1
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Jiang Y, Li S, Ramesh R. Identification of SMARCAL1 as a molecular target for small cell lung cancer treatment. Cancer Lett 2024; 592:216932. [PMID: 38735383 DOI: 10.1016/j.canlet.2024.216932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024]
Affiliation(s)
- Yuanyuan Jiang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, Shandong, China; Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Shuchang Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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2
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Sun BB, Wang GZ, Han SC, Yang FY, Guo H, Liu J, Liu YT, Zhou GB. Oncogenic functions and therapeutic potentials of targeted inhibition of SMARCAL1 in small cell lung cancer. Cancer Lett 2024; 592:216929. [PMID: 38697461 DOI: 10.1016/j.canlet.2024.216929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/05/2024]
Abstract
Small cell lung cancer (SCLC) is a recalcitrant cancer characterized by high frequency loss-of-function mutations in tumor suppressors with a lack of targeted therapy due to absence of high frequency gain-of-function abnormalities in oncogenes. SMARCAL1 is a member of the ATP-dependent chromatin remodeling protein SNF2 family that plays critical roles in DNA damage repair and genome stability maintenance. Here, we showed that SMARCAL1 was overexpressed in SCLC patient samples and was inversely associated with overall survival of the patients. SMARCAL1 was required for SCLC cell proliferation and genome integrity. Mass spectrometry revealed that PAR6B was a downstream SMARCAL1 signal molecule which rescued inhibitory effects caused by silencing of SMARCAL1. By screening of 36 FDA-approved clinically available agents related to DNA damage repair, we found that an aza-anthracenedione, pixantrone, was a potent SMARCAL1 inhibitor which suppressed the expression of SMARCAL1 and PAR6B at protein level. Pixantrone caused DNA damage and exhibited inhibitory effects on SCLC cells in vitro and in a patient-derived xenograft mouse model. These results indicated that SMARCAL1 functions as an oncogene in SCLC, and pixantrone as a SMARCAL1 inhibitor bears therapeutic potentials in this deadly disease.
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Affiliation(s)
- Bei-Bei Sun
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Gui-Zhen Wang
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Si-Chong Han
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fu-Ying Yang
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hua Guo
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yu-Tao Liu
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Guang-Biao Zhou
- State Key Laboratory of Molecular Oncology and Department of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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3
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Kang S, Yoo J, Myung K. PCNA cycling dynamics during DNA replication and repair in mammals. Trends Genet 2024; 40:526-539. [PMID: 38485608 DOI: 10.1016/j.tig.2024.02.006] [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: 01/17/2024] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 06/06/2024]
Abstract
Proliferating cell nuclear antigen (PCNA) is a eukaryotic replicative DNA clamp. Furthermore, DNA-loaded PCNA functions as a molecular hub during DNA replication and repair. PCNA forms a closed homotrimeric ring that encircles the DNA, and association and dissociation of PCNA from DNA are mediated by clamp-loader complexes. PCNA must be actively released from DNA after completion of its function. If it is not released, abnormal accumulation of PCNA on chromatin will interfere with DNA metabolism. ATAD5 containing replication factor C-like complex (RLC) is a PCNA-unloading clamp-loader complex. ATAD5 deficiency causes various DNA replication and repair problems, leading to genome instability. Here, we review recent progress regarding the understanding of the action mechanisms of PCNA unloading complex in DNA replication/repair pathways.
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Affiliation(s)
- Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Juyeong Yoo
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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4
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Schreuder A, Wendel TJ, Dorresteijn CGV, Noordermeer SM. (Single-stranded DNA) gaps in understanding BRCAness. Trends Genet 2024:S0168-9525(24)00100-8. [PMID: 38789375 DOI: 10.1016/j.tig.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
The tumour-suppressive roles of BRCA1 and 2 have been attributed to three seemingly distinct functions - homologous recombination, replication fork protection, and single-stranded (ss)DNA gap suppression - and their relative importance is under debate. In this review, we examine the origin and resolution of ssDNA gaps and discuss the recent advances in understanding the role of BRCA1/2 in gap suppression. There are ample data showing that gap accumulation in BRCA1/2-deficient cells is linked to genomic instability and chemosensitivity. However, it remains unclear whether there is a causative role and the function of BRCA1/2 in gap suppression cannot unambiguously be dissected from their other functions. We therefore conclude that the three functions of BRCA1 and 2 are closely intertwined and not mutually exclusive.
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Affiliation(s)
- Anne Schreuder
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Tiemen J Wendel
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Carlo G V Dorresteijn
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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5
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Batenburg NL, Sowa DJ, Walker JR, Andres SN, Zhu XD. CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells. Nucleic Acids Res 2024; 52:5067-5087. [PMID: 38416570 PMCID: PMC11109976 DOI: 10.1093/nar/gkae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024] Open
Abstract
CSB (Cockayne syndrome group B) and SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent, regulator of chromatin, subfamily A-like 1) are DNA translocases that belong to the SNF2 helicase family. They both are enriched at stalled replication forks. While SMARCAL1 is recruited by RPA32 to stalled forks, little is known about whether RPA32 also regulates CSB's association with stalled forks. Here, we report that CSB directly interacts with RPA, at least in part via a RPA32C-interacting motif within the N-terminal region of CSB. Modeling of the CSB-RPA32C interaction suggests that CSB binds the RPA32C surface previously shown to be important for binding of UNG2 and SMARCAL1. We show that this interaction is necessary for promoting fork slowing and fork degradation in BRCA2-deficient cells but dispensable for mediating restart of stalled forks. CSB competes with SMARCAL1 for RPA32 at stalled forks and acts non-redundantly with SMARCAL1 to restrain fork progression in response to mild replication stress. In contrast to CSB stimulated restart of stalled forks, SMARCAL1 inhibits restart of stalled forks in BRCA2-deficient cells, likely by suppressing BIR-mediated repair of collapsed forks. Loss of CSB leads to re-sensitization of SMARCAL1-depleted BRCA2-deficient cells to chemodrugs, underscoring a role of CSB in targeted cancer therapy.
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Affiliation(s)
- Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Dana J Sowa
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sara N Andres
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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6
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Yu H, Han X, Wang W, Zhang Y, Xiang L, Bai D, Zhang L, Weng Z, Lv K, Song L, Luo W, Yin N, Zhang Y, Feng T, Wang L, Xie G. Modified Unit-Mediated Strand Displacement Reactions for Direct Detection of Single Nucleotide Variants in Active Double-Stranded DNA. ACS NANO 2024; 18:12401-12411. [PMID: 38701333 DOI: 10.1021/acsnano.4c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Accurate identification of single nucleotide variants (SNVs) in key driver genes holds a significant value for disease diagnosis and treatment. Fluorescent probes exhibit tremendous potential in specific, high-resolution, and rapid detection of SNVs. However, additional steps are required in most post-PCR assays to convert double-stranded DNA (dsDNA) products into single-stranded DNA (ssDNA), enabling them to possess hybridization activity to trigger subsequent reactions. This process not only prolongs the complexity of the experiment but also introduces the risk of losing target information. In this study, we proposed two strategies for enriching active double-stranded DNA, involving PCR based on obstructive groups and cleavable units. Building upon this, we explored the impact of modified units on the strand displacement reaction (SDR) and assessed their discriminatory efficacy for mutations. The results showed that detection of low variant allele frequencies (VAF) as low as 0.1% can be achieved. The proposed strategy allowed orthogonal identification of 45 clinical colorectal cancer tissue samples with 100% specificity, and the results were generally consistent with sequencing results. Compared to existing methods for enriching active targets, our approach offers a more diverse set of enrichment strategies, characterized by the advantage of being simple and fast and preserving original information to the maximum extent. The objective of this study is to offer an effective solution for the swift and facile acquisition of active double-stranded DNA. We anticipate that our work will facilitate the practical applications of SDR based on dsDNA.
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Affiliation(s)
- Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yangli Zhang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Linguo Xiang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zhi Weng
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ke Lv
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Na Yin
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yaoyi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tong Feng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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7
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Tian T, Chen J, Zhao H, Li Y, Xia F, Huang J, Han J, Liu T. UFL1 triggers replication fork degradation by MRE11 in BRCA1/2-deficient cells. Nat Chem Biol 2024:10.1038/s41589-024-01611-7. [PMID: 38649452 DOI: 10.1038/s41589-024-01611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
The stabilization of stalled forks has emerged as a crucial mechanism driving resistance to poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA1/2-deficient tumors. Here, we identify UFL1, a UFM1-specific E3 ligase, as a pivotal regulator of fork stability and the response to PARP inhibitors in BRCA1/2-deficient cells. On replication stress, UFL1 localizes to stalled forks and catalyzes the UFMylation of PTIP, a component of the MLL3/4 methyltransferase complex, specifically at lysine 148. This modification facilitates the assembly of the PTIP-MLL3/4 complex, resulting in the enrichment of H3K4me1 and H3K4me3 at stalled forks and subsequent recruitment of the MRE11 nuclease. Consequently, loss of UFL1, disruption of PTIP UFMylation or overexpression of the UFM1 protease UFSP2 protects nascent DNA strands from extensive degradation and confers resistance to PARP inhibitors in BRCA1/2-deficient cells. These findings provide mechanistic insights into the processes underlying fork instability in BRCA1/2-deficient cells and offer potential therapeutic avenues for the treatment of BRCA1/2-deficient tumors.
