1
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Pang QY, Chiu YC, Huang RYJ. Regulating epithelial-mesenchymal plasticity from 3D genome organization. Commun Biol 2024; 7:750. [PMID: 38902393 PMCID: PMC11190238 DOI: 10.1038/s42003-024-06441-w] [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: 09/26/2022] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a dynamic process enabling polarized epithelial cells to acquire mesenchymal features implicated in development and carcinoma progression. As our understanding evolves, it is clear the reversible execution of EMT arises from complex epigenomic regulation involving histone modifications and 3-dimensional (3D) genome structural changes, leading to a cascade of transcriptional events. This review summarizes current knowledge on chromatin organization in EMT, with a focus on hierarchical structures of the 3D genome and chromatin accessibility changes.
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Affiliation(s)
- Qing You Pang
- Neuro-Oncology Research Laboratory, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Yi-Chia Chiu
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Ruby Yun-Ju Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
- Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, 10051, Taiwan.
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
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2
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Keller KM, Koetsier J, Schild L, Amo-Addae V, Eising S, van den Handel K, Ober K, Koopmans B, Essing A, van den Boogaard ML, Langenberg KPS, Jäger N, Kool M, Pfister S, Dolman MEM, Molenaar JJ, van Hooff SR. The potential of PARP as a therapeutic target across pediatric solid malignancies. BMC Cancer 2023; 23:310. [PMID: 37020198 PMCID: PMC10077757 DOI: 10.1186/s12885-022-10319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/15/2022] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Pediatric cancer is the leading cause of disease-related death in children and the need for better therapeutic options remains urgent. Due to the limited number of patients, target and drug development for pediatrics is often supplemented by data from studies focused on adult cancers. Recent evidence shows that pediatric cancers possess different vulnerabilities that should be explored independently from adult cancers. METHODS Using the publicly available Genomics of Drug Sensitivity in Cancer database, we explore therapeutic targets and biomarkers specific to the pediatric solid malignancies Ewing sarcoma, medulloblastoma, neuroblastoma, osteosarcoma, and rhabdomyosarcoma. Results are validated using cell viability assays and high-throughput drug screens are used to identify synergistic combinations. RESULTS Using published drug screening data, PARP is identified as a drug target of interest across multiple different pediatric malignancies. We validate these findings, and we show that efficacy can be improved when combined with conventional chemotherapeutics, namely topoisomerase inhibitors. Additionally, using gene set enrichment analysis, we identify ribosome biogenesis as a potential biomarker for PARP inhibition in pediatric cancer cell lines. CONCLUSION Collectively, our results provide evidence to support the further development of PARP inhibition and the combination with TOP1 inhibition as a therapeutic approach in solid pediatric malignancies. Additionally, we propose ribosome biogenesis as a component to PARP inhibitor sensitivity that should be further investigated to help maximize the potential utility of PARP inhibition and combinations across pediatric solid malignancies.
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Affiliation(s)
- Kaylee M Keller
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Joost Koetsier
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Linda Schild
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Vicky Amo-Addae
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Selma Eising
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Kimberley Ober
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Bianca Koopmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Anke Essing
- Princess Máxima Center for Pediatric 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 Pediatric 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
| | - Stefan Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - M Emmy M Dolman
- Princess Máxima Center for Pediatric 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, Sydney, NSW, Australia
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Department of Pharmaceutical Sciences, University Utrecht, Utrecht, the Netherlands.
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3
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Zhang H, Gao H, Gu Y, John A, Wei L, Huang M, Yu J, Adeosun AA, Weinshilboum RM, Wang L. 3D CRISPR screen in prostate cancer cells reveals PARP inhibitor sensitization through TBL1XR1-SMC3 interaction. Front Oncol 2022; 12:999302. [PMID: 36523978 PMCID: PMC9746894 DOI: 10.3389/fonc.2022.999302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/14/2022] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribose) (PAR) polymerase inhibitors (PARPi) either have been approved or being tested in the clinic for the treatment of a variety of cancers with homologous recombination deficiency (HRD). However, cancer cells can develop resistance to PARPi drugs through various mechanisms, and new biomarkers and combination therapeutic strategies need to be developed to support personalized treatment. In this study, a genome-wide CRISPR screen was performed in a prostate cancer cell line with 3D culture condition which identified novel signals involved in DNA repair pathways. One of these genes, TBL1XR1, regulates sensitivity to PARPi in prostate cancer cells. Mechanistically, we show that TBL1XR1 interacts with and stabilizes SMC3 on chromatin and promotes γH2AX spreading along the chromatin of the cells under DNA replication stress. TBL1XR1-SMC3 double knockdown (knockout) cells have comparable sensitivity to PARPi compared to SMC3 knockdown or TBL1XR1 knockout cells, and more sensitivity than WT cells. Our findings provide new insights into mechanisms underlying response to PARPi or platin compounds in the treatment of malignancies.
