101
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Casimir L, Zimmer S, Racine-Brassard F, Goudreau F, Jacques PÉ, Maréchal A. Chronic treatment with ATR and CHK1 inhibitors does not substantially increase the mutational burden of human cells. Mutat Res 2023; 827:111834. [PMID: 37531716 DOI: 10.1016/j.mrfmmm.2023.111834] [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: 04/21/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023]
Abstract
DNA replication stress (RS) entails the frequent slow down and arrest of replication forks by a variety of conditions that hinder accurate and processive genome duplication. Elevated RS leads to genome instability, replication catastrophe and eventually cell death. RS is particularly prevalent in cancer cells and its exacerbation to unsustainable levels by chemotherapeutic agents remains a cornerstone of cancer treatments. The adverse consequences of RS are normally prevented by the ATR and CHK1 checkpoint kinases that stabilize stressed forks, suppress origin firing and promote cell cycle arrest when replication is perturbed. Specific inhibitors of these kinases have been developed and shown to potentiate RS and cell death in multiple in vitro cancer settings. Ongoing clinical trials are now probing their efficacy against various cancer types, either as single agents or in combination with mainstay chemotherapeutics. Despite their promise as valuable additions to the anti-cancer pharmacopoeia, we still lack a genome-wide view of the potential mutagenicity of these new drugs. To investigate this question, we performed chronic long-term treatments of TP53-depleted human cancer cells with ATR and CHK1 inhibitors (ATRi, AZD6738/ceralasertib and CHK1i, MK8776/SCH-900776). ATR or CHK1 inhibition did not significantly increase the mutational burden of cells, nor generate specific mutational signatures. Indeed, no notable changes in the numbers of base substitutions, short insertions/deletions and larger scale rearrangements were observed despite induction of replication-associated DNA breaks during treatments. Interestingly, ATR inhibition did induce a slight increase in closely-spaced mutations, a feature previously attributed to translesion synthesis DNA polymerases. The results suggest that ATRi and CHK1i do not have substantial mutagenic effects in vitro when used as standalone agents.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Goudreau
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
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102
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Zhang T, Rawal Y, Jiang H, Kwon Y, Sung P, Greenberg RA. Break-induced replication orchestrates resection-dependent template switching. Nature 2023; 619:201-208. [PMID: 37316655 PMCID: PMC10937050 DOI: 10.1038/s41586-023-06177-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 05/05/2023] [Indexed: 06/16/2023]
Abstract
Break-induced telomere synthesis (BITS) is a RAD51-independent form of break-induced replication that contributes to alternative lengthening of telomeres1,2. This homology-directed repair mechanism utilizes a minimal replisome comprising proliferating cell nuclear antigen (PCNA) and DNA polymerase-δ to execute conservative DNA repair synthesis over many kilobases. How this long-tract homologous recombination repair synthesis responds to complex secondary DNA structures that elicit replication stress remains unclear3-5. Moreover, whether the break-induced replisome orchestrates additional DNA repair events to ensure processivity is also unclear. Here we combine synchronous double-strand break induction with proteomics of isolated chromatin segments (PICh) to capture the telomeric DNA damage response proteome during BITS1,6. This approach revealed a replication stress-dominated response, highlighted by repair synthesis-driven DNA damage tolerance signalling through RAD18-dependent PCNA ubiquitination. Furthermore, the SNM1A nuclease was identified as the major effector of ubiquitinated PCNA-dependent DNA damage tolerance. SNM1A recognizes the ubiquitin-modified break-induced replisome at damaged telomeres, and this directs its nuclease activity to promote resection. These findings show that break-induced replication orchestrates resection-dependent lesion bypass, with SNM1A nuclease activity serving as a critical effector of ubiquitinated PCNA-directed recombination in mammalian cells.
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Affiliation(s)
- Tianpeng Zhang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yashpal Rawal
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Haoyang Jiang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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103
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Duan Y, Zhuang L, Xu Y, Cheng H, Xia J, Lu T, Chen Y. Design, synthesis, and biological evaluation of pyrido[3,2-d]pyrimidine derivatives as novel ATR inhibitors. Bioorg Chem 2023; 136:106535. [PMID: 37086581 DOI: 10.1016/j.bioorg.2023.106535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/24/2023]
Abstract
Targeting ataxia telangiectasia mutated and Rad3-related (ATR) kinase is being pursued as a new therapeutic strategy for the treatment of advanced solid tumor with specific DNA damage response deficiency. Herein, we report a series of pyrido[3,2-d]pyrimidine derivatives with potent ATR inhibitory activity through structure-based drug design. Among them, the representative compound 10q exhibited excellent potency against ATR in both biochemical and cellular assays. More importantly, 10q exhibited good liver microsomes stability in different species and also showed moderate inhibitory activity against HT-29 cells in combination treatment with the ATM inhibitor AZD1390. Thus, this work provides a promising lead compound against ATR for further study.
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Affiliation(s)
- Yunxin Duan
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Lili Zhuang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yerong Xu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Haodong Cheng
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Jiawei Xia
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Yadong Chen
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China.
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104
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Hammad M, Raftari M, Cesário R, Salma R, Godoy P, Emami SN, Haghdoost S. Roles of Oxidative Stress and Nrf2 Signaling in Pathogenic and Non-Pathogenic Cells: A Possible General Mechanism of Resistance to Therapy. Antioxidants (Basel) 2023; 12:1371. [PMID: 37507911 PMCID: PMC10376708 DOI: 10.3390/antiox12071371] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The coordinating role of nuclear factor erythroid-2-related factor 2 (Nrf2) in cellular function is undeniable. Evidence indicates that this transcription factor exerts massive regulatory functions in multiple signaling pathways concerning redox homeostasis and xenobiotics, macromolecules, and iron metabolism. Being the master regulator of antioxidant system, Nrf2 controls cellular fate, influencing cell proliferation, differentiation, apoptosis, resistance to therapy, and senescence processes, as well as infection disease success. Because Nrf2 is the key coordinator of cell defence mechanisms, dysregulation of its signaling has been associated with carcinogenic phenomena and infectious and age-related diseases. Deregulation of this cytoprotective system may also interfere with immune response. Oxidative burst, one of the main microbicidal mechanisms, could be impaired during the initial phagocytosis of pathogens, which could lead to the successful establishment of infection and promote susceptibility to infectious diseases. There is still a knowledge gap to fill regarding the molecular mechanisms by which Nrf2 orchestrates such complex networks involving multiple pathways. This review describes the role of Nrf2 in non-pathogenic and pathogenic cells.
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Affiliation(s)
- Mira Hammad
- University of Caen Normandy, UMR6252 CIMAP/ARIA, GANIL, 14000 Caen, France
| | - Mohammad Raftari
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Rute Cesário
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Rima Salma
- University of Caen Normandy, UMR6252 CIMAP/ARIA, GANIL, 14000 Caen, France
| | - Paulo Godoy
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - S Noushin Emami
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
- Natural Resources Institute, University of Greenwich, London ME4 4TB, UK
| | - Siamak Haghdoost
- University of Caen Normandy, UMR6252 CIMAP/ARIA, GANIL, 14000 Caen, France
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
- Advanced Resource Center for HADrontherapy in Europe (ARCHADE), 14000 Caen, France
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105
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Gu L, Hickey RJ, Malkas LH. Therapeutic Targeting of DNA Replication Stress in Cancer. Genes (Basel) 2023; 14:1346. [PMID: 37510250 PMCID: PMC10378776 DOI: 10.3390/genes14071346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/30/2023] Open
Abstract
This article reviews the currently used therapeutic strategies to target DNA replication stress for cancer treatment in the clinic, highlighting their effectiveness and limitations due to toxicity and drug resistance. Cancer cells experience enhanced spontaneous DNA damage due to compromised DNA replication machinery, elevated levels of reactive oxygen species, loss of tumor suppressor genes, and/or constitutive activation of oncogenes. Consequently, these cells are addicted to DNA damage response signaling pathways and repair machinery to maintain genome stability and support survival and proliferation. Chemotherapeutic drugs exploit this genetic instability by inducing additional DNA damage to overwhelm the repair system in cancer cells. However, the clinical use of DNA-damaging agents is limited by their toxicity and drug resistance often arises. To address these issues, the article discusses a potential strategy to target the cancer-associated isoform of proliferating cell nuclear antigen (caPCNA), which plays a central role in the DNA replication and damage response network. Small molecule and peptide agents that specifically target caPCNA can selectively target cancer cells without significant toxicity to normal cells or experimental animals.
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Affiliation(s)
- Long Gu
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Robert J Hickey
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Linda H Malkas
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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106
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Gan X, Zhang Y, Jiang D, Shi J, Zhao H, Xie C, Wang Y, Xu J, Zhang X, Cai G, Wang H, Huang J, Chen X. Proper RPA acetylation promotes accurate DNA replication and repair. Nucleic Acids Res 2023; 51:5565-5583. [PMID: 37140030 PMCID: PMC10287905 DOI: 10.1093/nar/gkad291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
The single-stranded DNA (ssDNA) binding protein complex RPA plays a critical role in promoting DNA replication and multiple DNA repair pathways. However, how RPA is regulated to achieve its functions precisely in these processes remains elusive. Here, we found that proper acetylation and deacetylation of RPA are required to regulate RPA function in promoting high-fidelity DNA replication and repair. We show that yeast RPA is acetylated on multiple conserved lysines by the acetyltransferase NuA4 upon DNA damage. Mimicking constitutive RPA acetylation or blocking its acetylation causes spontaneous mutations with the signature of micro-homology-mediated large deletions or insertions. In parallel, improper RPA acetylation/deacetylation impairs DNA double-strand break (DSB) repair by the accurate gene conversion or break-induced replication while increasing the error-prone repair by single-strand annealing or alternative end joining. Mechanistically, we show that proper acetylation and deacetylation of RPA ensure its normal nuclear localization and ssDNA binding ability. Importantly, mutation of the equivalent residues in human RPA1 also impairs RPA binding on ssDNA, leading to attenuated RAD51 loading and homologous recombination repair. Thus, timely RPA acetylation and deacetylation likely represent a conserved mechanism promoting high-fidelity replication and repair while discriminating the error-prone repair mechanisms in eukaryotes.