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Affiliation(s)
- Tian Tian
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Junliang Chen
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Huacun Zhao
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yulin Li
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Feiyu Xia
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Huang
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jinhua Han
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ting Liu
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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8
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Ye Z, Xu S, Shi Y, Cheng X, Zhang Y, Roy S, Namjoshi S, Longo MA, Link TM, Schlacher K, Peng G, Yu D, Wang B, Tainer JA, Ahmed Z. GRB2 stabilizes RAD51 at reversed replication forks suppressing genomic instability and innate immunity against cancer. Nat Commun 2024; 15:2132. [PMID: 38459011 PMCID: PMC10923831 DOI: 10.1038/s41467-024-46283-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
Growth factor receptor-bound protein 2 (GRB2) is a cytoplasmic adapter for tyrosine kinase signaling and a nuclear adapter for homology-directed-DNA repair. Here we find nuclear GRB2 protects DNA at stalled replication forks from MRE11-mediated degradation in the BRCA2 replication fork protection axis. Mechanistically, GRB2 binds and inhibits RAD51 ATPase activity to stabilize RAD51 on stalled replication forks. In GRB2-depleted cells, PARP inhibitor (PARPi) treatment releases DNA fragments from stalled forks into the cytoplasm that activate the cGAS-STING pathway to trigger pro-inflammatory cytokine production. Moreover in a syngeneic mouse metastatic ovarian cancer model, GRB2 depletion in the context of PARPi treatment reduced tumor burden and enabled high survival consistent with immune suppression of cancer growth. Collective findings unveil GRB2 function and mechanism for fork protection in the BRCA2-RAD51-MRE11 axis and suggest GRB2 as a potential therapeutic target and an enabling predictive biomarker for patient selection for PARPi and immunotherapy combination.
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Affiliation(s)
- Zu Ye
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Shengfeng Xu
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yin Shi
- Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xueqian Cheng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuan Zhang
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sunetra Roy
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sarita Namjoshi
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michael A Longo
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Todd M Link
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Katharina Schlacher
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dihua Yu
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bin Wang
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John A Tainer
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Zamal Ahmed
- Departments of Molecular and Cellular Oncology and Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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9
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Yates M, Marois I, St-Hilaire E, Ronato DA, Djerir B, Brochu C, Morin T, Hammond-Martel I, Gezzar-Dandashi S, Casimir L, Drobetsky E, Cappadocia L, Masson JY, Wurtele H, Maréchal A. SMARCAL1 ubiquitylation controls its association with RPA-coated ssDNA and promotes replication fork stability. PLoS Biol 2024; 22:e3002552. [PMID: 38502677 PMCID: PMC10950228 DOI: 10.1371/journal.pbio.3002552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Impediments in replication fork progression cause genomic instability, mutagenesis, and severe pathologies. At stalled forks, RPA-coated single-stranded DNA (ssDNA) activates the ATR kinase and directs fork remodeling, 2 key early events of the replication stress response. RFWD3, a recently described Fanconi anemia (FA) ubiquitin ligase, associates with RPA and promotes its ubiquitylation, facilitating late steps of homologous recombination (HR). Intriguingly, RFWD3 also regulates fork progression, restart and stability via poorly understood mechanisms. Here, we used proteomics to identify putative RFWD3 substrates during replication stress in human cells. We show that RFWD3 interacts with and ubiquitylates the SMARCAL1 DNA translocase directly in vitro and following DNA damage in vivo. SMARCAL1 ubiquitylation does not trigger its subsequent proteasomal degradation but instead disengages it from RPA thereby regulating its function at replication forks. Proper regulation of SMARCAL1 by RFWD3 at stalled forks protects them from excessive MUS81-mediated cleavage in response to UV irradiation, thereby limiting DNA replication stress. Collectively, our results identify RFWD3-mediated SMARCAL1 ubiquitylation as a novel mechanism that modulates fork remodeling to avoid genome instability triggered by aberrant fork processing.
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Affiliation(s)
- Maïlyn Yates
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Isabelle Marois
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Edlie St-Hilaire
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
| | - Daryl A. Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Billel Djerir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Chloé Brochu
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Théo Morin
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | | | | | - Lisa Casimir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Elliot Drobetsky
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Laurent Cappadocia
- Faculty of Sciences, Department of Chemistry, Université du Québec à Montréal, Montréal, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Hugo Wurtele
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
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10
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Leuzzi G, Vasciaveo A, Taglialatela A, Chen X, Firestone TM, Hickman AR, Mao W, Thakar T, Vaitsiankova A, Huang JW, Cuella-Martin R, Hayward SB, Kesner JS, Ghasemzadeh A, Nambiar TS, Ho P, Rialdi A, Hebrard M, Li Y, Gao J, Gopinath S, Adeleke OA, Venters BJ, Drake CG, Baer R, Izar B, Guccione E, Keogh MC, Guerois R, Sun L, Lu C, Califano A, Ciccia A. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. Cell 2024; 187:861-881.e32. [PMID: 38301646 PMCID: PMC10980358 DOI: 10.1016/j.cell.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 07/23/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 limits endogenous DNA damage, thereby suppressing cGAS-STING-dependent signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a PD-L1 transcriptional regulatory element, thereby promoting PD-L1 expression in cancer cells. SMARCAL1 loss hinders the ability of tumor cells to induce PD-L1 in response to genomic instability, enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a promising target for cancer immunotherapy.
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Affiliation(s)
- Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alessandro Vasciaveo
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | | | - Wendy Mao
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tanay Thakar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alina Vaitsiankova
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jordan S Kesner
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ali Ghasemzadeh
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tarun S Nambiar
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander Rialdi
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxime Hebrard
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jinmei Gao
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | | | | | | | - Charles G Drake
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Urology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Raphael Guerois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lu Sun
- EpiCypher Inc., Durham, NC 27709, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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11
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Chen J, Wu M, Yang Y, Ruan C, Luo Y, Song L, Wu T, Huang J, Yang B, Liu T. TFIP11 promotes replication fork reversal to preserve genome stability. Nat Commun 2024; 15:1262. [PMID: 38341452 PMCID: PMC10858868 DOI: 10.1038/s41467-024-45684-3] [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: 04/28/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Replication fork reversal, a critical protective mechanism against replication stress in higher eukaryotic cells, is orchestrated via a series of coordinated enzymatic reactions. The Bloom syndrome gene product, BLM, a member of the highly conserved RecQ helicase family, is implicated in this process, yet its precise regulation and role remain poorly understood. In this study, we demonstrate that the GCFC domain-containing protein TFIP11 forms a complex with the BLM helicase. TFIP11 exhibits a preference for binding to DNA substrates that mimic the structure generated at stalled replication forks. Loss of either TFIP11 or BLM leads to the accumulation of the other protein at stalled forks. This abnormal accumulation, in turn, impairs RAD51-mediated fork reversal and slowing, sensitizes cells to replication stress-inducing agents, and enhances chromosomal instability. These findings reveal a previously unidentified regulatory mechanism that modulates the activities of BLM and RAD51 at stalled forks, thereby impacting genome integrity.
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Affiliation(s)
- Junliang Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China
| | - Mingjie Wu
- The Trauma Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chunyan Ruan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Yi Luo
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Lizhi Song
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Wu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Bing Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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12
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Spegg V, Altmeyer M. Genome maintenance meets mechanobiology. Chromosoma 2024; 133:15-36. [PMID: 37581649 PMCID: PMC10904543 DOI: 10.1007/s00412-023-00807-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023]
Abstract
Genome stability is key for healthy cells in healthy organisms, and deregulated maintenance of genome integrity is a hallmark of aging and of age-associated diseases including cancer and neurodegeneration. To maintain a stable genome, genome surveillance and repair pathways are closely intertwined with cell cycle regulation and with DNA transactions that occur during transcription and DNA replication. Coordination of these processes across different time and length scales involves dynamic changes of chromatin topology, clustering of fragile genomic regions and repair factors into nuclear repair centers, mobilization of the nuclear cytoskeleton, and activation of cell cycle checkpoints. Here, we provide a general overview of cell cycle regulation and of the processes involved in genome duplication in human cells, followed by an introduction to replication stress and to the cellular responses elicited by perturbed DNA synthesis. We discuss fragile genomic regions that experience high levels of replication stress, with a particular focus on telomere fragility caused by replication stress at the ends of linear chromosomes. Using alternative lengthening of telomeres (ALT) in cancer cells and ALT-associated PML bodies (APBs) as examples of replication stress-associated clustered DNA damage, we discuss compartmentalization of DNA repair reactions and the role of protein properties implicated in phase separation. Finally, we highlight emerging connections between DNA repair and mechanobiology and discuss how biomolecular condensates, components of the nuclear cytoskeleton, and interfaces between membrane-bound organelles and membraneless macromolecular condensates may cooperate to coordinate genome maintenance in space and time.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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13
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González-Acosta D, Lopes M. DNA replication and replication stress response in the context of nuclear architecture. Chromosoma 2024; 133:57-75. [PMID: 38055079 PMCID: PMC10904558 DOI: 10.1007/s00412-023-00813-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
The DNA replication process needs to be coordinated with other DNA metabolism transactions and must eventually extend to the full genome, regardless of chromatin status, gene expression, secondary structures and DNA lesions. Completeness and accuracy of DNA replication are crucial to maintain genome integrity, limiting transformation in normal cells and offering targeting opportunities for proliferating cancer cells. DNA replication is thus tightly coordinated with chromatin dynamics and 3D genome architecture, and we are only beginning to understand the underlying molecular mechanisms. While much has recently been discovered on how DNA replication initiation is organised and modulated in different genomic regions and nuclear territories-the so-called "DNA replication program"-we know much less on how the elongation of ongoing replication forks and particularly the response to replication obstacles is affected by the local nuclear organisation. Also, it is still elusive how specific components of nuclear architecture participate in the replication stress response. Here, we review known mechanisms and factors orchestrating replication initiation, and replication fork progression upon stress, focusing on recent evidence linking genome organisation and nuclear architecture with the cellular responses to replication interference, and highlighting open questions and future challenges to explore this exciting new avenue of research.
