1
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Luo R, Wu J, Chen X, Liu Y, Liu D, Song E, Luo ML. ATR/Chk1 interacting lncRNA modulates DNA damage response to induce breast cancer chemoresistance. CELL INSIGHT 2024; 3:100183. [PMID: 39148723 PMCID: PMC11325286 DOI: 10.1016/j.cellin.2024.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 08/17/2024]
Abstract
The ATR-Chk1 pathway is essential in cellular responses to DNA damage and replication stress, whereas the role of long noncoding RNAs (lncRNAs) in regulating this pathway remains largely unknown. In this study, we identify an ATR and Chk1 interacting lncRNA (ACIL, also known as LRRC75A-AS1 or SNHG29), which promotes the phosphorylation of Chk1 by ATR upon DNA damages. High ACIL levels are associated with chemoresistance to DNA damaging agents and poor outcome of breast cancer patients. ACIL knockdown sensitizes breast cancer cells to DNA damaging drugs in vitro and in vivo. ACIL protects cancer cells against DNA damages by inducing cell cycle arrest, stabilizing replication forks and inhibiting unscheduled origin firing, thereby guarding against replication catastrophe and contributing to DNA damage repair. These findings demonstrate a lncRNA-dependent mechanism of activating the ATR-Chk1 pathway and highlight the potential of utilizing ACIL as a predictive biomarker for chemotherapy sensitivity, as well as targeting ACIL to reverse chemoresistance in breast cancer.
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Affiliation(s)
- Rong Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- The First Department of Breast Cancer, The Third Affiliated Hospital, Kunming Medical University, Kunming, China
| | - Jiannan Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xueman Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yulan Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dequan Liu
- The First Department of Breast Cancer, The Third Affiliated Hospital, Kunming Medical University, Kunming, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Man-Li Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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2
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Bennett LG, Vernon EG, Thanendran V, Jones CM, Gamble A, Staples CJ. MRNIP limits ssDNA gaps during replication stress. Nucleic Acids Res 2024; 52:8320-8331. [PMID: 38917325 DOI: 10.1093/nar/gkae546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Replication repriming by the specialized primase-polymerase PRIMPOL ensures the continuity of DNA synthesis during replication stress. PRIMPOL activity generates residual post-replicative single-stranded nascent DNA gaps, which are linked with mutagenesis and chemosensitivity in BRCA1/2-deficient models, and which are suppressed by replication fork reversal mediated by the DNA translocases SMARCAL1 and ZRANB3. Here, we report that the MRE11 regulator MRNIP limits the prevalence of PRIMPOL and MRE11-dependent ssDNA gaps in cells in which fork reversal is perturbed either by treatment with the PARP inhibitor Olaparib, or by depletion of SMARCAL1 or ZRANB3. MRNIP-deficient cells are sensitive to PARP inhibition and accumulate PRIMPOL-dependent DNA damage, supportive of a pro-survival role for MRNIP linked to the regulation of gap prevalence. In MRNIP-deficient cells, post-replicative gap filling is driven in S-phase by UBC13-mediated template switching involving REV1 and the TLS polymerase Pol-ζ. Our findings represent the first report of modulation of post-replicative ssDNA gap dynamics by a direct MRE11 regulator.
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Affiliation(s)
- Laura G Bennett
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Ellen G Vernon
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Vithursha Thanendran
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Caryl M Jones
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Amelia Gamble
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
| | - Christopher J Staples
- North West Cancer Research Institute, North Wales Medical School, Bangor, Gwynedd, Wales LL57 2UW, UK
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3
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Schneider HE, Schmitt LM, Job A, Lankat-Buttgereit B, Gress T, Buchholz M, Gallmeier E. Synthetic lethality between ATR and POLA1 reveals a potential new target for individualized cancer therapy. Neoplasia 2024; 57:101038. [PMID: 39128273 DOI: 10.1016/j.neo.2024.101038] [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: 05/30/2024] [Revised: 08/06/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
The ATR-CHK1 pathway plays a fundamental role in the DNA damage response and is therefore an attractive target in cancer therapy. The antitumorous effect of ATR inhibitors is at least partly caused by synthetic lethality between ATR and various DNA repair genes. In previous studies, we have identified members of the B-family DNA polymerases as potential lethal partner for ATR, i.e. POLD1 and PRIM1. In this study, we validated and characterized the synthetic lethality between ATR and POLA1. First, we applied a model of ATR-deficient DLD-1 human colorectal cancer cells to confirm synthetic lethality by using chemical POLA1 inhibition. Analyzing cell cycle and apoptotic markers via FACS and Western blotting, we were able to show that apoptosis and S phase arrest contributed to the increased sensitivity of ATR-deficient cancer cells towards POLA1 inhibitors. Importantly, siRNA-mediated POLA1 depletion in ATR-deficient cells caused similar effects in regard to impaired cell viability and cumulation of apoptotic markers, thus excluding toxic effects of chemical POLA1 inhibition. Conversely, we demonstrated that siRNA-mediated POLA1 depletion sensitized several cancer cell lines towards chemical inhibition of ATR and its main effector kinase CHK1. In conclusion, the synthetic lethality between ATR/CHK1 and POLA1 might represent a novel and promising approach for individualized cancer therapy: First, alterations of POLA1 could serve as a screening parameter for increased sensitivity towards ATR and CHK1 inhibitors. Second, alterations in the ATR-CHK1 pathway might predict in increased sensitivity towards POLA1 inhibitors.
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Affiliation(s)
- Hanna Elisabeth Schneider
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany; Department of Medicine A - Hematology, Oncology and Pneumology, University Hospital Münster, Muenster, Germany
| | - Lisa-Maria Schmitt
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Albert Job
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Brigitte Lankat-Buttgereit
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Thomas Gress
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Malte Buchholz
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany
| | - Eike Gallmeier
- Center for Tumor Biology and Immunology, Department of Gastroenterology, Endocrinology and Metabolism, University Hospital of Marburg, Philipps-University Marburg, Marburg, Germany; Department of Internal Medicine II - Gastroenterology, Oncology and Metabolism, Hospital Memmingen, Memmingen, Germany.
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4
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Hieber C, Mustafa AHM, Neuroth S, Henninger S, Wollscheid HP, Zabkiewicz J, Lazenby M, Alvares C, Mahboobi S, Butter F, Brenner W, Bros M, Krämer OH. Inhibitors of the tyrosine kinases FMS-like tyrosine kinase-3 and WEE1 induce apoptosis and DNA damage synergistically in acute myeloid leukemia cells. Biomed Pharmacother 2024; 177:117076. [PMID: 38971011 DOI: 10.1016/j.biopha.2024.117076] [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: 04/21/2024] [Revised: 06/16/2024] [Accepted: 06/29/2024] [Indexed: 07/08/2024] Open
Abstract
Hyperactive FMS-like receptor tyrosine kinase-3 mutants with internal tandem duplications (FLT3-ITD) are frequent driver mutations of aggressive acute myeloid leukemia (AML). Inhibitors of FLT3 produce promising results in rationally designed cotreatment schemes. Since FLT3-ITD modulates DNA replication and DNA repair, valid anti-leukemia strategies could rely on a combined inhibition of FLT3-ITD and regulators of cell cycle progression and DNA integrity. These include the WEE1 kinase which controls cell cycle progression, nucleotide synthesis, and DNA replication origin firing. We investigated how pharmacological inhibition of FLT3 and WEE1 affected the survival and genomic integrity of AML cell lines and primary AML cells. We reveal that promising clinical grade and preclinical inhibitors of FLT3 and WEE1 synergistically trigger apoptosis in leukemic cells that express FLT3-ITD. An accumulation of single and double strand DNA damage precedes this process. Mass spectrometry-based proteomic analyses show that FLT3-ITD and WEE1 sustain the expression of the ribonucleotide reductase subunit RRM2, which provides dNTPs for DNA replication. Unlike their strong pro-apoptotic effects on leukemia cells with FLT3-ITD, inhibitors of FLT3 and WEE1 do not damage healthy human blood cells and murine hematopoietic stem cells. Thus, pharmacological inhibition of FLT3-ITD and WEE1 might become an improved, rationally designed therapeutic option.
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Affiliation(s)
- Christoph Hieber
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany; Department of Dermatology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | - Al-Hassan M Mustafa
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany; Department of Zoology, Faculty of Science, Aswan University, Aswan, Egypt.
| | - Sarah Neuroth
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | - Sven Henninger
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | | | - Joanna Zabkiewicz
- Department of Haematology, Cardiff Experimental Cancer Medicine Centre, Cardiff University, Wales, UK.
| | - Michelle Lazenby
- Department of Haematology, Cardiff Experimental Cancer Medicine Centre, Cardiff University, Wales, UK.
| | - Caroline Alvares
- Department of Haematology, Cardiff Experimental Cancer Medicine Centre, Cardiff University, Wales, UK.
| | - Siavosh Mahboobi
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany.
| | - Falk Butter
- Institute of Molecular Biology, Ackermannweg 4, Mainz 55128, Germany; Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institute, Greifswald 17493, Germany.
| | - Walburgis Brenner
- Department of Obstetrics and Gynecology, University Medical Center, Mainz 55131, Germany.
| | - Matthias Bros
- Department of Dermatology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center of Johannes Gutenberg University Mainz, Mainz 55131, Germany.
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5
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Jordan MR, Oakley GG, Mayo LD, Balakrishnan L, Turchi JJ. The Effect of Replication Protein A Inhibition and Post-Translational Modification on ATR Kinase Signaling. RESEARCH SQUARE 2024:rs.3.rs-4570504. [PMID: 39108493 PMCID: PMC11302688 DOI: 10.21203/rs.3.rs-4570504/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
The ATR kinase responds to elevated levels of single-stranded DNA (ssDNA) to activate the G2/M checkpoint, regulate origin utilization, preserve fork stability, and allow DNA repair towards ensuring genome integrity. The intrinsic replication stress in cancer cells makes this pathway an attractive therapeutic target. The ssDNA that drives ATR signaling is sensed by the ssDNA-binding protein replication protein A (RPA), which acts as a platform for ATRIP recruitment and subsequent ATR activation by TopBP1. We have developed chemical RPA inhibitors (RPAi) that block RPA-ssDNA interactions, termed RPA-DBi, and RPA protein-protein interactions, termed RPA-PPIi; both activities are required for ATR activation. Here, we employ a biochemically reconstituted ATR kinase signaling pathway and demonstrate that both RPA-DBi and RPA-PPIi abrogate ATR-dependent phosphorylation of downstream target proteins. We demonstrate that RPA post-translational modifications (PTMs) impact ATR kinase activation but do not alter sensitivity to RPAi. Specifically, phosphorylation of RPA32 and TopBP1 stimulate, while RPA70 acetylation has no effect on ATR phosphorylation of target proteins. Collectively, this work reveals the RPAi mechanism of action to inhibit ATR signaling that can be regulated by RPA PTMs and offers insight into the anti-cancer activity of ATR pathway targeted cancer therapeutics.
