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Waheed Y, Mojumdar A, Shafiq M, de Marco A, De March M. The fork remodeler helicase-like transcription factor in cancer development: all at once. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167280. [PMID: 38851303 DOI: 10.1016/j.bbadis.2024.167280] [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: 02/06/2024] [Revised: 04/20/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
The Helicase-like Transcription Factor (HLTF) is a member of the SNF2-family of fork remodelers, primarily studied for its capacity to provide DNA Damage Tolerance (DDT) and to induce replication fork reversal (RFR). HLTF is recruited at stalled forks where both its ATPase motor and HIP116 Rad5p N-terminal (HIRAN) domains are necessary for regulating its interaction with DNA. HIRAN bestows specificity to ssDNA 3'-end and imparts branch migration as well as DNA remodeling capabilities facilitating damage repair. Both expression regulation and mutation rate affect HLTF activity. Gene hypermethylation induces loss of HLTF function, in particular in colorectal cancer (CRC), implying a tumour suppressor role. Surprisingly, a correlation between hypermethylation and HLTF mRNA upregulation has also been observed, even within the same cancer type. In many cancers, both complex mutation patterns and the presence of gene Copy Number Variations (CNVs) have been reported. These conditions affect the amount of functional HLTF and question the physiological role of this fork remodeler. This review offers a systematic collection of the presently strewed information regarding HLTF, its structural and functional characteristics, the multiple roles in DDT and the regulation in cancer progression highlighting new research perspectives.
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Affiliation(s)
- Yossma Waheed
- Department of Environmental and Biological Sciences, University of Nova Gorica, Vipaska Cesta 13, SI-5000 Nova Gorica, Slovenia; National Institute of Science and Technology, Sector H-12, Islamabad Capital Territory, Pakistan
| | - Aditya Mojumdar
- Department of Biochemistry and Microbiology, University of Victoria, BC V8W 2Y2, Victoria, Canada
| | - Mohammad Shafiq
- Department of Environmental and Biological Sciences, University of Nova Gorica, Vipaska Cesta 13, SI-5000 Nova Gorica, Slovenia
| | - Ario de Marco
- Department of Environmental and Biological Sciences, University of Nova Gorica, Vipaska Cesta 13, SI-5000 Nova Gorica, Slovenia
| | - Matteo De March
- Department of Environmental and Biological Sciences, University of Nova Gorica, Vipaska Cesta 13, SI-5000 Nova Gorica, Slovenia.
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2
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Wang Y, Tan Y, Yang S, Wei J, Wei Y, Chen J. HLTF/SERPINE1 Axis Plays a Crucial Pro-Oncogenic Role in the Progression from Cervical Precancerous Lesions to Cervical Carcinoma in vitro. Gynecol Obstet Invest 2024:1-12. [PMID: 39348822 DOI: 10.1159/000540384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 07/14/2024] [Indexed: 10/02/2024]
Abstract
OBJECTIVES Cervical carcinoma (CC) is prevalent among women worldwide with increasing risk. Finding effective methods for treating CC is of utmost importance. The aim of this study was to investigate the effect of SERPINE1 on the progression of cervical precancerous lesions to CC. DESIGN This study used transcriptome sequencing and in vitro cell line. Participants/Materials: Cervical precancerous lesions and CC samples and human cervical epithelial immortalized cell line H8, human CC cell lines HeLa, and CaSki were involved in this study. SETTING AND METHODS Next-generation sequencing was applied to identify 100 differentially expressed genes from cervical precancerous lesions and CC samples. With the application of the Search Tool for the Retrieval of Interacting Genes (STRING) database, we carried out the protein-protein interaction network analysis, thus screening out serine protease inhibitor clade E member 1 (SERPINE1) with significant upregulation in CC cells. The helicase-like transcription factor (HLTF) was predicted as the upstream transcription factor using Human Transcription Factor Database (HumanTFDB). The chromatin immunoprecipitation (ChIP) experiment was conducted to validate the interaction between SERPINE1 and HLTF. The immunohistochemistry was employed to determine the expression of SERPINE1 and HLTF in CC tissues. Following the upregulation or downregulation of SERPINE1 and HLTF, the real-time quantitative reverse transcription polymerase chain reaction was carried out to assess mRNA expression levels of SERPINE1 and HLTF in cells. Cell viability, migration, and invasion were evaluated using MTT assay, cell scratch assay, and Transwell assay, respectively. Western blot analysis was conducted to assess changes in the expression levels of matrix metalloproteinases and proteins related to epithelial-mesenchymal transition (EMT). RESULTS The ChIP experiment confirmed the interaction between HLTF and SERPINE1. HLTF and SERPINE1 were upregulated in CC tissues and cells, and silencing SERPINE1 inhibited the EMT process and viability, migration, and invasion of CC cells. However, overexpression of SERPINE1 in CC cells showed the opposite trend. Rescue experiments demonstrated that silencing HLTF repressed CC cell viability, migration, and invasion, which could be restored by overexpressing SERPINE1. LIMITATIONS The effect of the HLTF/SERPINE1 axis on CC malignant progression has not been confirmed by in vivo experiments. CONCLUSION HLTF transcriptionally activates SERPINE1, promoting the progression from cervical precancerous lesions to CC.
