF intensify the autophagic flux. Increased vesicular trafficking leads to an enlargement of the lysosomes and the production of large vacuoles containing viral particles. HLTF induction in HTLV-1-infected cells significantly increases the percentage of defective virions. In conclusion, HLTF-mediated activation of the autophagic flux blunts the infectious replication cycle of HTLV-1, revealing an original mode of viral restriction.
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Affiliation(s)
- Aurélie Beauvois
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Hélène Gazon
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Pradeep Singh Chauhan
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Majeed Jamakhani
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Jean-Rock Jacques
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Marc Thiry
- Laboratory of Cell and Tissue Biology, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
| | - Emmanuel Dejardin
- Laboratory of Molecular Immunology & Signal Transduction, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
| | - Emmanuel Di Valentin
- Viral Vectors Platform, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000Liège, Belgium
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000Liège, Belgium
| | - Jean-Marie Péloponèse
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, 34094, Montpellier, France
| | - Makon-Sébastien Njock
- Laboratory of Pneumology, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, University Hospital of Liège, 4000Liège, Belgium
| | | | - Masao Matsuoka
- Department of Hematology, Kumamoto University, 860-8556, Kumamoto, Japan
| | - Malik Hamaïdia
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
| | - Luc Willems
- Laboratory of Molecular and Cellular Epigenetics, Grappe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, 4000, Liège, Belgium
- Molecular Biology, Teaching and Research Center, University of Liège, 5030, Gembloux, Belgium
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Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD, Wollscheid HP. Nuclear myosin VI maintains replication fork stability. Nat Commun 2023; 14:3787. [PMID: 37355687 PMCID: PMC10290672 DOI: 10.1038/s41467-023-39517-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 06/26/2023] Open
Abstract
The actin cytoskeleton is of fundamental importance for cellular structure and plasticity. However, abundance and function of filamentous actin in the nucleus are still controversial. Here we show that the actin-based molecular motor myosin VI contributes to the stabilization of stalled or reversed replication forks. In response to DNA replication stress, myosin VI associates with stalled replication intermediates and cooperates with the AAA ATPase Werner helicase interacting protein 1 (WRNIP1) in protecting these structures from DNA2-mediated nucleolytic attack. Using functionalized affinity probes to manipulate myosin VI levels in a compartment-specific manner, we provide evidence for the direct involvement of myosin VI in the nucleus and against a contribution of the abundant cytoplasmic pool during the replication stress response.
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Affiliation(s)
- Jie Shi
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Kristine Hauschulte
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Srijana Maharjan
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Mainz Biomed N.V., Robert-Koch-Str. 50, D - 55129, Mainz, Germany
| | - Valerie Arz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Max Planck School Matter to Life, Jahnstr. 29, D - 69120, Heidelberg, Germany
| | - Jonas V Schaefer
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Birgit Dreier
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Andreas Plückthun
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 15, D - 55128, Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
| | - Hans-Peter Wollscheid
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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35
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Tan Y, Wu D, Liu ZY, Yu HQ, Zheng XR, Lin XT, Bie P, Zhang LD, Xie CM. Degradation of helicase-like transcription factor (HLTF) by β-TrCP promotes hepatocarcinogenesis via activation of the p62/mTOR axis. J Mol Cell Biol 2023; 15:mjad012. [PMID: 36822623 PMCID: PMC10478628 DOI: 10.1093/jmcb/mjad012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/27/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Helicase-like transcription factor (HLTF) has been found to be involved in the maintenance of genome stability and tumour suppression, but whether its downregulation in cancers is associated with posttranslational regulation remains unclear. Here, we observed that HLTF was significantly downregulated in hepatocellular carcinoma (HCC) tissues and positively associated with the survival of HCC patients. Mechanistically, the decreased expression of HLTF in HCC was attributed to elevated β-TrCP-mediated ubiquitination and degradation. Knockdown of HLTF enhanced p62 transcriptional activity and mammalian target of rapamycin (mTOR) activation, leading to HCC tumourigenesis. Inhibition of mTOR effectively blocked β-TrCP overexpression- or HLTF knockdown-mediated HCC tumourigenesis and metastasis. Furthermore, in clinical tissues, decreased HLTF expression was positively correlated with elevated expression of β-TrCP, p62, or p-mTOR in HCC patients. Overall, our data not only uncover new roles of HLTF in HCC cell proliferation and metastasis, but also reveal a novel posttranslational modification of HLTF by β-TrCP, indicating that the β-TrCP/HLTF/p62/mTOR axis may be a new oncogenic driver involved in HCC development. This finding provides a potential therapeutic strategy for HCC patients by targeting the β-TrCP/HLTF/p62/mTOR axis.