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Affiliation(s)
- Huan Zhang
- School of Medicine, Nantong University, Nantong, China
| | - Huanyao Gao
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Yayun Gu
- School of Medicine, Nantong University, Nantong, China
| | - August John
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Lixuan Wei
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Minhong Huang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Adeyemi A. Adeosun
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Richard M. Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
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4
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Hou W, Li Y, Zhang J, Xia Y, Wang X, Chen H, Lou H. Cohesin in DNA damage response and double-strand break repair. Crit Rev Biochem Mol Biol 2022; 57:333-350. [PMID: 35112600 DOI: 10.1080/10409238.2022.2027336] [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: 08/05/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress on how cohesin regulates the DNA damage checkpoint activation and repair pathway choice, emphasizing postreplicative cohesin loading and DI-cohesion establishment in yeasts and mammals. DI-cohesion and RC-cohesion show distinct features in many aspects. DI-cohesion near or far from the break sites might undergo different regulations and execute different tasks in DDR and DSB repair. Furthermore, some open questions in this field and the significance of this new scenario to our understanding of genome stability maintenance and cohesinopathies are discussed.
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Affiliation(s)
- Wenya Hou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yan Li
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jiaxin Zhang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yisui Xia
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xueting Wang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Hongxiang Chen
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Huiqiang Lou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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5
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Mfarej MG, Skibbens RV. Genetically induced redox stress occurs in a yeast model for Roberts syndrome. G3 (BETHESDA, MD.) 2022; 12:6460337. [PMID: 34897432 PMCID: PMC9210317 DOI: 10.1093/g3journal/jkab426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 12/31/2022]
Abstract
Roberts syndrome (RBS) is a multispectrum developmental disorder characterized by severe limb, craniofacial, and organ abnormalities and often intellectual disabilities. The genetic basis of RBS is rooted in loss-of-function mutations in the essential N-acetyltransferase ESCO2 which is conserved from yeast (Eco1/Ctf7) to humans. ESCO2/Eco1 regulate many cellular processes that impact chromatin structure, chromosome transmission, gene expression, and repair of the genome. The etiology of RBS remains contentious with current models that include transcriptional dysregulation or mitotic failure. Here, we report evidence that supports an emerging model rooted in defective DNA damage responses. First, the results reveal that redox stress is elevated in both eco1 and cohesion factor Saccharomyces cerevisiae mutant cells. Second, we provide evidence that Eco1 and cohesion factors are required for the repair of oxidative DNA damage such that ECO1 and cohesin gene mutations result in reduced cell viability and hyperactivation of DNA damage checkpoints that occur in response to oxidative stress. Moreover, we show that mutation of ECO1 is solely sufficient to induce endogenous redox stress and sensitizes mutant cells to exogenous genotoxic challenges. Remarkably, antioxidant treatment desensitizes eco1 mutant cells to a range of DNA damaging agents, raising the possibility that modulating the cellular redox state may represent an important avenue of treatment for RBS and tumors that bear ESCO2 mutations.
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Affiliation(s)
- Michael G Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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6
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Morgan SM, Tanizawa H, Caruso LB, Hulse M, Kossenkov A, Madzo J, Keith K, Tan Y, Boyle S, Lieberman PM, Tempera I. The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity. Nat Commun 2022; 13:187. [PMID: 35039491 PMCID: PMC8764100 DOI: 10.1038/s41467-021-27894-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) persists in human B-cells by maintaining its chromatinized episomes within the nucleus. We have previously shown that cellular factor Poly [ADP-ribose] polymerase 1 (PARP1) binds the EBV genome, stabilizes CTCF binding at specific loci, and that PARP1 enzymatic activity correlates with maintaining a transcriptionally active latency program. To better understand PARP1's role in regulating EBV latency, here we functionally characterize the effect of PARP enzymatic inhibition on episomal structure through in situ HiC mapping, generating a complete 3D structure of the EBV genome. We also map intragenomic contact changes after PARP inhibition to global binding of chromatin looping factors CTCF and cohesin across the EBV genome. We find that PARP inhibition leads to fewer total unique intragenomic interactions within the EBV episome, yet new chromatin loops distinct from the untreated episome are also formed. This study also illustrates that PARP inhibition alters gene expression at the regions where chromatin looping is most effected. We observe that PARP1 inhibition does not alter cohesin binding sites but does increase its frequency of binding at those sites. Taken together, these findings demonstrate that PARP has an essential role in regulating global EBV chromatin structure and latent gene expression.
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Affiliation(s)
- Sarah M Morgan
- The Wistar Institute, Philadelphia, PA, USA
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | | | | | - Michael Hulse
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | | | - Jozef Madzo
- The Coriell Institute for Medical Research, Camden, NJ, USA
| | - Kelsey Keith
- The Coriell Institute for Medical Research, Camden, NJ, USA
| | - Yinfei Tan
- Fox Chase Cancer Center, Philadelphia, PA, USA
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7
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Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma. Nat Commun 2022; 13:281. [PMID: 35022408 PMCID: PMC8755833 DOI: 10.1038/s41467-021-27704-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/07/2021] [Indexed: 02/08/2023] Open
Abstract
SUMOylation is a post-translational modification of proteins that regulates these proteins’ localization, turnover or function. Aberrant SUMOylation is frequently found in cancers but its origin remains elusive. Using a genome-wide transposon mutagenesis screen in a MYC-driven B-cell lymphoma model, we here identify the SUMO isopeptidase (or deconjugase) SENP6 as a tumor suppressor that links unrestricted SUMOylation to tumor development and progression. Notably, SENP6 is recurrently deleted in human lymphomas and SENP6 deficiency results in unrestricted SUMOylation. Mechanistically, SENP6 loss triggers release of DNA repair- and genome maintenance-associated protein complexes from chromatin thereby impairing DNA repair in response to DNA damages and ultimately promoting genomic instability. In line with this hypothesis, SENP6 deficiency drives synthetic lethality to Poly-ADP-Ribose-Polymerase (PARP) inhibition. Together, our results link SENP6 loss to defective genome maintenance and reveal the potential therapeutic application of PARP inhibitors in B-cell lymphoma. SUMOylation is a post-translational modification that has been shown to be altered in cancer. Here, the authors show that loss of the SUMO isopeptidase SENP6 leads to unrestricted SUMOylation and genomic instability promoting lymphomagenesis and generating vulnerability to PARP inhibition.
