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Guan Y, He H, Guo Y, Zhang L. Essential roles of Rad6 in conidial property, stress tolerance, and pathogenicity of Beauveria bassiana. Virulence 2024; 15:2362748. [PMID: 38860453 PMCID: PMC11174126 DOI: 10.1080/21505594.2024.2362748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
Rad6 functions as a ubiquitin-conjugating protein that regulates cellular processes in many fungal species. However, its role in filamentous entomopathogenic fungi remains poorly understood. This study characterizes Rad6 in Beauveria bassiana, a filamentous fungus widely employed as a critical fungicide globally. The results demonstrate a significant association between Rad6 and conidial properties, heat shock response, and UV-B tolerance. Concurrently, the mutant strain exhibited heightened sensitivity to oxidative stress, cell wall interfering agents, DNA damage stress, and prolonged heat shock. Furthermore, the absence of Rad6 significantly extended the median lethal time (LT50) of Galleria mellonella infected by B. bassiana. This delay could be attributed to reduced Pr1 proteases and extracellular cuticle-degrading enzymes, diminished dimorphic transition rates, and dysregulated antioxidant enzymes. Additionally, the absence of Rad6 had a more pronounced effect on genetic information processing, metabolism, and cellular processes under normal conditions. However, its impact was limited to metabolism in oxidative stress. This study offers a comprehensive understanding of the pivotal roles of Rad6 in conidial and hyphal stress tolerance, environmental adaptation, and the pathogenesis of Beauveria bassiana.
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Affiliation(s)
- Yi Guan
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Haomin He
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Yuhan Guo
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Longbin Zhang
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian, China
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2
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Hoang PM, Torre D, Jaynes P, Ho J, Mohammed K, Alvstad E, Lam WY, Khanchandani V, Lee JM, Toh CMC, Lee RX, Anbuselvan A, Lee S, Sebra RP, Martin J Walsh, Marazzi I, Kappei D, Guccione E, Jeyasekharan AD. A PRMT5-ZNF326 axis mediates innate immune activation upon replication stress. SCIENCE ADVANCES 2024; 10:eadm9589. [PMID: 38838142 DOI: 10.1126/sciadv.adm9589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
DNA replication stress (RS) is a widespread phenomenon in carcinogenesis, causing genomic instability and extensive chromatin alterations. DNA damage leads to activation of innate immune signaling, but little is known about transcriptional regulators mediating such signaling upon RS. Using a chemical screen, we identified protein arginine methyltransferase 5 (PRMT5) as a key mediator of RS-dependent induction of interferon-stimulated genes (ISGs). This response is also associated with reactivation of endogenous retroviruses (ERVs). Using quantitative mass spectrometry, we identify proteins with PRMT5-dependent symmetric dimethylarginine (SDMA) modification induced upon RS. Among these, we show that PRMT5 targets and modulates the activity of ZNF326, a zinc finger protein essential for ISG response. Our data demonstrate a role for PRMT5-mediated SDMA in the context of RS-induced transcriptional induction, affecting physiological homeostasis and cancer therapy.
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Affiliation(s)
- Phuong Mai Hoang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Denis Torre
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jessica Ho
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Kevin Mohammed
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Alvstad
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Wan Yee Lam
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jie Min Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Chin Min Clarissa Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Akshaya Anbuselvan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, South Korea
| | - Robert P Sebra
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA 92697, USA
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetic and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Haematology-Oncology, National University Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Bonzi LC, Spinks RK, Donelson JM, Munday PL, Ravasi T, Schunter C. Timing-specific parental effects of ocean warming in a coral reef fish. Proc Biol Sci 2024; 291:20232207. [PMID: 38772423 DOI: 10.1098/rspb.2023.2207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/04/2024] [Indexed: 05/23/2024] Open
Abstract
Population and species persistence in a rapidly warming world will be determined by an organism's ability to acclimate to warmer conditions, especially across generations. There is potential for transgenerational acclimation but the importance of ontogenetic timing in the transmission of environmentally induced parental effects remains mostly unknown. We aimed to disentangle the effects of two critical ontogenetic stages (juvenile development and reproduction) to the new-generation acclimation potential, by exposing the spiny chromis damselfish Acanthochromis polyacanthus to simulated ocean warming across two generations. By using hepatic transcriptomics, we discovered that the post-hatching developmental environment of the offspring themselves had little effect on their acclimation potential at 2.5 months of life. Instead, the developmental experience of parents increased regulatory RNA production and protein synthesis, which could improve the offspring's response to warming. Conversely, parental reproduction and offspring embryogenesis in warmer water elicited stress response mechanisms in the offspring, with suppression of translation and mitochondrial respiration. Mismatches between parental developmental and reproductive temperatures deeply affected offspring gene expression profiles, and detrimental effects were evident when warming occurred both during parents' development and reproduction. This study reveals that the previous generation's developmental temperature contributes substantially to thermal acclimation potential during early life; however, exposure at reproduction as well as prolonged heat stress will likely have adverse effects on the species' persistence.
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Affiliation(s)
- L C Bonzi
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong , Hong Kong
| | - R K Spinks
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- Blue Carbon Section, Department of Climate Change, Energy, the Environment and Water, Australian Government , Brisbane 4000, Australia
| | - J M Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- College of Science and Engineering, James Cook University , Townsville 4810, Australia
| | - P L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- College of Science and Engineering, James Cook University , Townsville 4810, Australia
| | - T Ravasi
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University , Okinawa 904-0495, Japan
| | - C Schunter
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong , Hong Kong
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong , Hong Kong
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Ding Y, Li L, Han D, Wang S, Chen X. Head and Neck Malignant Paragangliomas: Experience from a Single Institution. EAR, NOSE & THROAT JOURNAL 2024; 103:298-304. [PMID: 34654328 DOI: 10.1177/01455613211052338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Objectives: To summarize the clinicopathological and genetic features of malignant paragangliomas in head and neck cancer and to explore the appropriate treatment options for this rare lesion. Methods: Six patients harboring head and neck malignant paraganglioma from Beijing Tongren Hospital were retrospectively reviewed. The clinicopathological characteristics, gene mutations, and prognosis of these patients were analyzed. Results: Of these 6 patients, 3 were male and 3 were female; 4 patients harbored malignant carotid body tumors, and two had malignant vagal paragangliomas. Three patients had cervical lymph node metastasis, two presented with lung and bone metastasis, and 1 had lung and liver metastasis. Of the 6 patients, four underwent surgical resection, and the other two patients denied surgery and instead received chemotherapy with paclitaxel, ifosfamide, and dacarbazine. These 2 patients with vagal paraganglioma received postoperative radiotherapy. All 6 patients are still alive at the present time, with a median follow-up time of 66 months. Positive Ki-67 expression in tumor tissue ranged from 1% to 40%. Genetic mutations in SDHD, SDHB, ATR, and MAP3K13 were identified in 4 patients. Conclusions: After comprehensive treatment, head and neck malignant paraganglioma can attain a favorable prognosis. Genetic mutations are commonly detected in patients with malignant paragangliomas. This study also identified mutations in ATR and MAP3K13 in these patients.
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Affiliation(s)
- Yiming Ding
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Lifeng Li
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Demin Han
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Shaozhong Wang
- Otolaryngology of Qinghai Provincial People's Hospital, Xining, Qinghai Province, China
| | - Xiaohong Chen
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
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Beaudreau N, Page TM, Drolet D, McKindsey CW, Howland KL, Calosi P. Using a metabolomics approach to investigate the sensitivity of a potential Arctic-invader and its Arctic sister-species to marine heatwaves and traditional harvesting disturbances. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170167. [PMID: 38242480 DOI: 10.1016/j.scitotenv.2024.170167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
Coastal species are threatened by fishing practices and changing environmental conditions, such as marine heatwaves (MHW). The mechanisms that confer tolerance to such stressors in marine invertebrates are poorly understood. However, differences in tolerance among different species may be attributed to their geographical distribution. To test the tolerance of species occupying different thermal ranges, we used two closely related bivalves the softshell clam Mya arenaria (Linnaeus, 1758), a cold-temperate invader with demonstrated potential for establishment in the Arctic, and the blunt gaper Mya truncata (Linnaeus, 1758), a native polar species. Clams were subjected to a thermal stress, mimicking a MHW, and harvesting stress in a controlled environment. Seven acute temperature changes (2, 7, 12, 17, 22, 27, and 32 °C) were tested at two harvesting disturbance intensities (with, without). Survival was measured after 12 days and three tissues (gills, mantle, and posterior adductor muscle) collected from surviving individuals for targeted metabolomic profiling. MHW tolerance differed significantly between species: 26.9 °C for M. arenaria and 17.8 °C for M. truncata, with a negligeable effect of harvesting. At the upper thermal limit, M. arenaria displayed a more profound metabolomic remodelling when compared to M. truncata, and this varied greatly between tissue types. Network analysis revealed differences in pathway utilization at the upper MHW limit, with M. arenaria displaying a greater reliance on multiple DNA repair and expression and cell signalling pathways, while M. truncata was limited to fewer pathways. This suggests that M. truncata is ill equipped to cope with warming environments. MHW patterning in the Northwest Atlantic may be a strong predictor of population survival and future range shifts in these two clam species. As polar environments undergo faster rates of warming compared to the global average, M. truncata may be outcompeted by M. arenaria expanding into its native range.
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Affiliation(s)
- Nicholas Beaudreau
- Laboratoire de Physiologie Écologique et Évolutive Marine, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Tessa M Page
- Laboratoire de Physiologie Écologique et Évolutive Marine, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - David Drolet
- Fisheries and Oceans Canada, Demersal and Benthic Science Branch, Institut Maurice-Lamontagne, Mont-Joli, Québec, Canada
| | - Christopher W McKindsey
- Fisheries and Oceans Canada, Demersal and Benthic Science Branch, Institut Maurice-Lamontagne, Mont-Joli, Québec, Canada
| | - Kimberly L Howland
- Fisheries and Oceans Canada, Arctic and Aquatic Research Division, Freshwater Institute, Winnipeg, Manitoba, Canada
| | - Piero Calosi
- Laboratoire de Physiologie Écologique et Évolutive Marine, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada.