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Affiliation(s)
- Ye Tan
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Di Wu
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ze-Yu Liu
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Hong-Qiang Yu
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiang-Ru Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Xiao-Tong Lin
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ping Bie
- Department of Hepatobiliary and Pancreatic Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Lei-Da Zhang
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Chuan-Ming Xie
- Key Laboratory of Hepatobiliary and Pancreatic Surgery, Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
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36
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Cen X, Lu Y, Lu J, Zhan P, Cheng Y, Luo C, Liu J, Xie C, Wang F. Upregulation of helicase-like transcription factor predicts poor prognosis and facilitates hepatocellular carcinoma progression. Hum Cell 2023:10.1007/s13577-023-00917-3. [PMID: 37227687 DOI: 10.1007/s13577-023-00917-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 05/12/2023] [Indexed: 05/26/2023]
Abstract
Helicase-like transcription factor (HLTF) belongs to the family of SWI/SNF proteins, which has been reported to exert oncogenic function in several human cancers. However, to date, its functional role in hepatocellular carcinoma (HCC) has not been revealed. Here, we found that HLTF was highly expressed in HCC tissues compared to nontumor tissues. Additionally, upregulation of HLTF was significantly associated with poor prognosis of patients with HCC. Functional experiments demonstrated that knockdown of HLTF expression significantly inhibited the proliferation, migration, and invasion of HCC cells in vitro, and suppressed tumor growth in vivo. In conclusion, our results suggest that upregulation of HLTF is associated with the development of HCC, and HLTF may be a potential therapeutic target for HCC treatment.
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Affiliation(s)
- Xuesong Cen
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China
| | - Yuyan Lu
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China
| | - Jing Lu
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China
| | - Ping Zhan
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China
| | - Yizhe Cheng
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China
| | - Changhong Luo
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China
| | - Jie Liu
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China
| | - Chengrong Xie
- Xiamen Translational Medical Key Laboratory of Digestive System Tumor, Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, 209 South Hubin Road, Xiamen, 361004, Fujian Province, China.
| | - Fuqiang Wang
- Department of Hepatobiliary Surgery, Xiamen Key Laboratory of Liver Diseases, Xiamen Hospital of Traditional Chinese Medicine, Beijing University of Chinese Medicine, 1739 Xianyue Road, Xiamen, 361001, Fujian Province, China.
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37
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Jennings L, Walters HA, Mason JM. FBH1 deficiency sensitizes cells to WEE1 inhibition by promoting mitotic catastrophe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540841. [PMID: 37292855 PMCID: PMC10245586 DOI: 10.1101/2023.05.15.540841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
WEE1 kinase phosphorylates CDK1 and CDK2 to regulate origin firing and mitotic entry. Inhibition of WEE1 has become an attractive target for cancer therapy due to the simultaneous induction of replication stress and inhibition of the G2/M checkpoint. WEE1 inhibition in cancer cells with high levels of replication stress results in induction of replication catastrophe and mitotic catastrophe. To increase potential as a single agent chemotherapeutic, a better understanding of genetic alterations that impact cellular responses to WEE1 inhibition is warranted. Here, we investigate the impact of loss of the helicase, FBH1, on the cellular response to WEE1 inhibition. FBH1-deficient cells have a reduction in ssDNA and double strand break signaling indicating FBH1 is required for induction of replication stress response in cells treated with WEE1 inhibitors. Despite the defect in the replication stress response, FBH1-deficiency sensitizes cells to WEE1 inhibition by increasing mitotic catastrophe. We propose loss of FBH1 is resulting in replication-associated damage that requires the WEE1-dependent G2 checkpoint for repair.