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6
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Liu Z, Jiang H, Lee SY, Kong N, Chan YW. FANCM promotes PARP inhibitor resistance by minimizing ssDNA gap formation and counteracting resection inhibition. Cell Rep 2024; 43:114464. [PMID: 38985669 DOI: 10.1016/j.celrep.2024.114464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/22/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024] Open
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPis) exhibit remarkable anticancer activity in tumors with homologous recombination (HR) gene mutations. However, the role of other DNA repair proteins in PARPi-induced lethality remains elusive. Here, we reveal that FANCM promotes PARPi resistance independent of the core Fanconi anemia (FA) complex. FANCM-depleted cells retain HR proficiency, acting independently of BRCA1 in response to PARPis. FANCM depletion leads to increased DNA damage in the second S phase after PARPi exposure, driven by elevated single-strand DNA (ssDNA) gap formation behind replication forks in the first S phase. These gaps arise from both 53BP1- and primase and DNA directed polymerase (PRIMPOL)-dependent mechanisms. Notably, FANCM-depleted cells also exhibit reduced resection of collapsed forks, while 53BP1 deletion restores resection and mitigates PARPi sensitivity. Our results suggest that FANCM counteracts 53BP1 to repair PARPi-induced DNA damage. Furthermore, FANCM depletion leads to increased chromatin bridges and micronuclei formation after PARPi treatment, elucidating the mechanism underlying extensive cell death in FANCM-depleted cells.
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Affiliation(s)
- Zeyuan Liu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Huadong Jiang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Sze Yuen Lee
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Nannan Kong
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ying Wai Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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7
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Gnugnoli M, Rinaldi C, Casari E, Pizzul P, Bonetti D, Longhese MP. Proteasome-mediated degradation of long-range nucleases negatively regulates resection of DNA double-strand breaks. iScience 2024; 27:110373. [PMID: 39071887 PMCID: PMC11277358 DOI: 10.1016/j.isci.2024.110373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/30/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024] Open
Abstract
Homologous recombination is initiated by the nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection is a two-step process. In the short-range step, the MRX (Mre11-Rad50-Xrs2) complex, together with Sae2, incises the 5'-terminated strand at the DSB end and resects back toward the DNA end. Then, the long-range resection nucleases Exo1 and Dna2 further elongate the resected DNA tracts. We found that mutations lowering proteasome functionality bypass the need for Sae2 in DSB resection. In particular, the dysfunction of the proteasome subunit Rpn11 leads to hyper-resection and increases the levels of both Exo1 and Dna2 to such an extent that it allows the bypass of the requirement for either Exo1 or Dna2, but not for both. These observations, along with the finding that Exo1 and Dna2 are ubiquitylated, indicate a role of the proteasome in restraining DSB resection by negatively controlling the abundance of the long-range resection nucleases.
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Affiliation(s)
- Marco Gnugnoli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
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Majumder B, Nataraj NB, Maitreyi L, Datta S. Mismatch repair-proficient tumor footprints in the sands of immune desert: mechanistic constraints and precision platforms. Front Immunol 2024; 15:1414376. [PMID: 39100682 PMCID: PMC11294168 DOI: 10.3389/fimmu.2024.1414376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Mismatch repair proficient (MMRp) tumors of colorectal origin are one of the prevalent yet unpredictable clinical challenges. Despite earnest efforts, optimal treatment modalities have yet to emerge for this class. The poor prognosis and limited actionability of MMRp are ascribed to a low neoantigen burden and a desert-like microenvironment. This review focuses on the critical roadblocks orchestrated by an immune evasive mechanistic milieu in the context of MMRp. The low density of effector immune cells, their weak spatiotemporal underpinnings, and the high-handedness of the IL-17-TGF-β signaling are intertwined and present formidable challenges for the existing therapies. Microbiome niche decorated by Fusobacterium nucleatum alters the metabolic program to maintain an immunosuppressive state. We also highlight the evolving strategies to repolarize and reinvigorate this microenvironment. Reconstruction of anti-tumor chemokine signaling, rational drug combinations eliciting T cell activation, and reprograming the maladapted microbiome are exciting developments in this direction. Alternative vulnerability of other DNA damage repair pathways is gaining momentum. Integration of liquid biopsy and ex vivo functional platforms provide precision oncology insights. We illustrated the perspectives and changing landscape of MMRp-CRC. The emerging opportunities discussed in this review can turn the tide in favor of fighting the treatment dilemma for this elusive cancer.
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9
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Xu H, Gitto SB, Ho GY, Medvedev S, Shield-Artin K, Kim H, Beard S, Kinose Y, Wang X, Barker HE, Ratnayake G, Hwang WT, Hansen RJ, Strouse B, Milutinovic S, Hassig C, Wakefield MJ, Vandenberg CJ, Scott CL, Simpkins F. CHK1 inhibitor SRA737 is active in PARP inhibitor resistant and CCNE1 amplified ovarian cancer. iScience 2024; 27:109978. [PMID: 39021796 PMCID: PMC11253285 DOI: 10.1016/j.isci.2024.109978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 04/05/2024] [Accepted: 05/11/2024] [Indexed: 07/20/2024] Open
Abstract
High-grade serous ovarian cancers (HGSOCs) with homologous recombination deficiency (HRD) are initially responsive to poly (ADP-ribose) polymerase inhibitors (PARPi), but resistance ultimately emerges. HGSOC with CCNE1 amplification (CCNE1 amp) are associated with resistance to PARPi and platinum treatments. High replication stress in HRD and CCNE1 amp HGSOC leads to increased reliance on checkpoint kinase 1 (CHK1), a key regulator of cell cycle progression and the replication stress response. Here, we investigated the anti-tumor activity of the potent, highly selective, orally bioavailable CHK1 inhibitor (CHK1i), SRA737, in both acquired PARPi-resistant BRCA1/2 mutant and CCNE1 amp HGSOC models. We demonstrated that SRA737 increased replication stress and induced subsequent cell death in vitro. SRA737 monotherapy in vivo prolonged survival in CCNE1 amp models, suggesting a potential biomarker for CHK1i therapy. Combination SRA737 and PARPi therapy increased tumor regression in both PARPi-resistant and CCNE1 amp patient-derived xenograft models, warranting further study in these HGSOC subgroups.
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Affiliation(s)
- Haineng Xu
- Ovarian Cancer Research Center, Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah B. Gitto
- Ovarian Cancer Research Center, Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gwo-Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Sergey Medvedev
- Ovarian Cancer Research Center, Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristy Shield-Artin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Hyoung Kim
- Ovarian Cancer Research Center, Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sally Beard
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Yasuto Kinose
- Ovarian Cancer Research Center, Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaolei Wang
- Ovarian Cancer Research Center, Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Australian Ovarian Cancer Study
- Research Division, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Ryan J. Hansen
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW 2145, Australia
| | - Bryan Strouse
- Sierra Oncology, Inc, 885 West Georgia Street, Suite 2150, Vancouver, BC V6C 3E8, Canada
| | - Snezana Milutinovic
- Sierra Oncology, Inc, 885 West Georgia Street, Suite 2150, Vancouver, BC V6C 3E8, Canada
| | - Christian Hassig
- Sierra Oncology, Inc, 885 West Georgia Street, Suite 2150, Vancouver, BC V6C 3E8, Canada
| | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
- The Royal Women’s Hospital, Parkville, VIC 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC 3010, Australia
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Fiona Simpkins
- Ovarian Cancer Research Center, Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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10
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Dennen MS, Kockler ZW, Roberts SA, Burkholder AB, Klimczak LJ, Gordenin DA. Hypomorphic mutation in the large subunit of replication protein A affects mutagenesis by human APOBEC cytidine deaminases in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601081. [PMID: 38979205 PMCID: PMC11230362 DOI: 10.1101/2024.06.27.601081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Human APOBEC single-strand (ss) specific DNA and RNA cytidine deaminases change cytosines to uracils and function in antiviral innate immunity, RNA editing, and can cause hypermutation in chromosomes. The resulting uracils can be directly replicated, resulting in C to T mutations, or uracil-DNA glycosylase can convert the uracils to abasic (AP) sites which are then fixed as C to T or C to G mutations by translesion DNA polymerases. We noticed that in yeast and in human cancers, contributions of C to T and C to G mutations depends on the origin of ssDNA mutagenized by APOBECs. Since ssDNA in eukaryotic genomes readily binds to replication protein A (RPA) we asked if RPA could affect APOBEC-induced mutation spectrum in yeast. For that purpose, we expressed human APOBECs in the wild-type yeast and in strains carrying a hypomorph mutation rfa1-t33 in the large RPA subunit. We confirmed that the rfa1-t33 allele can facilitate mutagenesis by APOBECs. We also found that the rfa1-t33 mutation changed the ratio of APOBEC3A-induced T to C and T to G mutations in replicating yeast to resemble a ratio observed in long-persistent ssDNA in yeast and in cancers. We present the data suggesting that RPA may shield APOBEC formed uracils in ssDNA from Ung1, thereby facilitating C to T mutagenesis through the accurate copying of uracils by replicative DNA polymerases. Unexpectedly, we also found that for uracils shielded from Ung1 by wild-type RPA the mutagenic outcome is reduced in the presence of translesion DNA polymerase zeta.
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Affiliation(s)
- Matthew S Dennen
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709
| | - Zachary W Kockler
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709
| | - Steven A Roberts
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405
| | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, 27709, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Durham, NC, 27709
| | - Dmitry A Gordenin
- Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709
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11
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Jo U, Arakawa Y, Zimmermann A, Taniyama D, Mizunuma M, Jenkins LM, Maity T, Kumar S, Zenke FT, Takebe N, Pommier Y. The Novel ATR Inhibitor M1774 Induces Replication Protein Overexpression and Broad Synergy with DNA-targeted Anticancer Drugs. Mol Cancer Ther 2024; 23:911-923. [PMID: 38466804 DOI: 10.1158/1535-7163.mct-23-0402] [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: 06/25/2023] [Revised: 12/09/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Ataxia telangiectasia and Rad3-related (ATR) checkpoint kinase inhibitors are in clinical trials. Here we explored the molecular pharmacology and therapeutic combination strategies of the oral ATR inhibitor M1774 (Tuvusertib) with DNA-damaging agents (DDA). As single agent, M1774 suppressed cancer cell viability at nanomolar concentrations, showing greater activity than ceralasertib and berzosertib, but less potency than gartisertib and elimusertib in the small cell lung cancer H146, H82, and DMS114 cell lines. M1774 also efficiently blocked the activation of the ATR-CHK1 checkpoint pathway caused by replication stress induced by TOP1 inhibitors. Combination with non-toxic dose of M1774 enhanced TOP1 inhibitor-induced cancer cell death by enabling unscheduled replication upon replicative damage, thereby increasing genome instability. Tandem mass tag-based quantitative proteomics uncovered that M1774, in the presence of DDA, forces the expression of proteins activating replication (CDC45) and G2-M progression (PLK1 and CCNB1). In particular, the fork protection complex proteins (TIMELESS and TIPIN) were enriched. Low dose of M1774 was found highly synergistic with a broad spectrum of clinical DDAs including TOP1 inhibitors (SN-38/irinotecan, topotecan, exatecan, and exatecan), the TOP2 inhibitor etoposide, cisplatin, the RNA polymerase II inhibitor lurbinectedin, and the PARP inhibitor talazoparib in various models including cancer cell lines, patient-derived organoids, and mouse xenograft models. Furthermore, we demonstrate that M1774 reverses chemoresistance to anticancer DDAs in cancer cells lacking SLFN11 expression, suggesting that SLFN11 can be utilized for patient selection in upcoming clinical trials.