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Tan J, Egelston CA, Guo W, Stark JM, Lee PP. STING signalling compensates for low tumour mutation burden to drive anti-tumour immunity. EBioMedicine 2024; 101:105035. [PMID: 38401418 PMCID: PMC10904200 DOI: 10.1016/j.ebiom.2024.105035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND While mutation-derived neoantigens are well recognized in generating anti-tumour T cell response, increasing evidences highlight the complex association between tumour mutation burden (TMB) and tumour infiltrating lymphocytes (TILs). The exploration of non-TMB determinants of active immune response could improve the prognosis prediction and provide guidance for current immunotherapy. METHODS The transcriptomic and whole exome sequence data in The Cancer Genome Atlas were used to examine the relationship between TMB and exhausted CD8+ T cells (Tex), as an indicator of tumour antigen-specific T cells across nine major cancer types. Computational clustering analysis was performed on 4510 tumours to identify different immune profiles. NanoString gene expression analysis and single cell RNA-seq analysis using fresh human breast cancer were performed for finding validation. FINDINGS TMB was found to be poorly correlated with active immune response in various cancer types. Patient clustering analysis revealed a group of tumours with abundant Tex but low TMB. In those tumours, we observed significantly higher expression of the stimulator of interferon genes (STING) signalling. Dendritic cells, particularly those of BATF3+ lineage, were also found to be essential for accumulation of Tex within tumours. Mechanistically, loss of genomic and cellular integrity, marked by decreased DNA damage repair, defective replication stress response, and increased apoptosis were shown to drive STING activation. INTERPRETATION These results highlight that TMB alone does not fully predict tumour immune profiles, with STING signalling compensating for low TMB in non-hypermutated tumours to enhance anti-tumour immunity. Translating these results, STING agonists may benefit patients with non-hypermutated tumours. STING activation may serve as an additional biomarker to predict response to immune checkpoint blockades alongside TMB. Our research also unravelled the interplay between genomic instability and STING activation, informing potential combined chemotherapy targeting the axis of genomic integrity and immunotherapy. FUNDING City of Hope Christopher Family Endowed Innovation Fund for Alzheimer's Disease and Breast Cancer Research in honor of Vineta Christopher; Breast Cancer Alliance Early Career Investigator Award; National Cancer Institute of the National Institutes of Health under award number R01CA256989 and R01CA240392.
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Affiliation(s)
- Jiayi Tan
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Colt A Egelston
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Weihua Guo
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Peter P Lee
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
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Mavroeidi D, Georganta A, Panagiotou E, Syrigos K, Souliotis VL. Targeting ATR Pathway in Solid Tumors: Evidence of Improving Therapeutic Outcomes. Int J Mol Sci 2024; 25:2767. [PMID: 38474014 DOI: 10.3390/ijms25052767] [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: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The DNA damage response (DDR) system is a complicated network of signaling pathways that detects and repairs DNA damage or induces apoptosis. Critical regulators of the DDR network include the DNA damage kinases ataxia telangiectasia mutated Rad3-related kinase (ATR) and ataxia-telangiectasia mutated (ATM). The ATR pathway coordinates processes such as replication stress response, stabilization of replication forks, cell cycle arrest, and DNA repair. ATR inhibition disrupts these functions, causing a reduction of DNA repair, accumulation of DNA damage, replication fork collapse, inappropriate mitotic entry, and mitotic catastrophe. Recent data have shown that the inhibition of ATR can lead to synthetic lethality in ATM-deficient malignancies. In addition, ATR inhibition plays a significant role in the activation of the immune system by increasing the tumor mutational burden and neoantigen load as well as by triggering the accumulation of cytosolic DNA and subsequently inducing the cGAS-STING pathway and the type I IFN response. Taken together, we review stimulating data showing that ATR kinase inhibition can alter the DDR network, the immune system, and their interplay and, therefore, potentially provide a novel strategy to improve the efficacy of antitumor therapy, using ATR inhibitors as monotherapy or in combination with genotoxic drugs and/or immunomodulators.
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Affiliation(s)
- Dimitra Mavroeidi
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Anastasia Georganta
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Emmanouil Panagiotou
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Konstantinos Syrigos
- Third Department of Medicine, Sotiria General Hospital for Chest Diseases, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Vassilis L Souliotis
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece
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Lin C, Schoenherr RM, Voytovich UJ, Ivey RG, Kennedy JJ, Whiteaker JR, Wang P, Paulovich AG. RNA and phosphoprotein profiles of TP53- and PTEN-knockouts in MCF10A at baseline and responding to DNA damage. Sci Data 2024; 11:27. [PMID: 38177134 PMCID: PMC10766633 DOI: 10.1038/s41597-023-02829-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
A wealth of proteogenomic data has been generated using cancer samples to deepen our understanding of the mechanisms of cancer and how biological networks are altered in association with somatic mutation of tumor suppressor genes, such as TP53 and PTEN. To generate functional signatures of TP53 or PTEN loss, we profiled the RNA and phosphoproteomes of the MCF10A epithelial cell line, along with its congenic TP53- or PTEN-knockout derivatives, upon perturbation with the monofunctional DNA alkylating agent methyl methanesulfonate (MMS) vs. mock treatment. To enable quantitative and reproducible mass spectrometry data generation, the cell lines were SILAC-labeled (stable isotope labeling with amino acids in cell culture), and the experimental design included label swapping and biological replicates. All data are publicly available and may be used to advance our understanding of the TP53 and PTEN tumor suppressor genes and to provide functional signatures for bioinformatic analyses of proteogenomic datasets.
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Affiliation(s)
- ChenWei Lin
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | | | | | - Pei Wang
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Syed A, Filandr F, Patterson-Fortin J, Bacolla A, Ravindranathan R, Zhou J, McDonald D, Albuhluli M, Verway-Cohen A, Newman J, Tsai MS, Jones D, Schriemer D, D’Andrea A, Tainer J. Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity. Nucleic Acids Res 2023; 51:9920-9937. [PMID: 37665033 PMCID: PMC10570058 DOI: 10.1093/nar/gkad727] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Polymerase theta (Polθ) acts in DNA replication and repair, and its inhibition is synthetic lethal in BRCA1 and BRCA2-deficient tumor cells. Novobiocin (NVB) is a first-in-class inhibitor of the Polθ ATPase activity, and it is currently being tested in clinical trials as an anti-cancer drug. Here, we investigated the molecular mechanism of NVB-mediated Polθ inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational and cellular assays, we found NVB is a non-competitive inhibitor of ATP hydrolysis. NVB sugar group deletion resulted in decreased potency and reduced HX-MS interactions, supporting a specific NVB binding orientation. Collective results revealed that NVB binds to an allosteric site to block DNA binding, both in vitro and in cells. Comparisons of The Cancer Genome Atlas (TCGA) tumors and matched controls implied that POLQ upregulation in tumors stems from its role in replication stress responses to increased cell proliferation: this can now be tested in fifteen tumor types by NVB blocking ssDNA-stimulation of ATPase activity, required for Polθ function at replication forks and DNA damage sites. Structural and functional insights provided in this study suggest a path for developing NVB derivatives with improved potency for Polθ inhibition by targeting ssDNA binding with entropically constrained small molecules.
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Affiliation(s)
- Aleem Syed
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jeffrey Patterson-Fortin
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ramya Ravindranathan
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jia Zhou
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Drew T McDonald
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohammed E Albuhluli
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amy Verway-Cohen
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph A Newman
- Center for Medicines Discovery, University of Oxford, OX1 3QU, UK
| | - Miaw-Sheue Tsai
- Biological and System Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Alan D D’Andrea
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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10
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Chang YC, Lin K, Baxley RM, Durrett W, Wang L, Stojkova O, Billmann M, Ward H, Myers CL, Bielinsky AK. RNF4 and USP7 cooperate in ubiquitin-regulated steps of DNA replication. Open Biol 2023; 13:230068. [PMID: 37607592 PMCID: PMC10444366 DOI: 10.1098/rsob.230068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
DNA replication requires precise regulation achieved through post-translational modifications, including ubiquitination and SUMOylation. These modifications are linked by the SUMO-targeted E3 ubiquitin ligases (STUbLs). Ring finger protein 4 (RNF4), one of only two mammalian STUbLs, participates in double-strand break repair and resolving DNA-protein cross-links. However, its role in DNA replication has been poorly understood. Using CRISPR/Cas9 genetic screens, we discovered an unexpected dependency of RNF4 mutants on ubiquitin specific peptidase 7 (USP7) for survival in TP53-null retinal pigment epithelial cells. TP53-/-/RNF4-/-/USP7-/- triple knockout (TKO) cells displayed defects in DNA replication that cause genomic instability. These defects were exacerbated by the proteasome inhibitor bortezomib, which limited the nuclear ubiquitin pool. A shortage of free ubiquitin suppressed the ataxia telangiectasia and Rad3-related (ATR)-mediated checkpoint response, leading to increased cell death. In conclusion, RNF4 and USP7 work cooperatively to sustain a functional level of nuclear ubiquitin to maintain the integrity of the genome.
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Affiliation(s)
- Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kevin Lin
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wesley Durrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Olivera Stojkova
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Henry Ward
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Andrs M, Stoy H, Boleslavska B, Chappidi N, Kanagaraj R, Nascakova Z, Menon S, Rao S, Oravetzova A, Dobrovolna J, Surendranath K, Lopes M, Janscak P. Excessive reactive oxygen species induce transcription-dependent replication stress. Nat Commun 2023; 14:1791. [PMID: 36997515 PMCID: PMC10063555 DOI: 10.1038/s41467-023-37341-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
Elevated levels of reactive oxygen species (ROS) reduce replication fork velocity by causing dissociation of the TIMELESS-TIPIN complex from the replisome. Here, we show that ROS generated by exposure of human cells to the ribonucleotide reductase inhibitor hydroxyurea (HU) promote replication fork reversal in a manner dependent on active transcription and formation of co-transcriptional RNA:DNA hybrids (R-loops). The frequency of R-loop-dependent fork stalling events is also increased after TIMELESS depletion or a partial inhibition of replicative DNA polymerases by aphidicolin, suggesting that this phenomenon is due to a global replication slowdown. In contrast, replication arrest caused by HU-induced depletion of deoxynucleotides does not induce fork reversal but, if allowed to persist, leads to extensive R-loop-independent DNA breakage during S-phase. Our work reveals a link between oxidative stress and transcription-replication interference that causes genomic alterations recurrently found in human cancer.
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Affiliation(s)
- Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Nagaraja Chappidi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Radhakrishnan Kanagaraj
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, London, UK
- School of Life Sciences, University of Bedfordshire, Luton, UK
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, India
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Shruti Menon
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- School of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Satyajeet Rao
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Anna Oravetzova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jana Dobrovolna
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kalpana Surendranath
- Genome Engineering Laboratory, School of Life Sciences, University of Westminster, London, UK
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, India
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Pavel Janscak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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12
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Kong LX, Wang Z, Shou YK, Zhou XD, Zong YW, Tong T, Liao M, Han Q, Li Y, Cheng L, Ren B. The FnBPA from methicillin-resistant Staphylococcus aureus promoted development of oral squamous cell carcinoma. J Oral Microbiol 2022; 14:2098644. [PMID: 35859766 PMCID: PMC9291692 DOI: 10.1080/20002297.2022.2098644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is the most common tumor in the oral cavity. Methicillin-resistant Staphylococcus aureus (MRSA) were highly detected in OSCC patients; however, the interactions and mechanisms between drug-resistant bacteria (MRSA) and OSCC are not clear. Aim The aim of this study was to investigate the promotion of MRSA on the development of OSCC. Methods MRSA and MSSA (methicillin-susceptible) strains were employed to investigate the effect on the proliferation of OSCC in vitro and vivo. Results All of the MRSA strains significantly increased the proliferation of OSCC cells and MRSA arrested the cell cycles of OSCC cells in the S phase. MRSA activated the expression of TLR-4, NF-κB and c-fos in OSCC cells. MRSA also promoted the development of squamous cell carcinoma in vivo. The virulence factor fnbpA gene was significantly upregulated in all MRSA strains. By neutralizing FnBPA, the promotions of MRSA on OSCC cell proliferation and development of squamous cell carcinoma were significantly decreased. Meanwhile, the activation of c-fos and NF-κB by MRSA was also significantly decreased by FnBPA antibody. Conclusion MRSA promoted development of OSCC, and the FnBPA protein was the critical virulence factor. Targeting virulence factors is a new method to block the interaction between a drug-resistant pathogen and development of tumors.