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Affiliation(s)
- Lucy Jennings
- Department of Genetics and Biochemistry, Clemson University, Clemson University
| | | | - Jennifer M. Mason
- Department of Genetics and Biochemistry, Clemson University, Clemson University
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38
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Zou Y, Pei J, Long H, Lan L, Dong K, Wang T, Li M, Zhao Z, Zhu L, Zhang G, Jin X, Wang Y, Wen Z, Wei M, Feng Y. H4S47 O-GlcNAcylation regulates the activation of mammalian replication origins. Nat Struct Mol Biol 2023:10.1038/s41594-023-00998-6. [PMID: 37202474 DOI: 10.1038/s41594-023-00998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
Abstract
The transmission and maintenance of genetic information in eukaryotic cells relies on the faithful duplication of the entire genome. In each round of division, excessive replication origins are licensed, with only a fraction activated to give rise to bi-directional replication forks in the context of chromatin. However, it remains elusive how eukaryotic replication origins are selectively activated. Here we demonstrate that O-GlcNAc transferase (OGT) enhances replication initiation by catalyzing H4S47 O-GlcNAcylation. Mutation of H4S47 impairs DBF4-dependent protein kinase (DDK) recruitment on chromatin, causing reduced phosphorylation of the replicative helicase mini-chromosome maintenance (MCM) complex and compromised DNA unwinding. Our short nascent-strand sequencing results further confirm the importance of H4S47 O-GlcNAcylation in origin activation. We propose that H4S47 O-GlcNAcylation directs origin activation through facilitating MCM phosphorylation, and this may shed light on the control of replication efficiency by chromatin environment.
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Affiliation(s)
- Yingying Zou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Jiayao Pei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Haizhen Long
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Liting Lan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kejian Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Tingting Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Ming Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Zhexuan Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Lirun Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Gangxuan Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Xin Jin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Yang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Zengqi Wen
- School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Min Wei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Yunpeng Feng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China.
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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.
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40
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Moore CE, Yalcindag SE, Czeladko H, Ravindranathan R, Wijesekara Hanthi Y, Levy JC, Sannino V, Schindler D, Ciccia A, Costanzo V, Elia AE. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks. J Cell Biol 2023; 222:e202106022. [PMID: 37036693 PMCID: PMC10097976 DOI: 10.1083/jcb.202106022] [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: 06/03/2021] [Revised: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 04/11/2023] Open
Abstract
Replication fork reversal is an important mechanism to protect the stability of stalled forks and thereby preserve genomic integrity. While multiple enzymes have been identified that can remodel forks, their regulation remains poorly understood. Here, we demonstrate that the ubiquitin ligase RFWD3, whose mutation causes Fanconi Anemia, promotes recruitment of the DNA translocase ZRANB3 to stalled replication forks and ubiquitinated sites of DNA damage. Using electron microscopy, we show that RFWD3 stimulates fork remodeling in a ZRANB3-epistatic manner. Fork reversal is known to promote nascent DNA degradation in BRCA2-deficient cells. Consistent with a role for RFWD3 in fork reversal, inactivation of RFWD3 in these cells rescues fork degradation and collapse, analogous to ZRANB3 inactivation. RFWD3 loss impairs ZRANB3 localization to spontaneous nuclear foci induced by inhibition of the PCNA deubiquitinase USP1. We demonstrate that RFWD3 promotes PCNA ubiquitination and interaction with ZRANB3, providing a mechanism for RFWD3-dependent recruitment of ZRANB3. Together, these results uncover a new role for RFWD3 in regulating ZRANB3-dependent fork remodeling.
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Affiliation(s)
- Chandler E. Moore
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Selin E. Yalcindag
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hanna Czeladko
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramya Ravindranathan
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yodhara Wijesekara Hanthi
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Juliana C. Levy
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Detlev Schindler
- Department of Human Genetics, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Alberto Ciccia
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Andrew E.H. Elia
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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41
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Liu W, Saito Y, Jackson J, Bhowmick R, Kanemaki MT, Vindigni A, Cortez D. RAD51 bypasses the CMG helicase to promote replication fork reversal. Science 2023; 380:382-387. [PMID: 37104614 PMCID: PMC10302453 DOI: 10.1126/science.add7328] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/25/2023] [Indexed: 04/29/2023]
Abstract
Replication fork reversal safeguards genome integrity as a replication stress response. DNA translocases and the RAD51 recombinase catalyze reversal. However, it remains unknown why RAD51 is required and what happens to the replication machinery during reversal. We find that RAD51 uses its strand exchange activity to circumvent the replicative helicase, which remains bound to the stalled fork. RAD51 is not required for fork reversal if the helicase is unloaded. Thus, we propose that RAD51 creates a parental DNA duplex behind the helicase that is used as a substrate by the DNA translocases for branch migration to create a reversed fork structure. Our data explain how fork reversal happens while maintaining the helicase in a position poised to restart DNA synthesis and complete genome duplication.