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Affiliation(s)
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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14
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Khatib JB, Nicolae CM, Moldovan GL. Role of Translesion DNA Synthesis in the Metabolism of Replication-associated Nascent Strand Gaps. J Mol Biol 2024; 436:168275. [PMID: 37714300 PMCID: PMC10842951 DOI: 10.1016/j.jmb.2023.168275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Translesion DNA synthesis (TLS) is a DNA damage tolerance pathway utilized by cells to overcome lesions encountered throughout DNA replication. During replication stress, cancer cells show increased dependency on TLS proteins for cellular survival and chemoresistance. TLS proteins have been described to be involved in various DNA repair pathways. One of the major emerging roles of TLS is single-stranded DNA (ssDNA) gap-filling, primarily after the repriming activity of PrimPol upon encountering a lesion. Conversely, suppression of ssDNA gap accumulation by TLS is considered to represent a mechanism for cancer cells to evade the toxicity of chemotherapeutic agents, specifically in BRCA-deficient cells. Thus, TLS inhibition is emerging as a potential treatment regimen for DNA repair-deficient tumors.
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Affiliation(s)
- Jude B Khatib
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA. https://twitter.com/JudeBKhatib
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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15
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Zhao Y, Hou K, Li Y, Hao S, Liu Y, Na Y, Li C, Cui J, Xu X, Wu X, Wang H. Human HELQ regulates DNA end resection at DNA double-strand breaks and stalled replication forks. Nucleic Acids Res 2023; 51:12207-12223. [PMID: 37897354 PMCID: PMC10711563 DOI: 10.1093/nar/gkad940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/15/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Following a DNA double strand break (DSB), several nucleases and helicases coordinate to generate single-stranded DNA (ssDNA) with 3' free ends, facilitating precise DNA repair by homologous recombination (HR). The same nucleases can act on stalled replication forks, promoting nascent DNA degradation and fork instability. Interestingly, some HR factors, such as CtIP and BRCA1, have opposite regulatory effects on the two processes, promoting end resection at DSB but inhibiting the degradation of nascent DNA on stalled forks. However, the reason why nuclease actions are regulated by different mechanisms in two DNA metabolism is poorly understood. We show that human HELQ acts as a DNA end resection regulator, with opposing activities on DNA end resection at DSBs and on stalled forks as seen for other regulators. Mechanistically, HELQ helicase activity is required for EXO1-mediated DSB end resection, while ssDNA-binding capacity of HELQ is required for its recruitment to stalled forks, facilitating fork protection and preventing chromosome aberrations caused by replication stress. Here, HELQ synergizes with CtIP but not BRCA1 or BRCA2 to protect stalled forks. These findings reveal an unanticipated role of HELQ in regulating DNA end resection at DSB and stalled forks, which is important for maintaining genome stability.
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Affiliation(s)
- Yuqin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Kaiping Hou
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Youhang Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yu Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yinan Na
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Chao Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jian Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, China Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
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16
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Palumbieri MD, Merigliano C, González-Acosta D, Kuster D, Krietsch J, Stoy H, von Känel T, Ulferts S, Welter B, Frey J, Doerdelmann C, Sanchi A, Grosse R, Chiolo I, Lopes M. Nuclear actin polymerization rapidly mediates replication fork remodeling upon stress by limiting PrimPol activity. Nat Commun 2023; 14:7819. [PMID: 38016948 PMCID: PMC10684888 DOI: 10.1038/s41467-023-43183-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase and observed their rapid extension in number and length upon genotoxic treatments, frequently taking contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork remodeling is linked to deregulated chromatin loading of PrimPol, which promotes unrestrained and discontinuous DNA synthesis and limits the recruitment of RAD51 and SMARCAL1 to nascent DNA. Moreover, defective nuclear actin polymerization upon mild replication interference induces chromosomal instability in a PRIMPOL-dependent manner. Hence, by limiting PrimPol activity, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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Affiliation(s)
| | - Chiara Merigliano
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | | | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Department of Cellular and Molecular Medicine, Copenhagen University, Copenhagen, Denmark
| | - Thomas von Känel
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Svenja Ulferts
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Welter
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Joël Frey
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Cyril Doerdelmann
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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17
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Rastokina A, Cebrián J, Mozafari N, Mandel NH, Smith CI, Lopes M, Zain R, Mirkin S. Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers. Nucleic Acids Res 2023; 51:8532-8549. [PMID: 37216608 PMCID: PMC10484681 DOI: 10.1093/nar/gkad441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/02/2023] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Friedreich's ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron of the human FXN gene that occur during both intergenerational transmissions and in somatic cells. Here we describe an experimental system to analyze large-scale repeat expansions in cultured human cells. It employs a shuttle plasmid that can replicate from the SV40 origin in human cells or be stably maintained in S. cerevisiae utilizing ARS4-CEN6. It also contains a selectable cassette allowing us to detect repeat expansions that accumulated in human cells upon plasmid transformation into yeast. We indeed observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system to study large-scale repeat expansions in human cells. Further, GAA•TTC repeats stall replication fork progression, while the frequency of repeat expansions appears to depend on proteins implicated in replication fork stalling, reversal, and restart. Locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers, which interfere with triplex formation at GAA•TTC repeats in vitro, prevented the expansion of these repeats in human cells. We hypothesize, therefore, that triplex formation by GAA•TTC repeats stall replication fork progression, ultimately leading to repeat expansions during replication fork restart.
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Affiliation(s)
| | - Jorge Cebrián
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | | | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
- Center for Rare Diseases, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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18
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Liu H, Xu C, Diplas BH, Brown A, Strickland LM, Yao H, Ling J, McLendon RE, Keir ST, Ashley DM, He Y, Waitkus MS. Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells. Neuro Oncol 2023; 25:1563-1575. [PMID: 36689342 PMCID: PMC10484176 DOI: 10.1093/neuonc/noad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Telomere maintenance mechanisms are required to enable the replicative immortality of malignant cells. While most cancers activate the enzyme telomerase, a subset of cancers uses telomerase-independent mechanisms termed alternative lengthening of telomeres (ALT). ALT occurs via homology-directed-repair mechanisms and is frequently associated with ATRX mutations. We previously showed that a subset of adult glioblastoma (GBM) patients with ATRX-expressing ALT-positive tumors harbored loss-of-function mutations in the SMARCAL1 gene, which encodes an annealing helicase involved in replication fork remodeling and the resolution of replication stress. However, the causative relationship between SMARCAL1 deficiency, tumorigenesis, and de novo telomere synthesis is not understood. METHODS We used a patient-derived ALT-positive GBM cell line with native SMARCAL1 deficiency to investigate the role of SMARCAL1 in ALT-mediated de novo telomere synthesis, replication stress, and gliomagenesis in vivo. RESULTS Inducible rescue of SMARCAL1 expression suppresses ALT indicators and inhibits de novo telomere synthesis in GBM and osteosarcoma cells, suggesting that SMARCAL1 deficiency plays a functional role in ALT induction in cancers that natively lack SMARCAL1 function. SMARCAL1-deficient ALT-positive cells can be serially propagated in vivo in the absence of detectable telomerase activity, demonstrating that the SMARCAL1-deficient ALT phenotype maintains telomeres in a manner that promotes tumorigenesis. CONCLUSIONS SMARCAL1 deficiency is permissive to ALT and promotes gliomagenesis. Inducible rescue of SMARCAL1 in ALT-positive cell lines permits the dynamic modulation of ALT activity, which will be valuable for future studies aimed at understanding the mechanisms of ALT and identifying novel anticancer therapeutics that target the ALT phenotype.
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Affiliation(s)
- Heng Liu
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Cheng Xu
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Bill H Diplas
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Alexandrea Brown
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Laura M Strickland
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Haipei Yao
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Jinjie Ling
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Roger E McLendon
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Stephen T Keir
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Matthew S Waitkus
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
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19
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Batenburg NL, Walker JR, Zhu XD. CSB Regulates Pathway Choice in Response to DNA Replication Stress Induced by Camptothecin. Int J Mol Sci 2023; 24:12419. [PMID: 37569794 PMCID: PMC10418903 DOI: 10.3390/ijms241512419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Topoisomerase inhibitor camptothecin (CPT) induces fork stalling and is highly toxic to proliferating cells. However, how cells respond to CPT-induced fork stalling has not been fully characterized. Here, we report that Cockayne syndrome group B (CSB) protein inhibits PRIMPOL-dependent fork repriming in response to a low dose of CPT. At a high concentration of CPT, CSB is required to promote the restart of DNA replication through MUS81-RAD52-POLD3-dependent break-induced replication (BIR). In the absence of CSB, resumption of DNA synthesis at a high concentration of CPT can occur through POLQ-LIG3-, LIG4-, or PRIMPOL-dependent pathways, which are inhibited, respectively, by RAD51, BRCA1, and BRCA2 proteins. POLQ and LIG3 are core components of alternative end joining (Alt-EJ), whereas LIG4 is a core component of nonhomologous end joining (NHEJ). These results suggest that CSB regulates fork restart pathway choice following high-dosage CPT-induced fork stalling, promoting BIR but inhibiting Alt-EJ, NHEJ, and fork repriming. We find that loss of CSB and BRCA2 is a toxic combination to genomic stability and cell survival at a high concentration of CPT, which is likely due to accumulation of ssDNA gaps, underscoring an important role of CSB in regulating the therapy response in cancers lacking functional BRCA2.