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Affiliation(s)
- Li-Xin Kong
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zheng Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yu-Ke Shou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xue-Dong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ya-Wen Zong
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ting Tong
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Min Liao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Qi Han
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yan Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Operative Dentistry and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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13
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Li X, Wang L, Liu X, Zheng Z, Kong D. Cellular regulation and stability of DNA replication forks in eukaryotic cells. DNA Repair (Amst) 2022; 120:103418. [DOI: 10.1016/j.dnarep.2022.103418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/03/2022]
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14
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Zhang J, Chan DW, Lin SY. Exploiting DNA Replication Stress as a Therapeutic Strategy for Breast Cancer. Biomedicines 2022; 10:2775. [PMID: 36359297 PMCID: PMC9687274 DOI: 10.3390/biomedicines10112775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 09/19/2023] Open
Abstract
Proliferating cells rely on DNA replication to ensure accurate genome duplication. Cancer cells, including breast cancer cells, exhibit elevated replication stress (RS) due to the uncontrolled oncogenic activation, loss of key tumor suppressors, and defects in the DNA repair machinery. This intrinsic vulnerability provides a great opportunity for therapeutic exploitation. An increasing number of drug candidates targeting RS in breast cancer are demonstrating promising efficacy in preclinical and early clinical trials. However, unresolved challenges lie in balancing the toxicity of these drugs while maintaining clinical efficacy. Furthermore, biomarkers of RS are urgently required to guide patient selection. In this review, we introduce the concept of targeting RS, detail the current therapies that target RS, and highlight the integration of RS with immunotherapies for breast cancer treatment. Additionally, we discuss the potential biomarkers to optimizing the efficacy of these therapies. Together, the continuous advances in our knowledge of targeting RS would benefit more patients with breast cancer.
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Affiliation(s)
- Jing Zhang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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15
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Cao TQ, Wainwright DA, Lee-Chang C, Miska J, Sonabend AM, Heimberger AB, Lukas RV. Next Steps for Immunotherapy in Glioblastoma. Cancers (Basel) 2022; 14:4023. [PMID: 36011015 PMCID: PMC9406905 DOI: 10.3390/cancers14164023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Outcomes for glioblastoma (GBM) patients undergoing standard of care treatment remain poor. Here we discuss the portfolio of previously investigated immunotherapies for glioblastoma, including vaccine therapy and checkpoint inhibitors, as well as novel emerging therapeutic approaches. In addition, we explore the factors that potentially influence response to immunotherapy, which should be considered in future research aimed at improving immunotherapy efficacy.
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Affiliation(s)
- Toni Q. Cao
- Department of Neurology, Northwestern University, Chicago, IL 60611, USA
| | - Derek A. Wainwright
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
- Lou & Jean Malnati Brain Tumor Institute, Chicago, IL 60611, USA
- Department of Medicine, Division of Hematology/Oncology, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Department of Microbiology-Immunology, Northwestern University, Chicago, IL 60611, USA
| | - Catalina Lee-Chang
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
- Lou & Jean Malnati Brain Tumor Institute, Chicago, IL 60611, USA
| | - Jason Miska
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
- Lou & Jean Malnati Brain Tumor Institute, Chicago, IL 60611, USA
| | - Adam M. Sonabend
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
- Lou & Jean Malnati Brain Tumor Institute, Chicago, IL 60611, USA
| | - Amy B. Heimberger
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60611, USA
- Lou & Jean Malnati Brain Tumor Institute, Chicago, IL 60611, USA
| | - Rimas V. Lukas
- Department of Neurology, Northwestern University, Chicago, IL 60611, USA
- Lou & Jean Malnati Brain Tumor Institute, Chicago, IL 60611, USA
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16
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Kim SM, Forsburg SL. Determinants of RPA megafoci localization to the nuclear periphery in response to replication stress. G3 (BETHESDA, MD.) 2022; 12:jkac116. [PMID: 35567482 PMCID: PMC9258583 DOI: 10.1093/g3journal/jkac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Upon replication stress, ssDNA, coated by the ssDNA-binding protein RPA, accumulates and generates a signal to activate the replication stress response. Severe replication stress induced by the loss of minichromosome maintenance helicase subunit Mcm4 in the temperature-sensitive Schizosaccharomyces pombe degron mutant (mcm4-dg) results in the formation of a large RPA focus that is translocated to the nuclear periphery. We show that resection and repair processes and chromatin remodeler Swr1/Ino80 are involved in the large RPA foci formation and its relocalization to nuclear periphery. This concentrated accumulation of RPA increases the recruitment of Cds1 to chromatin and results in an aberrant cell cycle that lacks MBF-mediated G1/S accumulation of Tos4. These findings reveal a distinct replication stress response mediated by localized accumulation of RPA that allows the evasion of cell cycle arrest.
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Affiliation(s)
- Seong Min Kim
- Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Susan L Forsburg
- Corresponding author: Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90007, USA.
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17
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Fabry LAR, Triantafyllopoulou A. [The role of the response to DNA damage in granulomatous diseases]. Z Rheumatol 2022; 81:881-887. [PMID: 36006470 PMCID: PMC9732071 DOI: 10.1007/s00393-022-01260-y] [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] [Accepted: 07/20/2022] [Indexed: 12/14/2022]
Abstract
Granulomas are organized aggregates of immune cells, which are formed in response to a persistent stimulus and are found in various rheumatic diseases, including sarcoidosis, rheumatoid arthritis and granulomatosis with polyangiitis. The core of granulomas contains a multitude of different macrophage subtypes, including multinucleated macrophages and foam cells. The mechanisms which induce the formation of granulomas are not well understood; however, recent data show that the DNA damage response regulates granuloma macrophage differentiation.
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Affiliation(s)
- Lea A R Fabry
- Medizinische Klinik m.S. Rheumatologie und Klinische Immunologie, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland.
- Deutsches Rheuma Forschungszentrum, ein Institut der Leibniz Gemeinschaft, Berlin, Deutschland.
| | - Antigoni Triantafyllopoulou
- Medizinische Klinik m.S. Rheumatologie und Klinische Immunologie, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland.
- Deutsches Rheuma Forschungszentrum, ein Institut der Leibniz Gemeinschaft, Berlin, Deutschland.
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18
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Keller KM, Krausert S, Gopisetty A, Luedtke D, Koster J, Schubert NA, Rodríguez A, van Hooff SR, Stichel D, Dolman MEM, Vassal G, Pfister SM, Caron HN, Stancato LF, Molenaar JJ, Jäger N, Kool M. Target Actionability Review: a systematic evaluation of replication stress as a therapeutic target for paediatric solid malignancies. Eur J Cancer 2021; 162:107-117. [PMID: 34963094 DOI: 10.1016/j.ejca.2021.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Owing to the high numbers of paediatric cancer-related deaths, advances in therapeutic options for childhood cancer is a heavily studied field, especially over the past decade. Classical chemotherapy offers some therapeutic benefit but has proven long-term complications in survivors, and there is an urgent need to identify novel target-driven therapies. Replication stress is a major cause of genomic instability in cancer, triggering the stalling of the replication fork. Failure of molecular response by DNA damage checkpoints, DNA repair mechanisms and restarting the replication forks can exacerbate replication stress and initiate cell death pathways, thus presenting as a novel therapeutic target. To bridge the gap between preclinical evidence and clinical utility thereof, we apply the literature-driven systematic target actionability review methodology to published proof-of-concept (PoC) data related to the process of replication stress. METHODS A meticulous PubMed literature search was performed to gather replication stress-related articles (published between 2014 and 2021) across 16 different paediatric solid tumour types. Articles that fulfilled inclusion criteria were uploaded into the R2 informatics platform [r2.amc.nl] and assessed by critical appraisal. Key evidence based on nine pre-established PoC modules was summarised, and scores based on the quality and outcome of each study were assigned by two separate reviewers. Articles with discordant modules/scores were re-scored by a third independent reviewer, and a final consensus score was agreed upon by adjudication between all three reviewers. To visualise the final scores, an interactive heatmap summarising the evidence and scores associated with each PoC module across all, including paediatric tumour types, were generated. RESULTS AND CONCLUSIONS 145 publications related to targeting replication stress in paediatric tumours were systematically reviewed with an emphasis on DNA repair pathways and cell cycle checkpoint control. Although various targets in these pathways have been studied in these diseases to different extents, the results of this extensive literature search show that ATR, CHK1, PARP or WEE1 are the most promising targets using either single agents or in combination with chemotherapy or radiotherapy in neuroblastoma, osteosarcoma, high-grade glioma or medulloblastoma. Targeting these pathways in other paediatric malignancies may work as well, but here, the evidence was more limited. The evidence for other targets (such as ATM and DNA-PK) was also limited but showed promising results in some malignancies and requires more studies in other tumour types. Overall, we have created an extensive overview of targeting replication stress across 16 paediatric tumour types, which can be explored using the interactive heatmap on the R2 target actionability review platform [https://hgserver1.amc.nl/cgi-bin/r2/main.cgi?option=imi2_targetmap_v1].