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Affiliation(s)
- Wenpeng Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rahul Bhowmick
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Masato T. Kanemaki
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
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42
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Wang YC, Kelso AA, Karamafrooz A, Chen YH, Chen WK, Cheng CT, Qi Y, Gu L, Malkas L, Taglialatela A, Kung HJ, Moldovan GL, Ciccia A, Stark JM, Ann DK. Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA ubiquitination. Cell Rep 2023; 42:112296. [PMID: 36961817 PMCID: PMC10517088 DOI: 10.1016/j.celrep.2023.112296] [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: 09/20/2021] [Revised: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 03/25/2023] Open
Abstract
The arginine dependency of cancer cells creates metabolic vulnerability. In this study, we examine the impact of arginine availability on DNA replication and genotoxicity resistance. Using DNA combing assays, we find that limiting extracellular arginine results in the arrest of cancer cells at S phase and a slowing or stalling of DNA replication. The translation of new histone H4 is arginine dependent and influences DNA replication. Increased proliferating cell nuclear antigen (PCNA) occupancy and helicase-like transcription factor (HLTF)-catalyzed PCNA K63-linked polyubiquitination protect arginine-starved cells from DNA damage. Arginine-deprived cancer cells display tolerance to genotoxicity in a PCNA K63-linked polyubiquitination-dependent manner. Our findings highlight the crucial role of extracellular arginine in nutrient-regulated DNA replication and provide potential avenues for the development of cancer treatments.
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Affiliation(s)
- Yi-Chang Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Andrew A Kelso
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Adak Karamafrooz
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yi-Hsuan Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Wei-Kai Chen
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Chun-Ting Cheng
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Yue Qi
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Long Gu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Linda Malkas
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hsing-Jien Kung
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, ROC
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA.
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Mansilla SF, Bertolin AP, Venerus Arbilla S, Castaño BA, Jahjah T, Singh JK, Siri SO, Castro MV, de la Vega MB, Quinet A, Wiesmüller L, Gottifredi V. Polymerase iota (Pol ι) prevents PrimPol-mediated nascent DNA synthesis and chromosome instability. SCIENCE ADVANCES 2023; 9:eade7997. [PMID: 37058556 PMCID: PMC10104471 DOI: 10.1126/sciadv.ade7997] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Recent studies have described a DNA damage tolerance pathway choice that involves a competition between PrimPol-mediated repriming and fork reversal. Screening different translesion DNA synthesis (TLS) polymerases by the use of tools for their depletion, we identified a unique role of Pol ι in regulating such a pathway choice. Pol ι deficiency unleashes PrimPol-dependent repriming, which accelerates DNA replication in a pathway that is epistatic with ZRANB3 knockdown. In Pol ι-depleted cells, the excess participation of PrimPol in nascent DNA elongation reduces replication stress signals, but thereby also checkpoint activation in S phase, triggering chromosome instability in M phase. This TLS-independent function of Pol ι requires its PCNA-interacting but not its polymerase domain. Our findings unravel an unanticipated role of Pol ι in protecting the genome stability of cells from detrimental changes in DNA replication dynamics caused by PrimPol.
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Affiliation(s)
| | - Agostina P. Bertolin
- Fundación Instituto Leloir, CONICET, 1405 Buenos Aires, Argentina
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Bryan A. Castaño
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany
| | - Tiya Jahjah
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
| | - Jenny K. Singh
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
| | | | | | | | - Annabel Quinet
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
- Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany
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Di Biagi L, Malacaria E, Aiello FA, Valenzisi P, Marozzi G, Franchitto A, Pichierri P. RAD52 prevents accumulation of Polα-dependent replication gaps at perturbed replication forks in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536536. [PMID: 37090680 PMCID: PMC10120653 DOI: 10.1101/2023.04.12.536536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Replication gaps can arise as a consequence of perturbed DNA replication and their accumulation might undermine the stability of the genome. Loss of RAD52, a protein involved in the regulation of fork reversal, promotes accumulation of parental ssDNA gaps during replication perturbation. Here, we demonstrate that this is due to the engagement of Polα downstream of the extensive degradation of perturbed replication forks after their reversal, and is not dependent on PrimPol. Polα is hyper-recruited at parental ssDNA in the absence of RAD52, and this recruitment is dependent on fork reversal enzymes and RAD51. Of note, we report that the interaction between Polα and RAD51 is stimulated by RAD52 inhibition, and Polα-dependent gap accumulation requires nucleation of RAD51 suggesting that it occurs downstream strand invasion. Altogether, our data indicate that RAD51-Polα-dependent repriming is essential to promote fork restart and limit DNA damage accumulation when RAD52 function is disabled.