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8
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Modeling DNA trapping of anticancer therapeutic targets using missense mutations identifies dominant synthetic lethal interactions. Proc Natl Acad Sci U S A 2021; 118:2100240118. [PMID: 33782138 DOI: 10.1073/pnas.2100240118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Genetic screens can identify synthetic lethal (SL) interactions and uncover potential anticancer therapeutic targets. However, most SL screens have utilized knockout or knockdown approaches that do not accurately mimic chemical inhibition of a target protein. Here, we test whether missense mutations can be utilized as a model for a type of protein inhibition that creates a dominant gain-of-function cytotoxicity. We expressed missense mutations in the FEN1 endonuclease and the replication-associated helicase, CHL1, that inhibited enzymatic activity but retained substrate binding, and found that these mutations elicited a dominant SL phenotype consistent with the generation of cytotoxic protein-DNA or protein-protein intermediates. Genetic screens with nuclease-defective hFEN1 and helicase-deficient yCHL1 captured dominant SL interactions, in which ectopic expression of the mutant form, in the presence of the wild-type form, caused SL in specific mutant backgrounds. Expression of nuclease-defective hFEN1 in yeast elicited DNA binding-dependent dominant SL with homologous recombination mutants. In contrast, dominant SL interactions with helicase-deficient yCHL1 were observed in spindle-associated, Ctf18-alternative replication factor C (Ctf18-RFC) clamp loader complex, and cohesin mutant backgrounds. These results highlight the different mechanisms underlying SL interactions that occur in the presence of an inhibited form of the target protein and point to the utility of modeling trapping mutations in pursuit of more clinically relevant SL interactions.
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9
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Chin CV, Antony J, Ketharnathan S, Labudina A, Gimenez G, Parsons KM, He J, George AJ, Pallotta MM, Musio A, Braithwaite A, Guilford P, Hannan RD, Horsfield JA. Cohesin mutations are synthetic lethal with stimulation of WNT signaling. eLife 2020; 9:e61405. [PMID: 33284104 PMCID: PMC7746233 DOI: 10.7554/elife.61405] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
Mutations in genes encoding subunits of the cohesin complex are common in several cancers, but may also expose druggable vulnerabilities. We generated isogenic MCF10A cell lines with deletion mutations of genes encoding cohesin subunits SMC3, RAD21, and STAG2 and screened for synthetic lethality with 3009 FDA-approved compounds. The screen identified several compounds that interfere with transcription, DNA damage repair and the cell cycle. Unexpectedly, one of the top 'hits' was a GSK3 inhibitor, an agonist of Wnt signaling. We show that sensitivity to GSK3 inhibition is likely due to stabilization of β-catenin in cohesin-mutant cells, and that Wnt-responsive gene expression is highly sensitized in STAG2-mutant CMK leukemia cells. Moreover, Wnt activity is enhanced in zebrafish mutant for cohesin subunits stag2b and rad21. Our results suggest that cohesin mutations could progress oncogenesis by enhancing Wnt signaling, and that targeting the Wnt pathway may represent a novel therapeutic strategy for cohesin-mutant cancers.
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Affiliation(s)
- Chue Vin Chin
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Jisha Antony
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Sarada Ketharnathan
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Anastasia Labudina
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Gregory Gimenez
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
| | - Kate M Parsons
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Jinshu He
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Amee J George
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
| | - Maria Michela Pallotta
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR)PisaItaly
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR)PisaItaly
| | - Antony Braithwaite
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
| | - Parry Guilford
- Department of Biochemistry, University of OtagoDunedinNew Zealand
| | - Ross D Hannan
- The John Curtin School of Medical Research, The Australian National UniversityCanberraAustralia
- Department of Biochemistry and Molecular Biology, University of MelbourneParkvilleAustralia
- Sir Peter MacCallum Department of Oncology, University of MelbourneParkvilleAustralia
- School of Biomedical Sciences, University of QueenslandSt LuciaAustralia
| | - Julia A Horsfield
- Department of Pathology, Otago Medical School, University of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of AucklandAucklandNew Zealand
- Genetics Otago Research Centre, University of OtagoDunedinNew Zealand
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10
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Subhi O, Schulten HJ, Bagatian N, Al-Dayini R, Karim S, Bakhashab S, Alotibi R, Al-Ahmadi A, Ata M, Elaimi A, Al-Muhayawi S, Mansouri M, Al-Ghamdi K, Hamour OA, Jamal A, Al-Maghrabi J, Al-Qahtani MH. Genetic relationship between Hashimoto`s thyroiditis and papillary thyroid carcinoma with coexisting Hashimoto`s thyroiditis. PLoS One 2020; 15:e0234566. [PMID: 32603365 PMCID: PMC7326236 DOI: 10.1371/journal.pone.0234566] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/28/2020] [Indexed: 12/30/2022] Open
Abstract