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Affiliation(s)
- Kaylee M Keller
- Princess Máxima Center for Paediatric Oncology, Utrecht, the Netherlands
| | - Sonja Krausert
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Apurva Gopisetty
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dan Luedtke
- Eli Lilly and Company, Indianapolis, IN, USA
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Nil A Schubert
- Princess Máxima Center for Paediatric Oncology, Utrecht, the Netherlands
| | | | - Sander R van Hooff
- Princess Máxima Center for Paediatric Oncology, Utrecht, the Netherlands
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Emmy M Dolman
- Princess Máxima Center for Paediatric Oncology, Utrecht, the Netherlands; Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia; School of Women's and Children's Health, Faculty of Medicine, UNSW Sydney, NSW Australia
| | - Gilles Vassal
- Department of Clinical Research, Gustave Roussy, Villejuif, France
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | | | | | - Jan J Molenaar
- Princess Máxima Center for Paediatric Oncology, Utrecht, the Netherlands
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marcel Kool
- Princess Máxima Center for Paediatric Oncology, Utrecht, the Netherlands; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
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19
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McGrail DJ, Pilié PG, Dai H, Lam TNA, Liang Y, Voorwerk L, Kok M, Zhang XHF, Rosen JM, Heimberger AB, Peterson CB, Jonasch E, Lin SY. Replication stress response defects are associated with response to immune checkpoint blockade in nonhypermutated cancers. Sci Transl Med 2021; 13:eabe6201. [PMID: 34705519 DOI: 10.1126/scitranslmed.abe6201] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick G Pilié
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Truong Nguyen Anh Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yulong Liang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leonie Voorwerk
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Marleen Kok
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.,Department of Medical Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Xiang H-F Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy B Heimberger
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Christine B Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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20
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BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model. Proc Natl Acad Sci U S A 2021; 118:2108421118. [PMID: 34607954 PMCID: PMC8521688 DOI: 10.1073/pnas.2108421118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
BRCA1 germline mutations are associated with an increased risk of breast and ovarian cancer. Recent findings of others suggest that BRCA1 mutation carriers also bear an increased risk of esophageal and gastric cancer. Here, we employ a Brca1/Trp53 mouse model to show that unresolved replication stress (RS) in BRCA1 heterozygous cells drives esophageal tumorigenesis in a model of the human equivalent. This model employs 4-nitroquinoline-1-oxide (4NQO) as an RS-inducing agent. Upon drinking 4NQO-containing water, Brca1 heterozygous mice formed squamous cell carcinomas of the distal esophagus and forestomach at a much higher frequency and speed (∼90 to 120 d) than did wild-type (WT) mice, which remained largely tumor free. Their esophageal tissue, but not that of WT control mice, revealed evidence of overt RS as reflected by intracellular CHK1 phosphorylation and 53BP1 staining. These Brca1 mutant tumors also revealed higher genome mutation rates than those of control animals; the mutational signature SBS4, which is associated with tobacco-induced tumorigenesis; and a loss of Brca1 heterozygosity (LOH). This uniquely accelerated Brca1 tumor model is also relevant to human esophageal squamous cell carcinoma, an often lethal tumor.
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21
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Katheeja MN, Das SP, Laha S. The budding yeast protein Chl1p is required for delaying progression through G1/S phase after DNA damage. Cell Div 2021; 16:4. [PMID: 34493312 PMCID: PMC8424871 DOI: 10.1186/s13008-021-00072-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022] Open
Abstract
Background The budding yeast protein Chl1p is a nuclear protein required for sister-chromatid cohesion, transcriptional silencing, rDNA recombination, ageing and plays an instrumental role in chromatin remodeling. This helicase is known to preserve genome integrity and spindle length in S-phase. Here we show additional roles of Chl1p at G1/S phase of the cell cycle following DNA damage. Results G1 arrested cells when exposed to DNA damage are more sensitive and show bud emergence with faster kinetics in chl1 mutants compared to wild-type cells. Also, more damage to DNA is observed in chl1 cells. The viability falls synergistically in rad24chl1 cells. The regulation of Chl1p on budding kinetics in G1 phase falls in line with Rad9p/Chk1p and shows a synergistic effect with Rad24p/Rad53p. rad9chl1 and chk1chl1 shows similar bud emergence as the single mutants chl1, rad9 and chk1. Whereas rad24chl1 and rad53chl1 shows faster bud emergence compared to the single mutants rad24, rad53 and chl1. In presence of MMS induced damage, synergistic with Rad24p indicates Chl1p’s role as a checkpoint at G1/S acting parallel to damage checkpoint pathway. The faster movement of DNA content through G1/S phase and difference in phosphorylation profile of Rad53p in wild type and chl1 cells confirms the checkpoint defect in chl1 mutant cells. Further, we have also confirmed that the checkpoint defect functions in parallel to the damage checkpoint pathway of Rad24p. Conclusion Chl1p shows Rad53p independent bud emergence and Rad53p dependent checkpoint activity in presence of damage. This confirms its requirement in two different pathways to maintain the G1/S arrest when cells are exposed to damaging agents. The bud emergence kinetics and DNA segregation were similar to wild type when given the same damage in nocodazole treated chl1 cells which establishes the absence of any role of Chl1p at the G2/M phase. The novelty of this paper lies in revealing the versatile role of Chl1p in checkpoints as well as repair towards regulating G1/S transition. Chl1p thus regulates the G1/S phase by affecting the G1 replication checkpoint pathway and shows an additive effect with Rad24p for Rad53p activation when damaging agents perturb the DNA. Apart from checkpoint activation, it also regulates the budding kinetics as a repair gene. Supplementary Information The online version contains supplementary material available at 10.1186/s13008-021-00072-x.
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Affiliation(s)
- Muhseena N Katheeja
- Cell Biology and Molecular Genetics Division, Yenepoya Research Centre, Yenepoya Medical College, Yenepoya (Deemed To Be University), University Road, 3rd floor, Academic block, Deralakatte, Mangalore, 575018, India
| | - Shankar Prasad Das
- Cell Biology and Molecular Genetics Division, Yenepoya Research Centre, Yenepoya Medical College, Yenepoya (Deemed To Be University), University Road, 3rd floor, Academic block, Deralakatte, Mangalore, 575018, India. .,Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VII M, 700 054, Kolkata, India.
| | - Suparna Laha
- Cell Biology and Molecular Genetics Division, Yenepoya Research Centre, Yenepoya Medical College, Yenepoya (Deemed To Be University), University Road, 3rd floor, Academic block, Deralakatte, Mangalore, 575018, India. .,Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VII M, 700 054, Kolkata, India.
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22
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Gao M, Guo G, Huang J, Hou X, Ham H, Kim W, Zhao F, Tu X, Zhou Q, Zhang C, Zhu Q, Liu J, Yan Y, Xu Z, Yin P, Luo K, Weroha J, Deng M, Billadeau DD, Lou Z. DOCK7 protects against replication stress by promoting RPA stability on chromatin. Nucleic Acids Res 2021; 49:3322-3337. [PMID: 33704464 PMCID: PMC8034614 DOI: 10.1093/nar/gkab134] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/21/2021] [Accepted: 03/02/2021] [Indexed: 02/05/2023] Open
Abstract
RPA is a critical factor for DNA replication and replication stress response. Surprisingly, we found that chromatin RPA stability is tightly regulated. We report that the GDP/GTP exchange factor DOCK7 acts as a critical replication stress regulator to promote RPA stability on chromatin. DOCK7 is phosphorylated by ATR and then recruited by MDC1 to the chromatin and replication fork during replication stress. DOCK7-mediated Rac1/Cdc42 activation leads to the activation of PAK1, which subsequently phosphorylates RPA1 at S135 and T180 to stabilize chromatin-loaded RPA1 and ensure proper replication stress response. Moreover, DOCK7 is overexpressed in ovarian cancer and depleting DOCK7 sensitizes cancer cells to camptothecin. Taken together, our results highlight a novel role for DOCK7 in regulation of the replication stress response and highlight potential therapeutic targets to overcome chemoresistance in cancer.
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Affiliation(s)
- Ming Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinzhou Huang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaonan Hou
- Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hyoungjun Ham
- Department of Biochemistry and Molecular Biology, Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Fei Zhao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chao Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jiaqi Liu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuanliang Yan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhijie Xu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - John Weroha
- Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel D Billadeau
- Department of Biochemistry and Molecular Biology, Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
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23
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Pieretti JC, Gonçalves MC, Nakazato G, Santos de Souza AC, Boudier A, Seabra AB. Multifunctional hybrid nanoplatform based on Fe 3O 4@Ag NPs for nitric oxide delivery: development, characterization, therapeutic efficacy, and hemocompatibility. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2021; 32:23. [PMID: 33675446 PMCID: PMC7936955 DOI: 10.1007/s10856-021-06494-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/15/2021] [Indexed: 05/03/2023]
Abstract
The combination of Fe3O4@Ag superparamagnetic hybrid nanoparticles and nitric oxide (NO) represents an innovative strategy for a localized NO delivery with a simultaneous antibacterial and antitumoral actions. Here, we report the design of Fe3O4@Ag hybrid nanoparticles, coated with a modified and nitrosated chitosan polymer, able to release NO in a biological medium. After their synthesis, physicochemical characterization confirmed the obtention of small NO-functionalized superparamagnetic Fe3O4@Ag NPs. Antibacterial assays demonstrated enhanced effects compared to control. Bacteriostatic effect against Gram-positive strains and bactericidal effect against E. coli were demonstrated. Moreover, NO-functionalized Fe3O4@Ag NPs demonstrated improved ability to reduce cancer cells viability and less cytotoxicity against non-tumoral cells compared to Fe3O4@Ag NPs. These effects were associated to the ability of these NPs act simultaneous as cytotoxic (necrosis inductors) and cytostatic compounds inducing S-phase cell cycle arrest. NPs also demonstrated low hemolysis ratio (<10%) at ideal work range, evidencing their potential for biomedical applications. Targeted and hemocompatible nitric oxide-releasing multi-functional hybrid nanoparticles for antitumor and antimicrobial applications.
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Affiliation(s)
- Joana Claudio Pieretti
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil
| | | | - Gerson Nakazato
- Department of Microbiology, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | | | - Ariane Boudier
- Université de Lorraine, CITHEFOR, F-54000, Nancy, France
| | - Amedea Barozzi Seabra
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo André, SP, Brazil.
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24
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Srivastava V, Wani MY, Al-Bogami AS, Ahmad A. Piperidine based 1,2,3-triazolylacetamide derivatives induce cell cycle arrest and apoptotic cell death in Candida auris. J Adv Res 2020; 29:121-135. [PMID: 33842010 PMCID: PMC8020347 DOI: 10.1016/j.jare.2020.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/18/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022] Open
Abstract
Introduction: The fungal pathogen Candida auris, is a serious threat to public health and is associated with bloodstream infections causing high mortality particularly in patients with serious medical problems. As this pathogen is generally resistant to all the available classes of antifungals, there is a constant demand for novel antifungal drugs with new mechanisms of antifungal action. Objective: Therefore, in this study we synthesised six novel piperidine based 1,2,3-triazolylacetamide derivatives (pta1-pta6) and tested their antifungal activity and mechanism of action against clinical C. auris isolates. Methods: Antifungal susceptibility testing was done to estimate MIC values of piperidine derivatives following CLSI recommended guidelines. MUSE Cell Analyzer was used to check cell viability and cell cycle arrest in C. auris after exposure to piperidine derivatives using different kits. Additionally, fluorescence microscopy was done to check the effect of test compound on C. auris membrane integrity and related apoptotic assays were performed to confirm cellular apoptosis using different apoptosis markers. Results: Out of the six derivatives; pta1, pta2 and pta3 showed highest active with MIC values from 0.24 to 0.97 μg/mL and MFC ranging from 0.97 to 3.9 μg/mL. Fungicidal behaviour of these compounds was confirmed by cell count and viability assay. Exposure to test compounds at sub-inhibitory and inhibitory concentrations resulted in disruption of C. auris plasma membrane. Further in-depth studies showed that these derivatives were able to induce apoptosis and cell cycle arrest in S-phase. Furthermore, the compounds demonstrated lower toxicity profile. Conclusion: Present study suggests that the novel derivatives (pta1-pta3) induce apoptotic cell death and cell cycle arrest in C. auris and could be potential candidates against C. auris infections.