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Affiliation(s)
- Yong Wang
- Department of Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yudi Tan
- Department of Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shasha Yang
- Department of Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinkong Wei
- Department of Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuying Wei
- Department of Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Junying Chen
- Department of Gynecology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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3
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Galli M, Frigerio C, Colombo CV, Casari E, Longhese MP, Clerici M. Exo1 cooperates with Tel1/ATM in promoting recombination events at DNA replication forks. iScience 2024; 27:110410. [PMID: 39081288 PMCID: PMC11284563 DOI: 10.1016/j.isci.2024.110410] [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: 03/06/2024] [Revised: 05/27/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Tel1/ataxia telangiectasia mutated (ATM) kinase plays multiple functions in response to DNA damage, promoting checkpoint-mediated cell-cycle arrest and repair of broken DNA. In addition, Saccharomyces cerevisiae Tel1 stabilizes replication forks that arrest upon the treatment with the topoisomerase poison camptothecin (CPT). We discover that inactivation of the Exo1 nuclease exacerbates the sensitivity of Tel1-deficient cells to CPT and other agents that hamper DNA replication. Furthermore, cells lacking both Exo1 and Tel1 activities exhibit sustained checkpoint activation in the presence of CPT, indicating that Tel1 and Exo1 limit the activation of a Mec1-dependent checkpoint. The absence of Tel1 or its kinase activity enhances recombination between inverted DNA repeats induced by replication fork blockage in an Exo1-dependent manner. Thus, we propose that Exo1 processes intermediates arising at stalled forks in tel1 mutants to promote DNA replication recovery and cell survival.
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Affiliation(s)
- Michela Galli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Chiara Frigerio
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Chiara Vittoria Colombo
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
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4
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Reginato G, Dello Stritto MR, Wang Y, Hao J, Pavani R, Schmitz M, Halder S, Morin V, Cannavo E, Ceppi I, Braunshier S, Acharya A, Ropars V, Charbonnier JB, Jinek M, Nussenzweig A, Ha T, Cejka P. HLTF disrupts Cas9-DNA post-cleavage complexes to allow DNA break processing. Nat Commun 2024; 15:5789. [PMID: 38987539 PMCID: PMC11237066 DOI: 10.1038/s41467-024-50080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
The outcome of CRISPR-Cas-mediated genome modifications is dependent on DNA double-strand break (DSB) processing and repair pathway choice. Homology-directed repair (HDR) of protein-blocked DSBs requires DNA end resection that is initiated by the endonuclease activity of the MRE11 complex. Using reconstituted reactions, we show that Cas9 breaks are unexpectedly not directly resectable by the MRE11 complex. In contrast, breaks catalyzed by Cas12a are readily processed. Cas9, unlike Cas12a, bridges the broken ends, preventing DSB detection and processing by MRE11. We demonstrate that Cas9 must be dislocated after DNA cleavage to allow DNA end resection and repair. Using single molecule and bulk biochemical assays, we next find that the HLTF translocase directly removes Cas9 from broken ends, which allows DSB processing by DNA end resection or non-homologous end-joining machineries. Mechanistically, the activity of HLTF requires its HIRAN domain and the release of the 3'-end generated by the cleavage of the non-target DNA strand by the Cas9 RuvC domain. Consequently, HLTF removes the H840A but not the D10A Cas9 nickase. The removal of Cas9 H840A by HLTF explains the different cellular impact of the two Cas9 nickase variants in human cells, with potential implications for gene editing.