Hashimoto's thyroiditis (HT) is present in the background of around 30% of papillary thyroid carcinomas (PTCs). The genetic predisposition effect of this autoimmune condition is not thoroughly understood. We analyzed the microarray expression profiles of 13 HT, eight PTCs with (w/) coexisting HT, six PTCs without (w/o) coexisting HT, six micro PTCs (mPTCs), and three normal thyroid (TN) samples. Based on a false discovery rate (FDR)-adjusted p-value ≤ 0.05 and a fold change (FC) > 2, four comparison groups were defined, which were HT vs. TN; PTC w/ HT vs. TN; PTC w/o HT vs. TN; and mPTC vs. TN. A Venn diagram displayed 15 different intersecting and non-intersecting differentially expressed gene (DEG) sets, of which a set of 71 DEGs, shared between the two comparison groups HT vs. TN ∩ PTC w/ HT vs. TN, harbored the relatively largest number of genes related to immune and inflammatory functions; oxidative stress and reactive oxygen species (ROS); DNA damage and DNA repair; cell cycle; and apoptosis. The majority of the 71 DEGs were upregulated and the most upregulated DEGs included a number of immunoglobulin kappa variable genes, and other immune-related genes, e.g., CD86 molecule (CD86), interleukin 2 receptor gamma (IL2RG), and interferon, alpha-inducible protein 6 (IFI6). Upregulated genes preferentially associated with other gene ontologies (GO) were, e.g., STAT1, MMP9, TOP2A, and BRCA2. Biofunctional analysis revealed pathways related to immunogenic functions. Further data analysis focused on the set of non-intersecting 358 DEGs derived from the comparison group of HT vs. TN, and on the set of 950 DEGs from the intersection of all four comparison groups. In conclusion, this study indicates that, besides immune/inflammation-related genes, also genes associated with oxidative stress, ROS, DNA damage, DNA repair, cell cycle, and apoptosis are comparably more deregulated in a data set shared between HT and PTC w/ HT. These findings are compatible with the conception of a genetic sequence where chronic inflammatory response is accompanied by deregulation of genes and biofunctions associated with oncogenic transformation. The generated data set may serve as a source for identifying candidate genes and biomarkers that are practical for clinical application.
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Affiliation(s)
- Ohoud Subhi
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
| | - Nadia Bagatian
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Roa'a Al-Dayini
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherin Bakhashab
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Alotibi
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alaa Al-Ahmadi
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Manar Ata
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Center of Innovation in Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saad Al-Muhayawi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majid Mansouri
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid Al-Ghamdi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Osman Abdel Hamour
- Department of Surgery, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Awatif Jamal
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jaudah Al-Maghrabi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mohammed Hussain Al-Qahtani
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Tackling Cancer with Yeast-Based Technologies. Trends Biotechnol 2019; 37:592-603. [DOI: 10.1016/j.tibtech.2018.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/24/2018] [Accepted: 11/30/2018] [Indexed: 12/19/2022]
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12
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Sardanyés J, Alarcón T. Noise-induced bistability in the fate of cancer phenotypic quasispecies: a bit-strings approach. Sci Rep 2018; 8:1027. [PMID: 29348614 PMCID: PMC5773630 DOI: 10.1038/s41598-018-19552-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/03/2018] [Indexed: 02/07/2023] Open
Abstract
Tumor cell populations are highly heterogeneous. Such heterogeneity, both at genotypic and phenotypic levels, is a key feature during tumorigenesis. How to investigate the impact of this heterogeneity in the dynamics of tumors cells becomes an important issue. Here we explore a stochastic model describing the competition dynamics between a pool of heterogeneous cancer cells with distinct phenotypes and healthy cells. This model is used to explore the role of demographic fluctuations on the transitions involving tumor clearance. Our results show that for large population sizes, when demographic fluctuations are negligible, there exists a sharp transition responsible for tumor cells extinction at increasing tumor cells' mutation rates. This result is consistent with a mean field model developed for the same system. The mean field model reveals only monostability scenarios, in which either the dominance of the tumor cells or the dominance of the healthy cells is found. Interestingly, the stochastic model shows that for small population sizes the monostability behavior disappears, involving the presence of noise-induced bistability. The impact of the initial populations of cells in the fate of the cell populations is investigated, as well as the transient times towards the healthy and the cancer states.
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Affiliation(s)
- Josep Sardanyés
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain.
- Barcelona Graduate School of Mathematics (BGSMath). Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain.
| | - Tomás Alarcón
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain.
- Barcelona Graduate School of Mathematics (BGSMath). Campus de Bellaterra, Edifici C, 08193 Bellaterra, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Barcelona, Spain.
