1
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Zhang Y, Liu X, Li Z, Li H, Miao Z, Wan B, Xu X. Advances on the Mechanisms and Therapeutic Strategies in Non-coding CGG Repeat Expansion Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04239-9. [PMID: 38780719 DOI: 10.1007/s12035-024-04239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Non-coding CGG repeat expansions within the 5' untranslated region are implicated in a range of neurological disorders, including fragile X-associated tremor/ataxia syndrome, oculopharyngeal myopathy with leukodystrophy, and oculopharyngodistal myopathy. This review outlined the general characteristics of diseases associated with non-coding CGG repeat expansions, detailing their clinical manifestations and neuroimaging patterns, which often overlap and indicate shared pathophysiological traits. We summarized the underlying molecular mechanisms of these disorders, providing new insights into the roles that DNA, RNA, and toxic proteins play. Understanding these mechanisms is crucial for the development of targeted therapeutic strategies. These strategies include a range of approaches, such as antisense oligonucleotides, RNA interference, genomic DNA editing, small molecule interventions, and other treatments aimed at correcting the dysregulated processes inherent in these disorders. A deeper understanding of the shared mechanisms among non-coding CGG repeat expansion disorders may hold the potential to catalyze the development of innovative therapies, ultimately offering relief to individuals grappling with these debilitating neurological conditions.
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Affiliation(s)
- Yutong Zhang
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Xuan Liu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Zeheng Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Hao Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
- Department of Neurology, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215124, China
| | - Zhigang Miao
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Bo Wan
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Xingshun Xu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China.
- The Institute of Neuroscience, Soochow University, Suzhou City, China.
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China.
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2
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Corazzi L, Ionasz VS, Andrejev S, Wang LC, Vouzas A, Giaisi M, Di Muzio G, Ding B, Marx AJM, Henkenjohann J, Allers MM, Gilbert DM, Wei PC. Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters. Nat Commun 2024; 15:3594. [PMID: 38678011 PMCID: PMC11055891 DOI: 10.1038/s41467-024-47934-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Recurrent DNA break clusters (RDCs) are replication-transcription collision hotspots; many are unique to neural progenitor cells. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unravel the replication features dictating RDC location and orientation. Most RDCs occur at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSBs), while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bound RNA reveals co-transcriptional dual-strand DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping RNA polymerase activity uncovers that head-to-head interactions between replication and transcription machinery result in 60% DSB contribution to the head-on compared to 40% for co-directional. Taken together we reveal TTR as a fragile class and show how the linear interaction between transcription and replication impacts genome stability.
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Affiliation(s)
- Lorenzo Corazzi
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Vivien S Ionasz
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Li-Chin Wang
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Athanasios Vouzas
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Marco Giaisi
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Giulia Di Muzio
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Boyu Ding
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Faculty of Medicine, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Anna J M Marx
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Jonas Henkenjohann
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - Michael M Allers
- German Cancer Research Center, 69120, Heidelberg, Germany
- Faculty of Medicine, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Pei-Chi Wei
- German Cancer Research Center, 69120, Heidelberg, Germany.
- Faculty of Bioscience, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany.
- Interdisciplinary Center for Neurosciences, Ruprecht-Karl-University of Heidelberg, 69120, Heidelberg, Germany.
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3
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Marlin R, Loger JS, Joachim C, Ebring C, Robert-Siegwald G, Pennont S, Rose M, Raguette K, Suez-Panama V, Ulric-Gervaise S, Lusbec S, Bera O, Vallard A, Aline-Fardin A, Colomba E, Jean-Laurent M. Copy number signatures and CCNE1 amplification reveal the involvement of replication stress in high-grade endometrial tumors oncogenesis. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00942-w. [PMID: 38564163 DOI: 10.1007/s13402-024-00942-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Managing high-grade endometrial cancer in Martinique poses significant challenges. The diversity of copy number alterations in high-grade endometrial tumors, often associated with a TP53 mutation, is a key factor complicating treatment. Due to the high incidence of high-grade tumors with poor prognosis, our study aimed to characterize the molecular signature of these tumors within a cohort of 25 high-grade endometrial cases. METHODS We conducted a comprehensive pangenomic analysis to categorize the copy number alterations involved in these tumors. Whole-Exome Sequencing (WES) and Homologous Recombination (HR) analysis were performed. The alterations obtained from the WES were classified into various signatures using the Copy Number Signatures tool available in COSMIC. RESULTS We identified several signatures that correlated with tumor stage and disctinct prognoses. These signatures all seem to be linked to replication stress, with CCNE1 amplification identified as the primary driver of oncogenesis in over 70% of tumors analyzed. CONCLUSION The identification of CCNE1 amplification, which is currently being explored as a therapeutic target in clinical trials, suggests new treatment strategies for high-grade endometrial cancer. This finding holds particular significance for Martinique, where access to care is challenging.
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Affiliation(s)
- Regine Marlin
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique.
| | - Jean-Samuel Loger
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Clarisse Joachim
- General Cancer Registry of Martinique, University Hospital of Martinique, Fort-de-France, Martinique
| | - Coralie Ebring
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
| | - Guillaume Robert-Siegwald
- MitoVasc Unit, SFR ICAT, Mitolab Team, UMR CNRS 6015 INSERM U1083, University of Angers, Angers, France
| | - Sabrina Pennont
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Mickaelle Rose
- Martinique Regional Oncology Platform, University Hospital of Martinique, Fort-de-France, Martinique
| | - Kevin Raguette
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Valerie Suez-Panama
- Biological Resource Center, University Hospital of Martinique, Fort-de-France, Martinique
| | - Sylviane Ulric-Gervaise
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Sylvie Lusbec
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
| | - Odile Bera
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Alexis Vallard
- Department of Oncology Hematology Urology, University Hospital of Martinique, Fort-de-France, Martinique
| | | | - Emeline Colomba
- Department of Cancer Medicine, Institut Gustave Roussy, University of Paris Saclay, Gif-sur-Yvette, France
| | - Mehdi Jean-Laurent
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
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4
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Yang SF, Nelson CB, Wells JK, Fernando M, Lu R, Allen JAM, Malloy L, Lamm N, Murphy VJ, Mackay JP, Deans AJ, Cesare AJ, Sobinoff AP, Pickett HA. ZNF827 is a single-stranded DNA binding protein that regulates the ATR-CHK1 DNA damage response pathway. Nat Commun 2024; 15:2210. [PMID: 38472229 PMCID: PMC10933417 DOI: 10.1038/s41467-024-46578-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
The ATR-CHK1 DNA damage response pathway becomes activated by the exposure of RPA-coated single-stranded DNA (ssDNA) that forms as an intermediate during DNA damage and repair, and as a part of the replication stress response. Here, we identify ZNF827 as a component of the ATR-CHK1 kinase pathway. We demonstrate that ZNF827 is a ssDNA binding protein that associates with RPA through concurrent binding to ssDNA intermediates. These interactions are dependent on two clusters of C2H2 zinc finger motifs within ZNF827. We find that ZNF827 accumulates at stalled forks and DNA damage sites, where it activates ATR and promotes the engagement of homologous recombination-mediated DNA repair. Additionally, we demonstrate that ZNF827 depletion inhibits replication initiation and sensitizes cancer cells to the topoisomerase inhibitor topotecan, revealing ZNF827 as a therapeutic target within the DNA damage response pathway.
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Affiliation(s)
- Sile F Yang
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Jadon K Wells
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Madushan Fernando
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Lisa Malloy
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Noa Lamm
- Nuclear Dynamics Group, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia.
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5
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Muñoz S, Blanco-Romero E, González-Acosta D, Rodriguez-Acebes S, Megías D, Lopes M, Méndez J. RAD51 restricts DNA over-replication from re-activated origins. EMBO J 2024; 43:1043-1064. [PMID: 38360996 PMCID: PMC10942984 DOI: 10.1038/s44318-024-00038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
Eukaryotic cells rely on several mechanisms to ensure that the genome is duplicated precisely once in each cell division cycle, preventing DNA over-replication and genomic instability. Most of these mechanisms limit the activity of origin licensing proteins to prevent the reactivation of origins that have already been used. Here, we have investigated whether additional controls restrict the extension of re-replicated DNA in the event of origin re-activation. In a genetic screening in cells forced to re-activate origins, we found that re-replication is limited by RAD51 and enhanced by FBH1, a RAD51 antagonist. In the presence of chromatin-bound RAD51, forks stemming from re-fired origins are slowed down, leading to frequent events of fork reversal. Eventual re-initiation of DNA synthesis mediated by PRIMPOL creates ssDNA gaps that facilitate the partial elimination of re-duplicated DNA by MRE11 exonuclease. In the absence of RAD51, these controls are abrogated and re-replication forks progress much longer than in normal conditions. Our study uncovers a safeguard mechanism to protect genome stability in the event of origin reactivation.
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Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Elena Blanco-Romero
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Daniel González-Acosta
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Sara Rodriguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Advanced Optical Microscopy Unit, Central Core Facilities, Instituto de Salud Carlos III, Madrid, Spain
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
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6
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Corazzi L, Ionasz V, Andrejev S, Wang LC, Vouzas A, Giaisi M, Di Muzio G, Ding B, Marx AJM, Henkenjohann J, Allers MM, Gilbert DM, Wei PC. Linear Interaction Between Replication and Transcription Shapes DNA Break Dynamics at Recurrent DNA Break Clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554340. [PMID: 37662334 PMCID: PMC10473677 DOI: 10.1101/2023.08.22.554340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Recurrent DNA break clusters (RDCs) are replication-transcription collision hotspots; many are unique to neural progenitor cells. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unraveled the replication features dictating RDC location and orientation. Most RDCs occur at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSBs), while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bound RNA revealed co-transcriptional dual-strand DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping RNA polymerase activity revealed that head-to-head interactions between replication and transcription machinery resulted in 60% DSB contribution to the head-on compared to 40% for co-directional. Our findings revealed TTR as a novel fragile class and highlighted how the linear interaction between transcription and replication impacts genome stability.