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Affiliation(s)
- Giordano Reginato
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Maria Rosaria Dello Stritto
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Yanbo Wang
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jingzhou Hao
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Schmitz
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Swagata Halder
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
- Biological Systems Engineering, Plaksha University, Mohali, Punjab, 140306, India
| | - Vincent Morin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Elda Cannavo
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ilaria Ceppi
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Stefan Braunshier
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ananya Acharya
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Virginie Ropars
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jean-Baptiste Charbonnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Andrè Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Taekjip Ha
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland.
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Wu CK, Shiu JL, Wu CL, Hung CF, Ho YC, Chen YT, Tung SY, Yeh CF, Shen CH, Liaw H, Su WP. APLF facilitates interstrand DNA crosslink repair and replication fork protection to confer cisplatin resistance. Nucleic Acids Res 2024; 52:5676-5697. [PMID: 38520407 PMCID: PMC11162786 DOI: 10.1093/nar/gkae211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Replication stress converts the stalled forks into reversed forks, which is an important protection mechanism to prevent fork degradation and collapse into poisonous DNA double-strand breaks (DSBs). Paradoxically, the mechanism also acts in cancer cells to contribute to chemoresistance against various DNA-damaging agents. PARP1 binds to and is activated by stalled forks to facilitate fork reversal. Aprataxin and polynucleotide kinase/phosphatase-like factor (APLF) binds to PARP1 through the poly(ADP-ribose) zinc finger (PBZ) domain and is known to be involved in non-homologous end joining (NHEJ). Here, we identify a novel function of APLF involved in interstrand DNA crosslink (ICL) repair and fork protection. We demonstrate that PARP1 activity facilitates the APLF recruitment to stalled forks, enabling the FANCD2 recruitment to stalled forks. The depletion of APLF sensitizes cells to cisplatin, impairs ICL repair, reduces the FANCD2 recruitment to stalled forks, and results in nascent DNA degradation by MRE11 nucleases. Additionally, cisplatin-resistant cancer cells show high levels of APLF and homologous recombination-related gene expression. The depletion of APLF sensitizes cells to cisplatin and results in fork instability. Our results reveal the novel function of APLF to facilitate ICL repair and fork protection, thereby contributing to cisplatin-resistant phenotypes of cancer cells.
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Affiliation(s)
- Cheng-Kuei Wu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
| | - Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Chao-Liang Wu
- Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Chi-Feng Hung
- Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Yen-Chih Ho
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Yen-Tzu Chen
- Department of Public Health & Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taiwan
| | - Sheng-Yung Tung
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Department of Urology, An Nan Hospital, China Medical University, Tainan, Taiwan
| | - Cheng-Fa Yeh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Che-Hung Shen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Wen-Pin Su
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Departments of Oncology and Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan 701, Taiwan
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6
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Yu G, Xiong Y, Xu Z, Zhang L, Zhou XA, Nie C, Li S, Wang W, Li X, Wang J. MBD1 protects replication fork stability by recruiting PARP1 and controlling transcription-replication conflicts. Cancer Gene Ther 2024; 31:94-107. [PMID: 37949945 DOI: 10.1038/s41417-023-00685-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
The replication-stress response is essential to ensure the faithful transmission of genetic information to daughter cells. Although several stress-resolution pathways have been identified to deal with replication stress, the precise regulatory mechanisms for replication fork stability are not fully understood. Our study identified Methyl-CpG Binding Domain 1 (MBD1) as essential for the maintaining genomic stability and protecting stalled replication forks in mammalian cells. Depletion of MBD1 increases DNA lesions and sensitivity to replication stress. Mechanistically, we found that loss of MBD1 leads to the dissociation of Poly(ADP-ribose) polymerase 1 (PARP1) from the replication fork, potentially accelerating fork progression and resulting in higher levels of transcription-replication conflicts (T-R conflicts). Using a proximity ligation assay combined with 5-ethynyl-2'-deoxyuridine, we revealed that the MBD1 and PARP1 proteins were recruited to stalled forks under hydroxyurea (HU) treatment. In addition, our study showed that the level of R-loops also increased in MBD1-delated cells. Without MBD1, stalled replication forks resulting from T-R conflicts were primarily degraded by the DNA2 nuclease. Our findings shed light on a new aspect of MBD1 in maintaining genome stability and providing insights into the mechanisms underlying replication stress response.