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Affiliation(s)
- Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yueyue Zhang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyao Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Han Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Chengyu Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Cai
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
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107
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A. Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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108
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Yeo XH, Sundararajan V, Wu Z, Phua ZJC, Ho YY, Peh KLE, Chiu YC, Tan TZ, Kappei D, Ho YS, Tan DSP, Tam WL, Huang RYJ. The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer. Commun Biol 2023; 6:660. [PMID: 37349576 PMCID: PMC10287694 DOI: 10.1038/s42003-023-05045-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
AXL is a receptor tyrosine kinase that is often overexpressed in cancers. It contributes to pathophysiology in cancer progression and therapeutic resistance, making it an emerging therapeutic target. The first-in-class AXL inhibitor bemcentinib (R428/BGB324) has been granted fast track designation by the U.S. Food and Drug Administration (FDA) in STK11-mutated advanced metastatic non-small cell lung cancer and was also reported to show selective sensitivity towards ovarian cancers (OC) with a Mesenchymal molecular subtype. In this study, we further explored AXL's role in mediating DNA damage responses by using OC as a disease model. AXL inhibition using R428 resulted in the increase of DNA damage with the concurrent upregulation of DNA damage response signalling molecules. Furthermore, AXL inhibition rendered cells more sensitive to the inhibition of ATR, a crucial mediator for replication stress. Combinatory use of AXL and ATR inhibitors showed additive effects in OC. Through SILAC co-immunoprecipitation mass spectrometry, we identified a novel binding partner of AXL, SAM68, whose loss in OC cells harboured phenotypes in DNA damage responses similar to AXL inhibition. In addition, AXL- and SAM68-deficiency or R428 treatment induced elevated levels of cholesterol and upregulated genes in the cholesterol biosynthesis pathway. There might be a protective role of cholesterol in shielding cancer cells against DNA damage induced by AXL inhibition or SMA68 deficiency.
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Affiliation(s)
- Xun Hui Yeo
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
| | - Vignesh Sundararajan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
| | - Zhengwei Wu
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
| | - Zi Jin Cheryl Phua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Yin Ying Ho
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros, Singapore, 138668, Republic of Singapore
| | - Kai Lay Esther Peh
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros, Singapore, 138668, Republic of Singapore
| | - Yi-Chia Chiu
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros, Singapore, 138668, Republic of Singapore
| | - David Shao Peng Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Republic of Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Republic of Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Ruby Yun-Ju Huang
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan.
- School of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
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109
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Menolfi D, Lee BJ, Zhang H, Jiang W, Bowen NE, Wang Y, Zhao J, Holmes A, Gershik S, Rabadan R, Kim B, Zha S. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion. Nat Commun 2023; 14:3618. [PMID: 37336885 DOI: 10.1038/s41467-023-39332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication and dNTP levels can be restored in Atr-deficient cells by suppressing origin firing, such as partial inhibition of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and importantly also other replication factors.
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Affiliation(s)
- Demis Menolfi
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Hanwen Zhang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Nicole E Bowen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yunyue Wang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Junfei Zhao
- Program for Mathematical Genomics, Department of Systems Biology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Antony Holmes
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Steven Gershik
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Raul Rabadan
- Program for Mathematical Genomics, Department of Systems Biology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY, 10032, USA.
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110
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Göder A, Quinlan A, Rainey MD, Bennett D, Shamavu D, Corso J, Santocanale C. PTBP1 enforces ATR-CHK1 signaling determining the potency of CDC7 inhibitors. iScience 2023; 26:106951. [PMID: 37378325 PMCID: PMC10291475 DOI: 10.1016/j.isci.2023.106951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
CDC7 kinase is crucial for DNA replication initiation and fork processing. CDC7 inhibition mildly activates the ATR pathway, which further limits origin firing; however, to date the relationship between CDC7 and ATR remains controversial. We show that CDC7 and ATR inhibitors are either synergistic or antagonistic depending on the degree of inhibition of each individual kinase. We find that Polypyrimidine Tract Binding Protein 1 (PTBP1) is important for ATR activity in response to CDC7 inhibition and genotoxic agents. Compromised PTBP1 expression makes cells defective in RPA recruitment, genomically unstable, and resistant to CDC7 inhibitors. PTBP1 deficiency affects the expression and splicing of many genes indicating a multifactorial impact on drug response. We find that an exon skipping event in RAD51AP1 contributes to checkpoint deficiency in PTBP1-deficient cells. These results identify PTBP1 as a key factor in replication stress response and define how ATR activity modulates the activity of CDC7 inhibitors.
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Affiliation(s)
- Anja Göder
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Aisling Quinlan
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Michael D. Rainey
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Declan Bennett
- School of Mathematical & Statistical Sciences, University of Galway, Galway H91TK33, Ireland
| | - Daniel Shamavu
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Jacqueline Corso
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Corrado Santocanale
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
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111
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Qin S, Kitty I, Hao Y, Zhao F, Kim W. Maintaining Genome Integrity: Protein Kinases and Phosphatases Orchestrate the Balancing Act of DNA Double-Strand Breaks Repair in Cancer. Int J Mol Sci 2023; 24:10212. [PMID: 37373360 DOI: 10.3390/ijms241210212] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
DNA double-strand breaks (DSBs) are the most lethal DNA damages which lead to severe genome instability. Phosphorylation is one of the most important protein post-translation modifications involved in DSBs repair regulation. Kinases and phosphatases play coordinating roles in DSB repair by phosphorylating and dephosphorylating various proteins. Recent research has shed light on the importance of maintaining a balance between kinase and phosphatase activities in DSB repair. The interplay between kinases and phosphatases plays an important role in regulating DNA-repair processes, and alterations in their activity can lead to genomic instability and disease. Therefore, study on the function of kinases and phosphatases in DSBs repair is essential for understanding their roles in cancer development and therapeutics. In this review, we summarize the current knowledge of kinases and phosphatases in DSBs repair regulation and highlight the advancements in the development of cancer therapies targeting kinases or phosphatases in DSBs repair pathways. In conclusion, understanding the balance of kinase and phosphatase activities in DSBs repair provides opportunities for the development of novel cancer therapeutics.
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Affiliation(s)
- Sisi Qin
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Ichiwa Kitty
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Chungcheongnam-do, Republic of Korea
| | - Yalan Hao
- Analytical Instrumentation Center, Hunan University, Changsha 410082, China
| | - Fei Zhao
- College of Biology, Hunan University, Changsha 410082, China
| | - Wootae Kim
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Chungcheongnam-do, Republic of Korea
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112
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Bouberhan S, Bar-Peled L, Matoba Y, Mazina V, Philp L, Rueda BR. The evolving role of DNA damage response in overcoming therapeutic resistance in ovarian cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2023; 6:345-357. [PMID: 37457127 PMCID: PMC10344720 DOI: 10.20517/cdr.2022.146] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/16/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023]
Abstract
Epithelial ovarian cancer (EOC) is treated in the first-line setting with combined platinum and taxane chemotherapy, often followed by a maintenance poly (ADP-ribose) polymerase inhibitor (PARPi). Responses to first-line treatment are frequent. For many patients, however, responses are suboptimal or short-lived. Over the last several years, multiple new classes of agents targeting DNA damage response (DDR) mechanisms have advanced through clinical development. In this review, we explore the preclinical rationale for the use of ATR inhibitors, CHK1 inhibitors, and WEE1 inhibitors, emphasizing their application to chemotherapy-resistant and PARPi-resistant ovarian cancer. We also present an overview of the clinical development of the leading drugs in each of these classes, emphasizing the rationale for monotherapy and combination therapy approaches.
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Affiliation(s)
- Sara Bouberhan
- Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Liron Bar-Peled
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yusuke Matoba
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA 02115 USA
| | - Varvara Mazina
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA 02115 USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lauren Philp
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA 02115 USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bo R. Rueda
- Department of Obstetrics and Gynecology, Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA 02115 USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA 02114, USA
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113
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Alghoul E, Basbous J, Constantinou A. Compartmentalization of the DNA damage response: Mechanisms and functions. DNA Repair (Amst) 2023; 128:103524. [PMID: 37320957 DOI: 10.1016/j.dnarep.2023.103524] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Cells have evolved an arsenal of molecular mechanisms to respond to continuous alterations in the primary structure of DNA. At the cellular level, DNA damage response proteins accumulate at sites of DNA damage and organize into nuclear foci. As recounted by Errol Friedberg, pioneering work on DNA repair in the 1930 s was stimulated by collaborations between physicists and geneticists. In recent years, the introduction of ideas from physics on self-organizing compartments has taken the field of cell biology by storm. Percolation and phase separation theories are increasingly used to model the self-assembly of compartments, called biomolecular condensates, that selectively concentrate molecules without a surrounding membrane. In this review, we discuss these concepts in the context of the DNA damage response. We discuss how studies of DNA repair foci as condensates can link molecular mechanisms with cell physiological functions, provide new insights into regulatory mechanisms, and open new perspectives for targeting DNA damage responses for therapeutic purposes.