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7
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Wei M, He X, Liu N, Deng H. Role of reactive oxygen species in ultraviolet-induced photodamage of the skin. Cell Div 2024; 19:1. [PMID: 38217019 PMCID: PMC10787507 DOI: 10.1186/s13008-024-00107-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/05/2024] [Indexed: 01/14/2024] Open
Abstract
Reactive oxygen species (ROS), such as superoxides (O2 •-) and hydroxyl groups (OH·), are short-lived molecules containing unpaired electrons. Intracellular ROS are believed to be mainly produced by the mitochondria and NADPH oxidase (NOX) and can be associated with various physiological processes, such as proliferation, cell signaling, and oxygen homeostasis. In recent years, many studies have indicated that ROS play crucial roles in regulating ultraviolet (UV)-induced photodamage of the skin, including exogenous aging, which accounts for 80% of aging. However, to the best of our knowledge, the detailed signaling pathways, especially those related to the mechanisms underlying apoptosis in which ROS are involved have not been reviewed previously. In this review, we elaborate on the biological characteristics of ROS and its role in regulating UV-induced photodamage of the skin.
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Affiliation(s)
- Min Wei
- Department of Dermatology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin He
- Department of Nephrology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Na Liu
- Department of Dermatology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Deng
- Department of Dermatology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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8
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Wendel S, Wallace NA. Interactions among human papillomavirus proteins and host DNA repair factors differ during the viral life cycle and virus-induced tumorigenesis. mSphere 2023; 8:e0042723. [PMID: 37850786 PMCID: PMC10732048 DOI: 10.1128/msphere.00427-23] [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] [Indexed: 10/19/2023] Open
Abstract
This review focuses on the impact of human papillomavirus (HPV) oncogenes on DNA repair pathways with a particular focus on how these relationships change as productive HPV infections transition to malignant lesions. We made specific efforts to incorporate advances in the understanding of HPV and DNA damage repair over the last 4 years. We apologize for any articles that we missed in compiling this report.
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Affiliation(s)
- Sebastian Wendel
- Kansas State University, Division of Biology, Manhattan, Kansas, USA
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9
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Lu M, Zhang X, Chu Q, Chen Y, Zhang P. Susceptibility Genes Associated with Multiple Primary Cancers. Cancers (Basel) 2023; 15:5788. [PMID: 38136334 PMCID: PMC10741435 DOI: 10.3390/cancers15245788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
With advancements in treatment and screening techniques, we have been witnessing an era where more cancer survivors harbor multiple primary cancers (MPCs), affecting approximately one in six patients. Identifying MPCs is crucial for tumor staging and subsequent treatment choices. However, the current clinicopathological criteria for clinical application are limited and insufficient, making it challenging to differentiate them from recurrences or metastases. The emergence of next-generation sequencing (NGS) technology has provided a genetic perspective for defining multiple primary cancers. Researchers have found that, when considering multiple tumor pairs, it is crucial not only to examine well-known essential mutations like MLH1/MSH2, EGFR, PTEN, BRCA1/2, CHEK2, and TP53 mutations but also to explore certain pleiotropic loci. Moreover, specific deleterious mutations may serve as regulatory factors in second cancer development following treatment. This review aims to discuss these susceptibility genes and provide an explanation of their functions based on the signaling pathway background. Additionally, the association network between genetic signatures and different tumor pairs will be summarized.
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Affiliation(s)
| | | | | | | | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (M.L.)
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10
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Wendel SO, Snow JA, Gu L, Banerjee NS, Malkas L, Wallace NA. The potential of PCNA inhibition as a therapeutic strategy in cervical cancer. J Med Virol 2023; 95:e29244. [PMID: 38010649 PMCID: PMC10683864 DOI: 10.1002/jmv.29244] [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: 08/23/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023]
Abstract
Cervical cancers are the fourth most common and most deadly cancer in women worldwide. Despite being a tremendous public health burden, few novel approaches to improve care for these malignancies have been introduced. We discuss the potential for proliferating cell nuclear antigen (PCNA) inhibition to address this need as well as the advantages and disadvantages for compounds that can therapeutically inhibit PCNA with a specific focus on cervical cancer.
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Affiliation(s)
| | - Jazmine A Snow
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Long Gu
- Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Nilam Sanjib Banerjee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Linda Malkas
- Beckman Research Institute of City of Hope, Duarte, California, USA
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11
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Choudhry SK, Neal ML, Li S, Navare AT, Van Eeuwen T, Wozniak RW, Mast FD, Rout MP, Aitchison JD. Nuclear pore complexes mediate subtelomeric gene silencing by regulating PCNA levels on chromatin. J Cell Biol 2023; 222:e202207060. [PMID: 37358474 PMCID: PMC10292210 DOI: 10.1083/jcb.202207060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/02/2023] [Accepted: 06/07/2023] [Indexed: 06/27/2023] Open
Abstract
The nuclear pore complex (NPC) physically interacts with chromatin and regulates gene expression. The Saccharomyces cerevisiae inner ring nucleoporin Nup170 has been implicated in chromatin organization and the maintenance of gene silencing in subtelomeric regions. To gain insight into how Nup170 regulates this process, we used protein-protein interactions, genetic interactions, and transcriptome correlation analyses to identify the Ctf18-RFC complex, an alternative proliferating cell nuclear antigen (PCNA) loader, as a facilitator of the gene regulatory functions of Nup170. The Ctf18-RFC complex is recruited to a subpopulation of NPCs that lack the nuclear basket proteins Mlp1 and Mlp2. In the absence of Nup170, PCNA levels on DNA are reduced, resulting in the loss of silencing of subtelomeric genes. Increasing PCNA levels on DNA by removing Elg1, which is required for PCNA unloading, rescues subtelomeric silencing defects in nup170Δ. The NPC, therefore, mediates subtelomeric gene silencing by regulating PCNA levels on DNA.
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Affiliation(s)
- Sanjeev Kumar Choudhry
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Maxwell L. Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Song Li
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Arti T. Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Trevor Van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | | | - Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Departments of Pediatrics and Biochemistry, University of Washington, Seattle, WA, USA
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12
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Trovato E, Fiorani D, Cartocci A, Cinotti E, Rubegni P. IGF1 synthesis after CO 2 fractional laser resurfacing (FLR): New insights in the treatment of scalp actinic keratoses. Lasers Surg Med 2023; 55:642-652. [PMID: 37222180 DOI: 10.1002/lsm.23680] [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: 02/21/2023] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
OBJECTIVES Actinic keratosis have a high risk of progression to a squamous cell carcinoma. Insulin-like growth factor 1 and its receptor play a relevant role in restoring repair of ultraviolet-induced cell damage. This pathway is reduced in patients older than 65 years. Ablative fractional laser resurfacing could normalize insulin-like growth factor 1 (IGF-1) secretion in elderly by recruiting new fibroblasts. The aim of the study is to evaluate restoration of IGF1 values by PCR in senescent fibroblasts after ablative fractional laser resurfacing. METHODS We enrolled 30 male patients with multiple actinic keratosis on the scalp, equally divided into two mirror areas of up to 50 cm2 , treating only the right one. We performed one skin biopsy for each area 30 days after treatment. Real-time PCR in fibroblasts was performed to assess the change in IGF1. At baseline and after 6 months, in vivo reflectance confocal microscopy examination was performed in all patients. RESULTS IGF1 values were increased in the treated side by about 60%. The right areas had fairly complete resolution of actinic keratosis at the last follow-up visit after 6 months with no appearance of new lesions. The mean number of actinic keratosis in the right area was reduced by more than 75% at four- and six-follow-up visits compared to the left area. The improvement in the right area was also evidenced by lower values of the mean AKASI (actinic keratosis area and severity index) score. Reflectance confocal microscopy showed a reduction of keratinocytic disarray and scales after treatment. DISCUSSION Taken together, all the clinical, laboratory, and in vivo results of our study allowed us to confirm that ablative fractional laser resurfacing is a valuable tool for the treatment of actinic keratosis and cancerization field, both for the management of clinically evident lesions and for preventing the occurrence of squamous cell carcinoma.
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Affiliation(s)
- Emanuele Trovato
- Unit of Dermatology, Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Diletta Fiorani
- Unit of Dermatology, Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | | | - Elisa Cinotti
- Unit of Dermatology, Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Pietro Rubegni
- Unit of Dermatology, Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
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13
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Mallick Ganguly O, Moulik S. Interactions of Mn complexes with DNA: the relevance of therapeutic applications towards cancer treatment. Dalton Trans 2023; 52:10639-10656. [PMID: 37475585 DOI: 10.1039/d3dt00659j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Manganese (Mn) is one of the most significant bio-metals that helps the body to form connective tissue, bones, blood clotting factors, and sex hormones. It is necessary for fat and carbohydrate metabolism, calcium absorption, blood sugar regulation, and normal brain and nerve functions. It accelerates the synthesis of proteins, vitamin C, and vitamin B. It is also involved in the catalysis of hematopoiesis, regulation of the endocrine level, and improvement of immune function. Again, Mn metalloenzymes like arginase, glutamine synthetase, phosphoenolpyruvate decarboxylase, and Mn superoxide dismutase (MnSOD) contribute to the metabolism processes and reduce oxidative stress against free radicals. Recent investigations have revealed that synthetic Mn-complexes act as antibacterial and antifungal agents. As a result, chemists and biologists have been actively involved in developing Mn-based drugs for the treatment of various diseases including cancer. Therefore, any therapeutic drugs based on manganese complexes would be invaluable for the treatment of cancer/infectious diseases and could be a better substitute for cisplatin and other related platinum based chemotherapeutic drugs. From this perspective, attempts have been made to discuss the interactions and nuclease activities of Mn(II/III/IV) complexes with DNA through which one can evaluate their therapeutic applications.