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Affiliation(s)
- Guihui Yu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Yundong Xiong
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Zhanzhan Xu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Lei Zhang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Chen Nie
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Shiwei Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China.
| | - Xiaoman Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China.
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China.
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7
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Hoes L, Voordeckers K, Dok R, Boeckx B, Steemans B, Gopaul D, Pasero P, Govers SK, Lambrechts D, Nuyts S, Verstrepen KJ. Ethanol induces replication fork stalling and membrane stress in immortalized laryngeal cells. iScience 2023; 26:108564. [PMID: 38213791 PMCID: PMC10783606 DOI: 10.1016/j.isci.2023.108564] [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: 07/13/2023] [Revised: 10/11/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
Although ethanol is a class I carcinogen and is linked to more than 700,000 cancer incidences, a clear understanding of the molecular mechanisms underlying ethanol-related carcinogenesis is still lacking. Further understanding of ethanol-related cell damage can contribute to reducing or treating alcohol-related cancers. Here, we investigated the effects of both short- and long-term exposure of human laryngeal epithelial cells to different ethanol concentrations. RNA sequencing shows that ethanol altered gene expression patterns in a time- and concentration-dependent way, affecting genes involved in ribosome biogenesis, cytoskeleton remodeling, Wnt signaling, and transmembrane ion transport. Additionally, ethanol induced a slower cell proliferation, a delayed cell cycle progression, and replication fork stalling. In addition, ethanol exposure resulted in morphological changes, which could be associated with membrane stress. Taken together, our data yields a comprehensive view of molecular changes associated with ethanol stress in epithelial cells of the upper aerodigestive tract.
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Affiliation(s)
- Lore Hoes
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Karin Voordeckers
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Bart Steemans
- Laboratory of Microbial Systems Cell Biology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Diyavarshini Gopaul
- Institute of Human Genetics, CNRS, University of Montpellier, 34396 Montpellier, France
| | - Philippe Pasero
- Institute of Human Genetics, CNRS, University of Montpellier, 34396 Montpellier, France
| | - Sander K. Govers
- Laboratory of Microbial Systems Cell Biology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospital Leuven, 3000 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
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8
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Kaur G, Helmer RA, Martinez-Marin D, Sennoune SR, Washburn RL, Martinez-Zaguilan R, Dufour JM, Chilton BS. Helicase-like transcription factor (Hltf)-deletion activates Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality. PLoS One 2023; 18:e0286109. [PMID: 37624843 PMCID: PMC10456192 DOI: 10.1371/journal.pone.0286109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/09/2023] [Indexed: 08/27/2023] Open
Abstract
Epigenetic mechanisms are integral to pancreatic β cell function. Promoter hypermethylation of the helicase like-transcription factor (HLTF) gene-a component of the cellular DNA damage response that contributes to genome stability-has been implicated in age-associated changes in β cells. To study HLTF, we generated global and β cell-specific (β) Hltf knockout (KO) immune competent (IC) and immune deficient (ID) Rag2-/IL2- mice. IC global and β Hltf KO mice were neonatal lethal whereas ID global and β Hltf KO newborn mice had normal survival. This focused our investigation on the effects of Rag2 interruption with common gamma chain interruption on β cell function/survival. Three-way transcriptomic (RNAseq) analyses of whole pancreata from IC and ID newborn β Hltf KO and wild type (Hltf +/+) controls combined with spatially resolved transcriptomic analysis of formalin fixed paraffin embedded tissue, immunohistochemistry and laser scanning confocal microscopy showed DNA damage caused by β Hltf KO in IC mice upregulated the Hmgb1-Rage axis and a gene signature for innate immune cells. Perforin-delivered granzyme A (GzmA) activation of DNase, Nme1, showed damaged nuclear single-stranded DNA (γH2AX immunostaining). This caspase-independent method of cell death was supported by transcriptional downregulation of Serpinc1 gene that encodes a serine protease inhibitor of GzmA. Increased transcriptional availability of complement receptors C3ar1 and C5ar1 likely invited crosstalk with Hmgb1 to amplify inflammation. This study explores the complex dialog between β cells and immune cells during development. It has implications for the initiation of type I diabetes in utero when altered gene expression that compromises genome stability invokes a localized inflammatory response.