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Affiliation(s)
- Emile Alghoul
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
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114
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Priya B, Ravi S, Kirubakaran S. Targeting ATM and ATR for cancer therapeutics: inhibitors in clinic. Drug Discov Today 2023:103662. [PMID: 37302542 DOI: 10.1016/j.drudis.2023.103662] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/22/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
The DNA Damage and Response (DDR) pathway ensures accurate information transfer from one generation to the next. Alterations in DDR functions have been connected to cancer predisposition, progression, and response to therapy. DNA double-strand break (DSB) is one of the most detrimental DNA defects, causing major chromosomal abnormalities such as translocations and deletions. ATR and ATM kinases recognize this damage and activate proteins involved in cell cycle checkpoint, DNA repair, and apoptosis. Cancer cells have a high DSB burden, and therefore rely on DSB repair for survival. Therefore, targeting DSB repair can sensitize cancer cells to DNA-damaging agents. This review focuses on ATM and ATR, their roles in DNA damage and repair pathways, challenges in targeting them, and inhibitors that are in current clinical trials.
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Affiliation(s)
- Bhanu Priya
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India
| | - Srimadhavi Ravi
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India
| | - Sivapriya Kirubakaran
- Chemistry, Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India.
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115
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Olson CL, Barbour AT, Wieser TA, Wuttke DS. RPA engages telomeric G-quadruplexes more effectively than CST. Nucleic Acids Res 2023; 51:5073-5086. [PMID: 37140062 PMCID: PMC10250233 DOI: 10.1093/nar/gkad315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/11/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
G-quadruplexes (G4s) are a set of stable secondary structures that form within guanine-rich regions of single-stranded nucleic acids that pose challenges for DNA maintenance. The G-rich DNA sequence at telomeres has a propensity to form G4s of various topologies. The human protein complexes Replication Protein A (RPA) and CTC1-STN1-TEN1 (CST) are implicated in managing G4s at telomeres, leading to DNA unfolding and allowing telomere replication to proceed. Here, we use fluorescence anisotropy equilibrium binding measurements to determine the ability of these proteins to bind various telomeric G4s. We find that the ability of CST to specifically bind G-rich ssDNA is substantially inhibited by the presence of G4s. In contrast, RPA tightly binds telomeric G4s, showing negligible changes in affinity for G4 structure compared to linear ssDNAs. Using a mutagenesis strategy, we found that RPA DNA-binding domains work together for G4 binding, and simultaneous disruption of these domains reduces the affinity of RPA for G4 ssDNA. The relative inability of CST to disrupt G4s, combined with the greater cellular abundance of RPA, suggests that RPA could act as a primary protein complex responsible for resolving G4s at telomeres.
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Affiliation(s)
- Conner L Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Alexandra T Barbour
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Thomas A Wieser
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
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116
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Menolfi D, Lee BJ, Zhang H, Jiang W, Bowen NE, Wang Y, Zhao J, Holmes A, Gershik S, Rabadan R, Kim B, Zha S. ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542515. [PMID: 37292881 PMCID: PMC10246007 DOI: 10.1101/2023.05.26.542515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently in early S phase, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication can be restored in Atr-deficient cells by pathways that suppress origin firing, such as downregulation of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and other replication factors.
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117
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Roshan P, Kuppa S, Mattice JR, Kaushik V, Chadda R, Pokhrel N, Tumala BR, Biswas A, Bothner B, Antony E, Origanti S. An Aurora B-RPA signaling axis secures chromosome segregation fidelity. Nat Commun 2023; 14:3008. [PMID: 37230964 PMCID: PMC10212944 DOI: 10.1038/s41467-023-38711-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
Errors in chromosome segregation underlie genomic instability associated with cancers. Resolution of replication and recombination intermediates and protection of vulnerable single-stranded DNA (ssDNA) intermediates during mitotic progression requires the ssDNA binding protein Replication Protein A (RPA). However, the mechanisms that regulate RPA specifically during unperturbed mitotic progression are poorly resolved. RPA is a heterotrimer composed of RPA70, RPA32 and RPA14 subunits and is predominantly regulated through hyperphosphorylation of RPA32 in response to DNA damage. Here, we have uncovered a mitosis-specific regulation of RPA by Aurora B kinase. Aurora B phosphorylates Ser-384 in the DNA binding domain B of the large RPA70 subunit and highlights a mode of regulation distinct from RPA32. Disruption of Ser-384 phosphorylation in RPA70 leads to defects in chromosome segregation with loss of viability and a feedback modulation of Aurora B activity. Phosphorylation at Ser-384 remodels the protein interaction domains of RPA. Furthermore, phosphorylation impairs RPA binding to DSS1 that likely suppresses homologous recombination during mitosis by preventing recruitment of DSS1-BRCA2 to exposed ssDNA. We showcase a critical Aurora B-RPA signaling axis in mitosis that is essential for maintaining genomic integrity.
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Affiliation(s)
- Poonam Roshan
- Department of Biology, St. Louis University, St. Louis, MO, 63103, USA
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Jenna R Mattice
- Department of Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53217, USA
| | - Brunda R Tumala
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Aparna Biswas
- Department of Biology, St. Louis University, St. Louis, MO, 63103, USA
| | - Brian Bothner
- Department of Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA.
| | - Sofia Origanti
- Department of Biology, St. Louis University, St. Louis, MO, 63103, USA.
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118
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Lin Y, Li J, Zhao H, McMahon A, McGhee K, Yan S. APE1 recruits ATRIP to ssDNA in an RPA-dependent and -independent manner to promote the ATR DNA damage response. eLife 2023; 12:e82324. [PMID: 37216274 PMCID: PMC10202453 DOI: 10.7554/elife.82324] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
Cells have evolved the DNA damage response (DDR) pathways in response to DNA replication stress or DNA damage. In the ATR-Chk1 DDR pathway, it has been proposed that ATR is recruited to RPA-coated single-stranded DNA (ssDNA) by direct ATRIP-RPA interaction. However, it remains elusive how ATRIP is recruited to ssDNA in an RPA-independent manner. Here, we provide evidence that APE1 directly associates ssDNA to recruit ATRIP onto ssDNA in an RPA-independent fashion. The N-terminal motif within APE1 is required and sufficient for the APE1-ATRIP interaction in vitro and the distinct APE1-ATRIP interaction is required for ATRIP recruitment to ssDNA and the ATR-Chk1 DDR pathway activation in Xenopus egg extracts. In addition, APE1 directly associates with RPA70 and RPA32 via two distinct motifs. Taken together, our evidence suggests that APE1 recruits ATRIP onto ssDNA in an RPA-dependent and -independent manner in the ATR DDR pathway.
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Affiliation(s)
- Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at CharlotteCharlotteUnited States
| | - Jia Li
- Department of Biological Sciences, University of North Carolina at CharlotteCharlotteUnited States
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at CharlotteCharlotteUnited States
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at CharlotteCharlotteUnited States
| | - Kelly McGhee
- Department of Biological Sciences, University of North Carolina at CharlotteCharlotteUnited States
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at CharlotteCharlotteUnited States
- School of Data Science, University of North Carolina at CharlotteCharlotteUnited States
- Center for Biomedical Engineering and Science, University of North Carolina at CharlotteCharlotteUnited States
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119
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Xu YJ, Bhadra S, Mahdi ATA, Dev K, Yurtsever I, Nakamura TM. Comprehensive mutational analysis of the checkpoint signaling function of Rpa1/Ssb1 in fission yeast. PLoS Genet 2023; 19:e1010691. [PMID: 37200372 DOI: 10.1371/journal.pgen.1010691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/31/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023] Open
Abstract
Replication protein A (RPA) is a heterotrimeric complex and the major single-strand DNA (ssDNA) binding protein in eukaryotes. It plays important roles in DNA replication, repair, recombination, telomere maintenance, and checkpoint signaling. Because RPA is essential for cell survival, understanding its checkpoint signaling function in cells has been challenging. Several RPA mutants have been reported previously in fission yeast. None of them, however, has a defined checkpoint defect. A separation-of-function mutant of RPA, if identified, would provide significant insights into the checkpoint initiation mechanisms. We have explored this possibility and carried out an extensive genetic screen for Rpa1/Ssb1, the large subunit of RPA in fission yeast, looking for mutants with defects in checkpoint signaling. This screen has identified twenty-five primary mutants that are sensitive to genotoxins. Among these mutants, two have been confirmed partially defective in checkpoint signaling primarily at the replication fork, not the DNA damage site. The remaining mutants are likely defective in other functions such as DNA repair or telomere maintenance. Our screened mutants, therefore, provide a valuable tool for future dissection of the multiple functions of RPA in fission yeast.