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Affiliation(s)
- Oishi Mallick Ganguly
- St Xavier's College, 30, Park St, Mullick Bazar, Park Street area, Kolkata, West Bengal 700016, India
| | - Shuvojit Moulik
- Suraksha Diagnostics Pvt Ltd, Newtown 12/1, Premises No. 02-0327, DG Block(Newtown), Action Area 1D, Newtown, Kolkata, West Bengal 700156, India.
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14
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Buyukcelebi K, Chen X, Abdula F, Elkafas H, Duval AJ, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Bulun SE, Wei JJ, Yue F, Adli M. Engineered MED12 mutations drive leiomyoma-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. Nat Commun 2023; 14:4057. [PMID: 37429859 DOI: 10.1038/s41467-023-39684-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
Nearly 70% of Uterine fibroid (UF) tumors are driven by recurrent MED12 hotspot mutations. Unfortunately, no cellular models could be generated because the mutant cells have lower fitness in 2D culture conditions. To address this, we employ CRISPR to precisely engineer MED12 Gly44 mutations in UF-relevant myometrial smooth muscle cells. The engineered mutant cells recapitulate several UF-like cellular, transcriptional, and metabolic alterations, including altered Tryptophan/kynurenine metabolism. The aberrant gene expression program in the mutant cells is, in part, driven by a substantial 3D genome compartmentalization switch. At the cellular level, the mutant cells gain enhanced proliferation rates in 3D spheres and form larger lesions in vivo with elevated production of collagen and extracellular matrix deposition. These findings indicate that the engineered cellular model faithfully models key features of UF tumors and provides a platform for the broader scientific community to characterize genomics of recurrent MED12 mutations.
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Affiliation(s)
- Kadir Buyukcelebi
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Xintong Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Fatih Abdula
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Hoda Elkafas
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Alexander James Duval
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Harun Ozturk
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Fidan Seker-Polat
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Ping Yin
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Yue Feng
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Serdar E Bulun
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Jian Jun Wei
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Mazhar Adli
- Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA.
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15
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Goodall DJ, Warecka D, Hawkins M, Rudolph CJ. Interplay between chromosomal architecture and termination of DNA replication in bacteria. Front Microbiol 2023; 14:1180848. [PMID: 37434703 PMCID: PMC10331603 DOI: 10.3389/fmicb.2023.1180848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Faithful transmission of the genome from one generation to the next is key to life in all cellular organisms. In the majority of bacteria, the genome is comprised of a single circular chromosome that is normally replicated from a single origin, though additional genetic information may be encoded within much smaller extrachromosomal elements called plasmids. By contrast, the genome of a eukaryote is distributed across multiple linear chromosomes, each of which is replicated from multiple origins. The genomes of archaeal species are circular, but are predominantly replicated from multiple origins. In all three cases, replication is bidirectional and terminates when converging replication fork complexes merge and 'fuse' as replication of the chromosomal DNA is completed. While the mechanics of replication initiation are quite well understood, exactly what happens during termination is far from clear, although studies in bacterial and eukaryotic models over recent years have started to provide some insight. Bacterial models with a circular chromosome and a single bidirectional origin offer the distinct advantage that there is normally just one fusion event between two replication fork complexes as synthesis terminates. Moreover, whereas termination of replication appears to happen in many bacteria wherever forks happen to meet, termination in some bacterial species, including the well-studied bacteria Escherichia coli and Bacillus subtilis, is more restrictive and confined to a 'replication fork trap' region, making termination even more tractable. This region is defined by multiple genomic terminator (ter) sites, which, if bound by specific terminator proteins, form unidirectional fork barriers. In this review we discuss a range of experimental results highlighting how the fork fusion process can trigger significant pathologies that interfere with the successful conclusion of DNA replication, how these pathologies might be resolved in bacteria without a fork trap system and how the acquisition of a fork trap might have provided an alternative and cleaner solution, thus explaining why in bacterial species that have acquired a fork trap system, this system is remarkably well maintained. Finally, we consider how eukaryotic cells can cope with a much-increased number of termination events.
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Affiliation(s)
- Daniel J. Goodall
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | | | - Christian J. Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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16
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Koch JP, Roth SM, Quintin A, Gavini J, Orlando E, Riedo R, Pozzato C, Hayrapetyan L, Aebersold R, Stroka DM, Aebersold DM, Medo M, Zimmer Y, Medová M. A DNA-PK phosphorylation site on MET regulates its signaling interface with the DNA damage response. Oncogene 2023; 42:2113-2125. [PMID: 37188738 PMCID: PMC10289896 DOI: 10.1038/s41388-023-02714-6] [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: 04/05/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
The DNA damage response (DDR) is intertwined with signaling pathways downstream of oncogenic receptor tyrosine kinases (RTKs). To drive research into the application of targeted therapies as radiosensitizers, a better understanding of this molecular crosstalk is necessary. We present here the characterization of a previously unreported MET RTK phosphosite, Serine 1016 (S1016) that represents a potential DDR-MET interface. MET S1016 phosphorylation increases in response to irradiation and is mainly targeted by DNA-dependent protein kinase (DNA-PK). Phosphoproteomics unveils an impact of the S1016A substitution on the overall long-term cell cycle regulation following DNA damage. Accordingly, the abrogation of this phosphosite strongly perturbs the phosphorylation of proteins involved in the cell cycle and formation of the mitotic spindle, enabling cells to bypass a G2 arrest upon irradiation and leading to the entry into mitosis despite compromised genome integrity. This results in the formation of abnormal mitotic spindles and a lower proliferation rate. Altogether, the current data uncover a novel signaling mechanism through which the DDR uses a growth factor receptor system for regulating and maintaining genome stability.
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Affiliation(s)
- Jonas P Koch
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Selina M Roth
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Aurélie Quintin
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Jacopo Gavini
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
| | - Eleonora Orlando
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Rahel Riedo
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Chiara Pozzato
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Liana Hayrapetyan
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
- Faculty of Science, University of Zürich, 8057, Zürich, Switzerland
| | - Deborah M Stroka
- Department for BioMedical Research, Visceral Surgery, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
| | - Daniel M Aebersold
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Matúš Medo
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Yitzhak Zimmer
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Michaela Medová
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland.
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland.
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17
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Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
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18
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Buyukcelebi K, Chen X, Abdula F, Duval A, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Wei JJ, Bulun S, Yue F, Adli M. Engineered MED12 mutations drive uterine fibroid-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. RESEARCH SQUARE 2023:rs.3.rs-2537075. [PMID: 36798375 PMCID: PMC9934745 DOI: 10.21203/rs.3.rs-2537075/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Uterine fibroid (UF) tumors originate from a mutated smooth muscle cell (SMC). Nearly 70% of these tumors are driven by hotspot recurrent somatic mutations in the MED12 gene; however, there are no tractable genetic models to study the biology of UF tumors because, under culture conditions, the non-mutant fibroblasts outgrow the mutant SMC cells, resulting in the conversion of the population to WT phenotype. The lack of faithful cellular models hampered our ability to delineate the molecular pathways downstream of MED12 mutations and identify therapeutics that may selectively target the mutant cells. To overcome this challenge, we employed CRISPR knock-in with a sensitive PCR-based screening strategy to precisely engineer cells with mutant MED12 Gly44, which constitutes 50% of MED12 exon two mutations. Critically, the engineered myometrial SMC cells recapitulate several UF-like cellular, transcriptional and metabolic alterations, including enhanced proliferation rates in 3D spheres and altered Tryptophan/kynurenine metabolism. Our transcriptomic analysis supported by DNA synthesis tracking reveals that MED12 mutant cells, like UF tumors, have heightened expression of DNA repair genes but reduced DNA synthesis rates. Consequently, these cells accumulate significantly higher rates of DNA damage and are selectively more sensitive to common DNA-damaging chemotherapy, indicating mutation-specific and therapeutically relevant vulnerabilities. Our high-resolution 3D chromatin interaction analysis demonstrates that the engineered MED12 mutations drive aberrant genomic activity due to a genome-wide chromatin compartmentalization switch. These findings indicate that the engineered cellular model faithfully models key features of UF tumors and provides a novel platform for the broader scientific community to characterize genomics of recurrent MED12 mutations and discover potential therapeutic targets.