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Affiliation(s)
- Gurvinder Kaur
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rebecca A. Helmer
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Dalia Martinez-Marin
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- Department of Immunology and Molecular Microbiology, Texas Tech University-Health Sciences Center, Lubbock, Texas, United States of America
| | - Souad R. Sennoune
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Rachel L. Washburn
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Raul Martinez-Zaguilan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jannette M. Dufour
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Beverly S. Chilton
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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9
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Ho YC, Ku CS, Tsai SS, Shiu JL, Jiang YZ, Miriam HE, Zhang HW, Chen YT, Chiu WT, Chang SB, Shen CH, Myung K, Chi P, Liaw H. PARP1 recruits DNA translocases to restrain DNA replication and facilitate DNA repair. PLoS Genet 2022; 18:e1010545. [PMID: 36512630 PMCID: PMC9794062 DOI: 10.1371/journal.pgen.1010545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/27/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
Replication fork reversal which restrains DNA replication progression is an important protective mechanism in response to replication stress. PARP1 is recruited to stalled forks to restrain DNA replication. However, PARP1 has no helicase activity, and the mechanism through which PARP1 participates in DNA replication restraint remains unclear. Here, we found novel protein-protein interactions between PARP1 and DNA translocases, including HLTF, SHPRH, ZRANB3, and SMARCAL1, with HLTF showing the strongest interaction among these DNA translocases. Although HLTF and SHPRH share structural and functional similarity, it remains unclear whether SHPRH contains DNA translocase activity. We further identified the ability of SHPRH to restrain DNA replication upon replication stress, indicating that SHPRH itself could be a DNA translocase or a helper to facilitate DNA translocation. Although hydroxyurea (HU) and MMS induce different types of replication stress, they both induce common DNA replication restraint mechanisms independent of intra-S phase activation. Our results suggest that the PARP1 facilitates DNA translocase recruitment to damaged forks, preventing fork collapse and facilitating DNA repair.
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Affiliation(s)
- Yen-Chih Ho
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Chen-Syun Ku
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Siang-Sheng Tsai
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yi-Zhen Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
| | - Hui Emmanuela Miriam
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Han-Wen Zhang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yen-Tzu Chen
- Department of Public Health & Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Che-Hung Shen
- National Institute of Cancer Research, National Health Research Institutes, Tainan City, Taiwan
| | - Kyungjae Myung
- IBS Center for Genomic Integrity, UNIST-gil 50, Ulsan, Republic of Korea
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei City, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
- * E-mail:
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Hydroxyurea-The Good, the Bad and the Ugly. Genes (Basel) 2021; 12:genes12071096. [PMID: 34356112 PMCID: PMC8304116 DOI: 10.3390/genes12071096] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Hydroxyurea (HU) is mostly referred to as an inhibitor of ribonucleotide reductase (RNR) and as the agent that is commonly used to arrest cells in the S-phase of the cycle by inducing replication stress. It is a well-known and widely used drug, one which has proved to be effective in treating chronic myeloproliferative disorders and which is considered a staple agent in sickle anemia therapy and—recently—a promising factor in preventing cognitive decline in Alzheimer’s disease. The reversibility of HU-induced replication inhibition also makes it a common laboratory ingredient used to synchronize cell cycles. On the other hand, prolonged treatment or higher dosage of hydroxyurea causes cell death due to accumulation of DNA damage and oxidative stress. Hydroxyurea treatments are also still far from perfect and it has been suggested that it facilitates skin cancer progression. Also, recent studies have shown that hydroxyurea may affect a larger number of enzymes due to its less specific interaction mechanism, which may contribute to further as-yet unspecified factors affecting cell response. In this review, we examine the actual state of knowledge about hydroxyurea and the mechanisms behind its cytotoxic effects. The practical applications of the recent findings may prove to enhance the already existing use of the drug in new and promising ways.
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