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Affiliation(s)
- Ludovica Di Biagi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d’Oro 305, 00136 Rome (Italy)
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Francesca Antonella Aiello
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d’Oro 305, 00136 Rome (Italy)
| | - Pasquale Valenzisi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Giorgia Marozzi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research Unit - Via delle Medaglie d’Oro 305, 00136 Rome (Italy)
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45
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Lim PX, Zaman M, Jasin M. BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536470. [PMID: 37090587 PMCID: PMC10120702 DOI: 10.1101/2023.04.11.536470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Highlights Gap suppression requires BRCA2 C-terminal RAD51 binding in mouse and human cells Brca2 heterozygosity in mice results in fork protection and gap suppression defects Gap suppression mitigates sensitivity to hmdU, but only when HDR is unperturbedHDR deficiency is the primary driver of chemotherapeutic sensitivity. eTOC blurb Lim et al . report that gap suppression as well as fork protection require BRCA2 stabilization of RAD51 filaments in human and mouse cells but have minimal impact on genome integrity, oncogenesis, and drug resistance. BRCA2 suppression of PRIMPOL-mediated replication gaps confers resistance to the nucleotide hmdU, incorporation of which leads to cytotoxic abasic sites.This effect is diminished when HDR is abrogated. Summary Tumor suppressor BRCA2 functions in homology-directed repair (HDR), protection of stalled replication forks, and suppression of replicative gaps. The relative contributions of these pathways to genome integrity and chemotherapy response are under scrutiny. Here, we report that mouse and human cells require a RAD51 filament stabilization motif in BRCA2 for both fork protection and gap suppression, but not HDR. Loss of fork protection and gap suppression do not compromise genome instability or shorten tumor latency in mice or cause replication stress in human mammary cells. By contrast, HDR deficiency increases spontaneous and replication stress-induced chromosome aberrations and tumor predisposition. Unlike with HDR, fork protection and gap suppression defects are also observed in Brca2 heterozygous mouse cells, likely due to reduced RAD51 stabilization at stalled forks and gaps. Gaps arise from PRIMPOL activity, which is associated with sensitivity to 5-hydroxymethyl-2’-deoxyuridine due to the formation of abasic sites by SMUG1 glycosylase and is exacerbated by poly(ADP-ribose) polymerase inhibition. However, HDR deficiency ultimately modulates sensitivity to chemotherapeutics, including PARP inhibitors.
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46
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Krishnan V. The RUNX Family of Proteins, DNA Repair, and Cancer. Cells 2023; 12:cells12081106. [PMID: 37190015 DOI: 10.3390/cells12081106] [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: 03/08/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
The RUNX family of transcription factors, including RUNX1, RUNX2, and RUNX3, are key regulators of development and can function as either tumor suppressors or oncogenes in cancer. Emerging evidence suggests that the dysregulation of RUNX genes can promote genomic instability in both leukemia and solid cancers by impairing DNA repair mechanisms. RUNX proteins control the cellular response to DNA damage by regulating the p53, Fanconi anemia, and oxidative stress repair pathways through transcriptional or non-transcriptional mechanisms. This review highlights the importance of RUNX-dependent DNA repair regulation in human cancers.
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Affiliation(s)
- Vaidehi Krishnan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
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47
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Andrs M, Stoy H, Boleslavska B, Chappidi N, Kanagaraj R, Nascakova Z, Menon S, Rao S, Oravetzova A, Dobrovolna J, Surendranath K, Lopes M, Janscak P. Excessive reactive oxygen species induce transcription-dependent replication stress. Nat Commun 2023; 14:1791. [PMID: 36997515 PMCID: PMC10063555 DOI: 10.1038/s41467-023-37341-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
Elevated levels of reactive oxygen species (ROS) reduce replication fork velocity by causing dissociation of the TIMELESS-TIPIN complex from the replisome. Here, we show that ROS generated by exposure of human cells to the ribonucleotide reductase inhibitor hydroxyurea (HU) promote replication fork reversal in a manner dependent on active transcription and formation of co-transcriptional RNA:DNA hybrids (R-loops). The frequency of R-loop-dependent fork stalling events is also increased after TIMELESS depletion or a partial inhibition of replicative DNA polymerases by aphidicolin, suggesting that this phenomenon is due to a global replication slowdown. In contrast, replication arrest caused by HU-induced depletion of deoxynucleotides does not induce fork reversal but, if allowed to persist, leads to extensive R-loop-independent DNA breakage during S-phase. Our work reveals a link between oxidative stress and transcription-replication interference that causes genomic alterations recurrently found in human cancer.