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19
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Fischer U, Meese E. Gene Amplification in Tumor Cells: Developed De Novo or Adopted from Stem Cells. Cells 2022; 12:cells12010148. [PMID: 36611942 PMCID: PMC9818554 DOI: 10.3390/cells12010148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Gene amplifications have been known for several decades as physiological processes in amphibian and flies, e.g., during eggshell development in Drosophila and as part of pathological processes in humans, specifically in tumors and drug-resistant cells. The long-held belief that a physiological gene amplification does not occur in humans was, however, fundamental questioned by findings that showed gene amplification in human stem cells. We hypothesis that the physiological and the pathological, i.e., tumor associated processes of gene amplification share at their beginning the same underlying mechanism. Re-replication was reported both in the context of tumor related genome instability and during restricted time windows in Drosophila development causing the known developmental gene amplification in Drosophila. There is also growing evidence that gene amplification and re-replication were present in human stem cells. It appears likely that stem cells utilize a re-replication mechanism that has been developed early in evolution as a powerful tool to increase gene copy numbers very efficiently. Here, we show that, several decades ago, there was already evidence of gene amplification in non-tumor mammalian cells, but that was not recognized at the time and interpreted accordingly. We give an overview on gene amplifications during normal mammalian development, the possible mechanism that enable gene amplification and hypothesize how tumors adopted this capability for gene amplification.
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20
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The Impact of Deleting Stem-Loop 1 of Epstein-Barr Virus-Encoded RNA 1 on Cell Proliferation. Viruses 2022; 14:v14112538. [PMID: 36423146 PMCID: PMC9696203 DOI: 10.3390/v14112538] [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: 10/10/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Epstein-Barr virus-encoded RNAs (EBERs) are two small, noncoding, structurally conserved transcripts, constitutively expressed at >106 copies per EBV-infected cell. They have been shown to drive cell growth. However, the mechanism(s) involved in EBER-induced proliferation is not clear. In this study, we investigated the molecular mechanisms and structural impact of EBER1. Sequences of EBER1 stem-loops (SL) 1, 3, and 4 were deleted, creating three mutants: ∆SL1, ∆SL3, and ∆SL4. These mutants were cloned into pHebo plasmids and expressed in Jurkat cell lines. Cells transfected with wildtype EBER1 and pHebo were used as controls. Cell proliferation was monitored by microscopy and flow cytometry. Microarray, qPCR, and Western blotting were used to investigate the cell cycle markers. We found significantly higher cell proliferation in wildtype EBER1 cells compared to pHebo, ∆SL1, and ∆SL3, but not ∆SL4 mutants. There was also significant upregulation of S-phase and G2/M phase markers in wildtype EBER1 and ∆SL4 mutant. Furthermore, CDT1, a factor for DNA replication, was upregulated in wildtype EBER1 and ∆SL4 mutant. However, in ∆SL1 mutant, CDT1 was significantly downregulated and translocated to the cytoplasm. These data indicate that the structure of EBER1 is important in cell proliferation.
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21
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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22
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Safeguarding DNA Replication: A Golden Touch of MiDAS and Other Mechanisms. Int J Mol Sci 2022; 23:ijms231911331. [PMID: 36232633 PMCID: PMC9570362 DOI: 10.3390/ijms231911331] [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: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
DNA replication is a tightly regulated fundamental process allowing the correct duplication and transfer of the genetic information from the parental cell to the progeny. It involves the coordinated assembly of several proteins and protein complexes resulting in replication fork licensing, firing and progression. However, the DNA replication pathway is strewn with hurdles that affect replication fork progression during S phase. As a result, cells have adapted several mechanisms ensuring replication completion before entry into mitosis and segregating chromosomes with minimal, if any, abnormalities. In this review, we describe the possible obstacles that a replication fork might encounter and how the cell manages to protect DNA replication from S to the next G1.
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23
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Pan-cancer analysis of co-occurring mutations in RAD52 and the BRCA1-BRCA2-PALB2 axis in human cancers. PLoS One 2022; 17:e0273736. [PMID: 36107942 PMCID: PMC9477347 DOI: 10.1371/journal.pone.0273736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
In human cells homologous recombination (HR) is critical for repair of DNA double strand breaks (DSBs) and rescue of stalled or collapsed replication forks. HR is facilitated by RAD51 which is loaded onto DNA by either BRCA2-BRCA1-PALB2 or RAD52. In human culture cells, double-knockdowns of RAD52 and genes in the BRCA1-BRCA2-PALB2 axis are lethal. Mutations in BRCA2, BRCA1 or PALB2 significantly impairs error free HR as RAD51 loading relies on RAD52 which is not as proficient as BRCA2-BRCA1-PALB2. RAD52 also facilitates Single Strand Annealing (SSA) that produces intra-chromosomal deletions. Some RAD52 mutations that affect the SSA function or decrease RAD52 association with DNA can suppress certain BRCA2 associated phenotypes in breast cancers. In this report we did a pan-cancer analysis using data reported on the Catalogue of Somatic Mutations in Cancers (COSMIC) to identify double mutants between RAD52 and BRCA1, BRCA2 or PALB2 that occur in cancer cells. We find that co-occurring mutations are likely in certain cancer tissues but not others. However, all mutations occur in a heterozygous state. Further, using computational and machine learning tools we identified only a handful of pathogenic or driver mutations predicted to significantly affect the function of the proteins. This supports previous findings that co-inactivation of RAD52 with any members of the BRCA2-BRCA1-PALB2 axis is lethal. Molecular modeling also revealed that pathogenic RAD52 mutations co-occurring with mutations in BRCA2-BRCA1-PALB2 axis are either expected to attenuate its SSA function or its interaction with DNA. This study extends previous breast cancer findings to other cancer types and shows that co-occurring mutations likely destabilize HR by similar mechanisms as in breast cancers.
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24
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Bukhari AB, Chan GK, Gamper AM. Targeting the DNA Damage Response for Cancer Therapy by Inhibiting the Kinase Wee1. Front Oncol 2022; 12:828684. [PMID: 35251998 PMCID: PMC8891215 DOI: 10.3389/fonc.2022.828684] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/21/2022] [Indexed: 12/15/2022] Open
Abstract
Cancer cells typically heavily rely on the G2/M checkpoint to survive endogenous and exogenous DNA damage, such as genotoxic stress due to genome instability or radiation and chemotherapy. The key regulator of the G2/M checkpoint, the cyclin-dependent kinase 1 (CDK1), is tightly controlled, including by its phosphorylation state. This posttranslational modification, which is determined by the opposing activities of the phosphatase cdc25 and the kinase Wee1, allows for a more rapid response to cellular stress than via the synthesis or degradation of modulatory interacting proteins, such as p21 or cyclin B. Reducing Wee1 activity results in ectopic activation of CDK1 activity and drives premature entry into mitosis with unrepaired or under-replicated DNA and causing mitotic catastrophe. Here, we review efforts to use small molecule inhibitors of Wee1 for therapeutic purposes, including strategies to combine Wee1 inhibition with genotoxic agents, such as radiation therapy or drugs inducing replication stress, or inhibitors of pathways that show synthetic lethality with Wee1. Furthermore, it become increasingly clear that Wee1 inhibition can also modulate therapeutic immune responses. We will discuss the mechanisms underlying combination treatments identifying both cell intrinsic and systemic anti-tumor activities.
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25
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Pan Y, Zuo H, Wen F, Huang F, Zhu Y, Cao L, Sha QQ, Li Y, Zhang H, Shi M, Liang C, Huang J, Zou L, Fan HY, Ju Z, Wang H, Shen L. HMCES safeguards genome integrity and long-term self-renewal of hematopoietic stem cells during stress responses. Leukemia 2022; 36:1123-1131. [PMID: 35039639 DOI: 10.1038/s41375-021-01499-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/04/2021] [Accepted: 12/10/2021] [Indexed: 12/28/2022]
Abstract
Hematopoietic stress drives quiescent hematopoietic stem cells (HSCs) to proliferate, generating reactive oxygen species (ROS) and oxidative DNA damage including abasic sites. Such a coupling between rapid DNA replication and a burst of abasic site formation during HSC stress responses, however, presents a challenge to accurately repair abasic sites located in replication-associated single-stranded DNA. Here we show that HMCES, a novel shield of abasic sites, plays pivotal roles in overcoming this challenge upon HSC activation. While HMCES was dispensable for steady-state hematopoiesis, Hmces-deficient HSCs exhibited compromised long-term self-renewal capacity in response to hematopoietic stress such as myeloablation and transplantation. Loss of HMCES resulted in accumulation of DNA lesions due to impaired resolution of abasic sites generated by activation-induced ROS in activated HSCs and broad downregulation of DNA damage response and repair pathways. Moreover, Hmces-deficient mice died from bone marrow failure after exposure to sublethal irradiation, which also produces ROS. Notably, dysregulation of HMCES occurs frequently in acute lymphocytic leukemia (ALL) and is associated with poor clinical outcomes. Together, our findings not only highlighted HMCES as a novel genome protector in activated HSCs, but also position it as a potential selective target against ALL while sparing normal hematopoiesis.
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Affiliation(s)
- Yinghao Pan
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Hongna Zuo
- MOE Key Laboratory of Regenerative Medicine, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Fei Wen
- MOE Key Laboratory of Regenerative Medicine, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Fei Huang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yezhang Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lanrui Cao
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qian-Qian Sha
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yang Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Huiying Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Miao Shi
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Chengzhen Liang
- Department of Orthopedics Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jun Huang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lin Zou
- Clinical Research Unit, Children's Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Heng-Yu Fan
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Zhenyu Ju
- MOE Key Laboratory of Regenerative Medicine, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China.
| | - Hu Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China.
| | - Li Shen
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China. .,Department of Orthopedics Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. .,Hangzhou Innovation Center, Zhejiang University, Hangzhou, China.