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Affiliation(s)
- Yong-Jie Xu
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Sankhadip Bhadra
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Alaa Taha A Mahdi
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Kamal Dev
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Ilknur Yurtsever
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Toru M Nakamura
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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120
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Li J, Zhao J, Gan X, Wang Y, Jiang D, Chen L, Wang F, Xu J, Pei H, Huang J, Chen X. The RPA-RNF20-SNF2H cascade promotes proper chromosome segregation and homologous recombination repair. Proc Natl Acad Sci U S A 2023; 120:e2303479120. [PMID: 37155876 PMCID: PMC10193940 DOI: 10.1073/pnas.2303479120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/27/2023] [Indexed: 05/10/2023] Open
Abstract
The human tumor suppressor Ring finger protein 20 (RNF20)-mediated histone H2B monoubiquitination (H2Bub) is essential for proper chromosome segregation and DNA repair. However, what is the precise function and mechanism of RNF20-H2Bub in chromosome segregation and how this pathway is activated to preserve genome stability remain unknown. Here, we show that the single-strand DNA-binding factor Replication protein A (RPA) interacts with RNF20 mainly in the S and G2/M phases and recruits RNF20 to mitotic centromeres in a centromeric R-loop-dependent manner. In parallel, RPA recruits RNF20 to chromosomal breaks upon DNA damage. Disruption of the RPA-RNF20 interaction or depletion of RNF20 increases mitotic lagging chromosomes and chromosome bridges and impairs BRCA1 and RAD51 loading and homologous recombination repair, leading to elevated chromosome breaks, genome instability, and sensitivities to DNA-damaging agents. Mechanistically, the RPA-RNF20 pathway promotes local H2Bub, H3K4 dimethylation, and subsequent SNF2H recruitment, ensuring proper Aurora B kinase activation at centromeres and efficient loading of repair proteins at DNA breaks. Thus, the RPA-RNF20-SNF2H cascade plays a broad role in preserving genome stability by coupling H2Bub to chromosome segregation and DNA repair.
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Affiliation(s)
- Jimin Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Jingyu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Fangwei Wang
- The Ministry of Education Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210009, China
| | - Huadong Pei
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057
| | - Jun Huang
- The Ministry of Education Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
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121
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Uchida C, Niida H, Sakai S, Iijima K, Kitagawa K, Ohhata T, Shiotani B, Kitagawa M. p130RB2 positively contributes to ATR activation in response to replication stress via the RPA32-ETAA1 axis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119484. [PMID: 37201767 DOI: 10.1016/j.bbamcr.2023.119484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 03/17/2023] [Accepted: 04/23/2023] [Indexed: 05/20/2023]
Abstract
Ataxia-telangiectasia mutated and Rad3-related (ATR) kinase is a crucial regulator of the cell cycle checkpoint and activated in response to DNA replication stress by two independent pathways via RPA32-ETAA1 and TopBP1. However, the precise activation mechanism of ATR by the RPA32-ETAA1 pathway remains unclear. Here, we show that p130RB2, a member of the retinoblastoma protein family, participates in the pathway under hydroxyurea-induced DNA replication stress. p130RB2 binds to ETAA1, but not TopBP1, and depletion of p130RB2 inhibits the RPA32-ETAA1 interaction under replication stress. Moreover, p130RB2 depletion reduces ATR activation accompanied by phosphorylation of its targets RPA32, Chk1, and ATR itself. It also causes improper re-progression of S phase with retaining single-stranded DNA after cancelation of the stress, which leads to an increase in the anaphase bridge phenotype and a decrease in cell survival. Importantly, restoration of p130RB2 rescued the disrupted phenotypes of p130RB2 knockdown cells. These results suggest positive involvement of p130RB2 in the RPA32-ETAA1-ATR axis and proper re-progression of the cell cycle to maintain genome integrity.
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Affiliation(s)
- Chiharu Uchida
- Advanced Research Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan.
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kenta Iijima
- Laboratory Animal Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kyoko Kitagawa
- Department of Environmental Health, University of Occupational and Environmental Health, Kitakyushu, Fukuoka 807-8555, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Bunsyo Shiotani
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
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122
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Williams KS, Secomb TW, El-Kareh AW. An autonomous mathematical model for the mammalian cell cycle. J Theor Biol 2023; 569:111533. [PMID: 37196820 DOI: 10.1016/j.jtbi.2023.111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 04/04/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
A mathematical model for the mammalian cell cycle is developed as a system of 13 coupled nonlinear ordinary differential equations. The variables and interactions included in the model are based on detailed consideration of available experimental data. A novel feature of the model is inclusion of cycle tasks such as origin licensing and initiation, nuclear envelope breakdown and kinetochore attachment, and their interactions with controllers (molecular complexes involved in cycle control). Other key features are that the model is autonomous, except for a dependence on external growth factors; the variables are continuous in time, without instantaneous resets at phase boundaries; mechanisms to prevent rereplication are included; and cycle progression is independent of cell size. Eight variables represent cell cycle controllers: the Cyclin D1-Cdk4/6 complex, APCCdh1, SCFβTrCP, Cdc25A, MPF, NuMA, the securin-separase complex, and separase. Five variables represent task completion, with four for the status of origins and one for kinetochore attachment. The model predicts distinct behaviors corresponding to the main phases of the cell cycle, showing that the principal features of the mammalian cell cycle, including restriction point behavior, can be accounted for in a quantitative mechanistic way based on known interactions among cycle controllers and their coupling to tasks. The model is robust to parameter changes, in that cycling is maintained over at least a five-fold range of each parameter when varied individually. The model is suitable for exploring how extracellular factors affect cell cycle progression, including responses to metabolic conditions and to anti-cancer therapies.
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Affiliation(s)
| | - Timothy W Secomb
- BIO5 Institute, University of Arizona, Tucson, AZ, USA; Department of Physiology, University of Arizona, Tucson, AZ, USA
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123
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Yano K, Shiotani B. Emerging strategies for cancer therapy by ATR inhibitors. Cancer Sci 2023. [PMID: 37189251 DOI: 10.1111/cas.15845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 05/17/2023] Open
Abstract
DNA replication stress (RS) causes genomic instability and vulnerability in cancer cells. To counteract RS, cells have evolved various mechanisms involving the ATR kinase signaling pathway, which regulates origin firing, cell cycle checkpoints, and fork stabilization to secure the fidelity of replication. However, ATR signaling also alleviates RS to support cell survival by driving RS tolerance, thereby contributing to therapeutic resistance. Cancer cells harboring genetic mutations and other changes that disrupt normal DNA replication increase the risk of DNA damage and the levels of RS, conferring addiction to ATR activity for sustainable replication and susceptibility to therapeutic approaches using ATR inhibitors (ATRis). Therefore, clinical trials are currently being conducted to evaluate the efficacy of ATRis as monotherapies or in combination with other drugs and biomarkers. In this review, we discuss recent advances in the elucidation of the mechanisms by which ATR functions in the RS response and its therapeutic relevance when utilizing ATRis.
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Affiliation(s)
- Kimiyoshi Yano
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Bunsyo Shiotani
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Tokyo, Japan
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124
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Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
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Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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125
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Cybulski C, Zamani N, Kluźniak W, Milano L, Wokołorczyk D, Stempa K, Rudnicka H, Zhang S, Zadeh M, Huzarski T, Jakubowska A, Dębniak T, Lener M, Szwiec M, Domagała P, Samani AA, Narod S, Gronwald J, Masson JY, Lubiński J, Akbari MR. Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank. Am J Hum Genet 2023; 110:648-662. [PMID: 36977412 PMCID: PMC10119148 DOI: 10.1016/j.ajhg.2023.03.002] [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: 12/06/2022] [Accepted: 03/02/2023] [Indexed: 03/29/2023] Open
Abstract
Several breast cancer susceptibility genes have been discovered, but more are likely to exist. To identify additional breast cancer susceptibility genes, we used the founder population of Poland and performed whole-exome sequencing on 510 women with familial breast cancer and 308 control subjects. We identified a rare mutation in ATRIP (GenBank: NM_130384.3: c.1152_1155del [p.Gly385Ter]) in two women with breast cancer. At the validation phase, we found this variant in 42/16,085 unselected Polish breast cancer-affected individuals and in 11/9,285 control subjects (OR = 2.14, 95% CI = 1.13-4.28, p = 0.02). By analyzing the sequence data of the UK Biobank study participants (450,000 individuals), we identified ATRIP loss-of-function variants among 13/15,643 breast cancer-affected individuals versus 40/157,943 control subjects (OR = 3.28, 95% CI = 1.76-6.14, p < 0.001). Immunohistochemistry and functional studies showed the ATRIP c.1152_1155del variant allele is weakly expressed compared to the wild-type allele, and truncated ATRIP fails to perform its normal function to prevent replicative stress. We showed that tumors of women with breast cancer who have a germline ATRIP mutation have loss of heterozygosity at the site of ATRIP mutation and genomic homologous recombination deficiency. ATRIP is a critical partner of ATR that binds to RPA coating single-stranded DNA at sites of stalled DNA replication forks. Proper activation of ATR-ATRIP elicits a DNA damage checkpoint crucial in regulating cellular responses to DNA replication stress. Based on our observations, we conclude ATRIP is a breast cancer susceptibility gene candidate linking DNA replication stress to breast cancer.
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Affiliation(s)
- Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Neda Zamani
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Wojciech Kluźniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Larissa Milano
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Dominika Wokołorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Klaudia Stempa
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Helena Rudnicka
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Shiyu Zhang
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada
| | - Maryam Zadeh
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tomasz Huzarski
- Department of Clinical Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Tadeusz Dębniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Marcin Lener
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Marek Szwiec
- Department of Surgery and Oncology, University of Zielona Góra, Zielona Góra, Poland
| | - Paweł Domagała
- Department of Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Amir Abbas Samani
- Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Humber River Hospital, University of Toronto, Toronto, ON, Canada
| | - Steven Narod
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Jan Lubiński
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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126
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Yates L, Tannous E, Morgan R, Burgers P, Zhang X. A DNA damage-induced phosphorylation circuit enhances Mec1 ATR Ddc2 ATRIP recruitment to Replication Protein A. Proc Natl Acad Sci U S A 2023; 120:e2300150120. [PMID: 36996117 PMCID: PMC10083555 DOI: 10.1073/pnas.2300150120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/31/2023] Open
Abstract
The cell cycle checkpoint kinase Mec1ATR and its integral partner Ddc2ATRIP are vital for the DNA damage and replication stress response. Mec1-Ddc2 "senses" single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA damage-induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2-RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1-Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn2+. Using electron microscopy and structural modeling approaches, we propose that Mec1-Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1-Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signaling.