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Affiliation(s)
- Vartika Srivastava
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Mohmmad Younus Wani
- University of Jeddah, College of Science, Department of Chemistry, Jeddah 21589, Saudi Arabia
| | - Abdullah Saad Al-Bogami
- University of Jeddah, College of Science, Department of Chemistry, Jeddah 21589, Saudi Arabia
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Infection Control Unit, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg 2193, South Africa
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25
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Faca VM, Sanford EJ, Tieu J, Comstock W, Gupta S, Marshall S, Yu H, Smolka MB. Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. Sci Rep 2020; 10:18056. [PMID: 33093574 PMCID: PMC7582137 DOI: 10.1038/s41598-020-74939-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
The maintenance of genomic stability relies on DNA damage sensor kinases that detect DNA lesions and phosphorylate an extensive network of substrates. The Mec1/ATR kinase is one of the primary sensor kinases responsible for orchestrating DNA damage responses. Despite the importance of Mec1/ATR, the current network of its identified substrates remains incomplete due, in part, to limitations in mass spectrometry-based quantitative phosphoproteomics. Phosphoproteomics suffers from lack of redundancy and statistical power for generating high confidence datasets, since information about phosphopeptide identity, site-localization, and quantitation must often be gleaned from a single peptide-spectrum match (PSM). Here we carefully analyzed the isotope label swapping strategy for phosphoproteomics, using data consistency among reciprocal labeling experiments as a central filtering rule for maximizing phosphopeptide identification and quantitation. We demonstrate that the approach allows drastic reduction of false positive quantitations and identifications even from phosphopeptides with a low number of spectral matches. Application of this approach identifies new Mec1/ATR-dependent signaling events, expanding our understanding of the DNA damage signaling network. Overall, the proposed quantitative phosphoproteomic approach should be generally applicable for investigating kinase signaling networks with high confidence and depth.
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Affiliation(s)
- Vitor Marcel Faca
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Biochemistry and Immunology and Cell-Based Therapy Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, 14049-900, Brazil
| | - Ethan J Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jennifer Tieu
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - William Comstock
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Shagun Gupta
- Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Shannon Marshall
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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26
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Ren X, Jiang K, Zhang F. The Multifaceted Roles of RCC1 in Tumorigenesis. Front Mol Biosci 2020; 7:225. [PMID: 33102517 PMCID: PMC7522611 DOI: 10.3389/fmolb.2020.00225] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/11/2020] [Indexed: 01/31/2023] Open
Abstract
RCC1 (regulator of chromosome condensation 1) is the only known guanine nucleotide exchange factor of Ran, a nuclear Ras-like G protein. RCC1 combines with chromatin and Ran to establish a concentration gradient of RanGTP, thereby participating in a series of cell physiological activities. In this review, we discuss the structure of RCC1 and describe how RCC1 affects the formation and function of the nuclear envelope, spindle formation, and nuclear transport. We mainly focus on the effect of RCC1 on the cell cycle during tumorigenesis and the recent research progress that has been made in relation to different tumor types.
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Affiliation(s)
- Xuanqi Ren
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Kai Jiang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Feng Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
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27
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Sarkar R, Patra U, Lo M, Mukherjee A, Biswas A, Chawla-Sarkar M. Rotavirus activates a noncanonical ATM-Chk2 branch of DNA damage response during infection to positively regulate viroplasm dynamics. Cell Microbiol 2020; 22:e13149. [PMID: 31845505 DOI: 10.1111/cmi.13149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022]
Abstract
Surveillance for maintaining genomic pristineness, a protective safeguard of great onco-preventive significance, has been dedicated in eukaryotic cells to a highly conserved and synchronised signalling cascade called DNA damage response (DDR). Not surprisingly, foreign genetic elements like those of viruses are often potential targets of DDR. Viruses have evolved novel ways to subvert this genome vigilance by twisting canonical DDR to a skewed, noncanonical response through selective hijacking of some DDR components while antagonising the others. Though reported for many DNA and a few RNA viruses, potential implications of DDR have not been addressed yet in case of infection with rotavirus (RV), a double-stranded RNA virus. In the present study, we aimed at the modulation of ataxia telangiectasia mutated (ATM)-checkpoint kinase 2 (Chk2) branch of DDR in response to RV infection in vitro. We found activation of the transducer kinase ATM and its downstream effector Chk2 in RV-SA11-infected cells, the activation response being maximal at 6-hr post infection. Moreover, ATM activation was found to be dependent on induction of the upstream sensor Mre11-Rad50-Nbs1 (MRN) complex. Interestingly, RV-SA11-mediated maximal induction of ATM-Chk2 pathway was revealed to be neither preceded by occurrence of nuclear DNA damage nor transduced to formation of damage-induced canonical nuclear foci. Subsequent investigations affirmed sequestration of MRN components as well as ATM-Chk2 proteins away from nucleus into cytosolic RV replication factories (viroplasms). Chemical intervention targeting ATM and Chk2 significantly inhibited fusion and maturation of viroplasms leading to attenuated viral propagation. Cumulatively, the current study describes RV-mediated activation of a noncanonical ATM-Chk2 branch of DDR skewed in favour of facilitated viroplasm fusion and productive viral perpetuation.
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Affiliation(s)
- Rakesh Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Mahadeb Lo
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Asim Biswas
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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28
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Posttranscriptional control of the replication stress response via TTP-mediated Claspin mRNA stabilization. Oncogene 2020; 39:3245-3257. [PMID: 32086441 DOI: 10.1038/s41388-020-1220-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 11/08/2022]
Abstract
ATR and CHK1 play key roles in the protection and recovery of the stalled replication forks. Claspin, an adaptor for CHK1 activation, is essential for DNA damage signaling and efficient replication fork progression. Here, we show that tristetraprolin (TTP), an mRNA-binding protein, can modulate the replication stress response via stabilization of Claspin mRNA. TTP depletion compromised specifically in the phosphorylation of CHK1, but not p53 or H2AX among other ATR substrates, and produced CHK1-defective replication phenotypes including accumulation of stalled replication forks. Importantly, the expression of siRNA-resistant TTP in TTP-deficient cells restored CHK1 phosphorylation and reduced the number of stalled replication forks as close to the control cells. Besides, we found that TTP was required for efficient replication fork progression even in the absence of exogenous DNA damage in a Claspin-dependent manner. Mechanistically, TTP was able to bind to the 3'-untranslated region of Claspin mRNA to increase the stability of Claspin mRNA which eventually contributed to the subsequent ATR-CHK1 activation upon DNA damage. Taken together, our results revealed an intimate link between TTP-dependent Claspin mRNA stability and ATR-CHK1-dependent replication fork stability to maintain replication fork integrity and chromosomal stability.
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29
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Li X. Epigenetics and cell cycle regulation in cystogenesis. Cell Signal 2019; 68:109509. [PMID: 31874209 DOI: 10.1016/j.cellsig.2019.109509] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022]
Abstract
The role of genetic mutations in the development of polycystic kidney disease (PKD), such as alterations in PKD1 and PKD2 genes in autosomal dominant PKD (ADPKD), is well understood. However, the significance of epigenetic mechanisms in the progression of PKD remains unclear and is increasingly being investigated. The term of epigenetics describes a range of mechanisms in genome function that do not solely result from the DNA sequence itself. Epigenetic information can be inherited during mammalian cell division to sustain phenotype specifically and physiologically responsive gene expression in the progeny cells. A multitude of functional studies of epigenetic modifiers and systematic genome-wide mapping of epigenetic marks reveal the importance of epigenomic mechanisms, including DNA methylation, histone/chromatin modifications and non-coding RNAs, in PKD pathologies. Deregulated proliferation is a characteristic feature of cystic renal epithelial cells. Moreover, defects in many of the molecules that regulate the cell cycle have been implicated in cyst formation and progression. Recent evidence suggests that alterations of DNA methylation and histone modifications on specific genes and the whole genome involved in cell cycle regulation and contribute to the pathogenesis of PKD. This review summarizes the recent advances of epigenetic mechanisms in PKD, which helps us to define the term of "PKD epigenetics" and group PKD epigenetic changes in three categories. In particularly, this review focuses on the interplay of epigenetic mechanisms with cell cycle regulation during normal cell cycle progression and cystic cell proliferation, and discusses the potential to detect and quantify DNA methylation from body fluids as diagnostic/prognostic biomarkers. Collectively, this review provides concepts and examples of epigenetics in cell cycle regulation to reveal a broad view of different aspects of epigenetics in biology and PKD, which may facilitate to identify possible novel therapeutic intervention points and to explore epigenetic biomarkers in PKD.
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Affiliation(s)
- Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States of America; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, United States of America.
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30
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Meng Y, Liu C, Shen L, Zhou M, Liu W, Kowolik C, Campbell JL, Zheng L, Shen B. TRAF6 mediates human DNA2 polyubiquitination and nuclear localization to maintain nuclear genome integrity. Nucleic Acids Res 2019; 47:7564-7579. [PMID: 31216032 PMCID: PMC6698806 DOI: 10.1093/nar/gkz537] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 12/14/2022] Open
Abstract
The multifunctional human DNA2 (hDNA2) nuclease/helicase is required to process DNA ends for homology-directed recombination repair (HDR) and to counteract replication stress. To participate in these processes, hDNA2 must localize to the nucleus and be recruited to the replication or repair sites. However, because hDNA2 lacks the nuclear localization signal that is found in its yeast homolog, it is unclear how its migration into the nucleus is regulated during replication or in response to DNA damage. Here, we report that the E3 ligase TRAF6 binds to and mediates the K63-linked polyubiquitination of hDNA2, increasing the stability of hDNA2 and promoting its nuclear localization. Inhibiting TRAF6-mediated polyubiquitination abolishes the nuclear localization of hDNA2, consequently impairing DNA end resection and HDR. Thus, the current study reveals a mechanism for the regulation of hDNA2 localization and establishes that TRAF6-mediated hDNA2 ubiquitination activates DNA repair pathways to maintain nuclear genome integrity.