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Affiliation(s)
| | | | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (N.L.B.); (J.R.W.)
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20
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Moore CE, Yalcindag SE, Czeladko H, Ravindranathan R, Wijesekara Hanthi Y, Levy JC, Sannino V, Schindler D, Ciccia A, Costanzo V, Elia AE. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks. J Cell Biol 2023; 222:e202106022. [PMID: 37036693 PMCID: PMC10097976 DOI: 10.1083/jcb.202106022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 04/11/2023] Open
Abstract
Replication fork reversal is an important mechanism to protect the stability of stalled forks and thereby preserve genomic integrity. While multiple enzymes have been identified that can remodel forks, their regulation remains poorly understood. Here, we demonstrate that the ubiquitin ligase RFWD3, whose mutation causes Fanconi Anemia, promotes recruitment of the DNA translocase ZRANB3 to stalled replication forks and ubiquitinated sites of DNA damage. Using electron microscopy, we show that RFWD3 stimulates fork remodeling in a ZRANB3-epistatic manner. Fork reversal is known to promote nascent DNA degradation in BRCA2-deficient cells. Consistent with a role for RFWD3 in fork reversal, inactivation of RFWD3 in these cells rescues fork degradation and collapse, analogous to ZRANB3 inactivation. RFWD3 loss impairs ZRANB3 localization to spontaneous nuclear foci induced by inhibition of the PCNA deubiquitinase USP1. We demonstrate that RFWD3 promotes PCNA ubiquitination and interaction with ZRANB3, providing a mechanism for RFWD3-dependent recruitment of ZRANB3. Together, these results uncover a new role for RFWD3 in regulating ZRANB3-dependent fork remodeling.
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Affiliation(s)
- Chandler E. Moore
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Selin E. Yalcindag
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hanna Czeladko
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramya Ravindranathan
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yodhara Wijesekara Hanthi
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Juliana C. Levy
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Detlev Schindler
- Department of Human Genetics, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Alberto Ciccia
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Andrew E.H. Elia
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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21
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Liu W, Saito Y, Jackson J, Bhowmick R, Kanemaki MT, Vindigni A, Cortez D. RAD51 bypasses the CMG helicase to promote replication fork reversal. Science 2023; 380:382-387. [PMID: 37104614 PMCID: PMC10302453 DOI: 10.1126/science.add7328] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/25/2023] [Indexed: 04/29/2023]
Abstract
Replication fork reversal safeguards genome integrity as a replication stress response. DNA translocases and the RAD51 recombinase catalyze reversal. However, it remains unknown why RAD51 is required and what happens to the replication machinery during reversal. We find that RAD51 uses its strand exchange activity to circumvent the replicative helicase, which remains bound to the stalled fork. RAD51 is not required for fork reversal if the helicase is unloaded. Thus, we propose that RAD51 creates a parental DNA duplex behind the helicase that is used as a substrate by the DNA translocases for branch migration to create a reversed fork structure. Our data explain how fork reversal happens while maintaining the helicase in a position poised to restart DNA synthesis and complete genome duplication.
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Affiliation(s)
- Wenpeng Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rahul Bhowmick
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Masato T. Kanemaki
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
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22
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Broderick R, Cherdyntseva V, Nieminuszczy J, Dragona E, Kyriakaki M, Evmorfopoulou T, Gagos S, Niedzwiedz W. Pathway choice in the alternative telomere lengthening in neoplasia is dictated by replication fork processing mediated by EXD2's nuclease activity. Nat Commun 2023; 14:2428. [PMID: 37105990 PMCID: PMC10140042 DOI: 10.1038/s41467-023-38029-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Telomerase-independent cancer proliferation via the alternative lengthening of telomeres (ALT) relies upon two distinct, largely uncharacterized, break-induced-replication (BIR) processes. How cancer cells initiate and regulate these terminal repair mechanisms is unknown. Here, we establish that the EXD2 nuclease is recruited to ALT telomeres to direct their maintenance. We demonstrate that EXD2 loss leads to telomere shortening, elevated telomeric sister chromatid exchanges, C-circle formation as well as BIR-mediated telomeric replication. We discover that EXD2 fork-processing activity triggers a switch between RAD52-dependent and -independent ALT-associated BIR. The latter is suppressed by EXD2 but depends specifically on the fork remodeler SMARCAL1 and the MUS81 nuclease. Thus, our findings suggest that processing of stalled replication forks orchestrates elongation pathway choice at ALT telomeres. Finally, we show that co-depletion of EXD2 with BLM, DNA2 or POLD3 confers synthetic lethality in ALT cells, identifying EXD2 as a potential druggable target for ALT-reliant cancers.
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Affiliation(s)
| | - Veronica Cherdyntseva
- Laboratory of Genetics, Center of Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation Academy of Athens (BRFAA), Athens, Greece
| | | | - Eleni Dragona
- Laboratory of Genetics, Center of Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation Academy of Athens (BRFAA), Athens, Greece
| | - Maria Kyriakaki
- Laboratory of Genetics, Center of Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation Academy of Athens (BRFAA), Athens, Greece
| | - Theodora Evmorfopoulou
- Laboratory of Genetics, Center of Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation Academy of Athens (BRFAA), Athens, Greece
| | - Sarantis Gagos
- Laboratory of Genetics, Center of Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation Academy of Athens (BRFAA), Athens, Greece.
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23
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Palumbieri MD, Merigliano C, Acosta DG, von Känel T, Welter B, Stoy H, Krietsch J, Ulferts S, Sanchi A, Grosse R, Chiolo I, Lopes M. Replication fork plasticity upon replication stress requires rapid nuclear actin polymerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534097. [PMID: 36993227 PMCID: PMC10055433 DOI: 10.1101/2023.03.24.534097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase, rapidly extending in number and thickness upon genotoxic treatments, and taking frequent contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork plasticity is linked to reduced recruitment of RAD51 and SMARCAL1 to nascent DNA. Conversely, PRIMPOL gains access to replicating chromatin, promoting unrestrained and discontinuous DNA synthesis, which is associated with increased chromosomal instability and decreased cellular resistance to replication stress. Hence, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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24
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Sohn EJ, Goralsky JA, Shay JW, Min J. The Molecular Mechanisms and Therapeutic Prospects of Alternative Lengthening of Telomeres (ALT). Cancers (Basel) 2023; 15:cancers15071945. [PMID: 37046606 PMCID: PMC10093677 DOI: 10.3390/cancers15071945] [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: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
As detailed by the end replication problem, the linear ends of a cell's chromosomes, known as telomeres, shorten with each successive round of replication until a cell enters into a state of growth arrest referred to as senescence. To maintain their immortal proliferation capacity, cancer cells must employ a telomere maintenance mechanism, such as telomerase activation or the Alternative Lengthening of Telomeres pathway (ALT). With only 10-15% of cancers utilizing the ALT mechanism, progress towards understanding its molecular components and associated hallmarks has only recently been made. This review analyzes the advances towards understanding the ALT pathway by: (1) detailing the mechanisms associated with engaging the ALT pathway as well as (2) identifying potential therapeutic targets of ALT that may lead to novel cancer therapeutic treatments. Collectively, these studies indicate that the ALT molecular mechanisms involve at least two distinct pathways induced by replication stress and damage at telomeres. We suggest exploiting tumor dependency on ALT is a promising field of study because it suggests new approaches to ALT-specific therapies for cancers with poorer prognosis. While substantial progress has been made in the ALT research field, additional progress will be required to realize these advances into clinical practices to treat ALT cancers and improve patient prognoses.
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Affiliation(s)
- Eric J Sohn
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia A Goralsky
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Jaewon Min
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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25
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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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26
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Abstract
High-fidelity DNA replication is critical for the faithful transmission of genetic information to daughter cells. Following genotoxic stress, specialized DNA damage tolerance pathways are activated to ensure replication fork progression. These pathways include translesion DNA synthesis, template switching and repriming. In this Review, we describe how DNA damage tolerance pathways impact genome stability, their connection with tumorigenesis and their effects on cancer therapy response. We discuss recent findings that single-strand DNA gap accumulation impacts chemoresponse and explore a growing body of evidence that suggests that different DNA damage tolerance factors, including translesion synthesis polymerases, template switching proteins and enzymes affecting single-stranded DNA gaps, represent useful cancer targets. We further outline how the consequences of DNA damage tolerance mechanisms could inform the discovery of new biomarkers to refine cancer therapies.
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Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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27
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Kavlashvili T, Liu W, Mohamed TM, Cortez D, Dewar JM. Replication fork uncoupling causes nascent strand degradation and fork reversal. Nat Struct Mol Biol 2023; 30:115-124. [PMID: 36593312 PMCID: PMC9868089 DOI: 10.1038/s41594-022-00871-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 10/14/2022] [Indexed: 01/03/2023]
Abstract
Genotoxins cause nascent strand degradation (NSD) and fork reversal during DNA replication. NSD and fork reversal are crucial for genome stability and are exploited by chemotherapeutic approaches. However, it is unclear how NSD and fork reversal are triggered. Additionally, the fate of the replicative helicase during these processes is unknown. We developed a biochemical approach to study synchronous, localized NSD and fork reversal using Xenopus egg extracts and validated this approach with experiments in human cells. We show that replication fork uncoupling stimulates NSD of both nascent strands and progressive conversion of uncoupled forks to reversed forks. Notably, the replicative helicase remains bound during NSD and fork reversal. Unexpectedly, NSD occurs before and after fork reversal, indicating that multiple degradation steps take place. Overall, our data show that uncoupling causes NSD and fork reversal and elucidate key events that precede fork reversal.