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13
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McCurdy SR, Levis MJ. Emerging molecular predictive and prognostic factors in acute myeloid leukemia. Leuk Lymphoma 2017; 59:2021-2039. [DOI: 10.1080/10428194.2017.1393669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shannon R. McCurdy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark J. Levis
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Kukolj E, Kaufmann T, Dick AE, Zeillinger R, Gerlich DW, Slade D. PARP inhibition causes premature loss of cohesion in cancer cells. Oncotarget 2017; 8:103931-103951. [PMID: 29262611 PMCID: PMC5732777 DOI: 10.18632/oncotarget.21879] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) regulate various aspects of cellular function including mitotic progression. Although PARP inhibitors have been undergoing various clinical trials and the PARP1/2 inhibitor olaparib was approved as monotherapy for BRCA-mutated ovarian cancer, their mode of action in killing tumour cells is not fully understood. We investigated the effect of PARP inhibition on mitosis in cancerous (cervical, ovary, breast and osteosarcoma) and non-cancerous cells by live-cell imaging. The clinically relevant inhibitor olaparib induced strong perturbations in mitosis, including problems with chromosome alignment at the metaphase plate, anaphase delay, and premature loss of cohesion (cohesion fatigue) after a prolonged metaphase arrest, resulting in sister chromatid scattering. PARP1 and PARP2 depletion suppressed the phenotype while PARP2 overexpression enhanced it, suggesting that olaparib-bound PARP1 and PARP2 rather than the lack of catalytic activity causes this phenotype. Olaparib-induced mitotic chromatid scattering was observed in various cancer cell lines with increased protein levels of PARP1 and PARP2, but not in non-cancer or cancer cell lines that expressed lower levels of PARP1 or PARP2. Interestingly, the sister chromatid scattering phenotype occurred only when olaparib was added during the S-phase preceding mitosis, suggesting that PARP1 and PARP2 entrapment at replication forks impairs sister chromatid cohesion. Clinically relevant DNA-damaging agents that impair replication progression such as topoisomerase inhibitors and cisplatin were also found to induce sister chromatid scattering and metaphase plate alignment problems, suggesting that these mitotic phenotypes are a common outcome of replication perturbation.
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Affiliation(s)
- Eva Kukolj
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Tanja Kaufmann
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Amalie E Dick
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Dea Slade
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
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15
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Benedetti L, Cereda M, Monteverde L, Desai N, Ciccarelli FD. Synthetic lethal interaction between the tumour suppressor STAG2 and its paralog STAG1. Oncotarget 2017; 8:37619-37632. [PMID: 28430577 PMCID: PMC5514935 DOI: 10.18632/oncotarget.16838] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/08/2017] [Indexed: 12/17/2022] Open
Abstract
Cohesin is a multi-protein complex that tethers sister chromatids during mitosis and mediates DNA repair, genome compartmentalisation and regulation of gene expression. Cohesin subunits frequently acquire cancer loss-of-function alterations and act as tumour suppressors in several tumour types. This has led to increased interest in cohesin as potential target in anti-cancer therapy. Here we show that the loss-of-function of STAG2, a core component of cohesin and an emerging tumour suppressor, leads to synthetic dependency of mutated cancer cells on its paralog STAG1. STAG1 and STAG2 share high sequence identity, encode mutually exclusive cohesin subunits and retain partially overlapping functions. We inhibited STAG1 and STAG2 in several cancer cell lines where the two genes have variable mutation and copy number status. In all cases, we observed that the simultaneous blocking of STAG1 and STAG2 significantly reduces cell proliferation. We further confirmed the synthetic lethal interaction developing a vector-free CRISPR system to induce STAG1/STAG2 double gene knockout. We provide strong evidence that STAG1 is a promising therapeutic target in cancers with inactivating alterations of STAG2.
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Affiliation(s)
- Lorena Benedetti
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Matteo Cereda
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - LeeAnn Monteverde
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Nikita Desai
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Francesca D. Ciccarelli
- Division of Cancer Studies, King's College London, London SE1 1UL, UK
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
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16
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Kuriki Y, Komatsu T, Ycas PD, Coulup SK, Carlson EJ, Pomerantz WCK. Meeting Proceedings ICBS2016-Translating the Power of Chemical Biology to Clinical Advances. ACS Chem Biol 2017; 12:869-877. [PMID: 28303709 DOI: 10.1021/acschembio.7b00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yugo Kuriki
- Graduate School
of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toru Komatsu
- Graduate School
of Pharmaceutical Sciences, University of Tokyo, 7-3-1, Hongo,
Bunkyo-ku, Tokyo 113-0033, Japan
- Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Peter D. Ycas
- Department of Chemistry, University of Minnesota, 312 Smith
Hall, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Sara K. Coulup
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - Erick J. Carlson
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, 312 Smith
Hall, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
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17
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Sardanyés J, Martínez R, Simó C, Solé R. Abrupt transitions to tumor extinction: a phenotypic quasispecies model. J Math Biol 2016; 74:1589-1609. [PMID: 27714432 DOI: 10.1007/s00285-016-1062-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 09/09/2016] [Indexed: 12/20/2022]
Abstract
The dynamics of heterogeneous tumor cell populations competing with healthy cells is an important topic in cancer research with deep implications in biomedicine. Multitude of theoretical and computational models have addressed this issue, especially focusing on the nature of the transitions governing tumor clearance as some relevant model parameters are tuned. In this contribution, we analyze a mathematical model of unstable tumor progression using the quasispecies framework. Our aim is to define a minimal model incorporating the dynamics of competition between healthy cells and a heterogeneous population of cancer cell phenotypes involving changes in replication-related genes (i.e., proto-oncogenes and tumor suppressor genes), in genes responsible for genomic stability, and in house-keeping genes. Such mutations or loss of genes result into different phenotypes with increased proliferation rates and/or increased genomic instabilities. Despite bifurcations in the classical deterministic quasispecies model are typically given by smooth, continuous shifts (i.e., transcritical bifurcations), we here identify a novel type of bifurcation causing an abrupt transition to tumor extinction. Such a bifurcation, named as trans-heteroclinic, is characterized by the exchange of stability between two distant fixed points (that do not collide) involving tumor persistence and tumor clearance. The increase of mutation and/or the decrease of the replication rate of tumor cells involves this catastrophic shift of tumor cell populations. The transient times near bifurcation thresholds are also characterized, showing a power law dependence of exponent [Formula: see text] of the transients as mutation is changed near the bifurcation value. These results are discussed in the context of targeted cancer therapy as a possible therapeutic strategy to force a catastrophic shift by simultaneously delivering mutagenic and cytotoxic drugs inside tumor cells.