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26
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Cleary JM, Wolpin BM, Dougan SK, Raghavan S, Singh H, Huffman B, Sethi NS, Nowak JA, Shapiro GI, Aguirre AJ, D'Andrea AD. Opportunities for Utilization of DNA Repair Inhibitors in Homologous Recombination Repair-Deficient and Proficient Pancreatic Adenocarcinoma. Clin Cancer Res 2021; 27:6622-6637. [PMID: 34285063 PMCID: PMC8678153 DOI: 10.1158/1078-0432.ccr-21-1367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/04/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022]
Abstract
Pancreatic cancer is rapidly progressive and notoriously difficult to treat with cytotoxic chemotherapy and targeted agents. Recent demonstration of the efficacy of maintenance PARP inhibition in germline BRCA mutated pancreatic cancer has raised hopes that increased understanding of the DNA damage response pathway will lead to new therapies in both homologous recombination (HR) repair-deficient and proficient pancreatic cancer. Here, we review the potential mechanisms of exploiting HR deficiency, replicative stress, and DNA damage-mediated immune activation through targeted inhibition of DNA repair regulatory proteins.
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Affiliation(s)
- James M Cleary
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
| | - Brian M Wolpin
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Srivatsan Raghavan
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Harshabad Singh
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Brandon Huffman
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Nilay S Sethi
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew J Aguirre
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Dana-Farber Brigham and Women's Cancer Center, Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts
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27
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Zwinderman MRH, Lobo TJ, van der Wouden PE, Spierings DCJ, van Vugt MATM, Lansdorp PM, Guryev V, Dekker FJ. Deposition Bias of Chromatin Proteins Inverts under DNA Replication Stress Conditions. ACS Chem Biol 2021; 16:2193-2201. [PMID: 34592816 PMCID: PMC8609521 DOI: 10.1021/acschembio.1c00321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Following DNA replication,
equal amounts of chromatin proteins
are distributed over sister chromatids by re-deposition of parental
chromatin proteins and deposition of newly synthesized chromatin proteins.
Molecular mechanisms balancing the allocation of new and old chromatin
proteins remain largely unknown. Here, we studied the genome-wide
distribution of new chromatin proteins relative to parental DNA template
strands and replication initiation zones using the double-click-seq.
Under control conditions, new chromatin proteins were preferentially
found on DNA replicated by the lagging strand machinery. Strikingly,
replication stress induced by hydroxyurea or curaxin treatment and
inhibition of ataxia telangiectasia and Rad3-related protein (ATR)
or p53 inactivation inverted the observed chromatin protein deposition
bias to the strand replicated by the leading strand polymerase in
line with previously reported effects on replication protein A occupancy.
We propose that asymmetric deposition of newly synthesized chromatin
proteins onto sister chromatids reflects differences in the processivity
of leading and lagging strand synthesis.
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Affiliation(s)
- Martijn R. H. Zwinderman
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Thamar Jessurun Lobo
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Petra E. van der Wouden
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Marcel A. T. M. van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Peter M. Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, V5Z 1L3 British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4 British Columbia, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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28
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Paulsen T, Malapati P, Shibata Y, Wilson B, Eki R, Benamar M, Abbas T, Dutta A. MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage. Nucleic Acids Res 2021; 49:11787-11799. [PMID: 34718766 PMCID: PMC8599734 DOI: 10.1093/nar/gkab984] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/05/2021] [Accepted: 10/27/2021] [Indexed: 12/23/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) are present within all eukaryotic organisms and actively contribute to gene expression changes. MicroDNA (200-1000bp) are the most abundant type of eccDNA and can amplify tRNA, microRNA, and novel si-like RNA sequences. Due to the heterogeneity of microDNA and the limited technology to directly quantify circular DNA molecules, the specific DNA repair pathways that contribute to microDNA formation have not been fully elucidated. Using a sensitive and quantitative assay that quantifies eight known abundant microDNA, we report that microDNA levels are dependent on resection after double-strand DNA break (DSB) and repair by Microhomology Mediated End Joining (MMEJ). Further, repair of DSB without resection by canonical Non-Homologous End Joining (c-NHEJ) diminishes microDNA formation. MicroDNA levels are induced locally even by a single site-directed DSB, suggesting that excision of genomic DNA by two closely spaced DSB is not necessary for microDNA formation. Consistent with all this, microDNA levels accumulate as cells undergo replication in S-phase, when DNA breaks and repair are elevated, and microDNA levels are decreased if DNA synthesis is prevented. Thus, formation of microDNA occurs during the repair of endogenous or induced DNA breaks by resection-based DNA repair pathways.
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Affiliation(s)
- Teressa Paulsen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Pumoli Malapati
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Rebeka Eki
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Mouadh Benamar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Tarek Abbas
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Radiation Oncology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
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29
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Zhu Y, Wang Y, Tao B, Han J, Chen H, Zhu Q, Huang L, He Y, Hong J, Li Y, Chen J, Huang J, Lo LJ, Peng J. Nucleolar GTPase Bms1 displaces Ttf1 from RFB-sites to balance progression of rDNA transcription and replication. J Mol Cell Biol 2021; 13:902-917. [PMID: 34791311 PMCID: PMC8800533 DOI: 10.1093/jmcb/mjab074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/24/2022] Open
Abstract
18S, 5.8S, and 28S ribosomal RNAs (rRNAs) are cotranscribed as a pre-ribosomal RNA (pre-rRNA) from the rDNA by RNA polymerase I whose activity is vigorous during the S-phase, leading to a conflict with rDNA replication. This conflict is resolved partly by replication-fork-barrier (RFB)-sites sequences located downstream of the rDNA and RFB-binding proteins such as Ttf1. However, how Ttf1 is displaced from RFB-sites to allow replication fork progression remains elusive. Here, we reported that loss-of-function of Bms1l, a nucleolar GTPase, upregulates rDNA transcription, causes replication-fork stall, and arrests cell cycle at the S-to-G2 transition; however, the G1-to-S transition is constitutively active characterized by persisting DNA synthesis. Concomitantly, ubf, tif-IA, and taf1b marking rDNA transcription, Chk2, Rad51, and p53 marking DNA-damage response, and Rpa2, PCNA, Fen1, and Ttf1 marking replication fork stall are all highly elevated in bms1l mutants. We found that Bms1 interacts with Ttf1 in addition to Rc1l. Finally, we identified RFB-sites for zebrafish Ttf1 through chromatin immunoprecipitation sequencing and showed that Bms1 disassociates the Ttf1‒RFB complex with its GTPase activity. We propose that Bms1 functions to balance rDNA transcription and replication at the S-phase through interaction with Rcl1 and Ttf1, respectively. TTF1 and Bms1 together might impose an S-phase checkpoint at the rDNA loci.
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Affiliation(s)
- Yanqing Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Yong Wang
- Taizhou Hospital, Zhejiang University, Taizhou, 317000 China
| | - Boxiang Tao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jinhua Han
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 China
| | - Hong Chen
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Qinfang Zhu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ling Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Yinan He
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jian Hong
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Yunqin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
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30
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Zhou X, Speer RM, Volk L, Hudson LG, Liu KJ. Arsenic co-carcinogenesis: Inhibition of DNA repair and interaction with zinc finger proteins. Semin Cancer Biol 2021; 76:86-98. [PMID: 33984503 PMCID: PMC8578584 DOI: 10.1016/j.semcancer.2021.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022]
Abstract
Arsenic is widely present in the environment and is associated with various population health risks including cancers. Arsenic exposure at environmentally relevant levels enhances the mutagenic effect of other carcinogens such as ultraviolet radiation. Investigation on the molecular mechanisms could inform the prevention and intervention strategies of arsenic carcinogenesis and co-carcinogenesis. Arsenic inhibition of DNA repair has been demonstrated to be an important mechanism, and certain DNA repair proteins have been identified to be extremely sensitive to arsenic exposure. This review will summarize the recent advances in understanding the mechanisms of arsenic carcinogenesis and co-carcinogenesis, including DNA damage induction and ROS generation, particularly how arsenic inhibits DNA repair through an integrated molecular mechanism which includes its interactions with sensitive zinc finger DNA repair proteins.
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Affiliation(s)
- Xixi Zhou
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Rachel M Speer
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Lindsay Volk
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
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31
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Aki T, Uemura K. Cell Death and Survival Pathways Involving ATM Protein Kinase. Genes (Basel) 2021; 12:genes12101581. [PMID: 34680975 PMCID: PMC8535589 DOI: 10.3390/genes12101581] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cell death is the ultimate form of cellular dysfunction, and is induced by a wide range of stresses including genotoxic stresses. During genotoxic stress, two opposite cellular reactions, cellular protection through DNA repair and elimination of damaged cells by the induction of cell death, can occur in both separate and simultaneous manners. ATM (ataxia telangiectasia mutated) kinase (hereafter referred to as ATM) is a protein kinase that plays central roles in the induction of cell death during genotoxic stresses. It has long been considered that ATM mediates DNA damage-induced cell death through inducing apoptosis. However, recent research progress in cell death modality is now revealing ATM-dependent cell death pathways that consist of not only apoptosis but also necroptosis, ferroptosis, and dysfunction of autophagy, a cellular survival mechanism. In this short review, we intend to provide a brief outline of cell death mechanisms in which ATM is involved, with emphasis on pathways other than apoptosis.