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Affiliation(s)
- Ukhyun Jo
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Yasuhiro Arakawa
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | - Daiki Taniyama
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Makito Mizunuma
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Tapan Maity
- Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Suresh Kumar
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | - Naoko Takebe
- Developmental Therapeutics Branch and Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch and Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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12
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Wakasa T, Nonaka K, Harada A, Ohkawa Y, Kikutake C, Suyama M, Kobunai T, Tsunekuni K, Matsuoka K, Kataoka Y, Ochiiwa H, Miyadera K, Sagara T, Oki E, Ohdo S, Maehara Y, Iimori M, Kitao H. The anti-tumor effect of trifluridine via induction of aberrant mitosis is unaffected by mutations modulating p53 activity. Cell Death Discov 2024; 10:307. [PMID: 38956056 PMCID: PMC11219725 DOI: 10.1038/s41420-024-02083-3] [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: 03/13/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
The fluorinated thymidine analog trifluridine (FTD) is a chemotherapeutic drug commonly used to treat cancer; however, the mechanism by which FTD induces cytotoxicity is not fully understood. In addition, the effect of gain-of-function (GOF) missense mutations of the TP53 gene (encoding p53), which promote cancer progression and chemotherapeutic drug resistance, on the chemotherapeutic efficacy of FTD is unclear. Here, we revealed the mechanisms by which FTD-induced aberrant mitosis and contributed to cytotoxicity in both p53-null and p53-GOF missense mutant cells. In p53-null mutant cells, FTD-induced DNA double-stranded breaks, single-stranded DNA accumulation, and the associated DNA damage responses during the G2 phase. Nevertheless, FTD-induced DNA damage and the related responses were not sufficient to trigger strict G2/M checkpoint arrest. Thus, these features were carried over into mitosis, resulting in chromosome breaks and bridges, and subsequent cytokinesis failure. Improper mitotic exit eventually led to cell apoptosis, caused by the accumulation of extensive DNA damage and the presence of micronuclei encapsulated in the disrupted nuclear envelope. Upon FTD treatment, the behavior of the p53-GOF-missense mutant, isogenic cell lines, generated by CRISPR/Cas9 genome editing, was similar to that of p53-null mutant cells. Thus, our data suggest that FTD treatment overrode the effect on gene expression induced by p53-GOF mutants and exerted its anti-tumor activity in a manner that was independent of the p53 function.
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Affiliation(s)
- Takeshi Wakasa
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
- Taiho Pharmaceutical Co. Ltd., Tokyo, Japan
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kentaro Nonaka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Kyushu Central Hospital of the Mutual Aid Association of Public School Teachers, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Chie Kikutake
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | | | | | | | | | | | | | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigehiro Ohdo
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Maehara
- Kyushu Central Hospital of the Mutual Aid Association of Public School Teachers, Fukuoka, Japan
| | - Makoto Iimori
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
- Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan.
| | - Hiroyuki Kitao
- Department of Molecular Cancer Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
- Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan.
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13
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Hoang PM, Torre D, Jaynes P, Ho J, Mohammed K, Alvstad E, Lam WY, Khanchandani V, Lee JM, Toh CMC, Lee RX, Anbuselvan A, Lee S, Sebra RP, Martin J Walsh, Marazzi I, Kappei D, Guccione E, Jeyasekharan AD. A PRMT5-ZNF326 axis mediates innate immune activation upon replication stress. SCIENCE ADVANCES 2024; 10:eadm9589. [PMID: 38838142 DOI: 10.1126/sciadv.adm9589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
DNA replication stress (RS) is a widespread phenomenon in carcinogenesis, causing genomic instability and extensive chromatin alterations. DNA damage leads to activation of innate immune signaling, but little is known about transcriptional regulators mediating such signaling upon RS. Using a chemical screen, we identified protein arginine methyltransferase 5 (PRMT5) as a key mediator of RS-dependent induction of interferon-stimulated genes (ISGs). This response is also associated with reactivation of endogenous retroviruses (ERVs). Using quantitative mass spectrometry, we identify proteins with PRMT5-dependent symmetric dimethylarginine (SDMA) modification induced upon RS. Among these, we show that PRMT5 targets and modulates the activity of ZNF326, a zinc finger protein essential for ISG response. Our data demonstrate a role for PRMT5-mediated SDMA in the context of RS-induced transcriptional induction, affecting physiological homeostasis and cancer therapy.
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Affiliation(s)
- Phuong Mai Hoang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Denis Torre
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jessica Ho
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Kevin Mohammed
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Alvstad
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Wan Yee Lam
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jie Min Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chin Min Clarissa Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akshaya Anbuselvan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, South Korea
| | - Robert P Sebra
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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14
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Goehring L, Keegan S, Lahiri S, Xia W, Kong M, Jimenez-Sainz J, Gupta D, Drapkin R, Jensen RB, Smith DJ, Rothenberg E, Fenyö D, Huang TT. Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency. Nat Commun 2024; 15:4716. [PMID: 38830843 PMCID: PMC11148086 DOI: 10.1038/s41467-024-48286-1] [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: 08/19/2023] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from replication stress and genotoxicity, but the specific mechanism(s) by which this is achieved to prevent early oncogenesis remains unclear. Here, we provide evidence that BRCA2 acts as a critical suppressor of head-on transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) and computational analysis, we identified origins (dormant origins) that are activated near the transcription termination sites (TTS) of highly expressed, long genes in response to replication stress. Dormant origins are a source for HO-TRCs, and drug treatments that inhibit dormant origin firing led to a reduction in HO-TRCs, R-loop formation, and DNA damage. Using super-resolution microscopy, we showed that HO-TRC events track with elongating RNA polymerase II, but not with transcription initiation. Importantly, RNase H2 is recruited to sites of HO-TRCs in a BRCA2-dependent manner to help alleviate toxic R-loops associated with HO-TRCs. Collectively, our results provide a mechanistic basis for how BRCA2 shields against genomic instability by preventing HO-TRCs through both direct and indirect means occurring at predetermined genomic sites based on the pre-cancer transcriptome.
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Affiliation(s)
- Liana Goehring
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Sarah Keegan
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sudipta Lahiri
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Wenxin Xia
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Michael Kong
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | | | - Dipika Gupta
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Duncan J Smith
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Eli Rothenberg
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - David Fenyö
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Institute for Systems Genetics, New York University School of Medicine, New York University School of Medicine, New York, NY, USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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15
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Do BT, Hsu PP, Vermeulen SY, Wang Z, Hirz T, Abbott KL, Aziz N, Replogle JM, Bjelosevic S, Paolino J, Nelson SA, Block S, Darnell AM, Ferreira R, Zhang H, Milosevic J, Schmidt DR, Chidley C, Harris IS, Weissman JS, Pikman Y, Stegmaier K, Cheloufi S, Su XA, Sykes DB, Vander Heiden MG. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress. Dev Cell 2024:S1534-5807(24)00327-7. [PMID: 38823395 DOI: 10.1016/j.devcel.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/14/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Control of cellular identity requires coordination of developmental programs with environmental factors such as nutrient availability, suggesting that perturbing metabolism can alter cell state. Here, we find that nucleotide depletion and DNA replication stress drive differentiation in human and murine normal and transformed hematopoietic systems, including patient-derived acute myeloid leukemia (AML) xenografts. These cell state transitions begin during S phase and are independent of ATR/ATM checkpoint signaling, double-stranded DNA break formation, and changes in cell cycle length. In systems where differentiation is blocked by oncogenic transcription factor expression, replication stress activates primed regulatory loci and induces lineage-appropriate maturation genes despite the persistence of progenitor programs. Altering the baseline cell state by manipulating transcription factor expression causes replication stress to induce genes specific for alternative lineages. The ability of replication stress to selectively activate primed maturation programs across different contexts suggests a general mechanism by which changes in metabolism can promote lineage-appropriate cell state transitions.
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Affiliation(s)
- Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peggy P Hsu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02113, USA; Rogel Cancer Center and Division of Hematology and Oncology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sidney Y Vermeulen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhishan Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Najihah Aziz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Bjelosevic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha A Nelson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samuel Block
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hanyu Zhang
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Jelena Milosevic
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Daniel R Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Christopher Chidley
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jonathan S Weissman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Stegmaier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA; Stem Cell Center, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, Riverside, CA 92521, USA
| | - Xiaofeng A Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02113, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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16
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Geraud M, Cristini A, Salimbeni S, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, Marinello J, Cordelier P, Trouche D, Favre G, Nicolas E, Capranico G, Sordet O. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep 2024; 43:114214. [PMID: 38761375 DOI: 10.1016/j.celrep.2024.114214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024] Open
Abstract
TDP1 removes transcription-blocking topoisomerase I cleavage complexes (TOP1ccs), and its inactivating H493R mutation causes the neurodegenerative syndrome SCAN1. However, the molecular mechanism underlying the SCAN1 phenotype is unclear. Here, we generate human SCAN1 cell models using CRISPR-Cas9 and show that they accumulate TOP1ccs along with changes in gene expression and genomic distribution of R-loops. SCAN1 cells also accumulate transcriptional DNA double-strand breaks (DSBs) specifically in the G1 cell population due to increased DSB formation and lack of repair, both resulting from abortive removal of transcription-blocking TOP1ccs. Deficient TDP1 activity causes increased DSB production, and the presence of mutated TDP1 protein hampers DSB repair by a TDP2-dependent backup pathway. This study provides powerful models to study TDP1 functions under physiological and pathological conditions and unravels that a gain of function of the mutated TDP1 protein, which prevents DSB repair, rather than a loss of TDP1 activity itself, could contribute to SCAN1 pathogenesis.
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Affiliation(s)
- Mathéa Geraud
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Simona Salimbeni
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France; Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Nicolas Bery
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Virginie Jouffret
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France; BigA Core Facility, Centre de Biologie Intégrative (CBI), Université de Toulouse, 31062 Toulouse, France
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Andrea Carla Ajello
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Lara Fernandez Martinez
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Pierre Cordelier
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Didier Trouche
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Estelle Nicolas
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy.
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France.