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Affiliation(s)
- Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wenpeng Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Taha M Mohamed
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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28
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Ho YC, Ku CS, Tsai SS, Shiu JL, Jiang YZ, Miriam HE, Zhang HW, Chen YT, Chiu WT, Chang SB, Shen CH, Myung K, Chi P, Liaw H. PARP1 recruits DNA translocases to restrain DNA replication and facilitate DNA repair. PLoS Genet 2022; 18:e1010545. [PMID: 36512630 PMCID: PMC9794062 DOI: 10.1371/journal.pgen.1010545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/27/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
Replication fork reversal which restrains DNA replication progression is an important protective mechanism in response to replication stress. PARP1 is recruited to stalled forks to restrain DNA replication. However, PARP1 has no helicase activity, and the mechanism through which PARP1 participates in DNA replication restraint remains unclear. Here, we found novel protein-protein interactions between PARP1 and DNA translocases, including HLTF, SHPRH, ZRANB3, and SMARCAL1, with HLTF showing the strongest interaction among these DNA translocases. Although HLTF and SHPRH share structural and functional similarity, it remains unclear whether SHPRH contains DNA translocase activity. We further identified the ability of SHPRH to restrain DNA replication upon replication stress, indicating that SHPRH itself could be a DNA translocase or a helper to facilitate DNA translocation. Although hydroxyurea (HU) and MMS induce different types of replication stress, they both induce common DNA replication restraint mechanisms independent of intra-S phase activation. Our results suggest that the PARP1 facilitates DNA translocase recruitment to damaged forks, preventing fork collapse and facilitating DNA repair.
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Affiliation(s)
- Yen-Chih Ho
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Chen-Syun Ku
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Siang-Sheng Tsai
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yi-Zhen Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
| | - Hui Emmanuela Miriam
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Han-Wen Zhang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yen-Tzu Chen
- Department of Public Health & Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Che-Hung Shen
- National Institute of Cancer Research, National Health Research Institutes, Tainan City, Taiwan
| | - Kyungjae Myung
- IBS Center for Genomic Integrity, UNIST-gil 50, Ulsan, Republic of Korea
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei City, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
- * E-mail:
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29
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Hodson C, van Twest S, Dylewska M, O'Rourke JJ, Tan W, Murphy VJ, Walia M, Abbouche L, Nieminuszczy J, Dunn E, Bythell-Douglas R, Heierhorst J, Niedzwiedz W, Deans AJ. Branchpoint translocation by fork remodelers as a general mechanism of R-loop removal. Cell Rep 2022; 41:111749. [PMID: 36476850 DOI: 10.1016/j.celrep.2022.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Co-transcriptional R loops arise from stalling of RNA polymerase, leading to the formation of stable DNA:RNA hybrids. Unresolved R loops promote genome instability but are counteracted by helicases and nucleases. Here, we show that branchpoint translocases are a third class of R-loop-displacing enzyme in vitro. In cells, deficiency in the Fanconi-anemia-associated branchpoint translocase FANCM causes R-loop accumulation, particularly after treatment with DNA:RNA-hybrid-stabilizing agents. This correlates with FANCM localization at R-loop-prone regions of the genome. Moreover, other branchpoint translocases associated with human disease, such as SMARCAL1 and ZRANB3, and those from lower organisms can also remove R loops in vitro. Branchpoint translocases are more potent than helicases in resolving R loops, indicating their evolutionary important role in R-loop suppression. In human cells, FANCM, SMARCAL1, and ZRANB3 depletion causes additive effects on R-loop accumulation and DNA damage. Our work reveals a mechanistic basis for R-loop displacement that is linked to genome stability.
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Affiliation(s)
- Charlotte Hodson
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Winnie Tan
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Mannu Walia
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lara Abbouche
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Elyse Dunn
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Jörg Heierhorst
- Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia; Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia.
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30
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Jackson LM, Moldovan GL. Mechanisms of PARP1 inhibitor resistance and their implications for cancer treatment. NAR Cancer 2022; 4:zcac042. [PMID: 36568963 PMCID: PMC9773381 DOI: 10.1093/narcan/zcac042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The discovery of synthetic lethality as a result of the combined loss of PARP1 and BRCA has revolutionized the treatment of DNA repair-deficient cancers. With the development of PARP inhibitors, patients displaying germline or somatic mutations in BRCA1 or BRCA2 were presented with a novel therapeutic strategy. However, a large subset of patients do not respond to PARP inhibitors. Furthermore, many of those who do respond eventually acquire resistance. As such, combating de novo and acquired resistance to PARP inhibitors remains an obstacle in achieving durable responses in patients. In this review, we touch on some of the key mechanisms of PARP inhibitor resistance, including restoration of homologous recombination, replication fork stabilization and suppression of single-stranded DNA gap accumulation, as well as address novel approaches for overcoming PARP inhibitor resistance.
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Affiliation(s)
- Lindsey M Jackson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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31
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Zhu C, Iwase M, Li Z, Wang F, Quinet A, Vindigni A, Shao J. Profilin-1 regulates DNA replication forks in a context-dependent fashion by interacting with SNF2H and BOD1L. Nat Commun 2022; 13:6531. [PMID: 36319634 PMCID: PMC9626489 DOI: 10.1038/s41467-022-34310-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/21/2022] [Indexed: 12/04/2022] Open
Abstract
DNA replication forks are tightly controlled by a large protein network consisting of well-known core regulators and many accessory factors which remain functionally undefined. In this study, we report previously unknown nuclear functions of the actin-binding factor profilin-1 (PFN1) in DNA replication, which occur in a context-dependent fashion and require its binding to poly-L-proline (PLP)-containing proteins instead of actin. In unperturbed cells, PFN1 increases DNA replication initiation and accelerates fork progression by binding and stimulating the PLP-containing nucleosome remodeler SNF2H. Under replication stress, PFN1/SNF2H increases fork stalling and functionally collaborates with fork reversal enzymes to enable the over-resection of unprotected forks. In addition, PFN1 binds and functionally attenuates the PLP-containing fork protector BODL1 to increase the resection of a subset of stressed forks. Accordingly, raising nuclear PFN1 level decreases genome stability and cell survival during replication stress. Thus, PFN1 is a multi-functional regulator of DNA replication with exploitable anticancer potential.
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Affiliation(s)
- Cuige Zhu
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mari Iwase
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ziqian Li
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Faliang Wang
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Annabel Quinet
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- UMR Genetic Stability Stem Cells and Radiation, University of Paris and University of Paris-Saclay, INSERM, iRCM/IBFJ CEA, Fontenay-aux-Roses, France
| | - Alessandro Vindigni
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jieya Shao
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Dibitetto D, Marshall S, Sanchi A, Liptay M, Badar J, Lopes M, Rottenberg S, Smolka MB. DNA-PKcs promotes fork reversal and chemoresistance. Mol Cell 2022; 82:3932-3942.e6. [PMID: 36130596 PMCID: PMC9588680 DOI: 10.1016/j.molcel.2022.08.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/25/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Abstract
The DNA-PKcs kinase mediates the repair of DNA double-strand breaks via classical non-homologous end joining (NHEJ). DNA-PKcs is also recruited to active replication forks, although a role for DNA-PKcs in the control of fork dynamics is unclear. Here, we identify a crucial role for DNA-PKcs in promoting fork reversal, a process that stabilizes stressed replication forks and protects genome integrity. DNA-PKcs promotes fork reversal and slowing in response to several replication stress-inducing agents in a manner independent of its role in NHEJ. Cells lacking DNA-PKcs activity show increased DNA damage during S-phase and cellular sensitivity to replication stress. Notably, prevention of fork slowing and reversal via DNA-PKcs inhibition efficiently restores chemotherapy sensitivity in BRCA2-deficient mammary tumors with acquired PARPi resistance. Together, our data uncover a new key regulator of fork reversal and show how DNA-PKcs signaling can be manipulated to alter fork dynamics and drug resistance in cancer.
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Affiliation(s)
- Diego Dibitetto
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Shannon Marshall
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Martin Liptay
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Jumana Badar
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Bern Center for Precision Medicine, University of Bern, 3012 Bern, Switzerland
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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Role of Cockayne Syndrome Group B Protein in Replication Stress: Implications for Cancer Therapy. Int J Mol Sci 2022; 23:ijms231810212. [PMID: 36142121 PMCID: PMC9499456 DOI: 10.3390/ijms231810212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 12/01/2022] Open
Abstract
A variety of endogenous and exogenous insults are capable of impeding replication fork progression, leading to replication stress. Several SNF2 fork remodelers have been shown to play critical roles in resolving this replication stress, utilizing different pathways dependent upon the nature of the DNA lesion, location on the DNA, and the stage of the cell cycle, to complete DNA replication in a manner preserving genetic integrity. Under certain conditions, however, the attempted repair may lead to additional genetic instability. Cockayne syndrome group B (CSB) protein, a SNF2 chromatin remodeler best known for its role in transcription-coupled nucleotide excision repair, has recently been shown to catalyze fork reversal, a pathway that can provide stability of stalled forks and allow resumption of DNA synthesis without chromosome breakage. Prolonged stalling of replication forks may collapse to give rise to DNA double-strand breaks, which are preferentially repaired by homology-directed recombination. CSB plays a role in repairing collapsed forks by promoting break-induced replication in S phase and early mitosis. In this review, we discuss roles of CSB in regulating the sources of replication stress, replication stress response, as well as the implications of CSB for cancer therapy.