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Affiliation(s)
- Josep Sardanyés
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain. .,Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - Regina Martínez
- Departament de Matemàtiques, Edifici C. Facultat de Ciències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Carles Simó
- Departament de Matemàtiques i Informàtica, Universitat de Barcelona, Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,The Santa Fe Institute, Santa Fe, New Mexico, USA
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18
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Yun J, Song SH, Kim HP, Han SW, Yi EC, Kim TY. Dynamic cohesin-mediated chromatin architecture controls epithelial-mesenchymal plasticity in cancer. EMBO Rep 2016; 17:1343-59. [PMID: 27466323 PMCID: PMC5007572 DOI: 10.15252/embr.201541852] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 06/03/2016] [Accepted: 06/22/2016] [Indexed: 01/26/2023] Open
Abstract
Epithelial to mesenchymal transition (EMT) and mesenchymal to epithelial transition (MET) are important interconnected events in tumorigenesis controlled by complex genetic networks. However, the cues that activate EMT-initiating factors and the mechanisms that reversibly connect EMT/MET are not well understood. Here, we show that cohesin-mediated chromatin organization coordinates EMT/MET by regulating mesenchymal genes. We report that RAD21, a subunit of the cohesin complex, is expressed in epithelial breast cancer cells, whereas its expression is decreased in mesenchymal cancer. Depletion of RAD21 in epithelial cancer cells causes transcriptional activation of TGFB1 and ITGA5, inducing EMT. Reduced binding of RAD21 changes intrachromosomal chromatin interactions within the TGFB1 and ITGA5 loci, creating an active transcriptional environment. Similarly, stem cell-like cancer cells also show an open chromatin structure at both genes, which correlates with high expression levels and mesenchymal fate characteristics. Conversely, overexpression of RAD21 in mesenchymal cancer cells induces MET-specific expression patterns. These findings indicate that dynamic cohesin-mediated chromatin structures are responsible for the initiation and regulation of essential EMT-related cell fate changes in cancer.
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Affiliation(s)
- Jiyeon Yun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sae-Won Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
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19
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SGO1 is involved in the DNA damage response in MYCN-amplified neuroblastoma cells. Sci Rep 2016; 6:31615. [PMID: 27539729 PMCID: PMC4990925 DOI: 10.1038/srep31615] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/25/2016] [Indexed: 11/08/2022] Open
Abstract
Shugoshin 1 (SGO1) is required for accurate chromosome segregation during mitosis and meiosis; however, its other functions, especially at interphase, are not clearly understood. Here, we found that downregulation of SGO1 caused a synergistic phenotype in cells overexpressing MYCN. Downregulation of SGO1 impaired proliferation and induced DNA damage followed by a senescence-like phenotype only in MYCN-overexpressing neuroblastoma cells. In these cells, SGO1 knockdown induced DNA damage, even during interphase, and this effect was independent of cohesin. Furthermore, MYCN-promoted SGO1 transcription and SGO1 expression tended to be higher in MYCN- or MYC-overexpressing cancers. Together, these findings indicate that SGO1 plays a role in the DNA damage response in interphase. Therefore, we propose that SGO1 represents a potential molecular target for treatment of MYCN-amplified neuroblastoma.
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20
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Yun J, Song SH, Kang JY, Park J, Kim HP, Han SW, Kim TY. Reduced cohesin destabilizes high-level gene amplification by disrupting pre-replication complex bindings in human cancers with chromosomal instability. Nucleic Acids Res 2016; 44:558-72. [PMID: 26420833 PMCID: PMC4737181 DOI: 10.1093/nar/gkv933] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 08/09/2015] [Accepted: 09/08/2015] [Indexed: 01/03/2023] Open
Abstract
Gene amplification is a hallmark of cancer with chromosomal instability although the underlying mechanism by which altered copy numbers are maintained is largely unclear. Cohesin, involved in sister chromatid cohesion, DNA repair, cell cycle progression and transcriptional regulation of key developmental genes, is frequently overexpressed in human cancer. Here we show that cohesin-dependent change in DNA replication controls the copy numbers of amplified genes in cancer cells with chromosomal instability. We found that the down-regulation of elevated cohesin leads to copy number-associated gene expression changes without disturbing chromosomal segregation. Highly amplified genes form typical long-range chromatin interactions, which are stabilized by enriched cohesin. The spatial proximities among cohesin binding sites within amplified genes are decreased by RAD21-knockdown, resulting in the rapid decline of amplified gene expression. After several passages, cohesin depletion inhibits DNA replication initiation by reducing the recruitment of pre-replication complexes such as minichromosome maintenance subunits 7 (MCM7), DNA polymerase α, and CDC45 at replication origins near the amplified regions, and as a result, decreases the DNA copy numbers of highly amplified genes. Collectively, our data demonstrate that cohesin-mediated chromatin organization and DNA replication are important for stabilizing gene amplification in cancer cells with chromosomal instability.
