151
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Piotto C, Biscontin A, Millino C, Mognato M. Functional validation of miRNAs targeting genes of DNA double-strand break repair to radiosensitize non-small lung cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:1102-1118. [PMID: 30389599 DOI: 10.1016/j.bbagrm.2018.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 10/18/2018] [Accepted: 10/23/2018] [Indexed: 01/10/2023]
Abstract
DNA-Double strand breaks (DSBs) generated by radiation therapy represent the most efficient lesions to kill tumor cells, however, the inherent DSB repair efficiency of tumor cells can cause cellular radioresistance and impact on therapeutic outcome. Genes of DSB repair represent a target for cancer therapy since their down-regulation can impair the repair process making the cells more sensitive to radiation. In this study, we analyzed the combination of ionizing radiation (IR) along with microRNA-mediated targeting of genes involved in DSB repair to sensitize human non-small cell lung cancer (NSCLC) cells. MicroRNAs are natural occurring modulators of gene expression and therefore represent an attractive strategy to affect the expression of DSB repair genes. As possible IR-sensitizing targets genes we selected genes of homologous recombination (HR) and non-homologous end joining (NHEJ) pathway (i.e. RAD51, BRCA2, PRKDC, XRCC5, LIG1). We examined these genes to determine whether they may be real targets of selected miRNAs by functional and biological validation. The in vivo effectiveness of miRNA treatments has been examined in cells over-expressing miRNAs and treated with IR. Taken together, our results show that hsa-miR-96-5p and hsa-miR-874-3p can directly regulate the expression of target genes. When these miRNAs are combined with IR can decrease the survival of NSCLC cells to a higher extent than that exerted by radiation alone, and similarly to radiation combined with specific chemical inhibitors of HR and NHEJ repair pathway.
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Affiliation(s)
- Celeste Piotto
- Department of Biology, School of Sciences, University of Padova, via U. Bassi 58 B, 35131 Padova, Italy
| | - Alberto Biscontin
- Department of Biology, School of Sciences, University of Padova, via U. Bassi 58 B, 35131 Padova, Italy
| | - Caterina Millino
- CRIBI Biotechnology Centre, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy
| | - Maddalena Mognato
- Department of Biology, School of Sciences, University of Padova, via U. Bassi 58 B, 35131 Padova, Italy.
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152
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Letters To the Editor. Radiat Res 2018; 190:650-653. [PMID: 30339058 DOI: 10.1667/rrlte6.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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153
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Tachon G, Cortes U, Guichet PO, Rivet P, Balbous A, Masliantsev K, Berger A, Boissonnade O, Wager M, Karayan-Tapon L. Cell Cycle Changes after Glioblastoma Stem Cell Irradiation: The Major Role of RAD51. Int J Mol Sci 2018; 19:ijms19103018. [PMID: 30282933 PMCID: PMC6213228 DOI: 10.3390/ijms19103018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 12/26/2022] Open
Abstract
“Glioma Stem Cells” (GSCs) are known to play a role in glioblastoma (GBM) recurrence. Homologous recombination (HR) defects and cell cycle checkpoint abnormalities can contribute concurrently to the radioresistance of GSCs. DNA repair protein RAD51 homolog 1 (RAD51) is a crucial protein for HR and its inhibition has been shown to sensitize GSCs to irradiation. The aim of this study was to examine the consequences of ionizing radiation (IR) for cell cycle progression in GSCs. In addition, we intended to assess the potential effect of RAD51 inhibition on cell cycle progression. Five radiosensitive GSC lines and five GSC lines that were previously characterized as radioresistant were exposed to 4Gy IR, and cell cycle analysis was done by fluorescence-activated cell sorting (FACS) at 24, 48, 72, and 96 h with or without RAD51 inhibitor. Following 4Gy IR, all GSC lines presented a significant increase in G2 phase at 24 h, which was maintained over 72 h. In the presence of RAD51 inhibitor, radioresistant GSCs showed delayed G2 arrest post-irradiation for up to 48 h. This study demonstrates that all GSCs can promote G2 arrest in response to radiation-induced DNA damage. However, following RAD51 inhibition, the cell cycle checkpoint response differed. This study contributes to the characterization of the radioresistance mechanisms of GSCs, thereby supporting the rationale of targeting RAD51-dependent repair pathways in view of radiosensitizing GSCs.
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Affiliation(s)
- Gaelle Tachon
- Laboratoire de Neurosciences Expérimentales et Cliniques (LNEC), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1084, Université de Poitiers, F-86073 Poitiers, France.
- Département de Cancérologie Biologique, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
- Faculté de Médecine-Pharmacie, Université de Poitiers, F-86021 Poitiers, France.
| | - Ulrich Cortes
- Département de Cancérologie Biologique, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
| | - Pierre-Olivier Guichet
- Laboratoire de Neurosciences Expérimentales et Cliniques (LNEC), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1084, Université de Poitiers, F-86073 Poitiers, France.