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Affiliation(s)
- Luke A. Yates
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
| | - Elias A. Tannous
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO63110
| | - R. Marc Morgan
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
| | - Peter M. Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO63110
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
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127
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Kim H, Villareal LB, Liu Z, Haneef M, Falcon DM, Martin DR, Lee H, Dame MK, Attili D, Chen Y, Varani J, Spence JR, Kovbasnjuk O, Colacino JA, Lyssiotis CA, Lin HC, Shah YM, Xue X. Transferrin Receptor-Mediated Iron Uptake Promotes Colon Tumorigenesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207693. [PMID: 36703617 PMCID: PMC10074045 DOI: 10.1002/advs.202207693] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Indexed: 05/17/2023]
Abstract
Transferrin receptor (TFRC) is the major mediator for iron entry into a cell. Under excessive iron conditions, TFRC is expected to be reduced to lower iron uptake and toxicity. However, the mechanism whereby TFRC expression is maintained at high levels in iron-enriched cancer cells and the contribution of TFRC to cancer development are enigmatic. Here the work shows TFRC is induced by adenomatous polyposis coli (APC) gene loss-driven β-catenin activation in colorectal cancer, whereas TFRC-mediated intratumoral iron accumulation potentiates β-catenin signaling by directly enhancing the activity of tankyrase. Disruption of TFRC leads to a reduction of colonic iron levels and iron-dependent tankyrase activity, which caused stabilization of axis inhibition protein 2 (AXIN2) and subsequent repression of the β-catenin/c-Myc/E2F Transcription Factor 1/DNA polymerase delta1 (POLD1) axis. POLD1 knockdown, iron chelation, and TFRC disruption increase DNA replication stress, DNA damage response, apoptosis, and reduce colon tumor growth. Importantly, a combination of iron chelators and DNA damaging agents increases DNA damage response and reduces colon tumor cell growth. TFRC-mediated iron import is at the center of a novel feed-forward loop that facilitates colonic epithelial cell survival. This discovery may provide novel strategies for colorectal cancer therapy.
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Affiliation(s)
- Hyeoncheol Kim
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Luke B Villareal
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Zhaoli Liu
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Mohammad Haneef
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Daniel M Falcon
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - David R Martin
- Department of PathologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Ho‐Joon Lee
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Michael K Dame
- Department of Internal MedicineDivision of GastroenterologyUniversity of MichiganAnn ArborMI48109USA
| | - Durga Attili
- Department of PathologyThe University of Michigan Medical SchoolAnn ArborMI48109USA
| | - Ying Chen
- Center for clinical research and translational medicineYangpu hospitalTongji University School of MedicineShanghai200090China
| | - James Varani
- Department of PathologyThe University of Michigan Medical SchoolAnn ArborMI48109USA
| | - Jason R. Spence
- Department of Internal MedicineDivision of GastroenterologyUniversity of MichiganAnn ArborMI48109USA
| | - Olga Kovbasnjuk
- Division of Gastroenterology and HepatologyDepartment of Medicinethe University of New MexicoAlbuquerqueNM87131USA
| | - Justin A Colacino
- Department of Environmental Health SciencesUniversity of MichiganAnn ArborMI48109USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Henry C Lin
- Section of GastroenterologyMedicine ServiceNew Mexico VA Health Care SystemAlbuquerqueNM87108USA
| | - Yatrik M Shah
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Xiang Xue
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
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128
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Garaycoechea JI, Quinlan C, Luijsterburg MS. Pathological consequences of DNA damage in the kidney. Nat Rev Nephrol 2023; 19:229-243. [PMID: 36702905 DOI: 10.1038/s41581-022-00671-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 01/27/2023]
Abstract
DNA lesions that evade repair can lead to mutations that drive the development of cancer, and cellular responses to DNA damage can trigger senescence and cell death, which are associated with ageing. In the kidney, DNA damage has been implicated in both acute and chronic kidney injury, and in renal cell carcinoma. The susceptibility of the kidney to chemotherapeutic agents that damage DNA is well established, but an unexpected link between kidney ciliopathies and the DNA damage response has also been reported. In addition, human genetic deficiencies in DNA repair have highlighted DNA crosslinks, DNA breaks and transcription-blocking damage as lesions that are particularly toxic to the kidney. Genetic tools in mice, as well as advances in kidney organoid and single-cell RNA sequencing technologies, have provided important insights into how specific kidney cell types respond to DNA damage. The emerging view is that in the kidney, DNA damage affects the local microenvironment by triggering a damage response and cell proliferation to replenish injured cells, as well as inducing systemic responses aimed at reducing exposure to genotoxic stress. The pathological consequences of DNA damage are therefore key to the nephrotoxicity of DNA-damaging agents and the kidney phenotypes observed in human DNA repair-deficiency disorders.
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Affiliation(s)
- Juan I Garaycoechea
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Catherine Quinlan
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
- Department of Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Australia
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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129
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Patel JA, Kim H. The TIMELESS effort for timely DNA replication and protection. Cell Mol Life Sci 2023; 80:84. [PMID: 36892674 PMCID: PMC9998586 DOI: 10.1007/s00018-023-04738-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023]
Abstract
Accurate replication of the genome is fundamental to cellular survival and tumor prevention. The DNA replication fork is vulnerable to DNA lesions and damages that impair replisome progression, and improper control over DNA replication stress inevitably causes fork stalling and collapse, a major source of genome instability that fuels tumorigenesis. The integrity of the DNA replication fork is maintained by the fork protection complex (FPC), in which TIMELESS (TIM) constitutes a key scaffold that couples the CMG helicase and replicative polymerase activities, in conjunction with its interaction with other proteins associated with the replication machinery. Loss of TIM or the FPC in general results in impaired fork progression, elevated fork stalling and breakage, and a defect in replication checkpoint activation, thus underscoring its pivotal role in protecting the integrity of both active and stalled replication forks. TIM is upregulated in multiple cancers, which may represent a replication vulnerability of cancer cells that could be exploited for new therapies. Here, we discuss recent advances on our understanding of the multifaceted roles of TIM in DNA replication and stalled fork protection, and how its complex functions are engaged in collaboration with other genome surveillance and maintenance factors.
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Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
- Stony Brook Cancer Center and Renaissance School of Medicine, Stony Brook University, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
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130
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Xu YJ, Bhadra S, Mahdi ATA, Dev K, Yurtsever I, Nakamura TM. Comprehensive mutational analysis of the checkpoint signaling function of Rpa1/Ssb1 in fission yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531248. [PMID: 36945624 PMCID: PMC10028789 DOI: 10.1101/2023.03.06.531248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Replication protein A (RPA) is a heterotrimeric complex and the major single-strand DNA (ssDNA) binding protein in eukaryotes. It plays important roles in DNA replication, repair, recombination, telomere maintenance, and checkpoint signaling. Because RPA is essential for cell survival, understanding its checkpoint signaling function in cells has been challenging. Several RPA mutants have been reported previously in fission yeast. None of them, however, has a defined checkpoint defect. A separation-of-function mutant of RPA, if identified, would provide significant insights into the checkpoint initiation mechanisms. We have explored this possibility and carried out an extensive genetic screening for Rpa1/Ssb1, the large subunit of RPA in fission yeast, looking for mutants with defects in checkpoint signaling. This screen has identified twenty-five primary mutants that are sensitive to genotoxins. Among these mutants, two have been confirmed partially defective in checkpoint signaling primarily at the replication fork, not the DNA damage site. The remaining mutants are likely defective in other functions such as DNA repair or telomere maintenance. Our screened mutants, therefore, provide a valuable tool for future dissection of the multiple functions of RPA in fission yeast. AUTHOR SUMMARY Originally discovered as a protein required for replication of simian virus SV40 DNA, replication protein A is now known to function in DNA replication, repair, recombination, telomere maintenance, and checkpoint signaling in all eukaryotes. The protein is a complex of three subunits and the two larger ones are essential for cell growth. This essential function however complicates the studies in living cells, and for this reason, its checkpoint function remains to be fully understood. We have carried out an genetic screening of the largest subunit of this protein in fission yeast, aiming to find a non-lethal mutant that lacks the checkpoint function. This extensive screen has uncovered two mutants with a partial defect in checkpoint signaling when DNA replication is arrested. Surprisingly, although the two mutants also have a defect in DNA repair, their checkpoint signaling remains largely functional in the presence of DNA damage. We have also uncovered twenty-three mutants with defects in DNA repair or telomere maintenance, but not checkpoint signaling. Therefore, the non-lethal mutants uncovered by this study provide a valuable tool for dissecting the multiple functions of this biologically important protein in fission yeast.