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Affiliation(s)
- Jiyeon Yun
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea
| | - Jee-Youn Kang
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea
| | - Jinah Park
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea
| | - Sae-Won Han
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Internal Medicine, Seoul National University Hospital, Seoul 110-744, Republic of Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University, Seoul 110-799, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 110-799, Republic of Korea Department of Internal Medicine, Seoul National University Hospital, Seoul 110-744, Republic of Korea
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21
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Abstract
Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer.
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Abstract
PURPOSE OF REVIEW The present study describes the recent advances in the identification of targetable genomic alterations in pediatric cancers, along with the progress and associated challenges in translating these findings into therapeutic benefit. RECENT FINDINGS Each field within pediatric cancer has rapidly and comprehensively begun to define genomic targets in tumors that potentially can improve the clinical outcome of patients, including hematologic malignancies (leukemia and lymphoma), solid malignancies (neuroblastoma, rhabdomyosarcoma, Ewing sarcoma, and osteosarcoma), and brain tumors (gliomas, ependymomas, and medulloblastomas). Although each tumor has specific and sometimes overlapping genomic targets, the translation to the clinic of new targeted trials and precision medicine protocols is still in its infancy. The first clinical tumor profiling studies in pediatric oncology have demonstrated feasibility and patient enthusiasm for the personalized medicine paradigm, but have yet to demonstrate clinical utility. Complexities influencing implementation include rapidly evolving sequencing technologies, tumor heterogeneity, and lack of access to targeted therapies. The return of incidental findings from the germline also remains a challenge, with evolving policy statements and accepted standards. SUMMARY The translation of genomic discoveries to the clinic in pediatric oncology continues to move forward at a brisk pace. Early adoption of genomics for tumor classification, risk stratification, and initial trials of targeted therapeutic agents has led to powerful results. As our experience grows in the integration of genomic and clinical medicine, the outcome for children with cancer should continue to improve.
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Abstract
Changes in technology are fundamentally reframing our concept of what constitutes a model organism. Nevertheless, research advances in the more traditional model organisms have enabled fresh and exciting opportunities for young scientists to establish new careers and offer the hope of comprehensive understanding of fundamental processes in life. New advances in translational research can be expected to heighten the importance of basic research in model organisms and expand opportunities. However, researchers must take special care and implement new resources to enable the newest members of the community to engage fully with the remarkable legacy of information in these fields.
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Affiliation(s)
- Jasper Rine
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3220
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24
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Audeh MW. Novel treatment strategies in triple-negative breast cancer: specific role of poly(adenosine diphosphate-ribose) polymerase inhibition. Pharmgenomics Pers Med 2014; 7:307-16. [PMID: 25342917 PMCID: PMC4205934 DOI: 10.2147/pgpm.s39765] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inhibitors of the poly(adenosine triphosphate-ribose) polymerase (PARP)-1 enzyme induce synthetic lethality in cancers with ineffective DNA (DNA) repair or homologous repair deficiency, and have shown promising clinical activity in cancers deficient in DNA repair due to germ-line mutation in BRCA1 and BRCA2. The majority of breast cancers arising in carriers of BRCA1 germ-line mutations, as well as half of those in BRCA2 carriers, are classified as triple-negative breast cancer (TNBC). TNBC is a biologically heterogeneous group of breast cancers characterized by the lack of immunohistochemical expression of the ER, PR, or HER2 proteins, and for which the current standard of care in systemic therapy is cytotoxic chemotherapy. Many "sporadic" cases of TNBC appear to have indicators of DNA repair dysfunction similar to those in BRCA-mutation carriers, suggesting the possible utility of PARP inhibitors in a subset of TNBC. Significant genetic heterogeneity has been observed within the TNBC cohort, creating challenges for interpretation of prior clinical trial data, and for the design of future clinical trials. Several PARP inhibitors are currently in clinical development in BRCA-mutated breast cancer. The use of PARP inhibitors in TNBC without BRCA mutation will require biomarkers that identify cancers with homologous repair deficiency in order to select patients likely to respond. Beyond mutations in the BRCA genes, dysfunction in other genes that interact with the homologous repair pathway may offer opportunities to induce synthetic lethality when combined with PARP inhibition.
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Affiliation(s)
- M William Audeh
- Division of Medical Oncology, Samuel Oschin Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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25
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Tapia-Alveal C, Lin SJ, O’Connell MJ. Functional interplay between cohesin and Smc5/6 complexes. Chromosoma 2014; 123:437-45. [PMID: 24981336 PMCID: PMC4169997 DOI: 10.1007/s00412-014-0474-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 12/14/2022]
Abstract
Chromosomes are subjected to massive reengineering as they are replicated, transcribed, repaired, condensed, and segregated into daughter cells. Among the engineers are three large protein complexes collectively known as the structural maintenance of chromosome (SMC) complexes: cohesin, condensin, and Smc5/6. As their names suggest, cohesin controls sister chromatid cohesion, condensin controls chromosome condensation, and while precise functions for Smc5/6 have remained somewhat elusive, most reports have focused on the control of recombinational DNA repair. Here, we focus on cohesin and Smc5/6 function. It is becoming increasingly clear that the functional repertoires of these complexes are greater than sister chromatid cohesion and recombination. These SMC complexes are emerging as interrelated and cooperating factors that control chromosome dynamics throughout interphase. However, they also release their embrace of sister chromatids to enable their segregation at anaphase, resetting the dynamic cycle of SMC-chromosome interactions.