- Département de Cancérologie Biologique, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
| | - Pierre Rivet
- Département de Cancérologie Biologique, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
| | - Anais Balbous
- Laboratoire de Neurosciences Expérimentales et Cliniques (LNEC), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1084, Université de Poitiers, F-86073 Poitiers, France.
- Département de Cancérologie Biologique, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
| | - Konstantin Masliantsev
- Laboratoire de Neurosciences Expérimentales et Cliniques (LNEC), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1084, Université de Poitiers, F-86073 Poitiers, France.
- Département de Cancérologie Biologique, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
- Faculté de Médecine-Pharmacie, Université de Poitiers, F-86021 Poitiers, France.
| | - Antoine Berger
- Département d'Oncologie Radiothérapie, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
| | - Odile Boissonnade
- Département d'Oncologie Radiothérapie, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
| | - Michel Wager
- Laboratoire de Neurosciences Expérimentales et Cliniques (LNEC), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1084, Université de Poitiers, F-86073 Poitiers, France.
- Faculté de Médecine-Pharmacie, Université de Poitiers, F-86021 Poitiers, France.
- Département de Neurochirurgie, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
| | - Lucie Karayan-Tapon
- Laboratoire de Neurosciences Expérimentales et Cliniques (LNEC), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1084, Université de Poitiers, F-86073 Poitiers, France.
- Département de Cancérologie Biologique, Centre Hospitalo-Universitaire de Poitiers, F-86021 Poitiers, France.
- Faculté de Médecine-Pharmacie, Université de Poitiers, F-86021 Poitiers, France.
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154
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Nieborowska-Skorska M, Maifrede S, Ye M, Toma M, Hewlett E, Gordon J, Le BV, Sliwinski T, Zhao H, Piwocka K, Valent P, Tulin AV, Childers W, Skorski T. Non-NAD-like PARP1 inhibitor enhanced synthetic lethal effect of NAD-like PARP inhibitors against BRCA1-deficient leukemia. Leuk Lymphoma 2018; 60:1098-1101. [PMID: 30277116 DOI: 10.1080/10428194.2018.1520988] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Margaret Nieborowska-Skorska
- a Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine , Temple University , Philadelphia , PA , USA
| | - Silvia Maifrede
- a Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine , Temple University , Philadelphia , PA , USA
| | - Min Ye
- b Temple University School of Pharmacy, Moulder Center for Drug Discovery Research , Philadelphia , PA , USA
| | - Monika Toma
- a Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine , Temple University , Philadelphia , PA , USA.,c Laboratory of Medical Genetics Faculty of Biology and Environmental Protection , University of Lodz , Lodz , Poland
| | - Elizabeth Hewlett
- b Temple University School of Pharmacy, Moulder Center for Drug Discovery Research , Philadelphia , PA , USA
| | - John Gordon
- b Temple University School of Pharmacy, Moulder Center for Drug Discovery Research , Philadelphia , PA , USA
| | - Bac Viet Le
- a Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine , Temple University , Philadelphia , PA , USA.,d Laboratory of Cytometry , Nencki Institute of Experimental Biology , Warsaw , Poland
| | - Tomasz Sliwinski
- c Laboratory of Medical Genetics Faculty of Biology and Environmental Protection , University of Lodz , Lodz , Poland
| | - Huaqing Zhao
- e Department of Clinical Sciences Lewis Katz School of Medicine , Temple University , Philadelphia , PA , USA
| | - Katarzyna Piwocka
- d Laboratory of Cytometry , Nencki Institute of Experimental Biology , Warsaw , Poland
| | - Peter Valent
- f Department of Internal Medicine I Division of Hematology & Hemostaseology and Ludwig-Boltzmann Cluster Oncology , Medical University of Vienna , Austria , Vienna
| | - Alexei V Tulin
- g Department of Biomedical Sciences School of Medicine and Health Sciences , University of North Dakota , Grand Forks , ND , USA
| | - Wayne Childers
- b Temple University School of Pharmacy, Moulder Center for Drug Discovery Research , Philadelphia , PA , USA
| | - Tomasz Skorski
- a Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine , Temple University , Philadelphia , PA , USA
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155
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Wang W, Daley JM, Kwon Y, Xue X, Krasner DS, Miller AS, Nguyen KA, Williamson EA, Shim EY, Lee SE, Hromas R, Sung P. A DNA nick at Ku-blocked double-strand break ends serves as an entry site for exonuclease 1 (Exo1) or Sgs1-Dna2 in long-range DNA end resection. J Biol Chem 2018; 293:17061-17069. [PMID: 30224356 DOI: 10.1074/jbc.ra118.004769] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/10/2018] [Indexed: 12/14/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is initiated by nucleolytic resection of the DNA break ends. The current model, being based primarily on genetic analyses in Saccharomyces cerevisiae and companion biochemical reconstitution studies, posits that end resection proceeds in two distinct stages. Specifically, the initiation of resection is mediated by the nuclease activity of the Mre11-Rad50-Xrs2 (MRX) complex in conjunction with its cofactor Sae2, and long-range resection is carried out by exonuclease 1 (Exo1) or the Sgs1-Top3-Rmi1-Dna2 ensemble. Using fully reconstituted systems, we show here that DNA with ends occluded by the DNA end-joining factor Ku70-Ku80 becomes a suitable substrate for long-range 5'-3' resection when a nick is introduced at a locale proximal to one of the Ku-bound DNA ends. We also show that Sgs1 can unwind duplex DNA harboring a nick, in a manner dependent on a species-specific interaction with the ssDNA-binding factor replication protein A (RPA). These biochemical systems and results will be valuable for guiding future endeavors directed at delineating the mechanistic intricacy of DNA end resection in eukaryotes.