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131
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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132
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Sun H, Ma L, Tsai YF, Abeywardana T, Shen B, Zheng L. Okazaki fragment maturation: DNA flap dynamics for cell proliferation and survival. Trends Cell Biol 2023; 33:221-234. [PMID: 35879148 PMCID: PMC9867784 DOI: 10.1016/j.tcb.2022.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 01/24/2023]
Abstract
Unsuccessful processing of Okazaki fragments leads to the accumulation of DNA breaks which are associated with many human diseases including cancer and neurodegenerative disorders. Recently, Okazaki fragment maturation (OFM) has received renewed attention regarding how unprocessed Okazaki fragments are sensed and repaired, and how inappropriate OFM impacts on genome stability and cell viability, especially in cancer cells. We provide an overview of the highly efficient and faithful canonical OFM pathways and their regulation of genomic integrity and cell survival. We also discuss how cells induce alternative error-prone OFM processes to promote cell survival in response to environmental stresses. Such stress-induced OFM processes may be important mechanisms driving mutagenesis, cellular evolution, and resistance to radio/chemotherapy and targeted therapeutics in human cancers.
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Affiliation(s)
- Haitao Sun
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Lingzi Ma
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Ya-Fang Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Tharindu Abeywardana
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
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Zhu S, Hou J, Gao H, Hu Q, Kloeber JA, Huang J, Zhao F, Zhou Q, Luo K, Wu Z, Tu X, Yin P, Lou Z. SUMOylation of HNRNPA2B1 modulates RPA dynamics during unperturbed replication and genotoxic stress responses. Mol Cell 2023; 83:539-555.e7. [PMID: 36702126 PMCID: PMC9975078 DOI: 10.1016/j.molcel.2023.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/17/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023]
Abstract
Replication protein A (RPA) is a major regulator of eukaryotic DNA metabolism involved in multiple essential cellular processes. Maintaining appropriate RPA dynamics is crucial for cells to prevent RPA exhaustion, which can lead to replication fork breakage and replication catastrophe. However, how cells regulate RPA availability during unperturbed replication and in response to stress has not been well elucidated. Here, we show that HNRNPA2B1SUMO functions as an endogenous inhibitor of RPA during normal replication. HNRNPA2B1SUMO associates with RPA through recognizing the SUMO-interacting motif (SIM) of RPA to inhibit RPA accumulation at replication forks and impede local ATR activation. Declining HNRNPA2SUMO induced by DNA damage will release nuclear soluble RPA to localize to chromatin and enable ATR activation. Furthermore, we characterize that HNRNPA2B1 hinders homologous recombination (HR) repair via limiting RPA availability, thus conferring sensitivity to PARP inhibitors. These findings establish HNRNPA2B1 as a critical player in RPA-dependent surveillance networks.
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Affiliation(s)
- Shouhai Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jing Hou
- Department of Breast Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
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134
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Priya B, Dubey G, Kirubakaran S. Exploring SPK98 for the Selective Sensitization of ATM- or P53-Deficient Cancer Cells. ACS OMEGA 2023; 8:4954-4962. [PMID: 36777575 PMCID: PMC9909806 DOI: 10.1021/acsomega.2c07356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Frequent mutation in the ATM/P53 signaling pathway has been documented in many human cancers. Reportedly, cancer cells with deficient P53/ATM pathways depend on functional Ataxia-telangiectasia and Rad3-related (ATR) protein for survival. This has prompted research in developing ATR inhibitors for the selective sensitization of cancer cells that are P53/ATM-deficient, but no clinical success has been attained thus far. This study explores the therapeutic potential of SPK98, an analogue of Torin2 in P53- and ATM-deficient cancer cells. Furthermore, the prospect of improving the therapeutic outcome of the genotoxic agent was also explored. SPK98 was shown to inhibit full-length human ATR protein purified from HEK293T cells. Cellular investigation using SPK98 demonstrated that it selectively sensitizes P53- and ATM-deficient cells at low concentrations compared to P53-/ATM-proficient cells. Furthermore, SPK98 drives the cancer cells toward cell death by promoting the formation of DNA double-strand breaks. Taken together, our findings suggest that SPK98 is a promising therapeutic molecule for P53- or ATM-deficient malignancy that merits additional preclinical investigation.
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Affiliation(s)
- Bhanu Priya
- Discipline
of Biological Engineering, Indian Institute
of Technology Gandhinagar, Gandhinagar 382355, Gujarat, India
| | - Gurudutt Dubey
- Discipline
of Chemistry, Indian Institute of Technology
Gandhinagar, Gandhinagar 382355, Gujarat, India
| | - Sivapriya Kirubakaran
- Discipline
of Chemistry, Indian Institute of Technology
Gandhinagar, Gandhinagar 382355, Gujarat, India
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135
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SMARCA4: Current status and future perspectives in non-small-cell lung cancer. Cancer Lett 2023; 554:216022. [PMID: 36450331 DOI: 10.1016/j.canlet.2022.216022] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
SMARCA4, also known as transcription activator, is an ATP-dependent catalytic subunit of SWI/SNF (SWItch/Sucrose NonFermentable) chromatin-remodeling complexes that participates in the regulation of chromatin structure and gene expression by supplying energy. As a tumor suppressor that has aberrant expression in ∼10% of non-small-cell lung cancers (NSCLCs), SMARCA4 possesses many biological functions, including regulating gene expression, differentiation and transcription. Furthermore, NSCLC patients with SMARCA4 alterations have a weak response to conventional chemotherapy and poor prognosis. Therefore, the mechanisms of SMARCA4 in NSCLC development urgently need to be explored to identify novel biomarkers and precise therapeutic strategies for this subtype. This review systematically describes the biological functions of SMARCA4 and its role in NSCLC development, metastasis, functional epigenetics and potential therapeutic approaches for NSCLCs with SMARCA4 alterations. Additionally, this paper explores the relationship and regulatory mechanisms shared by SMARCA4 and its mutually exclusive catalytic subunit SMARCA2. We aim to provide innovative treatment strategies and improve clinical outcomes for NSCLC patients with SMARCA4 alterations.
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136
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Molecular targets that sensitize cancer to radiation killing: From the bench to the bedside. Biomed Pharmacother 2023; 158:114126. [PMID: 36521246 DOI: 10.1016/j.biopha.2022.114126] [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: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a standard cytotoxic therapy against solid cancers. It uses ionizing radiation to kill tumor cells through damage to DNA, either directly or indirectly. Radioresistance is often associated with dysregulated DNA damage repair processes. Most radiosensitizers enhance radiation-mediated DNA damage and reduce the rate of DNA repair ultimately leading to accumulation of DNA damages, cell-cycle arrest, and cell death. Recently, agents targeting key signals in DNA damage response such as DNA repair pathways and cell-cycle have been developed. This new class of molecularly targeted radiosensitizing agents is being evaluated in preclinical and clinical studies to monitor their activity in potentiating radiation cytotoxicity of tumors and reducing normal tissue toxicity. The molecular pathways of DNA damage response are reviewed with a focus on the repair mechanisms, therapeutic targets under current clinical evaluation including ATM, ATR, CDK1, CDK4/6, CHK1, DNA-PKcs, PARP-1, Wee1, & MPS1/TTK and potential new targets (BUB1, and DNA LIG4) for radiation sensitization.
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137
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Groelly FJ, Fawkes M, Dagg RA, Blackford AN, Tarsounas M. Targeting DNA damage response pathways in cancer. Nat Rev Cancer 2023; 23:78-94. [PMID: 36471053 DOI: 10.1038/s41568-022-00535-5] [Citation(s) in RCA: 233] [Impact Index Per Article: 233.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Cells have evolved a complex network of biochemical pathways, collectively known as the DNA damage response (DDR), to prevent detrimental mutations from being passed on to their progeny. The DDR coordinates DNA repair with cell-cycle checkpoint activation and other global cellular responses. Genes encoding DDR factors are frequently mutated in cancer, causing genomic instability, an intrinsic feature of many tumours that underlies their ability to grow, metastasize and respond to treatments that inflict DNA damage (such as radiotherapy). One instance where we have greater insight into how genetic DDR abrogation impacts on therapy responses is in tumours with mutated BRCA1 or BRCA2. Due to compromised homologous recombination DNA repair, these tumours rely on alternative repair mechanisms and are susceptible to chemical inhibitors of poly(ADP-ribose) polymerase (PARP), which specifically kill homologous recombination-deficient cancer cells, and have become a paradigm for targeted cancer therapy. It is now clear that many other synthetic-lethal relationships exist between DDR genes. Crucially, some of these interactions could be exploited in the clinic to target tumours that become resistant to PARP inhibition. In this Review, we discuss state-of-the-art strategies for DDR inactivation using small-molecule inhibitors and highlight those compounds currently being evaluated in the clinic.