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17
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Ma J, Ren D, Wang Z, Li W, Li L, Liu T, Ye Q, Lei Y, Jian Y, Ma B, Fan Y, Liu J, Gao Y, Jin X, Huang H, Li L. CK2-dependent degradation of CBX3 dictates replication fork stalling and PARP inhibitor sensitivity. SCIENCE ADVANCES 2024; 10:eadk8908. [PMID: 38781342 PMCID: PMC11114232 DOI: 10.1126/sciadv.adk8908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
DNA replication is a vulnerable cellular process, and its deregulation leads to genomic instability. Here, we demonstrate that chromobox protein homolog 3 (CBX3) binds replication protein A 32-kDa subunit (RPA2) and regulates RPA2 retention at stalled replication forks. CBX3 is recruited to stalled replication forks by RPA2 and inhibits ring finger and WD repeat domain 3 (RFWD3)-facilitated replication restart. Phosphorylation of CBX3 at serine-95 by casein kinase 2 (CK2) kinase augments cadherin 1 (CDH1)-mediated CBX3 degradation and RPA2 dynamics at stalled replication forks, which permits replication fork restart. Increased expression of CBX3 due to gene amplification or CK2 inhibitor treatment sensitizes prostate cancer cells to poly(ADP-ribose) polymerase (PARP) inhibitors while inducing replication stress and DNA damage. Our work reveals CBX3 as a key regulator of RPA2 function and DNA replication, suggesting that CBX3 could serve as an indicator for targeted therapy of cancer using PARP inhibitors.
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Affiliation(s)
- Jian Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Dianyun Ren
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zixi Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wei Li
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Tianjie Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qi Ye
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yuzeshi Lei
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yanlin Jian
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Bohan Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yizeng Fan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Jing Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yang Gao
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Xin Jin
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Institute of Urologic Science and Technology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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18
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Yuan L, Liang X, He L. Insights into the Dissociation Process and Binding Pattern of the BRCT7/8-PHF8 Complex. ACS OMEGA 2024; 9:20819-20831. [PMID: 38764655 PMCID: PMC11097150 DOI: 10.1021/acsomega.3c09433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/27/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
DNA topoisomerase 2-binding protein 1 (Topbp1) plays a crucial role in activating the ataxia-telangiectasia mutated and rad3-related (ATR) complex to initiate DNA damage repair responses. For this process to occur, it is necessary for PHF8 to dissociate from Topbp1. Topbp1 binds to the acidic patch sequence (APS) of PHF8 through its C-terminal BRCT7/8 domain, and disrupting this interaction could be a promising strategy for cancer treatment. To investigate the dissociation process and binding pattern of BRCT7/8-PHF8, we employed enhanced sampling techniques, such as steered molecular dynamics (SMD) simulations and accelerated molecular dynamics (aMD) simulations, along with self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. Our results demonstrate that the dissociation of PHF8 from BRCT7/8 starts from the N-terminus, leading to the unfolding of the N-terminal helix. Additionally, we identified critical residues that play a pivotal role in this dissociation process. These findings provide valuable insights into the disassociation of PHF8 from BRCT7/8, which could potentially guide the development of novel drugs targeting Topbp1 for cancer therapy.
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Affiliation(s)
- Longxiao Yuan
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Xiaodan Liang
- School
of Computer Sciences and Technology, Tiangong
University, Tianjin 300387, China
| | - Lei He
- Institute
for Fetology, The First Affiliated Hospital
of Soochow University, Suzhou 215006, China
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19
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Marmolejo CO, Sanchez C, Lee J, Werner M, Roberts P, Hamperl S, Saldivar JC. A phosphorylation code coordinating transcription condensate dynamics with DNA replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593572. [PMID: 38765978 PMCID: PMC11100774 DOI: 10.1101/2024.05.10.593572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Chromatin is organized into compartments enriched with functionally-related proteins driving non-linear biochemical activities. Some compartments, e.g. transcription foci, behave as liquid condensates. While the principles governing the enrichment of proteins within condensates are being elucidated, mechanisms that coordinate condensate dynamics with other nuclear processes like DNA replication have not been identified. We show that at the G1/S cell cycle transition, large transcription condensates form at histone locus bodies (HLBs) in a cyclin-dependent kinase 1 and 2 (CDK1/2)-dependent manner. As cells progress through S phase, ataxia-telangiectasia and Rad3-related (ATR) accumulates within HLBs and dissolves the associated transcription condensates. Integration of CDK1/2 and ATR signaling creates a phosphorylation code within the intrinsically-disordered region of mediator subunit 1 (MED1) coordinating condensate dynamics with DNA replication. Disruption of this code results in imbalanced histone biosynthesis, and consequently, global DNA damage. We propose the spatiotemporal dynamics of transcription condensates are actively controlled via phosphorylation and essential for viability of proliferating cells.
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20
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Khan I, Kashani-Sabet M. Bromodomain inhibition targeting BPTF in the treatment of melanoma and other solid tumors. Clin Exp Metastasis 2024:10.1007/s10585-024-10265-7. [PMID: 38683257 DOI: 10.1007/s10585-024-10265-7] [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: 06/20/2023] [Accepted: 01/06/2024] [Indexed: 05/01/2024]
Abstract
Epigenetic mechanisms have been shown to play an important role in the development of cancer. These include the activation of chromatin remodeling factors in various malignancies, including bromodomain plant homeodomain (PHD) finger transcription factor (BPTF), the largest component of the human nucleosome remodeling factor (NURF). In the last few years, BPTF has been identified as a pro-tumorigenic factor in melanoma, stimulated by research into the molecular mechanisms underlying BPTF function. Developing therapy targeting the BPTF bromodomain would represent a significant advance. Melanoma therapy has been revolutionized by the efficacy of immunotherapeutic and targeted strategies, but the development of drug resistance calls for alternative therapeutic approaches. Recent work has shown both a biomarker as well as functional role for BPTF in melanoma progression and as a possible target for its therapy. BPTF was shown to stimulate the mitogen-activated protein kinase pathway, which is targeted by selective BRAF inhibitors. The advent of small molecule inhibitors that target bromodomain motifs has shown that bromodomains are druggable. By combining the bromodomain inhibitor bromosporine with existing treatments that target mutant BRAF, BPTF targeting has emerged as a novel and promising therapeutic approach for metastatic melanoma. This article summarizes the functional role of BPTF in tumor progression, reviews the clinical experience to date with bromodomain inhibitors, and discusses the promise of BPTF targeting in melanoma and other solid tumors.
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Affiliation(s)
- Imran Khan
- California Pacific Medical Center Research Institute, 475 Brannan St, Suite 130, San Francisco, CA, 94107, USA
| | - Mohammed Kashani-Sabet
- California Pacific Medical Center Research Institute, 475 Brannan St, Suite 130, San Francisco, CA, 94107, USA.
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21
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Pytko KG, Dannenberg RL, Eckert KA, Hedglin M. Replication of [AT/TA] 25 Microsatellite Sequences by Human DNA Polymerase δ Holoenzymes Is Dependent on dNTP and RPA Levels. Biochemistry 2024; 63:969-983. [PMID: 38623046 DOI: 10.1021/acs.biochem.4c00006] [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] [Indexed: 04/17/2024]
Abstract
Fragile sites are unstable genomic regions that are prone to breakage during stressed DNA replication. Several common fragile sites (CFS) contain A+T-rich regions including perfect [AT/TA] microsatellite repeats that may collapse into hairpins when in single-stranded DNA (ssDNA) form and coincide with chromosomal hotspots for breakage and rearrangements. While many factors contribute to CFS instability, evidence exists for replication stalling within [AT/TA] microsatellite repeats. Currently, it is unknown how stress causes replication stalling within [AT/TA] microsatellite repeats. To investigate this, we utilized FRET to characterize the structures of [AT/TA]25 sequences and also reconstituted lagging strand replication to characterize the progression of pol δ holoenzymes through A+T-rich sequences. The results indicate that [AT/TA]25 sequences adopt hairpins that are unwound by the major ssDNA-binding complex, RPA, and the progression of pol δ holoenzymes through A+T-rich sequences saturated with RPA is dependent on the template sequence and dNTP concentration. Importantly, the effects of RPA on the replication of [AT/TA]25 sequences are dependent on dNTP concentration, whereas the effects of RPA on the replication of A+T-rich, nonstructure-forming sequences are independent of dNTP concentration. Collectively, these results reveal complexities in lagging strand replication and provide novel insights into how [AT/TA] microsatellite repeats contribute to genome instability.
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Affiliation(s)
- Kara G Pytko
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Rachel L Dannenberg
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Kristin A Eckert
- Department of Pathology and Laboratory Medicine, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, United States
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
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22
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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23
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Rombaut D, Lefèvre C, Rached T, Bondu S, Letessier A, Mangione RM, Farhat B, Lesieur-Pasquier A, Castillo-Guzman D, Boussaid I, Friedrich C, Tourville A, De Carvalho M, Levavasseur F, Leduc M, Le Gall M, Battault S, Temple M, Houy A, Bouscary D, Willems L, Park S, Raynaud S, Cluzeau T, Clappier E, Fenaux P, Adès L, Margueron R, Wassef M, Alsafadi S, Chapuis N, Kosmider O, Solary E, Constantinou A, Stern MH, Droin N, Palancade B, Miotto B, Chédin F, Fontenay M. Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation. Nat Commun 2024; 15:3016. [PMID: 38589367 PMCID: PMC11001894 DOI: 10.1038/s41467-024-46547-7] [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: 12/07/2022] [Accepted: 02/29/2024] [Indexed: 04/10/2024] Open
Abstract
Myelodysplastic syndromes (MDS) with mutated SF3B1 gene present features including a favourable outcome distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we find that SF3B1-mutated MDS show reduced R-loop formation predominating in gene bodies associated with intron retention reduction, not found in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibit augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restores R-loop formation, slows down DNA replication forks and improves SF3B1-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress represents a hallmark of SF3B1-mutated MDS ineffective erythropoiesis, which could be used as a therapeutic target.
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Affiliation(s)
- David Rombaut
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Carine Lefèvre
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
| | - Tony Rached
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Sabrina Bondu
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Anne Letessier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | | | - Batoul Farhat
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Auriane Lesieur-Pasquier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Daisy Castillo-Guzman
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Ismael Boussaid
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Chloé Friedrich
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Aurore Tourville
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Magali De Carvalho
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Françoise Levavasseur
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marjorie Leduc
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Morgane Le Gall
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Sarah Battault
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marie Temple
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Alexandre Houy
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Didier Bouscary
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Lise Willems
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Sophie Park
- Department of Hematology, Centre Hospitalier Universitaire, Université de Grenoble Alpes, Grenoble, France
| | - Sophie Raynaud
- Laboratory of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Thomas Cluzeau
- Clinical Department of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Emmanuelle Clappier
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Laboratory of Hematology, Paris, France
| | - Pierre Fenaux
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Lionel Adès
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Raphael Margueron
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Michel Wassef
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nicolas Chapuis
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Olivier Kosmider
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Eric Solary
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nathalie Droin
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Miotto
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Michaela Fontenay
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France.
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France.
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France.
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France.