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Hao S, Wang Y, Zhao Y, Gao W, Cui W, Li Y, Cui J, Liu Y, Lin L, Xu X, Wang H. Dynamic switching of crotonylation to ubiquitination of H2A at lysine 119 attenuates transcription-replication conflicts caused by replication stress. Nucleic Acids Res 2022; 50:9873-9892. [PMID: 36062559 PMCID: PMC9508856 DOI: 10.1093/nar/gkac734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/20/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
The reversible post-translational modification (PTM) of proteins plays an important role in many cellular processes. Lysine crotonylation (Kcr) is a newly identified PTM, but its functional significance remains unclear. Here, we found that Kcr is involved in the replication stress response. We show that crotonylation of histone H2A at lysine 119 (H2AK119) and ubiquitination of H2AK119 are reversibly regulated by replication stress. Decrotonylation of H2AK119 by SIRT1 is a prerequisite for subsequent ubiquitination of H2AK119 by BMI1. Accumulation of ubiquitinated H2AK119 at reversed replication forks leads to the release of RNA Polymerase II and transcription repression in the vicinity of stalled replication forks. These effects attenuate transcription–replication conflicts (TRCs) and TRC-associated R-loop formation and DNA double-strand breaks. These findings suggest that decrotonylation and ubiquitination of H2A at lysine 119 act together to resolve replication stress-induced TRCs and protect genome stability.
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Affiliation(s)
- Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ya Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yuqin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Wen Gao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Wei Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Youhang Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jian Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yu Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Lixiu Lin
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, China Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
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35
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Gao J, Pickett HA. Targeting telomeres: advances in telomere maintenance mechanism-specific cancer therapies. Nat Rev Cancer 2022; 22:515-532. [PMID: 35790854 DOI: 10.1038/s41568-022-00490-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/31/2022]
Abstract
Cancer cells establish replicative immortality by activating a telomere-maintenance mechanism (TMM), be it telomerase or the alternative lengthening of telomeres (ALT) pathway. Targeting telomere maintenance represents an intriguing opportunity to treat the vast majority of all cancer types. Whilst telomerase inhibitors have historically been heralded as promising anticancer agents, the reality has been more challenging, and there are currently no therapeutic options for cancer types that use ALT despite their aggressive nature and poor prognosis. In this Review, we discuss the mechanistic differences between telomere maintenance by telomerase and ALT, the current methods used to detect each mechanism, the utility of these tests for clinical diagnosis, and recent developments in the therapeutic strategies being employed to target both telomerase and ALT. We present notable developments in repurposing established therapeutic agents and new avenues that are emerging to target cancer types according to which TMM they employ. These opportunities extend beyond inhibition of telomere maintenance, by finding and exploiting inherent weaknesses in the telomeres themselves to trigger rapid cellular effects that lead to cell death.
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Affiliation(s)
- Jixuan Gao
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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36
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Bhowmick R, Lerdrup M, Gadi SA, Rossetti GG, Singh MI, Liu Y, Halazonetis TD, Hickson ID. RAD51 protects human cells from transcription-replication conflicts. Mol Cell 2022; 82:3366-3381.e9. [PMID: 36002000 DOI: 10.1016/j.molcel.2022.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/02/2022] [Accepted: 07/16/2022] [Indexed: 12/16/2022]
Abstract
Oncogene activation during tumorigenesis promotes DNA replication stress (RS), which subsequently drives the formation of cancer-associated chromosomal rearrangements. Many episodes of physiological RS likely arise due to conflicts between the DNA replication and transcription machineries operating simultaneously at the same loci. One role of the RAD51 recombinase in human cells is to protect replication forks undergoing RS. Here, we have identified a key role for RAD51 in preventing transcription-replication conflicts (TRCs) from triggering replication fork breakage. The genomic regions most affected by RAD51 deficiency are characterized by being replicated and transcribed in early S-phase and show significant overlap with loci prone to cancer-associated amplification. Consistent with a role for RAD51 in protecting against transcription-replication conflicts, many of the adverse effects of RAD51 depletion are ameliorated by inhibiting early S-phase transcription. We propose a model whereby RAD51 suppresses fork breakage and subsequent inadvertent amplification of genomic loci prone to experiencing TRCs.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Mads Lerdrup
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Sampath Amitash Gadi
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Giacomo G Rossetti
- Department of Molecular Biology, University of Geneva, 30, quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Manika I Singh
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Ying Liu
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 30, quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Ian D Hickson
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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37
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The Biochemical Mechanism of Fork Regression in Prokaryotes and Eukaryotes—A Single Molecule Comparison. Int J Mol Sci 2022; 23:ijms23158613. [PMID: 35955746 PMCID: PMC9368896 DOI: 10.3390/ijms23158613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 02/04/2023] Open
Abstract
The rescue of stalled DNA replication forks is essential for cell viability. Impeded but still intact forks can be rescued by atypical DNA helicases in a reaction known as fork regression. This reaction has been studied at the single-molecule level using the Escherichia coli DNA helicase RecG and, separately, using the eukaryotic SMARCAL1 enzyme. Both nanomachines possess the necessary activities to regress forks: they simultaneously couple DNA unwinding to duplex rewinding and the displacement of bound proteins. Furthermore, they can regress a fork into a Holliday junction structure, the central intermediate of many fork regression models. However, there are key differences between these two enzymes. RecG is monomeric and unidirectional, catalyzing an efficient and processive fork regression reaction and, in the process, generating a significant amount of force that is used to displace the tightly-bound E. coli SSB protein. In contrast, the inefficient SMARCAL1 is not unidirectional, displays limited processivity, and likely uses fork rewinding to facilitate RPA displacement. Like many other eukaryotic enzymes, SMARCAL1 may require additional factors and/or post-translational modifications to enhance its catalytic activity, whereas RecG can drive fork regression on its own.
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38
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Halder S, Ranjha L, Taglialatela A, Ciccia A, Cejka P. Strand annealing and motor driven activities of SMARCAL1 and ZRANB3 are stimulated by RAD51 and the paralog complex. Nucleic Acids Res 2022; 50:8008-8022. [PMID: 35801922 PMCID: PMC9371921 DOI: 10.1093/nar/gkac583] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
SMARCAL1, ZRANB3 and HLTF are required for the remodeling of replication forks upon stress to promote genome stability. RAD51, along with the RAD51 paralog complex, were also found to have recombination-independent functions in fork reversal, yet the underlying mechanisms remained unclear. Using reconstituted reactions, we build upon previous data to show that SMARCAL1, ZRANB3 and HLTF have unequal biochemical capacities, explaining why they have non-redundant functions. SMARCAL1 uniquely anneals RPA-coated ssDNA, which depends on its direct interaction with RPA, but not on ATP. SMARCAL1, along with ZRANB3, but not HLTF efficiently employ ATPase driven translocase activity to rezip RPA-covered bubbled DNA, which was proposed to mimic elements of fork reversal. In contrast, ZRANB3 and HLTF but not SMARCAL1 are efficient in branch migration that occurs downstream in fork remodeling. We also show that low concentrations of RAD51 and the RAD51 paralog complex, RAD51B–RAD51C–RAD51D–XRCC2 (BCDX2), directly stimulate the motor-driven activities of SMARCAL1 and ZRANB3 but not HLTF, and the interplay is underpinned by physical interactions. Our data provide a possible mechanism explaining previous cellular experiments implicating RAD51 and BCDX2 in fork reversal.
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Affiliation(s)
- Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
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39
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Bisht D, Patne K, Rakesh R, Muthuswami R. On the Interaction Between SMARCAL1 and BRG1. Front Cell Dev Biol 2022; 10:870815. [PMID: 35784471 PMCID: PMC9243424 DOI: 10.3389/fcell.2022.870815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
SMARCAL1 and BRG1, both classified as ATP-dependent chromatin remodeling proteins, play a role in double-strand break DNA damage response pathways. Mutations in SMARCAL1 cause Schimke Immuno-osseous Dysplasia (SIOD) while mutations in BRG1 are associated with Coffin-Siris Syndrome (CSS4). In HeLa cells, SMARCAL1 and BRG1 co-regulate the expression of ATM, ATR, and RNAi genes on doxorubicin-induced DNA damage. Both the proteins are found to be simultaneously present on the promoter of these genes. Based on these results we hypothesized that SMARCAL1 and BRG1 interact with each other forming a complex. In this paper, we validate our hypothesis and show that SMARCAL1 and BRG1 do indeed interact with each other both in the absence and presence of doxorubicin. The formation of these complexes is dependent on the ATPase activity of both SMARCAL1 and BRG1. Using deletion constructs, we show that the HARP domains of SMARCAL1 mediate interaction with BRG1 while multiple domains of BRG1 are probably important for binding to SMARCAL1. We also show that SIOD-associated mutants fail to form a complex with BRG1. Similarly, CSS4-associated mutants of BRG1 fail to interact with SMARCAL1, thus, possibly contributing to the failure of the DNA damage response pathway and pathophysiology associated with SIOD and CSS4.