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Affiliation(s)
- Yuan Meng
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China.,Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Changwei Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Wenpeng Liu
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China.,Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Claudia Kowolik
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Judith L Campbell
- Division of Chemistry and Chemical Engineering, Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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31
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McGrail DJ, Lin CCJ, Dai H, Mo W, Li Y, Stephan C, Davies P, Lu Z, Mills GB, Lee JS, Lin SY. Defective Replication Stress Response Is Inherently Linked to the Cancer Stem Cell Phenotype. Cell Rep 2019; 23:2095-2106. [PMID: 29768207 DOI: 10.1016/j.celrep.2018.04.068] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 01/04/2018] [Accepted: 02/12/2018] [Indexed: 01/05/2023] Open
Abstract
Extensive spontaneous DNA damage from oncogene-induced replication stress is ubiquitous in precancerous lesions. While this damage induces differentiation, senescence, or apoptosis in normal cells, defects in DNA replication stress response (RSR) allow cells to continue proliferating, ultimately leading to early tumorigenesis. Using systems-level approaches, we developed a replication stress response defect gene signature that predicted risk of cancer development from hyperplastic lesions. Intriguingly, we found that replication stress response defects rewire non-malignant cells into a cancer stem cell (CSC)-like state, and analysis of CSCs indicated that they inherently harbor replication stress response defects. High-throughput drug screening to elucidate molecules required for survival of replication stress response defective cells identified a dependence on MEK/ERK signaling. Inhibition of this signaling cascade restored oncogene-induced senescence through a p53-independent MDM2/p21 axis. Moreover, MEK/ERK inhibition also depleted CSC populations. Together, these findings provide insights into the role of replication stress response defects in CSCs and an actionable pathway for therapeutic targeting.
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Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Curtis Chun-Jen Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Mo
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Clifford Stephan
- The Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Peter Davies
- The Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Zhimin Lu
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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32
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Kim W, Zhao F, Wu R, Qin S, Nowsheen S, Huang J, Zhou Q, Chen Y, Deng M, Guo G, Luo K, Lou Z, Yuan J. ZFP161 regulates replication fork stability and maintenance of genomic stability by recruiting the ATR/ATRIP complex. Nat Commun 2019; 10:5304. [PMID: 31757956 PMCID: PMC6876566 DOI: 10.1038/s41467-019-13321-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/23/2019] [Indexed: 12/03/2022] Open
Abstract
DNA replication stress-mediated activation of the ATR kinase pathway is important for maintaining genomic stability. In this study, we identified a zinc finger protein, ZFP161 that functions as a replication stress response factor in ATR activation. Mechanistically, ZFP161 acts as a scaffolding protein to facilitate the interaction between RPA and ATR/ATRIP. ZFP161 binds to RPA and ATR/ATRIP through distinct regions and stabilizes the RPA–ATR–ATRIP complex at stalled replication forks. This function of ZFP161 is important to the ATR signaling cascade and genome stability maintenance. In addition, ZFP161 knockout mice showed a defect in ATR activation and genomic instability. Furthermore, low expression of ZFP161 is associated with higher cancer risk and chromosomal instability. Overall, these findings suggest that ZFP161 coordinates ATR/Chk1 pathway activation and helps maintain genomic stability. The ATR pathway is active during DNA replication stress to maintain genome stability. Here the authors reveal the role of the zinc finger containing protein 161 (ZFP161) to facilitate replication fork stability by acting as a scaffold to facilitate the interaction between RPA and ATR/ATRIP.
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Affiliation(s)
- Wootae Kim
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fei Zhao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rentian Wu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sisi Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Somaira Nowsheen
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.,Mayo Clinic Medical Scientist Training Program, Mayo Clinic Alix School Of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qin Zhou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China.,Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China
| | - Min Deng
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guijie Guo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kuntian Luo
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA. .,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China. .,Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai, 200120, China.
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33
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Mutation in DNA Polymerase Beta Causes Spontaneous Chromosomal Instability and Inflammation-Associated Carcinogenesis in Mice. Cancers (Basel) 2019; 11:cancers11081160. [PMID: 31412651 PMCID: PMC6721533 DOI: 10.3390/cancers11081160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
DNA polymerase beta (Pol β) is a key enzyme in the base excision repair (BER) pathway. Pol β is mutated in approximately 40% of human tumors in small-scale studies. The 5´-deoxyribose-5-phosphate (dRP) lyase domain of Pol β is responsible for DNA end tailoring to remove the 5’ phosphate group. We previously reported that the dRP lyase activity of Pol β is critical to maintain DNA replication fork stability and prevent cellular transformation. In this study, we tested the hypothesis that the human gastric cancer associated variant of Pol β (L22P) has the ability to promote spontaneous chromosomal instability and carcinogenesis in mice. We constructed a Pol β L22P conditional knock-in mouse model and found that L22P enhances hyperproliferation and DNA double strand breaks (DSBs) in stomach cells. Moreover, mouse embryonic fibroblasts (MEFs) derived from L22P mice frequently induce abnormal numbers of chromosomes and centrosome amplification, leading to chromosome segregation errors. Importantly, L22P mice exhibit chronic inflammation accompanied by stomach tumors. These data demonstrate that the human cancer-associated variant of Pol β can contribute to chromosomal instability and cancer development.
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34
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Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst) 2019; 79:40-49. [PMID: 31102970 PMCID: PMC6570417 DOI: 10.1016/j.dnarep.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/20/2019] [Accepted: 05/04/2019] [Indexed: 12/31/2022]
Abstract
In response to the threat of DNA damage, cells exhibit a dramatic and multi-factorial response spanning from transcriptional changes to protein modifications, collectively known as the DNA damage response (DDR). Here, we review the literature surrounding the transcriptional response to DNA damage. We review differences in observed transcriptional responses as a function of cell cycle stage and emphasize the importance of experimental design in these transcriptional response studies. We additionally consider topics including structural challenges in the transcriptional response to DNA damage as well as the connection between transcription and protein abundance.
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Affiliation(s)
- Erica Silva
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA.
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA; Program in Bioinformatics, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
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35
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In yeast cells arrested at the early S-phase by hydroxyurea, rRNA gene promoters and chromatin are poised for transcription while rRNA synthesis is compromised. Mutat Res 2019; 815:20-29. [PMID: 31063901 DOI: 10.1016/j.mrfmmm.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/25/2019] [Accepted: 04/23/2019] [Indexed: 11/19/2022]
Abstract
Hydroxyurea (HU) is an inhibitor of ribonucleotide reductase that is used as a chemotherapeutic agent to treat a number of chronic diseases. Addition of HU to cell cultures causes reduction of the dNTP cellular pool below levels that are required for DNA replication. This trigger dividing cells to arrest in early S-phase of the cell cycle. Cell division hinges on ribosome biogenesis, which is tightly regulated by rRNA synthesis. Remarkably, HU represses the expression of some genes the products of which are required for rRNA maturation. To gain more information on the cellular response to HU, we employed the yeast Saccharomyces cerevisiae as model organism and analyzed the changing aspects of closed to open forms of rRNA gene chromatin during cell cycle arrest, the arrangement of RNA polymerase-I (RNAPI) on the open genes, the presence of RNAPI transcription-factors, transcription and rRNA maturation. The rRNA gene chromatin structure was analyzed by psoralen crosslinking and the distribution of RNAPI was investigated by chromatin endogenous cleavage. In HU arrested cells nearly all rRNA genes were in the open form of chromatin, but only a portion of them was engaged with RNAPI. Analyses by chromatin immuno-precipitation confirmed that the overall formation of transcription pre-initiation complexes remained unchanged, suggesting that the onset of rRNA gene activation was not significantly affected by HU. Moreover, the in vitro transcription run-on assay indicated that RNAPI retained most of its transcription elongation activity. However, in HU treated cells, we found that: (1) RNAPI accumulated next to the 5'-end of rRNA genes; (2) considerably less rRNA filaments were observed in electron micrographs of rDNA transcription units; and (3) rRNA maturation was compromised. It is established that HU inhibition of ribonucleotide reductase holds back DNA replication. This study indicates a hitherto unexplored cellular response to HU, namely altered rRNA synthesis, which could participate to hamper cell division.
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36
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Zhang T, Zhang Z, Shengzhao G, Li X, Liu H, Zhao Y. Strand break-induced replication fork collapse leads to C-circles, C-overhangs and telomeric recombination. PLoS Genet 2019; 15:e1007925. [PMID: 30716077 PMCID: PMC6382176 DOI: 10.1371/journal.pgen.1007925] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 02/20/2019] [Accepted: 01/01/2019] [Indexed: 12/16/2022] Open
Abstract
Telomerase-independent ALT (alternative lengthening of telomeres) cells are characterized by high frequency of telomeric homologous recombination (HR), C-rich extrachromosomal circles (C-circles) and C-rich terminal 5' overhangs (C-overhangs). However, underlying mechanism is poorly understood. Here, we show that both C-circle and C-overhang form when replication fork collapse is induced by strand break at telomeres. We find that endogenous DNA break predominantly occur on C-rich strand of telomeres in ALT cells, resulting in high frequency of replication fork collapse. While collapsed forks could be rescued by replication fork regression leading to telomeric homologous recombination, those unresolved are converted to C-circles and C-overhang at lagging and leading synthesized strand, respectively. Meanwhile, multiple hallmarks of ALT are provoked, suggesting that strand break-induced replication stress underlies ALT. These findings provide a molecular basis underlying telomeric HR and biogenesis of C-circle and C-overhang, thus implicating the specific mechanism to resolve strand break-induced replication defect at telomeres in ALT cells. 10 to 15% human cancers utilize telomerase-independent alternative lengthening of telomeres (ALT) to maintain their telomere length. Unexpectedly, we find that endogenous C-strand breaks predominantly exist in telomeres of ALT cells, which induce high frequency of replication fork collapse. While collapsed fork triggers fork regression machinery to restart the replication, leading to telomeric homologous recombination; those unresolved are converted to C-circle and C-overhang. These findings suggest that the formation of C-circle and C-overhang represents a unique manner for ALT cells to prevent chromosome instability induced by replication defect at telomeres. Moreover, multiple hallmarks of ALT are provoked during this process, demonstrating that DNA strand break at telomeres underlies ALT mechanism.
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Affiliation(s)
- Tianpeng Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zepeng Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Gong Shengzhao
- School of Chemical Engineering and Technology, Guangdong Engineering Technical Research Center for Green Household Chemicals, Guangdong Industry Technical College, Guangzhou, P.R.China
| | - Xiaocui Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
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37
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Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis. Sci Rep 2018; 8:7324. [PMID: 29743621 PMCID: PMC5943353 DOI: 10.1038/s41598-018-25530-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/24/2018] [Indexed: 12/05/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are frequently dysregulated in many human cancers. We sought to identify candidate oncogenic lncRNAs in human colon tumors by utilizing RNA sequencing data from 22 colon tumors and 22 adjacent normal colon samples from The Cancer Genome Atlas (TCGA). The analysis led to the identification of ~200 differentially expressed lncRNAs. Validation in an independent cohort of normal colon and patient-derived colon cancer cell lines identified a novel lncRNA, lincDUSP, as a potential candidate oncogene. Knockdown of lincDUSP in patient-derived colon tumor cell lines resulted in significantly decreased cell proliferation and clonogenic potential, and increased susceptibility to apoptosis. The knockdown of lincDUSP affects the expression of ~800 genes, and NCI pathway analysis showed enrichment of DNA damage response and cell cycle control pathways. Further, identification of lincDUSP chromatin occupancy sites by ChIRP-Seq demonstrated association with genes involved in the replication-associated DNA damage response and cell cycle control. Consistent with these findings, lincDUSP knockdown in colon tumor cell lines increased both the accumulation of cells in early S-phase and γH2AX foci formation, indicating increased DNA damage response induction. Taken together, these results demonstrate a key role of lincDUSP in the regulation of important pathways in colon cancer.