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32
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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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33
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Silva GLA, Tosi LRO, McCulloch R, Black JA. Unpicking the Roles of DNA Damage Protein Kinases in Trypanosomatids. Front Cell Dev Biol 2021; 9:636615. [PMID: 34422791 PMCID: PMC8377203 DOI: 10.3389/fcell.2021.636615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/13/2021] [Indexed: 12/31/2022] Open
Abstract
To preserve genome integrity when faced with DNA lesions, cells activate and coordinate a multitude of DNA repair pathways to ensure timely error correction or tolerance, collectively called the DNA damage response (DDR). These interconnecting damage response pathways are molecular signal relays, with protein kinases (PKs) at the pinnacle. Focused efforts in model eukaryotes have revealed intricate aspects of DNA repair PK function, including how they direct DDR pathways and how repair reactions connect to wider cellular processes, including DNA replication and transcription. The Kinetoplastidae, including many parasites like Trypanosoma spp. and Leishmania spp. (causative agents of debilitating, neglected tropical infections), exhibit peculiarities in several core biological processes, including the predominance of multigenic transcription and the streamlining or repurposing of DNA repair pathways, such as the loss of non-homologous end joining and novel operation of nucleotide excision repair (NER). Very recent studies have implicated ATR and ATM kinases in the DDR of kinetoplastid parasites, whereas DNA-dependent protein kinase (DNA-PKcs) displays uncertain conservation, questioning what functions it fulfills. The wide range of genetic manipulation approaches in these organisms presents an opportunity to investigate DNA repair kinase roles in kinetoplastids and to ask if further kinases are involved. Furthermore, the availability of kinase inhibitory compounds, targeting numerous eukaryotic PKs, could allow us to test the suitability of DNA repair PKs as novel chemotherapeutic targets. Here, we will review recent advances in the study of trypanosomatid DNA repair kinases.
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Affiliation(s)
- Gabriel L A Silva
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Jennifer Ann Black
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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34
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Yang J, Liu X, Huang Y, He L, Zhang W, Ren J, Wang Y, Wu J, Wu X, Shan L, Yang X, Sun L, Liang J, Zhang Y, Shang Y. TRPS1 drives heterochromatic origin refiring and cancer genome evolution. Cell Rep 2021; 34:108814. [PMID: 33691114 DOI: 10.1016/j.celrep.2021.108814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/18/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Exploitation of naturally occurring genetic mutations could empower the discovery of novel aspects of established cancer genes. We report here that TRPS1, a gene linked to the tricho-rhino-phalangeal syndrome (TRPS) and recently identified as a potential breast cancer driver, promotes breast carcinogenesis through regulating replication. Epigenomic decomposition of TRPS1 landscape reveals nearly half of H3K9me3-marked heterochromatic origins are occupied by TRPS1, where it encourages the chromatin loading of APC/C, resulting in uncontrolled origin refiring. TRPS1 binds to the genome through its atypical H3K9me3 reading via GATA and IKAROS domains, while TRPS-related mutations affect its chromatin binding, replication boosting, and tumorigenicity. Concordantly, overexpression of wild-type but not TRPS-associated mutants of TRPS1 is sufficient to drive cancer genome amplifications, which experience an extrachromosomal route and dynamically evolve to confer therapeutic resistance. Together, these results uncover a critical function of TRPS1 in driving heterochromatin origin firing and breast cancer genome evolution.
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Affiliation(s)
- Jianguo Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yunchao Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Wenting Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jie Ren
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaohan Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China.
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Medicine, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
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35
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Shah P, Hobson CM, Cheng S, Colville MJ, Paszek MJ, Superfine R, Lammerding J. Nuclear Deformation Causes DNA Damage by Increasing Replication Stress. Curr Biol 2021; 31:753-765.e6. [PMID: 33326770 PMCID: PMC7904640 DOI: 10.1016/j.cub.2020.11.037] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/22/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022]
Abstract
Cancer metastasis, i.e., the spreading of tumor cells from the primary tumor to distant organs, is responsible for the vast majority of cancer deaths. In the process, cancer cells migrate through narrow interstitial spaces substantially smaller in cross-section than the cell. During such confined migration, cancer cells experience extensive nuclear deformation, nuclear envelope rupture, and DNA damage. The molecular mechanisms responsible for the confined migration-induced DNA damage remain incompletely understood. Although in some cell lines, DNA damage is closely associated with nuclear envelope rupture, we show that, in others, mechanical deformation of the nucleus is sufficient to cause DNA damage, even in the absence of nuclear envelope rupture. This deformation-induced DNA damage, unlike nuclear-envelope-rupture-induced DNA damage, occurs primarily in S/G2 phase of the cell cycle and is associated with replication forks. Nuclear deformation, resulting from either confined migration or external cell compression, increases replication stress, possibly by increasing replication fork stalling, providing a molecular mechanism for the deformation-induced DNA damage. Thus, we have uncovered a new mechanism for mechanically induced DNA damage, linking mechanical deformation of the nucleus to DNA replication stress. This mechanically induced DNA damage could not only increase genomic instability in metastasizing cancer cells but could also cause DNA damage in non-migrating cells and tissues that experience mechanical compression during development, thereby contributing to tumorigenesis and DNA damage response activation.
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Affiliation(s)
- Pragya Shah
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chad M Hobson
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Svea Cheng
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marshall J Colville
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Matthew J Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Richard Superfine
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
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36
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Rapsomaniki MA, Maxouri S, Nathanailidou P, Garrastacho MR, Giakoumakis NN, Taraviras S, Lygeros J, Lygerou Z. In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity. NAR Genom Bioinform 2021; 3:lqaa112. [PMID: 33554116 PMCID: PMC7846089 DOI: 10.1093/nargab/lqaa112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/15/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023] Open
Abstract
DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. Here, we present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit a good correlation along the genome, robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to genome plasticity and a plethora of genotypic variations.
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Affiliation(s)
- Maria Anna Rapsomaniki
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Stella Maxouri
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Patroula Nathanailidou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | | | | | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - John Lygeros
- Automatic Control Laboratory, ETH Zurich, 8092 Zurich, Switzerland
| | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
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Targeted CRISPR screening identifies PRMT5 as synthetic lethality combinatorial target with gemcitabine in pancreatic cancer cells. Proc Natl Acad Sci U S A 2020; 117:28068-28079. [PMID: 33097661 DOI: 10.1073/pnas.2009899117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most challenging cancers to treat. Due to the asymptomatic nature of the disease and lack of curative treatment modalities, the 5-y survival rate of PDAC patients is one of the lowest of any cancer type. The recurrent genetic alterations in PDAC are yet to be targeted. Therefore, identification of effective drug combinations is desperately needed. Here, we performed an in vivo CRISPR screen in an orthotopic patient-derived xenograft (PDX) model to identify gene targets whose inhibition creates synergistic tumor growth inhibition with gemcitabine (Gem), a first- or second-line chemotherapeutic agent for PDAC treatment. The approach revealed protein arginine methyltransferase gene 5 (PRMT5) as an effective druggable candidate whose inhibition creates synergistic vulnerability of PDAC cells to Gem. Genetic depletion and pharmacological inhibition indicate that loss of PRMT5 activity synergistically enhances Gem cytotoxicity due to the accumulation of excessive DNA damage. At the molecular level, we show that inhibition of PRMT5 results in RPA depletion and impaired homology-directed DNA repair (HDR) activity. The combination (Gem + PRMT5 inhibition) creates conditional lethality and synergistic reduction of PDAC tumors in vivo. The findings demonstrate that unbiased genetic screenings combined with a clinically relevant model system is a practical approach in identifying synthetic lethal drug combinations for cancer treatment.
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38
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Vasilyeva TA, Marakhonov AV, Sukhanova NV, Kutsev SI, Zinchenko RA. Preferentially Paternal Origin of De Novo 11p13 Chromosome Deletions Revealed in Patients with Congenital Aniridia and WAGR Syndrome. Genes (Basel) 2020; 11:genes11070812. [PMID: 32708836 PMCID: PMC7397088 DOI: 10.3390/genes11070812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
The frequency of pathogenic large chromosome rearrangements detected in patients with different Mendelian diseases is truly diverse and can be remarkably high. Chromosome breaks could arise through different known mechanisms. Congenital PAX6-associated aniridia is a hereditary eye disorder caused by mutations or chromosome rearrangements involving the PAX6 gene. In our recent study, we identified 11p13 chromosome deletions in 30 out of 91 probands with congenital aniridia or WAGR syndrome (characterized by Wilms’ tumor, Aniridia, and Genitourinary abnormalities as well as mental Retardation). The loss of heterozygosity analysis (LOH) was performed in 10 families with de novo chromosome deletion in proband. In 7 out of 8 informative families, the analysis revealed that deletions occurred at the paternal allele. If paternal origin is not random, chromosome breaks could arise either (i) during spermiogenesis, which is possible due to specific male chromatin epigenetic program and its vulnerability to the breakage-causing factors, or (ii) in early zygotes at a time when chromosomes transmitted from different parents still carry epigenetic marks of the origin, which is also possible due to diverse and asymmetric epigenetic reprogramming occurring in male and female pronuclei. Some new data is needed to make a well-considered conclusion on the reasons for preferential paternal origin of 11p13 deletions.
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Affiliation(s)
- Tatyana A. Vasilyeva
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.A.V.); (S.I.K.); (R.A.Z.)
| | - Andrey V. Marakhonov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.A.V.); (S.I.K.); (R.A.Z.)
- Correspondence:
| | - Natella V. Sukhanova
- Central Clinical Hospital of the Russian Academy of Sciences, 119333 Moscow, Russia;
| | - Sergey I. Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.A.V.); (S.I.K.); (R.A.Z.)
| | - Rena A. Zinchenko
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (T.A.V.); (S.I.K.); (R.A.Z.)