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24
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Ngoi NYL, Pilié PG, McGrail DJ, Zimmermann M, Schlacher K, Yap TA. Targeting ATR in patients with cancer. Nat Rev Clin Oncol 2024; 21:278-293. [PMID: 38378898 DOI: 10.1038/s41571-024-00863-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Pharmacological inhibition of the ataxia telangiectasia and Rad3-related protein serine/threonine kinase (ATR; also known as FRAP-related protein (FRP1)) has emerged as a promising strategy for cancer treatment that exploits synthetic lethal interactions with proteins involved in DNA damage repair, overcomes resistance to other therapies and enhances antitumour immunity. Multiple novel, potent ATR inhibitors are being tested in clinical trials using biomarker-directed approaches and involving patients across a broad range of solid cancer types; some of these inhibitors have now entered phase III trials. Further insight into the complex interactions of ATR with other DNA replication stress response pathway components and with the immune system is necessary in order to optimally harness the potential of ATR inhibitors in the clinic and achieve hypomorphic targeting of the various ATR functions. Furthermore, a deeper understanding of the diverse range of predictive biomarkers of response to ATR inhibitors and of the intraclass differences between these agents could help to refine trial design and patient selection strategies. Key challenges that remain in the clinical development of ATR inhibitors include the optimization of their therapeutic index and the development of rational combinations with these agents. In this Review, we detail the molecular mechanisms regulated by ATR and their clinical relevance, and discuss the challenges that must be addressed to extend the benefit of ATR inhibitors to a broad population of patients with cancer.
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Affiliation(s)
- Natalie Y L Ngoi
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Patrick G Pilié
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Katharina Schlacher
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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25
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Chen S, Pan C, Huang J, Liu T. ATR limits Rad18-mediated PCNA monoubiquitination to preserve replication fork and telomerase-independent telomere stability. EMBO J 2024; 43:1301-1324. [PMID: 38467834 PMCID: PMC10987609 DOI: 10.1038/s44318-024-00066-9] [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: 09/14/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Upon replication fork stalling, the RPA-coated single-stranded DNA (ssDNA) formed behind the fork activates the ataxia telangiectasia-mutated and Rad3-related (ATR) kinase, concomitantly initiating Rad18-dependent monoubiquitination of PCNA. However, whether crosstalk exists between these two events and the underlying physiological implications of this interplay remain elusive. In this study, we demonstrate that during replication stress, ATR phosphorylates human Rad18 at Ser403, an adjacent residue to a previously unidentified PIP motif (PCNA-interacting peptide) within Rad18. This phosphorylation event disrupts the interaction between Rad18 and PCNA, thereby restricting the extent of Rad18-mediated PCNA monoubiquitination. Consequently, excessive accumulation of the tumor suppressor protein SLX4, now characterized as a novel reader of ubiquitinated PCNA, at stalled forks is prevented, contributing to the prevention of stalled fork collapse. We further establish that ATR preserves telomere stability in alternative lengthening of telomere (ALT) cells by restricting Rad18-mediated PCNA monoubiquitination and excessive SLX4 accumulation at telomeres. These findings shed light on the complex interplay between ATR activation, Rad18-dependent PCNA monoubiquitination, and SLX4-associated stalled fork processing, emphasizing the critical role of ATR in preserving replication fork stability and facilitating telomerase-independent telomere maintenance.
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Affiliation(s)
- Siyuan Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chen Pan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China.
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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26
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Vogt M, Classen S, Krause AK, Peter NJ, Petersen C, Rothkamm K, Borgmann K, Meyer F. USP7 Deregulation Impairs S Phase Specific DNA Repair after Irradiation in Breast Cancer Cells. Biomedicines 2024; 12:762. [PMID: 38672118 PMCID: PMC11047985 DOI: 10.3390/biomedicines12040762] [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: 02/15/2024] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The ubiquitin specific protease 7 (USP7) is a deubiquitinating enzyme with numerous substrates. Aberrant expression of USP7 is associated with tumor progression. This study aims to investigate how a deregulated USP7 expression affects chromosomal instability and prognosis of breast cancer patients in silico and radiosensitivity and DNA repair in breast cancer cells in vitro. The investigations in silico were performed using overall survival and USP7 mRNA expression data of breast cancer patients. The results showed that a high USP7 expression was associated with increased chromosomal instability and decreased overall survival. The in vitro experiments were performed in a luminal and a triple-negative breast cancer cell line. Proliferation, DNA repair, DNA replication stress, and survival after USP7 overexpression or inhibition and irradiation were analyzed. Both, USP7 inhibition and overexpression resulted in decreased cellular survival, distinct radiosensitization and an increased number of residual DNA double-strand breaks in the S phase following irradiation. RAD51 recruitment and base incorporation were decreased after USP7 inhibition plus irradiation and more single-stranded DNA was detected. The results show that deregulation of USP7 activity disrupts DNA repair in the S phase by increasing DNA replication stress and presents USP7 as a promising target to overcome the radioresistance of breast tumors.
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Affiliation(s)
| | | | | | | | | | | | | | - Felix Meyer
- Department of Radiotherapy & Radiation Oncology, Hubertus Wald Tumor Center—University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.V.); (S.C.); (A.K.K.); (N.-J.P.); (C.P.); (K.R.); (K.B.)
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27
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Mirsanaye AS, Hoffmann S, Weisser M, Mund A, Lopez Mendez B, Typas D, van den Boom J, Benedict B, Hendriks IA, Nielsen ML, Meyer H, Duxin JP, Montoya G, Mailand N. VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates. Nat Commun 2024; 15:2459. [PMID: 38503733 PMCID: PMC10950897 DOI: 10.1038/s41467-024-46760-4] [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: 07/20/2023] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
The hexameric AAA+ ATPase p97/VCP functions as an essential mediator of ubiquitin-dependent cellular processes, extracting ubiquitylated proteins from macromolecular complexes or membranes by catalyzing their unfolding. p97 is directed to ubiquitylated client proteins via multiple cofactors, most of which interact with the p97 N-domain. Here, we discover that FAM104A, a protein of unknown function also named VCF1 (VCP/p97 nuclear Cofactor Family member 1), acts as a p97 cofactor in human cells. Detailed structure-function studies reveal that VCF1 directly binds p97 via a conserved α-helical motif that recognizes the p97 N-domain with unusually high affinity, exceeding that of other cofactors. We show that VCF1 engages in joint p97 complex formation with the heterodimeric primary p97 cofactor UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates in cells. Mechanistically, VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 but has no intrinsic affinity for ubiquitin. Collectively, our findings establish VCF1 as an unconventional p97 cofactor that promotes p97-dependent protein turnover by facilitating p97-UFD1-NPL4 recruitment to ubiquitylated targets.
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Affiliation(s)
- Ann Schirin Mirsanaye
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Saskia Hoffmann
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Melanie Weisser
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Andreas Mund
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Dimitris Typas
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Johannes van den Boom
- Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Michael Lund Nielsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Hemmo Meyer
- Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117, Essen, Germany
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark.
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28
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Żabka A, Gocek N, Polit JT, Maszewski J. Oxidative replication stress induced by long-term exposure to hydroxyurea in root meristem cells of Vicia faba. PLANT CELL REPORTS 2024; 43:87. [PMID: 38460026 DOI: 10.1007/s00299-024-03187-x] [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: 01/03/2024] [Accepted: 02/28/2024] [Indexed: 03/11/2024]
Abstract
KEY MESSAGE Low concentrations of hydroxyurea, an inhibitor of DNA replication, induced oxidative and replicative stress in root apical meristem (RAM) cells of Vicia faba. Plant cells are constantly exposed to low-level endogenous stress factors that can affect DNA replication and lead to DNA damage. Long-term treatments of Vicia faba root apical meristems (RAMs) with HU leads to the appearance of atypical cells with intranuclear asynchrony. This rare form of abnormality was manifested by a gradual condensation of chromatin, from interphase to mitosis (so-called IM cells). Moreover, HU-treated root cells revealed abnormal chromosome structure, persisting DNA replication, and elevated levels of intracellular hydrogen peroxide (H2O2) and superoxide anion (O2∙-). Immunocytochemical studies have shown an increased number of fluorescent foci of H3 histones acetylated at lysine 56 (H3K56Ac; canonically connected with the DNA replication process). We show that continuous 3-day exposure to low concentrations (0.75 mM) of hydroxyurea (HU; an inhibitor of DNA replication) induces cellular response to reactive oxygen species and to DNA replication stress conditions.
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Affiliation(s)
- Aneta Żabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland.
| | - Natalia Gocek
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
| | - Justyna Teresa Polit
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
| | - Janusz Maszewski
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-236, Lodz, Poland
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29
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Ochs F, Green C, Szczurek AT, Pytowski L, Kolesnikova S, Brown J, Gerlich DW, Buckle V, Schermelleh L, Nasmyth KA. Sister chromatid cohesion is mediated by individual cohesin complexes. Science 2024; 383:1122-1130. [PMID: 38452070 DOI: 10.1126/science.adl4606] [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: 10/20/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024]
Abstract
Eukaryotic genomes are organized by loop extrusion and sister chromatid cohesion, both mediated by the multimeric cohesin protein complex. Understanding how cohesin holds sister DNAs together, and how loss of cohesion causes age-related infertility in females, requires knowledge as to cohesin's stoichiometry in vivo. Using quantitative super-resolution imaging, we identified two discrete populations of chromatin-bound cohesin in postreplicative human cells. Whereas most complexes appear dimeric, cohesin that localized to sites of sister chromatid cohesion and associated with sororin was exclusively monomeric. The monomeric stoichiometry of sororin:cohesin complexes demonstrates that sister chromatid cohesion is conferred by individual cohesin rings, a key prediction of the proposal that cohesion arises from the co-entrapment of sister DNAs.
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Affiliation(s)
- Fena Ochs
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Charlotte Green
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Lior Pytowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Sofia Kolesnikova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna Austria
| | - Jill Brown
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daniel Wolfram Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna Austria
| | - Veronica Buckle
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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30
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Yang X, Hu X, Yin J, Li W, Fu Y, Yang B, Fan J, Lu F, Qin T, Kang X, Zhuang X, Li F, Xiao R, Shi T, Song K, Li J, Chen G, Sun C. Comprehensive multi-omics analysis reveals WEE1 as a synergistic lethal target with hyperthermia through CDK1 super-activation. Nat Commun 2024; 15:2089. [PMID: 38453961 PMCID: PMC10920785 DOI: 10.1038/s41467-024-46358-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
Hyperthermic intraperitoneal chemotherapy's role in ovarian cancer remains controversial, hindered by limited understanding of hyperthermia-induced tumor cellular changes. This limits developing potent combinatory strategies anchored in hyperthermic intraperitoneal therapy (HIPET). Here, we perform a comprehensive multi-omics study on ovarian cancer cells under hyperthermia, unveiling a distinct molecular panorama, primarily characterized by rapid protein phosphorylation changes. Based on the phospho-signature, we pinpoint CDK1 kinase is hyperactivated during hyperthermia, influencing the global signaling landscape. We observe dynamic, reversible CDK1 activity, causing replication arrest and early mitotic entry post-hyperthermia. Subsequent drug screening shows WEE1 inhibition synergistically destroys cancer cells with hyperthermia. An in-house developed miniaturized device confirms hyperthermia and WEE1 inhibitor combination significantly reduces tumors in vivo. These findings offer additional insights into HIPET, detailing molecular mechanisms of hyperthermia and identifying precise drug combinations for targeted treatment. This research propels the concept of precise hyperthermic intraperitoneal therapy, highlighting its potential against ovarian cancer.