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38
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Flach J, Milyavsky M. Replication stress in hematopoietic stem cells in mouse and man. Mutat Res 2018; 808:74-82. [PMID: 29079268 DOI: 10.1016/j.mrfmmm.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 08/31/2017] [Accepted: 10/12/2017] [Indexed: 04/14/2023]
Abstract
Life-long blood regeneration relies on a rare population of self-renewing hematopoietic stem cells (HSCs). These cells' nearly unlimited self-renewal potential and lifetime persistence in the body signifies the need for tight control of their genome integrity. Their quiescent state, tightly linked with low metabolic activity, is one of the main strategies employed by HSCs to preserve an intact genome. On the other hand, HSCs need to be able to quickly respond to increased blood demands and rapidly increase their cellular output in order to fight infection-associated inflammation or extensive blood loss. This increase in proliferation rate, however, comes at the price of exposing HSCs to DNA damage inevitably associated with the process of DNA replication. Any interference with normal replication fork progression leads to a specialized molecular response termed replication stress (RS). Importantly, increased levels of RS are a hallmark feature of aged HSCs, where an accumulating body of evidence points to causative relationships between RS and the aging-associated impairment of the blood system's functional capacity. In this review, we present an overview of RS in HSCs focusing on its causes and consequences for the blood system of mice and men.
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Affiliation(s)
- Johanna Flach
- Department of Hematology and Medical Oncology & Institute of Molecular Oncology, University Medical Center Goettingen, Germany; Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Mannheim, Germany.
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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39
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Pai GM, Zielinski A, Koalick D, Ludwig K, Wang ZQ, Borgmann K, Pospiech H, Rubio I. TSC loss distorts DNA replication programme and sensitises cells to genotoxic stress. Oncotarget 2018; 7:85365-85380. [PMID: 27863419 PMCID: PMC5356742 DOI: 10.18632/oncotarget.13378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 10/26/2016] [Indexed: 01/14/2023] Open
Abstract
Tuberous Sclerosis (TSC) is characterized by exorbitant mTORC1 signalling and manifests as non-malignant, apoptosis-prone neoplasia. Previous reports have shown that TSC-/- cells are highly susceptible to mild, innocuous doses of genotoxic stress, which drive TSC-/- cells into apoptotic death. It has been argued that this hypersensitivity to stress derives from a metabolic/energetic shortfall in TSC-/- cells, but how metabolic dysregulation affects the DNA damage response and cell cycle alterations in TSC-/- cells exposed to genotoxic stress is not understood. We report here the occurrence of futile checkpoint responses and an unusual type of replicative stress (RS) in TSC1-/- fibroblasts exposed to low-dose genotoxins. This RS is characterized by elevated nucleotide incorporation rates despite only modest origin over-firing. Strikingly, an increased propensity for asymmetric fork progression and profuse chromosomal aberrations upon mild DNA damage confirmed that TSC loss indeed proved detrimental to stress adaptation. We conclude that low stress tolerance of TSC-/- cells manifests at the level of DNA replication control, imposing strong negative selection on genomic instability that could in turn detain TSC-mutant tumours benign.
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Affiliation(s)
- Govind M Pai
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, University Hospital, 07745 Jena, Germany
| | - Alexandra Zielinski
- Laboratory of Radiobiology & Experimental Radiooncology, Department of Radiotherapy and Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, Germany, 20246 Hamburg, Germany
| | - Dennis Koalick
- Leibniz Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Kristin Ludwig
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, University Hospital, 07745 Jena, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Kerstin Borgmann
- Laboratory of Radiobiology & Experimental Radiooncology, Department of Radiotherapy and Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, Germany, 20246 Hamburg, Germany
| | - Helmut Pospiech
- Leibniz Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Ignacio Rubio
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, University Hospital, 07745 Jena, Germany
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40
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Pietrobono S, Santini R, Gagliardi S, Dapporto F, Colecchia D, Chiariello M, Leone C, Valoti M, Manetti F, Petricci E, Taddei M, Stecca B. Targeted inhibition of Hedgehog-GLI signaling by novel acylguanidine derivatives inhibits melanoma cell growth by inducing replication stress and mitotic catastrophe. Cell Death Dis 2018; 9:142. [PMID: 29396391 PMCID: PMC5833413 DOI: 10.1038/s41419-017-0142-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022]
Abstract
Aberrant activation of the Hedgehog (HH) signaling is a critical driver in tumorigenesis. The Smoothened (SMO) receptor is one of the major upstream transducers of the HH pathway and a target for the development of anticancer agents. The SMO inhibitor Vismodegib (GDC-0449/Erivedge) has been approved for treatment of basal cell carcinoma. However, the emergence of resistance during Vismodegib treatment and the occurrence of numerous side effects limit its use. Our group has recently discovered and developed novel and potent SMO inhibitors based on acylguanidine or acylthiourea scaffolds. Here, we show that the two acylguanidine analogs, compound (1) and its novel fluoride derivative (2), strongly reduce growth and self-renewal of melanoma cells, inhibiting the level of the HH signaling target GLI1 in a dose-dependent manner. Both compounds induce apoptosis and DNA damage through the ATR/CHK1 axis. Mechanistically, they prevent G2 to M cell cycle transition, and induce signs of mitotic aberrations ultimately leading to mitotic catastrophe. In a melanoma xenograft mouse model, systemic treatment with 1 produced a remarkable inhibition of tumor growth without body weight loss in mice. Our data highlight a novel route for cell death induction by SMO inhibitors and support their use in therapeutic approaches for melanoma and, possibly, other types of cancer with active HH signaling.
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Affiliation(s)
| | - Roberta Santini
- Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy
| | | | - Francesca Dapporto
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica and Core Research Laboratory, Istituto Toscano Tumori, AOU Senese, Siena, Italy
| | - David Colecchia
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica and Core Research Laboratory, Istituto Toscano Tumori, AOU Senese, Siena, Italy
| | - Mario Chiariello
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica and Core Research Laboratory, Istituto Toscano Tumori, AOU Senese, Siena, Italy
| | - Cosima Leone
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Massimo Valoti
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Elena Petricci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Maurizio Taddei
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Barbara Stecca
- Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy. .,Department of Oncology, Careggi University Hospital, Florence, Italy.
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41
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Wright DJ, Day FR, Kerrison ND, Zink F, Cardona A, Sulem P, Thompson DJ, Sigurjonsdottir S, Gudbjartsson DF, Helgason A, Chapman JR, Jackson SP, Langenberg C, Wareham NJ, Scott RA, Thorsteindottir U, Ong KK, Stefansson K, Perry JR. Genetic variants associated with mosaic Y chromosome loss highlight cell cycle genes and overlap with cancer susceptibility. Nat Genet 2017; 49:674-679. [PMID: 28346444 PMCID: PMC5973269 DOI: 10.1038/ng.3821] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/26/2017] [Indexed: 12/14/2022]
Abstract
The Y chromosome is frequently lost in hematopoietic cells, which represents the most common somatic alteration in men. However, the mechanisms that regulate mosaic loss of chromosome Y (mLOY), and its clinical relevance, are unknown. We used genotype-array-intensity data and sequence reads from 85,542 men to identify 19 genomic regions (P < 5 × 10-8) that are associated with mLOY. Cumulatively, these loci also predicted X chromosome loss in women (n = 96,123; P = 4 × 10-6). Additional epigenome-wide methylation analyses using whole blood highlighted 36 differentially methylated sites associated with mLOY. The genes identified converge on aspects of cell proliferation and cell cycle regulation, including DNA synthesis (NPAT), DNA damage response (ATM), mitosis (PMF1, CENPN and MAD1L1) and apoptosis (TP53). We highlight the shared genetic architecture between mLOY and cancer susceptibility, in addition to inferring a causal effect of smoking on mLOY. Collectively, our results demonstrate that genotype-array-intensity data enables a measure of cell cycle efficiency at population scale and identifies genes implicated in aneuploidy, genome instability and cancer susceptibility.
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Affiliation(s)
- Daniel J. Wright
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Felix R. Day
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Nicola D. Kerrison
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Florian Zink
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
| | - Alexia Cardona
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Patrick Sulem
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
| | - Deborah J. Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | | | | | - J. Ross Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Steve P. Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Robert A. Scott
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Unnur Thorsteindottir
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Ken K. Ong
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., IS-101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - John R.B. Perry
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
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42
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An H, Yang L, Wang C, Gan Z, Gu H, Zhang T, Huang X, Liu Y, Li Y, Chang SJ, Lai J, Li YB, Chen S, Sun FL. Interactome Analysis Reveals a Novel Role for RAD6 in the Regulation of Proteasome Activity and Localization in Response to DNA Damage. Mol Cell Biol 2017; 37:e00419-16. [PMID: 28031328 PMCID: PMC5335506 DOI: 10.1128/mcb.00419-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/01/2016] [Accepted: 12/04/2016] [Indexed: 01/25/2023] Open
Abstract
RAD6, an E2 ubiquitin-conjugating enzyme, is a key node for determining different DNA damage repair pathways, controlling both the error-prone and the error-free DNA damage repair pathways through differential regulation of the ubiquitination of the proliferating cell nuclear antigen (PCNA) protein. However, whether other pathways are involved in the RAD6-mediated regulation of DNA damage repair is still unclear. To deeply understand the molecular mechanisms of RAD6 in DNA damage repair, we performed a proteomic analysis and identified the changes of the protein-protein interaction (PPI) networks of RAD6 before and after X-ray irradiation. Furthermore, our study indicated that a proteasome-related event is likely involved in the DNA damage repair process. Moreover, we found that RAD6 promotes proteasome activity and nuclear translocation by enhancing the degradation of PSMF1 and the lamin B receptor (LBR). Therefore, we provide a novel pathway that is employed by RAD6 in response to DNA damage.
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Affiliation(s)
- Hongli An
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Lu Yang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Chen Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Zhixue Gan
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Haihui Gu
- Department of Transfusion Medicine, Changhai Hospital, Second Military Medical University, Shanghai, Shanghai, People's Republic of China
| | - Tao Zhang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Xin Huang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Yan Liu
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Yufeng Li
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Shing-Jyh Chang
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan, Republic of China
| | - Jianghua Lai
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Ya-Bin Li
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Su Chen
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
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43
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Dass Singh M, Thomas P, Hor M, Almond T, Owens J, Hague W, Fenech M. Infant birth outcomes are associated with DNA damage biomarkers as measured by the cytokinesis block micronucleus cytome assay: the DADHI study. Mutagenesis 2017; 32:355-370. [DOI: 10.1093/mutage/gex001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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44
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Cellular responses to replication stress: Implications in cancer biology and therapy. DNA Repair (Amst) 2016; 49:9-20. [PMID: 27908669 DOI: 10.1016/j.dnarep.2016.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022]
Abstract
DNA replication is essential for cell proliferation. Any obstacles during replication cause replication stress, which may lead to genomic instability and cancer formation. In this review, we summarize the physiological DNA replication process and the normal cellular response to replication stress. We also outline specialized therapies in clinical trials based on current knowledge and future perspectives in the field.