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Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
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138
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Sundararajan V, Tan TZ, Lim D, Peng Y, Wengner AM, Ngoi NYL, Jeyasekharan AD, Tan DSP. Nuclear pCHK1 as a potential biomarker of increased sensitivity to ATR inhibition. J Pathol 2023; 259:194-204. [PMID: 36373784 PMCID: PMC10107453 DOI: 10.1002/path.6032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Excessive genomic instability coupled with abnormalities in DNA repair pathways induces high levels of 'replication stress' when cancer cells propagate. Rather than hampering cancer cell proliferation, novel treatment strategies are turning their attention towards targeting cell cycle checkpoint kinases (such as ATR, CHK1, WEE1, and others) along the DNA damage response and replicative stress response pathways, thereby allowing unrepaired DNA damage to be carried forward towards mitotic catastrophe and apoptosis. The selective ATR kinase inhibitor elimusertib (BAY 1895344) has demonstrated preclinical and clinical monotherapy activity; however, reliable predictive biomarkers of treatment benefit are still lacking. In this study, using gene expression profiling of 24 cell lines from different cancer types and in a panel of ovarian cancer cell lines, we found that nuclear-specific enrichment of checkpoint kinase 1 (CHK1) correlated with increased sensitivity to elimusertib. Using an advanced multispectral imaging system in subsequent cell line-derived xenograft specimens, we showed a trend between nuclear phosphorylated CHK1 (pCHK1) staining and increased sensitivity to the ATR inhibitor elimusertib, indicating the potential value of pCHK1 expression as a predictive biomarker of ATR inhibitor sensitivity. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Vignesh Sundararajan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Diana Lim
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Natalie Yan Li Ngoi
- Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - David Shao Peng Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, Singapore
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139
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DNA Damage Response Mechanisms in Head and Neck Cancer: Significant Implications for Therapy and Survival. Int J Mol Sci 2023; 24:ijms24032760. [PMID: 36769087 PMCID: PMC9917521 DOI: 10.3390/ijms24032760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Head and neck cancer (HNC) is a term collectively used to describe a heterogeneous group of tumors that arise in the oral cavity, larynx, nasopharynx, oropharynx, and hypopharynx, and represents the sixth most common type of malignancy worldwide. Despite advances in multimodality treatment, the disease has a recurrence rate of around 50%, and the prognosis of metastatic patients remains poor. HNCs are characterized by a high degree of genomic instability, which involves a vicious circle of accumulating DNA damage, defective DNA damage repair (DDR), and replication stress. Nonetheless, the damage that is induced on tumor cells by chemo and radiotherapy relies on defective DDR processes for a successful response to treatment, and may play an important role in the development of novel and more effective therapies. This review summarizes the current knowledge on the genes and proteins that appear to be deregulated in DDR pathways, their implication in HNC pathogenesis, and the rationale behind targeting these genes and pathways for the development of new therapies. We give particular emphasis on the therapeutic targets that have shown promising results at the pre-clinical stage and on those that have so far been associated with a therapeutic advantage in the clinical setting.
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140
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Nikfarjam S, Singh KK. DNA damage response signaling: A common link between cancer and cardiovascular diseases. Cancer Med 2023; 12:4380-4404. [PMID: 36156462 PMCID: PMC9972122 DOI: 10.1002/cam4.5274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/10/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022] Open
Abstract
DNA damage response (DDR) signaling ensures genomic and proteomic homeostasis to maintain a healthy genome. Dysregulation either in the form of down- or upregulation in the DDR pathways correlates with various pathophysiological states, including cancer and cardiovascular diseases (CVDs). Impaired DDR is studied as a signature mechanism for cancer; however, it also plays a role in ischemia-reperfusion injury (IRI), inflammation, cardiovascular function, and aging, demonstrating a complex and intriguing relationship between cancer and pathophysiology of CVDs. Accordingly, there are increasing number of reports indicating higher incidences of CVDs in cancer patients. In the present review, we thoroughly discuss (1) different DDR pathways, (2) the functional cross talk among different DDR mechanisms, (3) the role of DDR in cancer, (4) the commonalities and differences of DDR between cancer and CVDs, (5) the role of DDR in pathophysiology of CVDs, (6) interventional strategies for targeting genomic instability in CVDs, and (7) future perspective.
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Affiliation(s)
- Sepideh Nikfarjam
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Krishna K Singh
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada.,Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
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141
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Kitab B, Tsukiyama-Kohara K. Regulatory Role of Ribonucleotide Reductase Subunit M2 in Hepatocyte Growth and Pathogenesis of Hepatitis C Virus. Int J Mol Sci 2023; 24:ijms24032619. [PMID: 36768940 PMCID: PMC9916403 DOI: 10.3390/ijms24032619] [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: 12/20/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Hepatitis C virus (HCV) frequently causes chronic infection in the human liver, which may progress to advanced hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. HCV primarily infects highly differentiated quiescent hepatocytes and can modulate cell cycle-regulatory genes and proliferation pathways, which ultimately contribute to persistent infection and pathogenesis. On the other hand, several studies have shown differential regulation of HCV RNA and viral protein expression levels, depending on the proliferation state of hepatocytes and the phase of the cell cycle. HCV typically requires factors provided by host cells for efficient and persistent viral replication. Previously, we found that HCV infection upregulates the expression of ribonucleotide reductase subunit M2 (RRM2) in quiescent hepatocytes. RRM2 is a rate-limiting protein that catalyzes de novo synthesis of deoxyribonucleotide triphosphates, and its expression is highly regulated during various phases of the cell cycle. RRM2 functions as a pro-viral factor essential for HCV RNA synthesis, but its functional role in HCV-induced liver diseases remains unknown. Here, we present a comprehensive review of the role of the hepatocyte cell cycle, in correlation with RRM2 expression, in the regulation of HCV replication. We also discuss the potential relevance of this protein in the pathogenesis of HCV, particularly in the development of hepatocellular carcinoma.
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142
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Mechetin GV, Zharkov DO. DNA Damage Response and Repair in Boron Neutron Capture Therapy. Genes (Basel) 2023; 14:127. [PMID: 36672868 PMCID: PMC9859301 DOI: 10.3390/genes14010127] [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: 12/10/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Boron neutron capture therapy (BNCT) is an approach to the radiotherapy of solid tumors that was first outlined in the 1930s but has attracted considerable attention recently with the advent of a new generation of neutron sources. In BNCT, tumor cells accumulate 10B atoms that react with epithermal neutrons, producing energetic α particles and 7Li atoms that damage the cell's genome. The damage inflicted by BNCT appears not to be easily repairable and is thus lethal for the cell; however, the molecular events underlying the action of BNCT remain largely unaddressed. In this review, the chemistry of DNA damage during BNCT is outlined, the major mechanisms of DNA break sensing and repair are summarized, and the specifics of the repair of BNCT-induced DNA lesions are discussed.
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Affiliation(s)
- Grigory V. Mechetin
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
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143
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Gospodinov A, Dzhokova S, Petrova M, Ugrinova I. Chromatin regulators in DNA replication and genome stability maintenance during S-phase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:243-280. [PMID: 37061334 DOI: 10.1016/bs.apcsb.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The duplication of genetic information is central to life. The replication of genetic information is strictly controlled to ensure that each piece of genomic DNA is copied only once during a cell cycle. Factors that slow or stop replication forks cause replication stress. Replication stress is a major source of genome instability in cancer cells. Multiple control mechanisms facilitate the unimpeded fork progression, prevent fork collapse and coordinate fork repair. Chromatin alterations, caused by histone post-translational modifications and chromatin remodeling, have critical roles in normal replication and in avoiding replication stress and its consequences. This text reviews the chromatin regulators that ensure DNA replication and the proper response to replication stress. We also briefly touch on exploiting replication stress in therapeutic strategies. As chromatin regulators are frequently mutated in cancer, manipulating their activity could provide many possibilities for personalized treatment.
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Affiliation(s)
- Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Stefka Dzhokova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Petrova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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144
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Salguero C, Valladolid C, Robinson HMR, Smith GCM, Yap TA. Targeting ATR in Cancer Medicine. Cancer Treat Res 2023; 186:239-283. [PMID: 37978140 DOI: 10.1007/978-3-031-30065-3_14] [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] [Indexed: 11/19/2023]
Abstract
As a key component of the DNA Damage Response, the Ataxia telangiectasia and Rad3-related (ATR) protein is a promising druggable target that is currently widely evaluated in phase I-II-III clinical trials as monotherapy and in combinations with other rational antitumor agents, including immunotherapy, DNA repair inhibitors, chemo- and radiotherapy. Ongoing clinical studies for this drug class must address the optimization of the therapeutic window to limit overlapping toxicities and refine the target population that will most likely benefit from ATR inhibition. With advances in the development of personalized treatment strategies for patients with advanced solid tumors, many ongoing ATR inhibitor trials have been recruiting patients based on their germline and somatic molecular alterations, rather than relying solely on specific tumor subtypes. Although a spectrum of molecular alterations have already been identified as potential predictive biomarkers of response that may sensitize to ATR inhibition, these biomarkers must be analytically validated and feasible to measure robustly to allow for successful integration into the clinic. While several ATR inhibitors in development are poised to address a clinically unmet need, no ATR inhibitor has yet received FDA-approval. This chapter details the underlying rationale for targeting ATR and summarizes the current preclinical and clinical landscape of ATR inhibitors currently in evaluation, as their regulatory approval potentially lies close in sight.
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Affiliation(s)
- Carolina Salguero
- Department of Investigational Cancer Therapeutics (Phase I Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christian Valladolid
- Department of Investigational Cancer Therapeutics (Phase I Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Helen M R Robinson
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The Institute for Applied Cancer Science, and Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Boulevard, TX, 77030, Houston, USA.
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145
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Wong GCN, Chow KHM. DNA Damage Response-Associated Cell Cycle Re-Entry and Neuronal Senescence in Brain Aging and Alzheimer's Disease. J Alzheimers Dis 2023; 94:S429-S451. [PMID: 35848025 PMCID: PMC10473156 DOI: 10.3233/jad-220203] [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] [Accepted: 06/07/2022] [Indexed: 11/15/2022]
Abstract
Chronological aging is by far the strongest risk factor for age-related dementia and Alzheimer's disease. Senescent cells accumulated in the aging and Alzheimer's disease brains are now recognized as the keys to describing such an association. Cellular senescence is a classic phenomenon characterized by stable cell arrest, which is thought to be applicable only to dividing cells. Emerging evidence indicates that fully differentiated post-mitotic neurons are also capable of becoming senescent, with roles in contributing to both brain aging and disease pathogenesis. The key question that arises is the identity of the upstream triggers and the molecular mechanisms that underly such changes. Here, we highlight the potential role of persistent DNA damage response as the major driver of senescent phenotypes and discuss the current evidence and molecular mechanisms that connect DNA repair infidelity, cell cycle re-entry and terminal fate decision in committing neuronal cell senescence.