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Affiliation(s)
- Xiaohang Yang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, PR China
| | - Xingyuan Hu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Jingjing Yin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Wenting Li
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Shihezi University Shihezi, Xinjiang, 832000, PR China
| | - Yu Fu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Bin Yang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Junpeng Fan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Funian Lu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Tianyu Qin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Xiaoyan Kang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Xucui Zhuang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Fuxia Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Shihezi University Shihezi, Xinjiang, 832000, PR China
| | - Rourou Xiao
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, PR China
| | - Tingyan Shi
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, PR China
| | - Jing Li
- Department of Gynecologic Oncology, Sun Yat-sen Memorial Hospital, 33 Yingfeng Road, Guangzhou, 510000, PR China.
| | - Gang Chen
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
| | - Chaoyang Sun
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
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31
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Yu Y, Wang X, Fox J, Li Q, Yu Y, Hastings PJ, Chen K, Ira G. RPA and Rad27 limit templated and inverted insertions at DNA breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583931. [PMID: 38496432 PMCID: PMC10942419 DOI: 10.1101/2024.03.07.583931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ∼5-34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ). This process is exacerbated in mutants with low levels or mutated RPA ( rtt105 Δ; rfa1 -t33) or extensive resection mutant ( sgs1 Δ exo1 Δ). Templated insertions from various distant genomic locations also increase in these mutants as well as in rad27 Δ and originate from fragile regions of the genome. Among complex insertions, common events are insertions of two sequences, originating from the same locus and with inverted orientation. We propose that these inversions are also formed by microhomology-mediated template switching. Taken together, we propose that a shortage of RPA typical in cancer cells is one possible factor stimulating the formation of templated insertions.
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32
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Xu P, Liu Y, Liu C, Guey B, Li L, Melenec P, Ricci J, Ablasser A. The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Nature 2024; 627:873-879. [PMID: 38418882 PMCID: PMC10972748 DOI: 10.1038/s41586-024-07112-w] [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: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA demands tight regulatory mechanisms that are necessary to maintain cell and tissue homeostasis under normal conditions. Inside the cell nucleus, anchoring to nucleosomes and competition with chromatin architectural proteins jointly prohibit cGAS activation by genomic DNA8-15. However, the fate of nuclear cGAS and its role in cell physiology remains unclear. Here we show that the ubiquitin proteasomal system (UPS) degrades nuclear cGAS in cycling cells. We identify SPSB3 as the cGAS-targeting substrate receptor that associates with the cullin-RING ubiquitin ligase 5 (CRL5) complex to ligate ubiquitin onto nuclear cGAS. A cryo-electron microscopy structure of nucleosome-bound cGAS in a complex with SPSB3 reveals a highly conserved Asn-Asn (NN) minimal degron motif at the C terminus of cGAS that directs SPSB3 recruitment, ubiquitylation and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling, conferring heightened protection against infection by DNA viruses. Our research defines protein degradation as a determinant of cGAS regulation in the nucleus and provides structural insights into an element of cGAS that is amenable to therapeutic exploitation.
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Affiliation(s)
- Pengbiao Xu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Ying Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- School of Medicine, Jiangnan University, Wuxi, China
| | - Chong Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Baptiste Guey
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Lingyun Li
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Pauline Melenec
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Jonathan Ricci
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Ablasser
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Institute for Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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Yates M, Marois I, St-Hilaire E, Ronato DA, Djerir B, Brochu C, Morin T, Hammond-Martel I, Gezzar-Dandashi S, Casimir L, Drobetsky E, Cappadocia L, Masson JY, Wurtele H, Maréchal A. SMARCAL1 ubiquitylation controls its association with RPA-coated ssDNA and promotes replication fork stability. PLoS Biol 2024; 22:e3002552. [PMID: 38502677 PMCID: PMC10950228 DOI: 10.1371/journal.pbio.3002552] [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: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Impediments in replication fork progression cause genomic instability, mutagenesis, and severe pathologies. At stalled forks, RPA-coated single-stranded DNA (ssDNA) activates the ATR kinase and directs fork remodeling, 2 key early events of the replication stress response. RFWD3, a recently described Fanconi anemia (FA) ubiquitin ligase, associates with RPA and promotes its ubiquitylation, facilitating late steps of homologous recombination (HR). Intriguingly, RFWD3 also regulates fork progression, restart and stability via poorly understood mechanisms. Here, we used proteomics to identify putative RFWD3 substrates during replication stress in human cells. We show that RFWD3 interacts with and ubiquitylates the SMARCAL1 DNA translocase directly in vitro and following DNA damage in vivo. SMARCAL1 ubiquitylation does not trigger its subsequent proteasomal degradation but instead disengages it from RPA thereby regulating its function at replication forks. Proper regulation of SMARCAL1 by RFWD3 at stalled forks protects them from excessive MUS81-mediated cleavage in response to UV irradiation, thereby limiting DNA replication stress. Collectively, our results identify RFWD3-mediated SMARCAL1 ubiquitylation as a novel mechanism that modulates fork remodeling to avoid genome instability triggered by aberrant fork processing.
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Affiliation(s)
- Maïlyn Yates
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Isabelle Marois
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Edlie St-Hilaire
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
| | - Daryl A. Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Billel Djerir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Chloé Brochu
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Théo Morin
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | | | | | - Lisa Casimir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Elliot Drobetsky
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Laurent Cappadocia
- Faculty of Sciences, Department of Chemistry, Université du Québec à Montréal, Montréal, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Hugo Wurtele
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
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Zhao X, Singhal A, Park S, Kong J, Bachelder R, Ideker T. Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress. Cancer Discov 2024; 14:508-523. [PMID: 38236062 PMCID: PMC10905674 DOI: 10.1158/2159-8290.cd-23-0641] [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: 06/12/2023] [Revised: 10/25/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
Rapid proliferation is a hallmark of cancer associated with sensitivity to therapeutics that cause DNA replication stress (RS). Many tumors exhibit drug resistance, however, via molecular pathways that are incompletely understood. Here, we develop an ensemble of predictive models that elucidate how cancer mutations impact the response to common RS-inducing (RSi) agents. The models implement recent advances in deep learning to facilitate multidrug prediction and mechanistic interpretation. Initial studies in tumor cells identify 41 molecular assemblies that integrate alterations in hundreds of genes for accurate drug response prediction. These cover roles in transcription, repair, cell-cycle checkpoints, and growth signaling, of which 30 are shown by loss-of-function genetic screens to regulate drug sensitivity or replication restart. The model translates to cisplatin-treated cervical cancer patients, highlighting an RTK-JAK-STAT assembly governing resistance. This study defines a compendium of mechanisms by which mutations affect therapeutic responses, with implications for precision medicine. SIGNIFICANCE Zhao and colleagues use recent advances in machine learning to study the effects of tumor mutations on the response to common therapeutics that cause RS. The resulting predictive models integrate numerous genetic alterations distributed across a constellation of molecular assemblies, facilitating a quantitative and interpretable assessment of drug response. This article is featured in Selected Articles from This Issue, p. 384.
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Affiliation(s)
- Xiaoyu Zhao
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Akshat Singhal
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California
| | - Sungjoon Park
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
| | - JungHo Kong
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, California
| | - Robin Bachelder
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
| | - Trey Ideker
- Division of Human Genomics and Precision Medicine, Department of Medicine, University of California, San Diego, La Jolla, California
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, California
- Department of Bioengineering, University of California, San Diego, La Jolla, California
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Wang J, Meng X, Chen X, Xiao J, Yu X, Wu L, Li Z, Chen K, Zhang X, Xiong B, Feng J. Cinchophen induces RPA1 related DNA damage and apoptosis to impair ENS development of zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116032. [PMID: 38306819 DOI: 10.1016/j.ecoenv.2024.116032] [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: 11/14/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) have become contaminants widely distributed in the environment due to improper disposal and discharge. Previous study has found several components might involve in impairing enteric nervous system (ENS) development of zebrafish, including NSAIDs cinchophen. Deficient ENS development in fetal could lead to Hirschsprung disease (HSCR), a congenital neurocristopathy characterized by absence of enteric neurons in hindgut. However, the intrinsic mechanism of neurotoxicity of cinchophen is unclear. We confirmed that cinchophen could impair ENS development of zebrafish and transcriptome sequencing revealed that disfunction of Replication protein A1 (RPA1), which is involved in DNA replication and repairment, might be relevant to the neurotoxicity effects induced by cinchophen. Based on previous data of single cell RNA sequencing (scRNA-seq) of zebrafish gut cells, we observed that rpa1 mainly expressed in proliferating, differentiating ENS cells and neural crest progenitors. Interestingly, cinchophen induced apoptosis and impaired proliferation. Furthermore, cinchophen caused DNA damage and abnormal activation of ataxia telangiectasia mutated/ Rad3 related (ATM/ATR) and checkpoint kinase 2 (CHK2). Finally, molecular docking indicated cinchophen could bind and antagonize RPA1 more effectively. Our study might provide a better understanding and draw more attention to the role of environmental factors in the pathogenesis of HSCR. And the mechanism of cinchophen neurotoxicity would give theoretical guidance for clinical pharmacy.
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Affiliation(s)
- Jing Wang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xinyao Meng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xuyong Chen
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Xiao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaosi Yu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Luyao Wu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zejian Li
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Chen
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xuan Zhang
- Department of Pediatric Surgery, Pingshan District Maternal & Child Healthcare Hospital of Shenzhen, Shenzhen 518000, China
| | - Bo Xiong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jiexiong Feng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Bandau S, Alvarez V, Jiang H, Graff S, Sundaramoorthy R, Gierlinski M, Toman M, Owen-Hughes T, Sidoli S, Lamond A, Alabert C. RNA polymerase II promotes the organization of chromatin following DNA replication. EMBO Rep 2024; 25:1387-1414. [PMID: 38347224 PMCID: PMC10933433 DOI: 10.1038/s44319-024-00085-x] [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: 07/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
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Affiliation(s)
- Susanne Bandau
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Vanesa Alvarez
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Sarah Graff
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | | | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Matt Toman
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Simone Sidoli
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Constance Alabert
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK.
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37
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Day M, Tetik B, Parlak M, Almeida-Hernández Y, Räschle M, Kaschani F, Siegert H, Marko A, Sanchez-Garcia E, Kaiser M, Barker IA, Pearl LH, Oliver AW, Boos D. TopBP1 utilises a bipartite GINS binding mode to support genome replication. Nat Commun 2024; 15:1797. [PMID: 38413589 PMCID: PMC10899662 DOI: 10.1038/s41467-024-45946-0] [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: 06/21/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Activation of the replicative Mcm2-7 helicase by loading GINS and Cdc45 is crucial for replication origin firing, and as such for faithful genetic inheritance. Our biochemical and structural studies demonstrate that the helicase activator GINS interacts with TopBP1 through two separate binding surfaces, the first involving a stretch of highly conserved amino acids in the TopBP1-GINI region, the second a surface on TopBP1-BRCT4. The two surfaces bind to opposite ends of the A domain of the GINS subunit Psf1. Mutation analysis reveals that either surface is individually able to support TopBP1-GINS interaction, albeit with reduced affinity. Consistently, either surface is sufficient for replication origin firing in Xenopus egg extracts and becomes essential in the absence of the other. The TopBP1-GINS interaction appears sterically incompatible with simultaneous binding of DNA polymerase epsilon (Polε) to GINS when bound to Mcm2-7-Cdc45, although TopBP1-BRCT4 and the Polε subunit PolE2 show only partial competitivity in binding to Psf1. Our TopBP1-GINS model improves the understanding of the recently characterised metazoan pre-loading complex. It further predicts the coordination of three molecular origin firing processes, DNA polymerase epsilon arrival, TopBP1 ejection and GINS integration into Mcm2-7-Cdc45.