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45
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Wang P, Zhang H, Hou H, Wang Q, Li Y, Huang Y, Xie L, Gao F, He S, Li L. Cell cycle arrest induced by inhibitors of epigenetic modifications in maize (Zea mays) seedling leaves: characterization of the process and possible mechanisms involved. THE NEW PHYTOLOGIST 2016; 211:646-657. [PMID: 27040740 DOI: 10.1111/nph.13942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/20/2016] [Indexed: 06/05/2023]
Abstract
Epigenetic modifications play crucial roles in the regulation of chromatin architecture and are involved in cell cycle progression, including mitosis and meiosis. To explore the relationship between epigenetic modifications and the cell cycle, we treated maize (Zea mays) seedlings with six different epigenetic modification-related inhibitors and identified the postsynthetic phase (G2 ) arrest via flow cytometry analysis. Total H4K5ac levels were significantly increased and the distribution of H3S10ph signalling was obviously changed in mitosis under various treatments. Further statistics of the cells in different periods of mitosis confirmed that the cell cycle was arrested at preprophase. Concentrations of hydrogen peroxide were relatively higher in the treated plants and the antioxidant thiourea could negate the influence of the inhibitors. Moreover, all of the treated plants displayed negative results in the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labelling (TUNEL) and γ-H2AX immunostaining assays after exposure for 3 d. Additionally, the expression level of topoisomerase genes in the treated plants was relatively lower than that in the untreated plants. These results suggest that these inhibitors of epigenetic modifications could cause preprophase arrest via reactive oxygen species formation inhibiting the expression of DNA topoisomerase genes, accompanied by changes in the H4K5ac and H3S10ph histone modifications.
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Affiliation(s)
- Pu Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qing Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yingnan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Liangfu Xie
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fei Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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46
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Rybaczek D. Hydroxyurea-induced replication stress causes poly(ADP-ribose) polymerase-2 accumulation and changes its intranuclear location in root meristems of Vicia faba. JOURNAL OF PLANT PHYSIOLOGY 2016; 198:89-102. [PMID: 27155387 DOI: 10.1016/j.jplph.2016.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
Replication stress induced by 24 and 48h exposure to 2.5mM hydroxyurea (HU) increased the activity of poly(ADP-ribose) polymerase-2 (PARP-2; EC 2.4.2.30) in root meristem cells of Vicia faba. An increase in the number of PARP-2 foci was accompanied by their delocalization from peripheral areas to the interior of the nucleus. Our results indicate that the increase in PARP-2 was connected with an increase in S139-phosphorylated H2AX histones. The findings suggest the possible role of PARP-2 in replication stress. We also confirm that the intranuclear location of PARP-2 depends on the duration of HU-induced replication stress, confirming the role of PARP-2 as an indicator of stress intensity. Finally, we conclude that the more intense the HU-mediated replication stress, the greater the probability of PARP-2 activation or H2AXS139 phosphorylation, but also the greater the chance of increasing the efficiency of repair processes and a return to normal cell cycle progression.
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Affiliation(s)
- Dorota Rybaczek
- Department of Cytophysiology, Institute of Experimental Biology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90236 Łódź, Poland.
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47
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Mohanty S, Mohanty A, Sandoval N, Tran T, Bedell V, Wu J, Scuto A, Murata-Collins J, Weisenburger DD, Ngo VN. Cyclin D1 depletion induces DNA damage in mantle cell lymphoma lines. Leuk Lymphoma 2016; 58:676-688. [PMID: 27338091 DOI: 10.1080/10428194.2016.1198958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Elevated cyclin D1 (CCND1) expression levels in mantle cell lymphoma (MCL) are associated with aggressive clinical manifestations related to chemoresistance, but little is known about how this important proto-oncogene contributes to the resistance of MCL. Here, we showed that RNA interference-mediated depletion of CCND1 increased caspase-3 activities and induced apoptosis in the human MCL lines UPN-1 and JEKO-1. In vitro and xenotransplant studies revealed that the toxic effect of CCND1 depletion in MCL cells was likely due to increase in histone H2AX phosphorylation, a DNA damage marker. DNA fiber analysis suggested deregulated replication initiation after CCND1 depletion as a potential cause of DNA damage. Finally, in contrast to depletion or inhibition of cyclin-dependent kinase 4, CCND1 depletion increased chemosensitivity of MCL cells to replication inhibitors hydroxyurea and cytarabine. Our findings have an important implication for CCND1 as a potential therapeutic target in MCL patients who are refractory to standard chemotherapy.
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Affiliation(s)
- Suchismita Mohanty
- a Division of Hematopoietic Stem Cell and Leukemia Research , Beckman Research Institute , Duarte , CA , USA
| | - Atish Mohanty
- a Division of Hematopoietic Stem Cell and Leukemia Research , Beckman Research Institute , Duarte , CA , USA
| | - Natalie Sandoval
- a Division of Hematopoietic Stem Cell and Leukemia Research , Beckman Research Institute , Duarte , CA , USA
| | - Thai Tran
- b Irell & Manella Graduate School of Biological Sciences , Duarte , CA , USA
| | - Victoria Bedell
- c Department of Pathology , City of Hope National Medical Center , Duarte , CA , USA
| | - Jun Wu
- d Animal Resource Center , Beckman Research Institute of City of Hope , Duarte , CA , USA
| | - Anna Scuto
- c Department of Pathology , City of Hope National Medical Center , Duarte , CA , USA
| | - Joyce Murata-Collins
- c Department of Pathology , City of Hope National Medical Center , Duarte , CA , USA
| | - Dennis D Weisenburger
- c Department of Pathology , City of Hope National Medical Center , Duarte , CA , USA
| | - Vu N Ngo
- a Division of Hematopoietic Stem Cell and Leukemia Research , Beckman Research Institute , Duarte , CA , USA
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48
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Minakawa Y, Atsumi Y, Shinohara A, Murakami Y, Yoshioka KI. Gamma-irradiated quiescent cells repair directly induced double-strand breaks but accumulate persistent double-strand breaks during subsequent DNA replication. Genes Cells 2016; 21:789-97. [PMID: 27251002 DOI: 10.1111/gtc.12381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 04/26/2016] [Indexed: 01/31/2023]
Abstract
H2AX is expressed at very low levels in quiescent normal cells in vivo and in vitro. Such cells repair DNA double-strand breaks (DSBs) induced by γ-irradiation through a transient stabilization of H2AX. However, the resultant cells accumulate small numbers of irreparable (or persistent) DSBs via an unknown mechanism. We found that quiescent cells that had repaired DSBs directly induced by γ-rays were prone to accumulate DSBs during the subsequent DNA replication. Unlike directly induced DSBs, secondary DSBs were not efficiently repaired, although Rad51 and 53BP1 were recruited to these sites. H2AX was dramatically stabilized in response to DSBs directly caused by γ-rays, enabling γH2AX foci formation and DSB repair, whereas H2AX was barely stabilized in response to secondary DSBs, in which γH2AX foci were small and DSBs were not efficiently repaired. Our results show a pathway that leads to the persistent DSB formation after γ-irradiation.
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Affiliation(s)
- Yusuke Minakawa
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Biological Science and Technology, Tokyo University of Science, 6-1-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Yuko Atsumi
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akira Shinohara
- Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasufumi Murakami
- Biological Science and Technology, Tokyo University of Science, 6-1-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Ken-Ichi Yoshioka
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
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49
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Radulovic M, Baqader NO, Stoeber K, Godovac-Zimmermann J. Spatial Cross-Talk between Oxidative Stress and DNA Replication in Human Fibroblasts. J Proteome Res 2016; 15:1907-38. [PMID: 27142241 DOI: 10.1021/acs.jproteome.6b00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MS-based proteomics has been applied to a differential network analysis of the nuclear-cytoplasmic subcellular distribution of proteins between cell-cycle arrest: (a) at the origin activation checkpoint for DNA replication, or (b) in response to oxidative stress. Significant changes were identified for 401 proteins. Cellular response combines changes in trafficking and in total abundance to vary the local compartmental abundances that are the basis of cellular response. Appreciable changes for both perturbations were observed for 245 proteins, but cross-talk between oxidative stress and DNA replication is dominated by 49 proteins that show strong changes for both. Many nuclear processes are influenced by a spatial switch involving the proteins {KPNA2, KPNB1, PCNA, PTMA, SET} and heme/iron proteins HMOX1 and FTH1. Dynamic spatial distribution data are presented for proteins involved in caveolae, extracellular matrix remodelling, TGFβ signaling, IGF pathways, emerin complexes, mitochondrial protein import complexes, spliceosomes, proteasomes, and so on. The data indicate that for spatially heterogeneous cells cross-compartmental communication is integral to their system biology, that coordinated spatial redistribution for crucial protein networks underlies many functional changes, and that information on dynamic spatial redistribution of proteins is essential to obtain comprehensive pictures of cellular function. We describe how spatial data of the type presented here can provide priorities for further investigation of crucial features of high-level spatial coordination across cells. We suggest that the present data are related to increasing indications that much of subcellular protein transport is constitutive and that perturbation of these constitutive transport processes may be related to cancer and other diseases. A quantitative, spatially resolved nucleus-cytoplasm interaction network is provided for further investigations.
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Affiliation(s)
- Marko Radulovic
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom.,Insitute of Oncology and Radiology , Pasterova 14, 11000 Belgrade, Serbia
| | - Noor O Baqader
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Kai Stoeber
- Research Department of Pathology and UCL Cancer Institute, Rockefeller Building, University College London , University Street, London WC1E 6JJ, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Division of Medicine, University College London, Center for Nephrology , Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
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50
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Muñoz S, Méndez J. DNA replication stress: from molecular mechanisms to human disease. Chromosoma 2016; 126:1-15. [PMID: 26797216 DOI: 10.1007/s00412-016-0573-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/29/2022]
Abstract
The genome of proliferating cells must be precisely duplicated in each cell division cycle. Chromosomal replication entails risks such as the possibility of introducing breaks and/or mutations in the genome. Hence, DNA replication requires the coordinated action of multiple proteins and regulatory factors, whose deregulation causes severe developmental diseases and predisposes to cancer. In recent years, the concept of "replicative stress" (RS) has attracted much attention as it impinges directly on genomic stability and offers a promising new avenue to design anticancer therapies. In this review, we summarize recent progress in three areas: (1) endogenous and exogenous factors that contribute to RS, (2) molecular mechanisms that mediate the cellular responses to RS, and (3) the large list of diseases that are directly or indirectly linked to RS.
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Affiliation(s)
- Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain.
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