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39
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3D genome organization contributes to genome instability at fragile sites. Nat Commun 2020; 11:3613. [PMID: 32680994 PMCID: PMC7367836 DOI: 10.1038/s41467-020-17448-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 06/30/2020] [Indexed: 12/15/2022] Open
Abstract
Common fragile sites (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features were suggested to underlie CFS instability, however, these features are prevalent across the genome. Therefore, the molecular mechanisms underlying CFS instability remain unclear. Here, we explore the transcriptional profile and DNA replication timing (RT) under mild replication stress in the context of the 3D genome organization. The results reveal a fragility signature, comprised of a TAD boundary overlapping a highly transcribed large gene with APH-induced RT-delay. This signature enables precise mapping of core fragility regions in known CFSs and identification of novel fragile sites. CFS stability may be compromised by incomplete DNA replication and repair in TAD boundaries core fragility regions leading to genomic instability. The identified fragility signature will allow for a more comprehensive mapping of CFSs and pave the way for investigating mechanisms promoting genomic instability in cancer. Common fragile sites are regions susceptible to replication stress and are prone to chromosomal instability. Here, the authors, by analyzing the contribution of 3D chromatin organization, identify and characterize a fragility signature and precisely map these fragility regions.
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40
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DNA Damage: From Threat to Treatment. Cells 2020; 9:cells9071665. [PMID: 32664329 PMCID: PMC7408370 DOI: 10.3390/cells9071665] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022] Open
Abstract
DNA is the source of genetic information, and preserving its integrity is essential in order to sustain life. The genome is continuously threatened by different types of DNA lesions, such as abasic sites, mismatches, interstrand crosslinks, or single-stranded and double-stranded breaks. As a consequence, cells have evolved specialized DNA damage response (DDR) mechanisms to sustain genome integrity. By orchestrating multilayer signaling cascades specific for the type of lesion that occurred, the DDR ensures that genetic information is preserved overtime. In the last decades, DNA repair mechanisms have been thoroughly investigated to untangle these complex networks of pathways and processes. As a result, key factors have been identified that control and coordinate DDR circuits in time and space. In the first part of this review, we describe the critical processes encompassing DNA damage sensing and resolution. In the second part, we illustrate the consequences of partial or complete failure of the DNA repair machinery. Lastly, we will report examples in which this knowledge has been instrumental to develop novel therapies based on genome editing technologies, such as CRISPR-Cas.
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41
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Abstract
Cells confront DNA damage in every cell cycle. Among the most deleterious types of DNA damage are DNA double-strand breaks (DSBs), which can cause cell lethality if unrepaired or cancers if improperly repaired. In response to DNA DSBs, cells activate a complex DNA damage checkpoint (DDC) response that arrests the cell cycle, reprograms gene expression, and mobilizes DNA repair factors to prevent the inheritance of unrepaired and broken chromosomes. Here we examine the DDC, induced by DNA DSBs, in the budding yeast model system and in mammals.
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Affiliation(s)
- David P Waterman
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA;
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42
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Karakaidos P, Karagiannis D, Rampias T. Resolving DNA Damage: Epigenetic Regulation of DNA Repair. Molecules 2020; 25:molecules25112496. [PMID: 32471288 PMCID: PMC7321228 DOI: 10.3390/molecules25112496] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
Epigenetic research has rapidly evolved into a dynamic field of genome biology. Chromatin regulation has been proved to be an essential aspect for all genomic processes, including DNA repair. Chromatin structure is modified by enzymes and factors that deposit, erase, and interact with epigenetic marks such as DNA and histone modifications, as well as by complexes that remodel nucleosomes. In this review we discuss recent advances on how the chromatin state is modulated during this multi-step process of damage recognition, signaling, and repair. Moreover, we examine how chromatin is regulated when different pathways of DNA repair are utilized. Furthermore, we review additional modes of regulation of DNA repair, such as through the role of global and localized chromatin states in maintaining expression of DNA repair genes, as well as through the activity of epigenetic enzymes on non-nucleosome substrates. Finally, we discuss current and future applications of the mechanistic interplays between chromatin regulation and DNA repair in the context cancer treatment.
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Affiliation(s)
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA;
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
- Correspondence: ; Tel.: +30-210-659-7469
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43
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Mastro TL, Tripathi VP, Forsburg SL. Translesion synthesis polymerases contribute to meiotic chromosome segregation and cohesin dynamics in Schizosaccharomycespombe. J Cell Sci 2020; 133:jcs238709. [PMID: 32317395 PMCID: PMC7325440 DOI: 10.1242/jcs.238709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/26/2020] [Indexed: 12/17/2022] Open
Abstract
Translesion synthesis polymerases (TLSPs) are non-essential error-prone enzymes that ensure cell survival by facilitating DNA replication in the presence of DNA damage. In addition to their role in bypassing lesions, TLSPs have been implicated in meiotic double-strand break repair in several systems. Here, we examine the joint contribution of four TLSPs to meiotic progression in the fission yeast Schizosaccharomyces pombe. We observed a dramatic loss of spore viability in fission yeast lacking all four TLSPs, which is accompanied by disruptions in chromosome segregation during meiosis I and II. Rec8 cohesin dynamics are altered in the absence of the TLSPs. These data suggest that the TLSPs contribute to multiple aspects of meiotic chromosome dynamics.
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Affiliation(s)
- Tara L Mastro
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Vishnu P Tripathi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Susan L Forsburg
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA
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44
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Syeda AH, Dimude JU, Skovgaard O, Rudolph CJ. Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics. Front Microbiol 2020; 11:534. [PMID: 32351461 PMCID: PMC7174701 DOI: 10.3389/fmicb.2020.00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022] Open
Abstract
Each cell division requires the complete and accurate duplication of the entire genome. In bacteria, the duplication process of the often-circular chromosomes is initiated at a single origin per chromosome, resulting in two replication forks that traverse the chromosome in opposite directions. DNA synthesis is completed once the two forks fuse in a region diametrically opposite the origin. In some bacteria, such as Escherichia coli, the region where forks fuse forms a specialized termination area. Polar replication fork pause sites flanking this area can pause the progression of replication forks, thereby allowing forks to enter but not to leave. Transcription of all required genes has to take place simultaneously with genome duplication. As both of these genome trafficking processes share the same template, conflicts are unavoidable. In this review, we focus on recent attempts to add additional origins into various ectopic chromosomal locations of the E. coli chromosome. As ectopic origins disturb the native replichore arrangements, the problems resulting from such perturbations can give important insights into how genome trafficking processes are coordinated and the problems that arise if this coordination is disturbed. The data from these studies highlight that head-on replication–transcription conflicts are indeed highly problematic and multiple repair pathways are required to restart replication forks arrested at obstacles. In addition, the existing data also demonstrate that the replication fork trap in E. coli imposes significant constraints to genome duplication if ectopic origins are active. We describe the current models of how replication fork fusion events can cause serious problems for genome duplication, as well as models of how such problems might be alleviated both by a number of repair pathways as well as the replication fork trap system. Considering the problems associated both with head-on replication-transcription conflicts as well as head-on replication fork fusion events might provide clues of how these genome trafficking issues have contributed to shape the distinct architecture of bacterial chromosomes.
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Affiliation(s)
- Aisha H Syeda
- Department of Biology, University of York, York, United Kingdom
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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45
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Srinivasan G, Williamson EA, Kong K, Jaiswal AS, Huang G, Kim HS, Schärer O, Zhao W, Burma S, Sung P, Hromas R. MiR223-3p promotes synthetic lethality in BRCA1-deficient cancers. Proc Natl Acad Sci U S A 2019; 116:17438-17443. [PMID: 31395736 PMCID: PMC6717293 DOI: 10.1073/pnas.1903150116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Defects in DNA repair give rise to genomic instability, leading to neoplasia. Cancer cells defective in one DNA repair pathway can become reliant on remaining repair pathways for survival and proliferation. This attribute of cancer cells can be exploited therapeutically, by inhibiting the remaining repair pathway, a process termed synthetic lethality. This process underlies the mechanism of the Poly-ADP ribose polymerase-1 (PARP1) inhibitors in clinical use, which target BRCA1 deficient cancers, which is indispensable for homologous recombination (HR) DNA repair. HR is the major repair pathway for stressed replication forks, but when BRCA1 is deficient, stressed forks are repaired by back-up pathways such as alternative nonhomologous end-joining (aNHEJ). Unlike HR, aNHEJ is nonconservative, and can mediate chromosomal translocations. In this study we have found that miR223-3p decreases expression of PARP1, CtIP, and Pso4, each of which are aNHEJ components. In most cells, high levels of microRNA (miR) 223-3p repress aNHEJ, decreasing the risk of chromosomal translocations. Deletion of the miR223 locus in mice increases PARP1 levels in hematopoietic cells and enhances their risk of unprovoked chromosomal translocations. We also discovered that cancer cells deficient in BRCA1 or its obligate partner BRCA1-Associated Protein-1 (BAP1) routinely repress miR223-3p to permit repair of stressed replication forks via aNHEJ. Reconstituting the expression of miR223-3p in BRCA1- and BAP1-deficient cancer cells results in reduced repair of stressed replication forks and synthetic lethality. Thus, miR223-3p is a negative regulator of the aNHEJ DNA repair and represents a therapeutic pathway for BRCA1- or BAP1-deficient cancers.