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Affiliation(s)
- Claudia Tapia-Alveal
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Su-Jiun Lin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthew J. O’Connell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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26
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Liu C, Srihari S, Cao KAL, Chenevix-Trench G, Simpson PT, Ragan MA, Khanna KK. A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Res 2014; 42:6106-27. [PMID: 24792170 PMCID: PMC4041457 DOI: 10.1093/nar/gku284] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 02/06/2023] Open
Abstract
DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pathways, triggering cancerous potential in cells. Selective killing of cancer cells by sensitizing them to further DNA damage, especially by induction of DSBs, therefore requires careful modulation of DSB-repair pathways. Here, we review the latest knowledge on the two DSB-repair pathways, homologous recombination and non-homologous end joining in human, describing in detail the functions of their components and the key mechanisms contributing to the repair. Such an in-depth characterization of these pathways enables a more mechanistic understanding of how cells respond to therapies, and suggests molecules and processes that can be explored as potential therapeutic targets. One such avenue that has shown immense promise is via the exploitation of synthetic lethal relationships, for which the BRCA1-PARP1 relationship is particularly notable. Here, we describe how this relationship functions and the manner in which cancer cells acquire therapy resistance by restoring their DSB repair potential.
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Affiliation(s)
- Chao Liu
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Kim-Anh Lê Cao
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia Queensland Facility for Advanced Bioinformatics, The University of Queensland, St. Lucia 4072, Australia
| | | | - Peter T Simpson
- The University of Queensland Centre for Clinical Research, Herston, Brisbane, QLD 4029, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Kum Kum Khanna
- Queensland Facility for Advanced Bioinformatics, The University of Queensland, St. Lucia 4072, Australia
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Bailey ML, O'Neil NJ, van Pel DM, Solomon DA, Waldman T, Hieter P. Glioblastoma cells containing mutations in the cohesin component STAG2 are sensitive to PARP inhibition. Mol Cancer Ther 2014; 13:724-32. [PMID: 24356817 PMCID: PMC4130349 DOI: 10.1158/1535-7163.mct-13-0749] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Recent data have identified STAG2, a core subunit of the multifunctional cohesin complex, as a highly recurrently mutated gene in several types of cancer. We sought to identify a therapeutic strategy to selectively target cancer cells harboring inactivating mutations of STAG2 using two independent pairs of isogenic glioblastoma cell lines containing either an endogenous mutant STAG2 allele or a wild-type STAG2 allele restored by homologous recombination. We find that mutations in STAG2 are associated with significantly increased sensitivity to inhibitors of the DNA repair enzyme PARP. STAG2-mutated, PARP-inhibited cells accumulated in G2 phase and had a higher percentage of micronuclei, fragmented nuclei, and chromatin bridges compared with wild-type STAG2 cells. We also observed more 53BP1 foci in STAG2-mutated glioblastoma cells, suggesting that these cells have defects in DNA repair. Furthermore, cells with mutations in STAG2 were more sensitive than cells with wild-type STAG2 when PARP inhibitors were used in combination with DNA-damaging agents. These data suggest that PARP is a potential target for tumors harboring inactivating mutations in STAG2, and strongly recommend that STAG2 status be determined and correlated with therapeutic response to PARP inhibitors, both prospectively and retrospectively, in clinical trials.
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Affiliation(s)
- Melanie L Bailey
- Corresponding Author: Philip Hieter, Michael Smith Laboratories, 2185 East Mall, Room 323, University of British Columbia, Vancouver, British Columbia, Canada V6T1Z4.
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Abstract
Ewing Sarcoma is a developmental tumor characterized by balanced chromosomal translocations and formation of new fusion genes, which are the main hallmark of this rare entity. Despite the vast knowledge regarding the molecular aspects of this rare malignancy obtained in the last few years, including the discovery of new therapeutic targets, many questions still remain open. In this review we focus on the research on targeted therapies in this malignancy, and discussed some bottlenecks related to this such as the possible role of pathologists, the availability of samples, the lack of appropriate animal models, and the resources needed to carry out preclinical and clinical research.
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Altmeyer M, Toledo L, Gudjonsson T, Grøfte M, Rask MB, Lukas C, Akimov V, Blagoev B, Bartek J, Lukas J. The chromatin scaffold protein SAFB1 renders chromatin permissive for DNA damage signaling. Mol Cell 2013; 52:206-20. [PMID: 24055346 DOI: 10.1016/j.molcel.2013.08.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/08/2013] [Accepted: 08/14/2013] [Indexed: 01/25/2023]
Abstract
Although the general relevance of chromatin modifications for genotoxic stress signaling, cell-cycle checkpoint activation, and DNA repair is well established, how these modifications reach initial thresholds in order to trigger robust responses remains largely unexplored. Here, we identify the chromatin-associated scaffold attachment factor SAFB1 as a component of the DNA damage response and show that SAFB1 cooperates with histone acetylation to allow for efficient γH2AX spreading and genotoxic stress signaling. SAFB1 undergoes a highly dynamic exchange at damaged chromatin in a poly(ADP-ribose)-polymerase 1- and poly(ADP-ribose)-dependent manner and is required for unperturbed cell-cycle checkpoint activation and guarding cells against replicative stress. Altogether, our data reveal that transient recruitment of an architectural chromatin component is required in order to overcome physiological barriers by making chromatin permissive for DNA damage signaling, whereas the ensuing exclusion of SAFB1 may help prevent excessive signaling.
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Affiliation(s)
- Matthias Altmeyer
- Chromosome Stability and Dynamics Group, Department of Disease Biology, the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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