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Affiliation(s)
- Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Nagaraja Chappidi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Radhakrishnan Kanagaraj
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, London, UK
- School of Life Sciences, University of Bedfordshire, Luton, UK
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, India
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Shruti Menon
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- School of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Satyajeet Rao
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Anna Oravetzova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jana Dobrovolna
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kalpana Surendranath
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, London, UK
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, India
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Pavel Janscak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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Palumbieri MD, Merigliano C, Acosta DG, von Känel T, Welter B, Stoy H, Krietsch J, Ulferts S, Sanchi A, Grosse R, Chiolo I, Lopes M. Replication fork plasticity upon replication stress requires rapid nuclear actin polymerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534097. [PMID: 36993227 PMCID: PMC10055433 DOI: 10.1101/2023.03.24.534097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase, rapidly extending in number and thickness upon genotoxic treatments, and taking frequent contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork plasticity is linked to reduced recruitment of RAD51 and SMARCAL1 to nascent DNA. Conversely, PRIMPOL gains access to replicating chromatin, promoting unrestrained and discontinuous DNA synthesis, which is associated with increased chromosomal instability and decreased cellular resistance to replication stress. Hence, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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Wang YC, Kelso AA, Karamafrooz A, Chen YH, Chen WK, Cheng CT, Qi Y, Gu L, Malkas L, Kung HJ, Moldovan GL, Ciccia A, Stark JM, Ann DK. Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA polyubiquitination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526362. [PMID: 36778247 PMCID: PMC9915598 DOI: 10.1101/2023.01.31.526362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The unique arginine dependencies of cancer cell proliferation and survival creates metabolic vulnerability. Here, we investigate the impact of extracellular arginine availability on DNA replication and genotoxic resistance. Using DNA combing assays, we find that when extracellular arginine is limited, cancer cells are arrested at S-phase and DNA replication forks slow or stall instantly until arginine is re-supplied. The translation of new histone H4 is arginine-dependent and impacts DNA replication and the expression of newly synthesized histone H4 is reduced in the avascular nutrient-poor breast cancer xenograft tumor cores. Furthermore, we demonstrate that increased PCNA occupancy and HLTF-catalyzed PCNA K63-linked polyubiquitination protects arginine-starved cells from hydroxyurea-induced, DNA2-catalyzed nascent strand degradation. Finally, arginine-deprived cancer cells are tolerant to genotoxic insults in a PCNA K63-linked polyubiquitination-dependent manner. Together, these findings reveal that extracellular arginine is the "linchpin" for nutrient-regulated DNA replication. Such information could be leveraged to expand current modalities or design new drug targets against cancer.
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Affiliation(s)
- Yi-Chang Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Andrew A. Kelso
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Adak Karamafrooz
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yi-Hsuan Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Wei-Kai Chen
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Chun-Ting Cheng
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Yue Qi
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Long Gu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Linda Malkas
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Hsing-Jien Kung
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, ROC
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Jeremy M. Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
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50
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Replication gap suppression depends on the double-strand DNA binding activity of BRCA2. Nat Commun 2023; 14:446. [PMID: 36707518 PMCID: PMC9883520 DOI: 10.1038/s41467-023-36149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Replication stress (RS) is a major source of genomic instability and is intrinsic to cancer cells. RS is also the consequence of chemotherapeutic drugs for treating cancer. However, adaptation to RS is also a mechanism of resistance to chemotherapy. BRCA2 deficiency results in replication stress in human cells. BRCA2 protein's main functions include DNA repair by homologous recombination (HR) both at induced DNA double-strand breaks (DSB) and spontaneous replicative lesions. At stalled replication forks, BRCA2 protects the DNA from aberrant nucleolytic degradation and is thought to limit the appearance of ssDNA gaps by arresting replication and via post-replicative HR. However, whether and how BRCA2 acts to limit the formation of ssDNA gaps or mediate their repair, remains ill-defined. Here, we use breast cancer variants affecting different domains of BRCA2 to shed light on this function. We demonstrate that the N-terminal DNA binding domain (NTD), and specifically, its dsDNA binding activity, is required to prevent and repair/fill-in ssDNA gaps upon nucleotide depletion but not to limit PARPi-induced ssDNA gaps. Thus, these findings suggest that nucleotide depletion and PARPi trigger gaps via distinct mechanisms and that the NTD of BRCA2 prevents nucleotide depletion-induced ssDNA gaps.
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