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Affiliation(s)
- Matthew Day
- School of Biological and Behavioural Sciences, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Bilal Tetik
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Milena Parlak
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Räschle
- Molecular Genetics, Technical University Kaiserslautern, Paul-Ehrlich Straße 24, 67663, Kaiserslautern, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Heike Siegert
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Anika Marko
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Kaiser
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Isabel A Barker
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK.
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Dominik Boos
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany.
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Muñoz S, Barroso S, Badra-Fajardo N, Marqueta-Gracia JJ, García-Rubio ML, Ubieto-Capella P, Méndez J, Aguilera A. SIN3A histone deacetylase action counteracts MUS81 to promote stalled fork stability. Cell Rep 2024; 43:113778. [PMID: 38341854 PMCID: PMC10915396 DOI: 10.1016/j.celrep.2024.113778] [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: 07/19/2023] [Revised: 12/09/2023] [Accepted: 01/26/2024] [Indexed: 02/13/2024] Open
Abstract
During genome duplication, replication forks (RFs) can be stalled by different obstacles or by depletion of replication factors or nucleotides. A limited number of histone post-translational modifications at stalled RFs are involved in RF protection and restart. Provided the recent observation that the SIN3A histone deacetylase complex reduces transcription-replication conflicts, we explore the role of the SIN3A complex in protecting RFs under stressed conditions. We observe that Sin3A protein is enriched at replicating DNA in the presence of hydroxyurea. In this situation, Sin3A-depleted cells show increased RF stalling, H3 acetylation, and DNA breaks at stalled RFs. Under Sin3A depletion, RF recovery is impaired, and DNA damage accumulates. Importantly, these effects are partially dependent on the MUS81 endonuclease, which promotes DNA breaks and MRE11-dependent DNA degradation of such breaks. We propose that chromatin deacetylation triggered by the SIN3A complex limits MUS81 cleavage of stalled RFs, promoting genome stability when DNA replication is challenged.
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Affiliation(s)
- Sergio Muñoz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Nibal Badra-Fajardo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - José Javier Marqueta-Gracia
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Patricia Ubieto-Capella
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Juan Méndez
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
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Zhou M, Duan L, Chen J, Li Y, Yin Z, Song S, Cao Y, Luo P, Hu F, Yang G, Xu J, Liao T, Jin Y. The dynamic role of nucleoprotein SHCBP1 in the cancer cell cycle and its potential as a synergistic target for DNA-damaging agents in cancer therapy. Cell Commun Signal 2024; 22:131. [PMID: 38365687 PMCID: PMC10874017 DOI: 10.1186/s12964-024-01513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Malignant tumours seriously threaten human life and health, and effective treatments for cancer are still being explored. The ability of SHC SH2 domain-binding protein 1 (SHCBP1) to induce cell cycle disturbance and inhibit tumour growth has been increasingly studied, but its dynamic role in the tumour cell cycle and corresponding effects leading to mitotic catastrophe and DNA damage have rarely been studied. RESULTS In this paper, we found that the nucleoprotein SHCBP1 exhibits dynamic spatiotemporal expression during the tumour cell cycle, and SHCBP1 knockdown slowed cell cycle progression by inducing spindle disorder, as reflected by premature mitotic entry and multipolar spindle formation. This dysfunction was caused by G2/M checkpoint impairment mediated by downregulated WEE1 kinase and NEK7 (a member of the mammalian NIMA-related kinase family) expression and upregulated centromere/kinetochore protein Zeste White 10 (ZW10) expression. Moreover, both in vivo and in vitro experiments confirmed the significant inhibitory effects of SHCBP1 knockdown on tumour growth. Based on these findings, SHCBP1 knockdown in combination with low-dose DNA-damaging agents had synergistic tumouricidal effects on tumour cells. In response to this treatment, tumour cells were forced into the mitotic phase with considerable unrepaired DNA lesions, inducing mitotic catastrophe. These synergistic effects were attributed not only to the abrogation of the G2/M checkpoint and disrupted spindle function but also to the impairment of the DNA damage repair system, as demonstrated by mass spectrometry-based proteomic and western blotting analyses. Consistently, patients with low SHCBP1 expression in tumour tissue were more sensitive to radiotherapy. However, SHCBP1 knockdown combined with tubulin-toxic drugs weakened the killing effect of the drugs on tumour cells, which may guide the choice of chemotherapeutic agents in clinical practice. CONCLUSION In summary, we elucidated the role of the nucleoprotein SHCBP1 in tumour cell cycle progression and described a novel mechanism by which SHCBP1 regulates tumour progression and through which targeting SHCBP1 increases sensitivity to DNA-damaging agent therapy, indicating its potential as a cancer treatment.
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Affiliation(s)
- Mei Zhou
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Limin Duan
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Department of Critical Care Medicine, Institute of Anesthesia and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiangbin Chen
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Yumei Li
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Zhengrong Yin
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Siwei Song
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Yaqi Cao
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Ping Luo
- Department of Translational Medicine Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Fan Hu
- Medical Subcenter of HUST Analytical & Testing Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Guanghai Yang
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Tingting Liao
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
- Hubei Province Key Laboratory of Biological Targeted Therapy, MOE Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
- Hubei Province Engineering Research Center for Tumour-Targeted Biochemotherapy, Union HospitalTongji Medical CollegeHuazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
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40
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Yadav AK, Polasek-Sedlackova H. Quantity and quality of minichromosome maintenance protein complexes couple replication licensing to genome integrity. Commun Biol 2024; 7:167. [PMID: 38336851 PMCID: PMC10858283 DOI: 10.1038/s42003-024-05855-w] [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: 10/05/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Accurate and complete replication of genetic information is a fundamental process of every cell division. The replication licensing is the first essential step that lays the foundation for error-free genome duplication. During licensing, minichromosome maintenance protein complexes, the molecular motors of DNA replication, are loaded to genomic sites called replication origins. The correct quantity and functioning of licensed origins are necessary to prevent genome instability associated with severe diseases, including cancer. Here, we delve into recent discoveries that shed light on the novel functions of licensed origins, the pathways necessary for their proper maintenance, and their implications for cancer therapies.
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Affiliation(s)
- Anoop Kumar Yadav
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Polasek-Sedlackova
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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41
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Tischler JD, Tsuchida H, Bosire R, Oda TT, Park A, Adeyemi RO. FLIP(C1orf112)-FIGNL1 complex regulates RAD51 chromatin association to promote viability after replication stress. Nat Commun 2024; 15:866. [PMID: 38286805 PMCID: PMC10825145 DOI: 10.1038/s41467-024-45139-9] [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: 05/24/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Homologous recombination (HR) plays critical roles in repairing lesions that arise during DNA replication and is thus essential for viability. RAD51 plays important roles during replication and HR, however, how RAD51 is regulated downstream of nucleofilament formation and how the varied RAD51 functions are regulated is not clear. We have investigated the protein c1orf112/FLIP that previously scored in genome-wide screens for mediators of DNA inter-strand crosslink (ICL) repair. Upon ICL agent exposure, FLIP loss leads to marked cell death, elevated chromosomal instability, increased micronuclei formation, altered cell cycle progression and increased DNA damage signaling. FLIP is recruited to damage foci and forms a complex with FIGNL1. Both proteins have epistatic roles in ICL repair, forming a stable complex. Mechanistically, FLIP loss leads to increased RAD51 amounts and foci on chromatin both with or without exogenous DNA damage, defective replication fork progression and reduced HR competency. We posit that FLIP is essential for limiting RAD51 levels on chromatin in the absence of damage and for RAD51 dissociation from nucleofilaments to properly complete HR. Failure to do so leads to replication slowing and inability to complete repair.
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Affiliation(s)
- Jessica D Tischler
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Hiroshi Tsuchida
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | | | - Tommy T Oda
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- University of Washington, Seattle, 98195, USA
| | - Ana Park
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- University of Washington, Seattle, 98195, USA
| | - Richard O Adeyemi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
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42
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Borenäs M, Umapathy G, Lind DE, Lai WY, Guan J, Johansson J, Jennische E, Schmidt A, Kurhe Y, Gabre JL, Aniszewska A, Strömberg A, Bemark M, Hall MN, den Eynden JV, Hallberg B, Palmer RH. ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition. Proc Natl Acad Sci U S A 2024; 121:e2315242121. [PMID: 38154064 PMCID: PMC10769851 DOI: 10.1073/pnas.2315242121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
High-risk neuroblastoma (NB) is a significant clinical challenge. MYCN and Anaplastic Lymphoma Kinase (ALK), which are often involved in high-risk NB, lead to increased replication stress in cancer cells, suggesting therapeutic strategies. We previously identified an ATR (ataxia telangiectasia and Rad3-related)/ALK inhibitor (ATRi/ALKi) combination as such a strategy in two independent genetically modified mouse NB models. Here, we identify an underlying molecular mechanism, in which ALK signaling leads to phosphorylation of ATR and CHK1, supporting an effective DNA damage response. The importance of ALK inhibition is supported by mouse data, in which ATRi monotreatment resulted in a robust initial response, but subsequent relapse, in contrast to a 14-d ALKi/ATRi combination treatment that resulted in a robust and sustained response. Finally, we show that the remarkable response to the 14-d combined ATR/ALK inhibition protocol reflects a robust differentiation response, reprogramming tumor cells to a neuronal/Schwann cell lineage identity. Our results identify an ability of ATR inhibition to promote NB differentiation and underscore the importance of further exploring combined ALK/ATR inhibition in NB, particularly in high-risk patient groups with oncogene-induced replication stress.
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Affiliation(s)
- Marcus Borenäs
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Dan E. Lind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Wei-Yun Lai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Joel Johansson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Eva Jennische
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, Basel University, Basel4056, Switzerland
| | - Yeshwant Kurhe
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Jonatan L. Gabre
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent9000, Belgium
| | - Agata Aniszewska
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Anneli Strömberg
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg SE-405 30, Sweden
| | | | - Jimmy Van den Eynden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent9000, Belgium
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
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43
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Martinikova AS, Stoyanov M, Oravetzova A, Kok YP, Yu S, Dobrovolna J, Janscak P, van Vugt M, Macurek L. PPM1D activity promotes the replication stress caused by cyclin E1 overexpression. Mol Oncol 2024; 18:6-20. [PMID: 37067201 PMCID: PMC10766204 DOI: 10.1002/1878-0261.13433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/09/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023] Open
Abstract
Oncogene-induced replication stress has been recognized as a major cause of genome instability in cancer cells. Increased expression of cyclin E1 caused by amplification of the CCNE1 gene is a common cause of replication stress in various cancers. Protein phosphatase magnesium-dependent 1 delta (PPM1D) is a negative regulator of p53 and has been implicated in termination of the cell cycle checkpoint. Amplification of the PPM1D gene or frameshift mutations in its final exon promote tumorigenesis. Here, we show that PPM1D activity further increases the replication stress caused by overexpression of cyclin E1. In particular, we demonstrate that cells expressing a truncated mutant of PPM1D progress faster from G1 to S phase and fail to complete licensing of the replication origins. In addition, we show that transcription-replication collisions and replication fork slowing caused by CCNE1 overexpression are exaggerated in cells expressing the truncated PPM1D. Finally, replication speed and accumulation of focal DNA copy number alterations caused by induction of CCNE1 expression was rescued by pharmacological inhibition of PPM1D. We propose that increased activity of PPM1D suppresses the checkpoint function of p53 and thus promotes genome instability in cells expressing the CCNE1 oncogene.