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Affiliation(s)
- Genper Chi-Ngai Wong
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong
| | - Kim Hei-Man Chow
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Hong Kong
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146
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Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA. PLoS One 2023; 18:e0278396. [PMID: 36656834 PMCID: PMC9851514 DOI: 10.1371/journal.pone.0278396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/15/2022] [Indexed: 01/20/2023] Open
Abstract
Human Replication Protein A (hRPA) is a multidomain protein that interacts with ssDNA intermediates to provide the latter much-needed stability during DNA metabolism and maintain genomic integrity. Although the ssDNA organization with hRPA was studied recently through experimental means, characterizing the underlying mechanism at the atomic level remains challenging because of the dynamic domain architecture of hRPA and poorly understood heterogeneity of ssDNA-protein interactions. Here, we used a computational framework, precisely tailored to capture protein-ssDNA interactions, and investigated the binding of hRPA with a 60 nt ssDNA. Two distinct binding mechanisms are realized based on the hRPA domain flexibility. For a rigid domain architecture of hRPA, ssDNA binds sequentially with hRPA domains, resulting in slow association kinetics. The binding pathway involves the formation of stable and distinct intermediate states. On contrary, for a flexible domain architecture of hRPA, ssDNA binds synergistically to the A and B domains followed by the rest of hRPA. The domain dynamics in hRPA alleviates the free energy cost of domain orientation necessary for specific binding with ssDNA, leading to fast association kinetics along a downhill binding free energy landscape. An ensemble of free energetically degenerate intermediate states is encountered that makes it arduous to characterize them structurally. An excellent match between our results with the available experimental observations provides new insights into the rich dynamics of hRPA binding to ssDNA and in general paves the way to investigate intricate details of ssDNA-protein interactions, crucial for cellular functioning.
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147
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Zhao X, Zhuang Y, Wang B, Yuan B, Du S, Zeng Z. The miR-34a-5p-c-MYC-CHK1/CHK2 Axis Counteracts Cancer Stem Cell-Like Properties and Enhances Radiosensitivity in Hepatocellular Cancer Through Repression of the DNA Damage Response. Radiat Res 2023; 199:48-60. [PMID: 36445955 DOI: 10.1667/rade-22-00098.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/14/2022] [Indexed: 11/30/2022]
Abstract
Radiotherapy has become an increasingly widespread modality for treating hepatocellular cancer (HCC); however, the development of radioresistance significantly limits its effectiveness and invariably leads to tumor recurrence. Cancer stem cell (CSC) theory offers a potential explanation for tumor relapse and radioresistance, but the underlying mechanism remains unknown. Herein we investigate the role of miRNA in molecular regulation of stemness and radioresistance in HCC. Two HCC radiation-resistant cell lines (Huh7-RR and SMMC-7721-RR) were established by selecting the radioresistant subpopulation from HCC cells via clonogenic survival assays. MiRNA Sequencing was used to identify potential radiosensitivity involved miRNA in HCC-RR cells. Xenograft tumor mouse model was established for in vivo study. CSC properties were assessed using sphere formation assay and side population (SP) cells analysis. We found that miR-34a-5p was significantly downregulated in HCC-RR cells. Overexpression of miR-34a-5p counteracts CSC properties and enhances radiosensitivity in HCC. Mechanistic investigation revealed that c-MYC is the direct target of miR-34a-5p. Overexpression of miR-34a-5p reversed c-MYC-induced radioresistance. Moreover, we found that the specific molecular mechanism was that c-MYC activated CHK1 and CHK2, which are two key DNA damage checkpoint kinases, and facilitated the DNA damage response to radiation. Repression of the miR-34a-5p-cMYC-CHK1/CHK2 axis contributes to the acquisition of radioresistance in HCC cells. In summary, the miR-34a-5p-c-MYC-CHK1/CHK2 axis counteracts cancer stem cell-like properties and enhances radiosensitivity in hepatocellular cancer through repression of the DNA damage response.
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Affiliation(s)
- Xiaomei Zhao
- Departments of Radiation Oncology Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuan Zhuang
- Departments of Radiation Oncology Zhongshan Hospital, Fudan University, Shanghai, China
| | - Biao Wang
- Departments of Radiation Oncology Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baoying Yuan
- Departments of Radiation Oncology Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shisuo Du
- Departments of Radiation Oncology Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhaochong Zeng
- Departments of Radiation Oncology Zhongshan Hospital, Fudan University, Shanghai, China
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148
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Luan Y, Yu SY, Abazarikia A, Dong R, Kim SY. TAp63 determines the fate of oocytes against DNA damage. SCIENCE ADVANCES 2022; 8:eade1846. [PMID: 36542718 PMCID: PMC9770984 DOI: 10.1126/sciadv.ade1846] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Cyclophosphamide and doxorubicin lead to premature ovarian insufficiency as an off-target effect. However, their oocyte death pathway has been debated. Here, we clarified the precise mechanism of ovarian depletion induced by cyclophosphamide and doxorubicin. Dormant oocytes instead of activated oocytes with high PI3K activity were more sensitive to cyclophosphamide. Checkpoint kinase 2 (CHK2) inhibitor rather than GNF2 protected oocytes from cyclophosphamide and doxorubicin, as cyclophosphamide up-regulated p-CHK2 and depleted primordial follicles in Abl1 knockout mice. Contrary to previous reports, TAp63 is pivotal in cyclophosphamide and doxorubicin-induced oocyte death. Oocyte-specific Trp63 knockout mice prevented primordial follicle loss and maintained reproductive function from cyclophosphamide and doxorubicin, indicated by undetectable levels of BAX and cPARP. Here, we demonstrated that TAp63 is fundamental in determining the signaling of oocyte death against DNA damage. This study establishes the role of TAp63 as a target molecule of adjuvant therapies to protect the ovarian reserve from different classes of chemotherapy.
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Affiliation(s)
- Yi Luan
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Seok-Yeong Yu
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Amirhossein Abazarikia
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rosemary Dong
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - So-Youn Kim
- Olson Center for Women’s Health, Department of Obstetrics and Gynecology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
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149
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Sadek M, Sheth A, Zimmerman G, Hays E, Vélez-Cruz R. The role of SWI/SNF chromatin remodelers in the repair of DNA double strand breaks and cancer therapy. Front Cell Dev Biol 2022; 10:1071786. [PMID: 36605718 PMCID: PMC9810387 DOI: 10.3389/fcell.2022.1071786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Switch/Sucrose non-fermenting (SWI/SNF) chromatin remodelers hydrolyze ATP to push and slide nucleosomes along the DNA thus modulating access to various genomic loci. These complexes are the most frequently mutated epigenetic regulators in human cancers. SWI/SNF complexes are well known for their function in transcription regulation, but more recent work has uncovered a role for these complexes in the repair of DNA double strand breaks (DSBs). As radiotherapy and most chemotherapeutic agents kill cancer cells by inducing double strand breaks, by identifying a role for these complexes in double strand break repair we are also identifying a DNA repair vulnerability that can be exploited therapeutically in the treatment of SWI/SNF-mutated cancers. In this review we summarize work describing the function of various SWI/SNF subunits in the repair of double strand breaks with a focus on homologous recombination repair and discuss the implication for the treatment of cancers with SWI/SNF mutations.
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Affiliation(s)
- Maria Sadek
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Anand Sheth
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL, United States
| | - Grant Zimmerman
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL, United States
| | - Emily Hays
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Renier Vélez-Cruz
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL, United States
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
- Chicago College of Optometry, Midwestern University, Downers Grove, IL, United States
- Chicago College of Pharmacy, Midwestern University, Downers Grove, IL, United States
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150
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Li S, Wang T, Fei X, Zhang M. ATR Inhibitors in Platinum-Resistant Ovarian Cancer. Cancers (Basel) 2022; 14:cancers14235902. [PMID: 36497387 PMCID: PMC9740197 DOI: 10.3390/cancers14235902] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Platinum-resistant ovarian cancer (PROC) is one of the deadliest types of epithelial ovarian cancer, and it is associated with a poor prognosis as the median overall survival (OS) is less than 12 months. Targeted therapy is a popular emerging treatment method. Several targeted therapies, including those using bevacizumab and poly (ADP-ribose) polymerase inhibitor (PARPi), have been used to treat PROC. Ataxia telangiectasia and RAD3-Related Protein Kinase inhibitors (ATRi) have attracted attention as a promising class of targeted drugs that can regulate the cell cycle and influence homologous recombination (HR) repair. In recent years, many preclinical and clinical studies have demonstrated the efficacy of ATRis in PROC. This review focuses on the anticancer mechanism of ATRis and the progress of research on ATRis for PROC.
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Affiliation(s)
- Siyu Li
- Department of Medical Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230031, China
- Department of Oncology, Anhui Medical University, Hefei 230031, China
| | - Tao Wang
- Department of Medical Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230031, China
- Department of Oncology, Anhui Medical University, Hefei 230031, China
| | - Xichang Fei
- Department of Medical Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230031, China
- Department of Oncology, Anhui Medical University, Hefei 230031, China
| | - Mingjun Zhang
- Department of Medical Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230031, China
- Department of Oncology, Anhui Medical University, Hefei 230031, China
- Correspondence:
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