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40
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Giansanti C, Manzini V, Dickmanns A, Dickmanns A, Palumbieri MD, Sanchi A, Kienle SM, Rieth S, Scheffner M, Lopes M, Dobbelstein M. MDM2 binds and ubiquitinates PARP1 to enhance DNA replication fork progression. Cell Rep 2022; 39:110879. [PMID: 35649362 DOI: 10.1016/j.celrep.2022.110879] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/15/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022] Open
Abstract
The MDM2 oncoprotein antagonizes the tumor suppressor p53 by physical interaction and ubiquitination. However, it also sustains the progression of DNA replication forks, even in the absence of functional p53. Here, we show that MDM2 binds, inhibits, ubiquitinates, and destabilizes poly(ADP-ribose) polymerase 1 (PARP1). When cellular MDM2 levels are increased, this leads to accelerated progression of DNA replication forks, much like pharmacological inhibition of PARP1. Conversely, overexpressed PARP1 restores normal fork progression despite elevated MDM2. Strikingly, MDM2 profoundly reduces the frequency of fork reversal, revealed as four-way junctions through electron microscopy. Depletion of RECQ1 or the primase/polymerase (PRIMPOL) reverses the MDM2-mediated acceleration of the nascent DNA elongation rate. MDM2 also increases the occurrence of micronuclei, and it exacerbates camptothecin-induced cell death. In conclusion, high MDM2 levels phenocopy PARP inhibition in modulation of fork restart, representing a potential vulnerability of cancer cells.
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Affiliation(s)
- Celeste Giansanti
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Valentina Manzini
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Antje Dickmanns
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute of Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Maria Dilia Palumbieri
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - Sonja Rieth
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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41
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Ding L, Luo Y, Tian T, Chen X, Yang Y, Bu M, Han J, Yang B, Yan H, Liu T, Wu M, Zhang G, Xu Y, Zhu S, Huen MSY, Mao G, Huang J. RNF4 controls the extent of replication fork reversal to preserve genome stability. Nucleic Acids Res 2022; 50:5672-5687. [PMID: 35640614 PMCID: PMC9177969 DOI: 10.1093/nar/gkac447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/09/2022] [Accepted: 05/15/2022] [Indexed: 11/14/2022] Open
Abstract
Replication fork reversal occurs via a two-step process that entails reversal initiation and reversal extension. DNA topoisomerase IIalpha (TOP2A) facilitates extensive fork reversal, on one hand through resolving the topological stress generated by the initial reversal, on the other hand via its role in recruiting the SUMO-targeted DNA translocase PICH to stalled forks in a manner that is dependent on its SUMOylation by the SUMO E3 ligase ZATT. However, how TOP2A activities at stalled forks are precisely regulated remains poorly understood. Here we show that, upon replication stress, the SUMO-targeted ubiquitin E3 ligase RNF4 accumulates at stalled forks and targets SUMOylated TOP2A for ubiquitination and degradation. Downregulation of RNF4 resulted in aberrant activation of the ZATT–TOP2A–PICH complex at stalled forks, which in turn led to excessive reversal and elevated frequencies of fork collapse. These results uncover a previously unidentified regulatory mechanism that regulates TOP2A activities at stalled forks and thus the extent of fork reversal.
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Affiliation(s)
- Linli Ding
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yi Luo
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Tian Tian
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518033, Guangdong, China
| | - Xu Chen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Min Bu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jinhua Han
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Bing Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Haiyan Yan
- School of Medicine, Zhejiang University City of College, Hangzhou 310015, Zhejiang, China
| | - Ting Liu
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Mengjie Wu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine and Key laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310058, Zhejiang, China
| | - Guofei Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Yipeng Xu
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310058, Zhejiang, China
| | - Shaoxing Zhu
- Department of Urology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310058, Zhejiang, China
| | - Michael S Y Huen
- Department of Anatomy, The University of Hong Kong, Hong Kong, China
| | - Genxiang Mao
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou 310030, Zhejiang, China
| | - Jun Huang
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou 310030, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, Zhejiang, China
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Hou K, Yu Y, Li D, Zhang Y, Zhang K, Tong J, Yang K, Jia S. Alternative Lengthening of Telomeres and Mediated Telomere Synthesis. Cancers (Basel) 2022; 14:cancers14092194. [PMID: 35565323 PMCID: PMC9105334 DOI: 10.3390/cancers14092194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Alternative lengthing of telomere (ALT) is an important mechanism for maintaining telomere length and cell proliferation in telomerase-negative tumor cells. However, the molecular mechanism of ALT is still poorly understood. ALT occurs in a wide range of tumor types and usually associated with a worse clinical consequence. Here, we review the recent findings of ALT mechanisms, which promise ALT could be a valuable drug target for clinical telomerase-negative tumor treatment. Abstract Telomeres are DNA–protein complexes that protect eukaryotic chromosome ends from being erroneously repaired by the DNA damage repair system, and the length of telomeres indicates the replicative potential of the cell. Telomeres shorten during each division of the cell, resulting in telomeric damage and replicative senescence. Tumor cells tend to ensure cell proliferation potential and genomic stability by activating telomere maintenance mechanisms (TMMs) for telomere lengthening. The alternative lengthening of telomeres (ALT) pathway is the most frequently activated TMM in tumors of mesenchymal and neuroepithelial origin, and ALT also frequently occurs during experimental cellular immortalization of mesenchymal cells. ALT is a process that relies on homologous recombination (HR) to elongate telomeres. However, some processes in the ALT mechanism remain poorly understood. Here, we review the most recent understanding of ALT mechanisms and processes, which may help us to better understand how the ALT pathway is activated in cancer cells and determine the potential therapeutic targets in ALT pathway-stabilized tumors.
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Affiliation(s)
- Kailong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China;
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
| | - Yuyang Yu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Duda Li
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Yanduo Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Ke Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Jinkai Tong
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Kunxian Yang
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
- Correspondence: (K.Y.); (S.J.)
| | - Shuting Jia
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- Correspondence: (K.Y.); (S.J.)
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Feng W, Qi Z, Dong Z, Liu W, Xu M, Gao M, Liu S. LncRNA MT1DP promotes cadmium-induced DNA replication stress by inhibiting chromatin recruitment of SMARCAL1. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151078. [PMID: 34715232 DOI: 10.1016/j.scitotenv.2021.151078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/05/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) is a well-known carcinogenic metal and widespread environmental pollutant. The effect of Cd-induced carcinogenesis is partly due to accumulated DNA damage and chromosomal aberrations, but the exact mechanisms underlying the genotoxicity of Cd have not been clearly understood. Here, we found that one long non-coding RNA MT1DP is participated in Cd-induced DNA damage and replication stress. Through analyzing the residents from Cd-contaminated area in Southern China, we found that blood DNA repair genes are down-regulated in individuals with high urine Cd values compared to those with low urine Cd values, which contrast to the blood MT1DP levels. Through in vitro experiments, we found that MT1DP promotes Cd-induced DNA damage response, genome instability and replication fork stalling. Mechanically, upon Cd treatment, ATR is activated to enhance HIF-1α expression, which in turn promotes the transcription level of MT1DP. Subsequently MT1DP is recruited on the chromatin and binds to SMARCAL1 to competitive inhibit latter's interaction with RPA complexes, finally leading to increased replication stress and DNA damage. In summary, this study provides clear evidence for the role of epigenetic regulation on the genotoxic effect of Cd, and MT1DP-mediated replication stress may represent a novel mechanism for Cd-induced carcinogenesis.
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Affiliation(s)
- Wenya Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zijuan Qi
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China
| | - Zheng Dong
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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44
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Ler AAL, Carty MP. DNA Damage Tolerance Pathways in Human Cells: A Potential Therapeutic Target. Front Oncol 2022; 11:822500. [PMID: 35198436 PMCID: PMC8859465 DOI: 10.3389/fonc.2021.822500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022] Open
Abstract
DNA lesions arising from both exogenous and endogenous sources occur frequently in DNA. During DNA replication, the presence of unrepaired DNA damage in the template can arrest replication fork progression, leading to fork collapse, double-strand break formation, and to genome instability. To facilitate completion of replication and prevent the generation of strand breaks, DNA damage tolerance (DDT) pathways play a key role in allowing replication to proceed in the presence of lesions in the template. The two main DDT pathways are translesion synthesis (TLS), which involves the recruitment of specialized TLS polymerases to the site of replication arrest to bypass lesions, and homology-directed damage tolerance, which includes the template switching and fork reversal pathways. With some exceptions, lesion bypass by TLS polymerases is a source of mutagenesis, potentially contributing to the development of cancer. The capacity of TLS polymerases to bypass replication-blocking lesions induced by anti-cancer drugs such as cisplatin can also contribute to tumor chemoresistance. On the other hand, during homology-directed DDT the nascent sister strand is transiently utilised as a template for replication, allowing for error-free lesion bypass. Given the role of DNA damage tolerance pathways in replication, mutagenesis and chemoresistance, a more complete understanding of these pathways can provide avenues for therapeutic exploitation. A number of small molecule inhibitors of TLS polymerase activity have been identified that show synergy with conventional chemotherapeutic agents in killing cancer cells. In this review, we will summarize the major DDT pathways, explore the relationship between damage tolerance and carcinogenesis, and discuss the potential of targeting TLS polymerases as a therapeutic approach.