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Affiliation(s)
- Andra S. Martinikova
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Miroslav Stoyanov
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Anna Oravetzova
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Yannick P. Kok
- Department of Medical Oncology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Shibo Yu
- Department of Pathology and Medical Biology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Jana Dobrovolna
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
| | - Pavel Janscak
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
- Institute of Molecular Cancer ResearchUniversity of ZurichSwitzerland
| | - Marcel van Vugt
- Department of Medical Oncology, University Medical Center GroningenUniversity of GroningenThe Netherlands
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular GeneticsCzech Academy of SciencesPragueCzech Republic
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44
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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: 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: 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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45
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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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46
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Zhao Y, Hou K, Li Y, Hao S, Liu Y, Na Y, Li C, Cui J, Xu X, Wu X, Wang H. Human HELQ regulates DNA end resection at DNA double-strand breaks and stalled replication forks. Nucleic Acids Res 2023; 51:12207-12223. [PMID: 37897354 PMCID: PMC10711563 DOI: 10.1093/nar/gkad940] [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: 07/31/2023] [Revised: 09/15/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Following a DNA double strand break (DSB), several nucleases and helicases coordinate to generate single-stranded DNA (ssDNA) with 3' free ends, facilitating precise DNA repair by homologous recombination (HR). The same nucleases can act on stalled replication forks, promoting nascent DNA degradation and fork instability. Interestingly, some HR factors, such as CtIP and BRCA1, have opposite regulatory effects on the two processes, promoting end resection at DSB but inhibiting the degradation of nascent DNA on stalled forks. However, the reason why nuclease actions are regulated by different mechanisms in two DNA metabolism is poorly understood. We show that human HELQ acts as a DNA end resection regulator, with opposing activities on DNA end resection at DSBs and on stalled forks as seen for other regulators. Mechanistically, HELQ helicase activity is required for EXO1-mediated DSB end resection, while ssDNA-binding capacity of HELQ is required for its recruitment to stalled forks, facilitating fork protection and preventing chromosome aberrations caused by replication stress. Here, HELQ synergizes with CtIP but not BRCA1 or BRCA2 to protect stalled forks. These findings reveal an unanticipated role of HELQ in regulating DNA end resection at DSB and stalled forks, which is important for maintaining genome stability.
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Affiliation(s)
- Yuqin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Kaiping Hou
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Youhang Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yu Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yinan Na
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Chao Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jian Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, China Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
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47
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Lebdy R, Canut M, Patouillard J, Cadoret JC, Letessier A, Ammar J, Basbous J, Urbach S, Miotto B, Constantinou A, Abou Merhi R, Ribeyre C. The nucleolar protein GNL3 prevents resection of stalled replication forks. EMBO Rep 2023; 24:e57585. [PMID: 37965896 DOI: 10.15252/embr.202357585] [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: 06/02/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Faithful DNA replication requires specific proteins that protect replication forks and so prevent the formation of DNA lesions that may damage the genome. Identification of new proteins involved in this process is essential to understand how DNA lesions accumulate in cancer cells and how they tolerate them. Here, we show that human GNL3/nucleostemin, a GTP-binding protein localized mostly in the nucleolus and highly expressed in cancer cells, prevents nuclease-dependent resection of nascent DNA in response to replication stress. We demonstrate that inhibiting origin firing reduces resection. This suggests that the heightened replication origin activation observed upon GNL3 depletion largely drives the observed DNA resection probably due to the exhaustion of the available RPA pool. We show that GNL3 and DNA replication initiation factor ORC2 interact in the nucleolus and that the concentration of GNL3 in the nucleolus is required to limit DNA resection. We propose that the control of origin firing by GNL3 through the sequestration of ORC2 in the nucleolus is critical to prevent nascent DNA resection in response to replication stress.
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Affiliation(s)
- Rana Lebdy
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
- Faculty of Sciences, Genomics and Surveillance Biotherapy (GSBT) Laboratory, R. Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Marine Canut
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Julie Patouillard
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | | | - Anne Letessier
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Josiane Ammar
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Jihane Basbous
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, Inserm U1191, Université de Montpellier, Montpellier Cedex 5, France
| | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Angelos Constantinou
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Raghida Abou Merhi
- Faculty of Sciences, Genomics and Surveillance Biotherapy (GSBT) Laboratory, R. Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Cyril Ribeyre
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
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48
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Munk SHN, Merchut-Maya JM, Adelantado Rubio A, Hall A, Pappas G, Milletti G, Lee M, Johnsen LG, Guldberg P, Bartek J, Maya-Mendoza A. NAD + regulates nucleotide metabolism and genomic DNA replication. Nat Cell Biol 2023; 25:1774-1786. [PMID: 37957325 PMCID: PMC10709141 DOI: 10.1038/s41556-023-01280-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 10/06/2023] [Indexed: 11/15/2023]
Abstract
The intricate orchestration of enzymatic activities involving nicotinamide adenine dinucleotide (NAD+) is essential for maintaining metabolic homeostasis and preserving genomic integrity. As a co-enzyme, NAD+ plays a key role in regulating metabolic pathways, such as glycolysis and Kreb's cycle. ADP-ribosyltransferases (PARPs) and sirtuins rely on NAD+ to mediate post-translational modifications of target proteins. The activation of PARP1 in response to DNA breaks leads to rapid depletion of cellular NAD+ compromising cell viability. Therefore, the levels of NAD+ must be tightly regulated. Here we show that exogenous NAD+, but not its precursors, has a direct effect on mitochondrial activity. Short-term incubation with NAD+ boosts Kreb's cycle and the electron transport chain and enhances pyrimidine biosynthesis. Extended incubation with NAD+ results in depletion of pyrimidines, accumulation of purines, activation of the replication stress response and cell cycle arrest. Moreover, a combination of NAD+ and 5-fluorouridine selectively kills cancer cells that rely on de novo pyrimidine synthesis. We propose an integrated model of how NAD+ regulates nucleotide metabolism, with relevance to healthspan, ageing and cancer therapy.
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Affiliation(s)
| | | | | | - Arnaldur Hall
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - George Pappas
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - Giacomo Milletti
- DNA Replication and Cancer Group, Danish Cancer Institute, Copenhagen, Denmark
| | - MyungHee Lee
- DNA Replication and Cancer Group, Danish Cancer Institute, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | | | - Per Guldberg
- Molecular Diagnostics Group, Danish Cancer Institute, Copenhagen, Denmark
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark.
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SciLifeLab, Stockholm, Sweden.
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49
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Rios-Szwed DO, Alvarez V, Sanchez-Pulido L, Garcia-Wilson E, Jiang H, Bandau S, Lamond A, Alabert C. FAM111A regulates replication origin activation and cell fitness. Life Sci Alliance 2023; 6:e202302111. [PMID: 37793778 PMCID: PMC10551639 DOI: 10.26508/lsa.202302111] [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: 04/25/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
FAM111A is a replisome-associated protein and dominant mutations within its trypsin-like peptidase domain are linked to severe human developmental syndrome, the Kenny-Caffey syndrome. However, FAM111A functions remain unclear. Here, we show that FAM111A facilitates efficient activation of DNA replication origins. Upon hydroxyurea treatment, FAM111A-depleted cells exhibit reduced single-stranded DNA formation and a better survival rate. Unrestrained expression of FAM111A WT and patient mutants causes accumulation of DNA damage and cell death, only when the peptidase domain remains intact. Unrestrained expression of FAM111A WT also causes increased single-stranded DNA formation that relies on S phase entry, FAM111A peptidase activity but not its binding to proliferating cell nuclear antigen. Altogether, these data unveil how FAM111A promotes DNA replication under normal conditions and becomes harmful in a disease context.
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Affiliation(s)
- Diana O Rios-Szwed
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vanesa Alvarez
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Luis Sanchez-Pulido
- https://ror.org/01nrxwf90 MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh, UK
| | - Elisa Garcia-Wilson
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Hao Jiang
- https://ror.org/03h2bxq36 MCDB, Quantitative Proteomics Laboratory, School of Life Sciences, University of Dundee, Dundee, UK
| | - Susanne Bandau
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
| | - Angus Lamond
- https://ror.org/03h2bxq36 MCDB, Quantitative Proteomics Laboratory, School of Life Sciences, University of Dundee, Dundee, UK
| | - Constance Alabert
- https://ror.org/03h2bxq36 MCDB, School of Life Sciences, University of Dundee, Dundee, UK
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Leriche M, Bonnet C, Jana J, Chhetri G, Mennour S, Martineau S, Pennaneach V, Busso D, Veaute X, Bertrand P, Lambert S, Somyajit K, Uguen P, Vagner S. 53BP1 interacts with the RNA primer from Okazaki fragments to support their processing during unperturbed DNA replication. Cell Rep 2023; 42:113412. [PMID: 37963016 DOI: 10.1016/j.celrep.2023.113412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
RNA-binding proteins (RBPs) are found at replication forks, but their direct interaction with DNA-embedded RNA species remains unexplored. Here, we report that p53-binding protein 1 (53BP1), involved in the DNA damage and replication stress response, is an RBP that directly interacts with Okazaki fragments in the absence of external stress. The recruitment of 53BP1 to nascent DNA shows susceptibility to in situ ribonuclease A treatment and is dependent on PRIM1, which synthesizes the RNA primer of Okazaki fragments. Conversely, depletion of FEN1, resulting in the accumulation of uncleaved RNA primers, increases 53BP1 levels at replication forks, suggesting that RNA primers contribute to the recruitment of 53BP1 at the lagging DNA strand. 53BP1 depletion induces an accumulation of S-phase poly(ADP-ribose), which constitutes a sensor of unligated Okazaki fragments. Collectively, our data indicate that 53BP1 is anchored at nascent DNA through its RNA-binding activity, highlighting the role of an RNA-protein interaction at replication forks.
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Affiliation(s)
- Melissa Leriche
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Clara Bonnet
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Jagannath Jana
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Gita Chhetri
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Sabrina Mennour
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Sylvain Martineau
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Vincent Pennaneach
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Didier Busso
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France; Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France
| | - Xavier Veaute
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France; Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France; Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France
| | - Sarah Lambert
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Kumar Somyajit
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patricia Uguen
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France.
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