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Affiliation(s)
- Gayathri Srinivasan
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Elizabeth A Williamson
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Kimi Kong
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Aruna S Jaiswal
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Guangcun Huang
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 689-798, Republic of Korea
| | - Orlando Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 689-798, Republic of Korea
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229;
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 689-798, Republic of Korea
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46
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Petropoulos M, Champeris Tsaniras S, Taraviras S, Lygerou Z. Replication Licensing Aberrations, Replication Stress, and Genomic Instability. Trends Biochem Sci 2019; 44:752-764. [PMID: 31054805 DOI: 10.1016/j.tibs.2019.03.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/24/2019] [Accepted: 03/27/2019] [Indexed: 01/07/2023]
Abstract
Strict regulation of DNA replication is of fundamental significance for the maintenance of genome stability. Licensing of origins of DNA replication is a critical event for timely genome duplication. Errors in replication licensing control lead to genomic instability across evolution. Here, we present accumulating evidence that aberrant replication licensing is linked to oncogene-induced replication stress and poses a major threat to genome stability, promoting tumorigenesis. Oncogene activation can lead to defects in where along the genome and when during the cell cycle licensing takes place, resulting in replication stress. We also discuss the potential of replication licensing as a specific target for novel anticancer therapies.
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Affiliation(s)
- Michalis Petropoulos
- Department of Biology, School of Medicine, University of Patras, Patras 26504, Greece
| | | | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, Patras 26504, Greece.
| | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, Patras 26504, Greece.
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DNA Rereplication Is Susceptible to Nucleotide-Level Mutagenesis. Genetics 2019; 212:445-460. [PMID: 31028114 PMCID: PMC6553831 DOI: 10.1534/genetics.119.302194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
The initiation of eukaryotic DNA replication at replication origins is tightly regulated to prevent re-initiation and re-replication within each cell cycle. This regulation is critical for genome stability as re-replication is an extremely potent inducer... The sources of genome instability, a hallmark of cancer, remain incompletely understood. One potential source is DNA rereplication, which arises when the mechanisms that prevent the reinitiation of replication origins within a single cell cycle are compromised. Using the budding yeast Saccharomyces cerevisiae, we previously showed that DNA rereplication is extremely potent at inducing gross chromosomal alterations and that this arises in part because of the susceptibility of rereplication forks to break. Here, we examine the ability of DNA rereplication to induce nucleotide-level mutations. During normal replication these mutations are restricted by three overlapping error-avoidance mechanisms: the nucleotide selectivity of replicative polymerases, their proofreading activity, and mismatch repair. Using lys2InsEA14, a frameshift reporter that is poorly proofread, we show that rereplication induces up to a 30× higher rate of frameshift mutations and that this mutagenesis is due to passage of the rereplication fork, not secondary to rereplication fork breakage. Rereplication can also induce comparable rates of frameshift and base-substitution mutations in a more general mutagenesis reporter CAN1, when the proofreading activity of DNA polymerase ε is inactivated. Finally, we show that the rereplication-induced mutagenesis of both lys2InsEA14 and CAN1 disappears in the absence of mismatch repair. These results suggest that mismatch repair is attenuated during rereplication, although at most sequences DNA polymerase proofreading provides enough error correction to mitigate the mutagenic consequences. Thus, rereplication can facilitate nucleotide-level mutagenesis in addition to inducing gross chromosomal alterations, broadening its potential role in genome instability.
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Developmental Control of the Cell Cycle: Insights from Caenorhabditis elegans. Genetics 2019; 211:797-829. [PMID: 30846544 PMCID: PMC6404260 DOI: 10.1534/genetics.118.301643] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022] Open
Abstract
During animal development, a single fertilized egg forms a complete organism with tens to trillions of cells that encompass a large variety of cell types. Cell cycle regulation is therefore at the center of development and needs to be carried out in close coordination with cell differentiation, migration, and death, as well as tissue formation, morphogenesis, and homeostasis. The timing and frequency of cell divisions are controlled by complex combinations of external and cell-intrinsic signals that vary throughout development. Insight into how such controls determine in vivo cell division patterns has come from studies in various genetic model systems. The nematode Caenorhabditis elegans has only about 1000 somatic cells and approximately twice as many germ cells in the adult hermaphrodite. Despite the relatively small number of cells, C. elegans has diverse tissues, including intestine, nerves, striated and smooth muscle, and skin. C. elegans is unique as a model organism for studies of the cell cycle because the somatic cell lineage is invariant. Somatic cells divide at set times during development to produce daughter cells that adopt reproducible developmental fates. Studies in C. elegans have allowed the identification of conserved cell cycle regulators and provided insights into how cell cycle regulation varies between tissues. In this review, we focus on the regulation of the cell cycle in the context of C. elegans development, with reference to other systems, with the goal of better understanding how cell cycle regulation is linked to animal development in general.
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Munera López J, Ganuza A, Bogado SS, Muñoz D, Ruiz DM, Sullivan WJ, Vanagas L, Angel SO. Evaluation of ATM Kinase Inhibitor KU-55933 as Potential Anti- Toxoplasma gondii Agent. Front Cell Infect Microbiol 2019; 9:26. [PMID: 30815397 PMCID: PMC6381018 DOI: 10.3389/fcimb.2019.00026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/25/2019] [Indexed: 01/01/2023] Open
Abstract
Toxoplasma gondii is an apicomplexan protozoan parasite with a complex life cycle composed of multiple stages that infect mammals and birds. Tachyzoites rapidly replicate within host cells to produce acute infection during which the parasite disseminates to tissues and organs. Highly replicative cells are subject to Double Strand Breaks (DSBs) by replication fork collapse and ATM, a member of the phosphatidylinositol 3-kinase (PI3K) family, is a key factor that initiates DNA repair and activates cell cycle checkpoints. Here we demonstrate that the treatment of intracellular tachyzoites with the PI3K inhibitor caffeine or ATM kinase-inhibitor KU-55933 affects parasite replication rate in a dose-dependent manner. KU-55933 affects intracellular tachyzoite growth and induces G1-phase arrest. Addition of KU-55933 to extracellular tachyzoites also leads to a significant reduction of tachyzoite replication upon infection of host cells. ATM kinase phosphorylates H2A.X (γH2AX) to promote DSB damage repair. The level of γH2AX increases in tachyzoites treated with camptothecin (CPT), a drug that generates fork collapse, but this increase was not observed when co-administered with KU-55933. These findings support that KU-55933 is affecting the Toxoplasma ATM-like kinase (TgATM). The combination of KU-55933 and other DNA damaging agents such as methyl methane sulfonate (MMS) and CPT produce a synergic effect, suggesting that TgATM kinase inhibition sensitizes the parasite to damaged DNA. By contrast, hydroxyurea (HU) did not further inhibit tachyzoite replication when combined with KU-55933.
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Affiliation(s)
- Jonathan Munera López
- Laboratorio de Parasitología Molecular, IIB-INTECH, Consejo Nacional de Investigaciones Científicas (CONICET)-Universidad Nacional General San Martin (UNSAM), Chascomús, Argentina
| | - Agustina Ganuza
- Laboratorio de Parasitología Molecular, IIB-INTECH, Consejo Nacional de Investigaciones Científicas (CONICET)-Universidad Nacional General San Martin (UNSAM), Chascomús, Argentina
| | - Silvina S Bogado
- Laboratorio de Parasitología Molecular, IIB-INTECH, Consejo Nacional de Investigaciones Científicas (CONICET)-Universidad Nacional General San Martin (UNSAM), Chascomús, Argentina
| | - Daniela Muñoz
- Laboratorio de Parasitología Molecular, IIB-INTECH, Consejo Nacional de Investigaciones Científicas (CONICET)-Universidad Nacional General San Martin (UNSAM), Chascomús, Argentina
| | - Diego M Ruiz
- Laboratorio de Parasitología Molecular, IIB-INTECH, Consejo Nacional de Investigaciones Científicas (CONICET)-Universidad Nacional General San Martin (UNSAM), Chascomús, Argentina
| | - William J Sullivan
- Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States.,Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, IIB-INTECH, Consejo Nacional de Investigaciones Científicas (CONICET)-Universidad Nacional General San Martin (UNSAM), Chascomús, Argentina
| | - Sergio O Angel
- Laboratorio de Parasitología Molecular, IIB-INTECH, Consejo Nacional de Investigaciones Científicas (CONICET)-Universidad Nacional General San Martin (UNSAM), Chascomús, Argentina
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Griffin WC, Trakselis MA. The MCM8/9 complex: A recent recruit to the roster of helicases involved in genome maintenance. DNA Repair (Amst) 2019; 76:1-10. [PMID: 30743181 DOI: 10.1016/j.dnarep.2019.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/03/2019] [Indexed: 12/11/2022]
Abstract
There are several DNA helicases involved in seemingly overlapping aspects of homologous and homoeologous recombination. Mutations of many of these helicases are directly implicated in genetic diseases including cancer, rapid aging, and infertility. MCM8/9 are recent additions to the catalog of helicases involved in recombination, and so far, the evidence is sparse, making assignment of function difficult. Mutations in MCM8/9 correlate principally with primary ovarian failure/insufficiency (POF/POI) and infertility indicating a meiotic defect. However, they also act when replication forks collapse/break shuttling products into mitotic recombination and several mutations are found in various somatic cancers. This review puts MCM8/9 in context with other replication and recombination helicases to narrow down its genomic maintenance role. We discuss the known structure/function relationship, the mutational spectrum, and dissect the available cellular and organismal data to better define its role in recombination.
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Affiliation(s)
- Wezley C Griffin
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798, USA.
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