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Affiliation(s)
- Ashlynn Ai Li Ler
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
| | - Michael P. Carty
- Biochemistry, School of Biological and Chemical Sciences, The National University of Ireland (NUI) Galway, Galway, Ireland
- DNA Damage Response Laboratory, Centre for Chromosome Biology, NUI Galway, Galway, Ireland
- *Correspondence: Michael P. Carty,
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45
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Mohamed T, Adolph MB, Cortez D. Oligomerization of DNA replication regulatory protein RADX is essential to maintain replication fork stability. J Biol Chem 2022; 298:101672. [PMID: 35120927 PMCID: PMC8902620 DOI: 10.1016/j.jbc.2022.101672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 11/23/2022] Open
Abstract
Genome integrity requires complete and accurate DNA replication once per cell division cycle. Replication stress poses obstacles to this process that must be overcome to prevent replication fork collapse. An important regulator of replication fork stability is the RAD51 protein, which promotes replication fork reversal and protects nascent DNA strands from nuclease-mediated degradation. Many regulatory proteins control these RAD51 activities, including RADX, which binds both ssDNA and RAD51 at replication forks to ensure that fork reversal is confined to stalled forks. Many ssDNA-binding proteins function as hetero- or homo-oligomers. In this study, we addressed whether this is also the case for RADX. Using biochemical and genetic approaches, we found that RADX acts as a homo-oligomer to control replication fork stability. RADX oligomerizes using at least two different interaction surfaces, including one mapped to a C-terminal region. We demonstrate that mutations in this region prevent oligomerization and prevent RADX function in cells, and that addition of a heterologous dimerization domain to the oligomerization mutants restored their ability to regulate replication. Taken together, our results demonstrate that like many ssDNA-binding proteins, oligomerization is essential for RADX-mediated regulation of genome stability.
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Affiliation(s)
- Taha Mohamed
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Madison B Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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46
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Batenburg NL, Mersaoui SY, Walker JR, Coulombe Y, Hammond-Martel I, Wurtele H, Masson JY, Zhu XD. Cockayne syndrome group B protein regulates fork restart, fork progression and MRE11-dependent fork degradation in BRCA1/2-deficient cells. Nucleic Acids Res 2021; 49:12836-12854. [PMID: 34871413 PMCID: PMC8682776 DOI: 10.1093/nar/gkab1173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 11/08/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
Cockayne syndrome group B (CSB) protein has been implicated in the repair of a variety of DNA lesions that induce replication stress. However, little is known about its role at stalled replication forks. Here, we report that CSB is recruited to stalled forks in a manner dependent upon its T1031 phosphorylation by CDK. While dispensable for MRE11 association with stalled forks in wild-type cells, CSB is required for further accumulation of MRE11 at stalled forks in BRCA1/2-deficient cells. CSB promotes MRE11-mediated fork degradation in BRCA1/2-deficient cells. CSB possesses an intrinsic ATP-dependent fork reversal activity in vitro, which is activated upon removal of its N-terminal region that is known to autoinhibit CSB’s ATPase domain. CSB functions similarly to fork reversal factors SMARCAL1, ZRANB3 and HLTF to regulate slowdown in fork progression upon exposure to replication stress, indicative of a role of CSB in fork reversal in vivo. Furthermore, CSB not only acts epistatically with MRE11 to facilitate fork restart but also promotes RAD52-mediated break-induced replication repair of double-strand breaks arising from cleavage of stalled forks by MUS81 in BRCA1/2-deficient cells. Loss of CSB exacerbates chemosensitivity in BRCA1/2-deficient cells, underscoring an important role of CSB in the treatment of cancer lacking functional BRCA1/2.
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Affiliation(s)
- Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sofiane Y Mersaoui
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Yan Coulombe
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Ian Hammond-Martel
- Centre de recherche, de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, Québec H1T 2M4, Canada
| | - Hugo Wurtele
- Centre de recherche, de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, Québec H1T 2M4, Canada.,Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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47
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Lei KH, Yang HL, Chang HY, Yeh HY, Nguyen DD, Lee TY, Lyu X, Chastain M, Chai W, Li HW, Chi P. Crosstalk between CST and RPA regulates RAD51 activity during replication stress. Nat Commun 2021; 12:6412. [PMID: 34741010 PMCID: PMC8571288 DOI: 10.1038/s41467-021-26624-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
Replication stress causes replication fork stalling, resulting in an accumulation of single-stranded DNA (ssDNA). Replication protein A (RPA) and CTC1-STN1-TEN1 (CST) complex bind ssDNA and are found at stalled forks, where they regulate RAD51 recruitment and foci formation in vivo. Here, we investigate crosstalk between RPA, CST, and RAD51. We show that CST and RPA localize in close proximity in cells. Although CST stably binds to ssDNA with a high affinity at low ionic strength, the interaction becomes more dynamic and enables facilitated dissociation at high ionic strength. CST can coexist with RPA on the same ssDNA and target RAD51 to RPA-coated ssDNA. Notably, whereas RPA-coated ssDNA inhibits RAD51 activity, RAD51 can assemble a functional filament and exhibit strand-exchange activity on CST-coated ssDNA at high ionic strength. Our findings provide mechanistic insights into how CST targets and tethers RAD51 to RPA-coated ssDNA in response to replication stress.
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Affiliation(s)
- Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Han-Lin Yang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Dinh Duc Nguyen
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Tzu-Yu Lee
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Xinxing Lyu
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Megan Chastain
- Office of Research, Washington State University, Spokane, WA, USA
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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48
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Kent T, Clynes D. Alternative Lengthening of Telomeres: Lessons to Be Learned from Telomeric DNA Double-Strand Break Repair. Genes (Basel) 2021; 12:1734. [PMID: 34828344 PMCID: PMC8619803 DOI: 10.3390/genes12111734] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 12/25/2022] Open
Abstract
The study of the molecular pathways underlying cancer has given us important insights into how breaks in our DNA are repaired and the dire consequences that can occur when these processes are perturbed. Extensive research over the past 20 years has shown that the key molecular event underpinning a subset of cancers involves the deregulated repair of DNA double-strand breaks (DSBs) at telomeres, which in turn leads to telomere lengthening and the potential for replicative immortality. Here we discuss, in-depth, recent major breakthroughs in our understanding of the mechanisms underpinning this pathway known as the alternative lengthening of telomeres (ALT). We explore how this gives us important insights into how DSB repair at telomeres is regulated, with relevance to the cell-cycle-dependent regulation of repair, repair of stalled replication forks and the spatial regulation of DSB repair.
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Affiliation(s)
- Thomas Kent
- Molecular Haematology Unit, Radcliffe Department of Medicine, The MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK;
| | - David Clynes
- Department of Oncology, The MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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49
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Kang Z, Fu P, Alcivar AL, Fu H, Redon C, Foo TK, Zuo Y, Ye C, Baxley R, Madireddy A, Buisson R, Bielinsky AK, Zou L, Shen Z, Aladjem MI, Xia B. BRCA2 associates with MCM10 to suppress PRIMPOL-mediated repriming and single-stranded gap formation after DNA damage. Nat Commun 2021; 12:5966. [PMID: 34645815 PMCID: PMC8514439 DOI: 10.1038/s41467-021-26227-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/23/2021] [Indexed: 11/28/2022] Open
Abstract
The BRCA2 tumor suppressor protects genome integrity by promoting homologous recombination-based repair of DNA breaks, stability of stalled DNA replication forks and DNA damage-induced cell cycle checkpoints. BRCA2 deficient cells display the radio-resistant DNA synthesis (RDS) phenotype, however the mechanism has remained elusive. Here we show that cells without BRCA2 are unable to sufficiently restrain DNA replication fork progression after DNA damage, and the underrestrained fork progression is due primarily to Primase-Polymerase (PRIMPOL)-mediated repriming of DNA synthesis downstream of lesions, leaving behind single-stranded DNA gaps. Moreover, we find that BRCA2 associates with the essential DNA replication factor MCM10 and this association suppresses PRIMPOL-mediated repriming and ssDNA gap formation, while having no impact on the stability of stalled replication forks. Our findings establish an important function for BRCA2, provide insights into replication fork control during the DNA damage response, and may have implications in tumor suppression and therapy response. Tumor suppressor BRCA2 is known to stabilize and restart stalled DNA replication forks. Here the authors show that BRCA2 is recruited to the replication fork through its interaction with MCM10 and inhibits Primase-Polymerase-mediated repriming, lesion bypass and single strand DNA gap formation after DNA damage.
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Affiliation(s)
- Zhihua Kang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Pan Fu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Allen L Alcivar
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,Bristol-Myers Squibb Company, Bloomsbury, NJ, 08804, USA
| | - Haiqing Fu
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christophe Redon
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Yamei Zuo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Caiyong Ye
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.,School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Ryan Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Remi Buisson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Group, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
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50
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Keuper K, Wieland A, Räschle M, Storchova Z. Processes shaping cancer genomes - From mitotic defects to chromosomal rearrangements. DNA Repair (Amst) 2021; 107:103207. [PMID: 34425515 DOI: 10.1016/j.dnarep.2021.103207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/19/2022]
Abstract
Sequencing of cancer genomes revealed a rich landscape of somatic single nucleotide variants, structural changes of chromosomes, as well as chromosomal copy number alterations. These chromosome changes are highly variable, and simple translocations, deletions or duplications have been identified, as well as complex events that likely arise through activity of several interconnected processes. Comparison of the cancer genome sequencing data with our knowledge about processes important for maintenance of genome stability, namely DNA replication, repair and chromosome segregation, provides insights into the mechanisms that may give rise to complex chromosomal patterns, such as chromothripsis, a complex form of multiple focal chromosome rearrangements. In addition, observations gained from model systems that recapitulate the rearrangements patterns under defined experimental conditions suggest that mitotic errors and defective DNA replication and repair contribute to their formation. Here, we review the molecular mechanisms that contribute to formation of chromosomal aberrations observed in cancer genomes.
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Affiliation(s)
- Kristina Keuper
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Angela Wieland
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Markus Räschle
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Zuzana Storchova
- Department of Molecular Genetics, Paul-Ehrlich Strasse 24, University of Kaiserslautern, 67663, Kaiserslautern, Germany.
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