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Affiliation(s)
- Weibin Wang
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - James M Daley
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Youngho Kwon
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and.,Departments of Biochemistry and Structural Biology
| | - Xiaoyu Xue
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Danielle S Krasner
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Adam S Miller
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | - Kevin A Nguyen
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and
| | | | | | - Sang Eun Lee
- Radiation Oncology, and.,Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas 78229
| | | | - Patrick Sung
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 and .,Departments of Biochemistry and Structural Biology
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156
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Charlesworth CT, Camarena J, Cromer MK, Vaidyanathan S, Bak RO, Carte JM, Potter J, Dever DP, Porteus MH. Priming Human Repopulating Hematopoietic Stem and Progenitor Cells for Cas9/sgRNA Gene Targeting. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:89-104. [PMID: 30195800 PMCID: PMC6023838 DOI: 10.1016/j.omtn.2018.04.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/11/2022]
Abstract
Engineered nuclease-mediated gene targeting through homologous recombination (HR) in hematopoietic stem and progenitor cells (HSPCs) has the potential to treat a variety of genetic hematologic and immunologic disorders. Here, we identify critical parameters to reproducibly achieve high frequencies of RNA-guided (single-guide RNA [sgRNA]; CRISPR)-Cas9 nuclease (Cas9/sgRNA) and rAAV6-mediated HR at the β-globin (HBB) locus in HSPCs. We identified that by transducing HSPCs with rAAV6 post-electroporation, there was a greater than 2-fold electroporation-aided transduction (EAT) of rAAV6 endocytosis with roughly 70% of the cell population having undergone transduction within 2 hr. When HSPCs are cultured at low densities (1 × 105 cells/mL) prior to HBB targeting, HSPC expansion rates are significantly positively correlated with HR frequencies in vitro as well as in repopulating cells in immunodeficient NSG mice in vivo. We also show that culturing fluorescence-activated cell sorting (FACS)-enriched HBB-targeted HSPCs at low cell densities in the presence of the small molecules, UM171 and SR1, stimulates the expansion of gene-edited HSPCs as measured by higher engraftment levels in immunodeficient mice. This work serves not only as an optimized protocol for genome editing HSPCs at the HBB locus for the treatment of β-hemoglobinopathies but also as a foundation for editing HSPCs at other loci for both basic and translational research.
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Affiliation(s)
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Rasmus O Bak
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Jason M Carte
- Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA 92008, USA
| | - Jason Potter
- Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA 92008, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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157
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Abstract
Flaws in the DNA replication process have emerged as a leading driver of genome instability in human diseases. Alteration to replication fork progression is a defining feature of replication stress and the consequent failure to maintain fork integrity and complete genome duplication within a single round of S-phase compromises genetic integrity. This includes increased mutation rates, small and large scale genomic rearrangement and deleterious consequences for the subsequent mitosis that result in the transmission of additional DNA damage to the daughter cells. Therefore, preserving fork integrity and replication competence is an important aspect of how cells respond to replication stress and avoid genetic change. Homologous recombination is a pivotal pathway in the maintenance of genome integrity in the face of replication stress. Here we review our recent understanding of the mechanisms by which homologous recombination acts to protect, restart and repair replication forks. We discuss the dynamics of these genetically distinct functions and their contribution to faithful mitoticsegregation.
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158
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Reyes J, Chen JY, Stewart-Ornstein J, Karhohs KW, Mock CS, Lahav G. Fluctuations in p53 Signaling Allow Escape from Cell-Cycle Arrest. Mol Cell 2018; 71:581-591.e5. [PMID: 30057196 PMCID: PMC6282757 DOI: 10.1016/j.molcel.2018.06.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 04/10/2018] [Accepted: 06/20/2018] [Indexed: 02/09/2023]
Abstract
Biological signals need to be robust and filter small fluctuations yet maintain sensitivity to signals across a wide range of magnitudes. Here, we studied how fluctuations in DNA damage signaling relate to maintenance of long-term cell-cycle arrest. Using live-cell imaging, we quantified division profiles of individual human cells in the course of 1 week after irradiation. We found a subset of cells that initially establish cell-cycle arrest and then sporadically escape and divide. Using fluorescent reporters and mathematical modeling, we determined that fluctuations in the oscillatory pattern of the tumor suppressor p53 trigger a sharp switch between p21 and CDK2, leading to escape from arrest. Transient perturbation of p53 stability mimicked the noise in individual cells and was sufficient to trigger escape from arrest. Our results show that the self-reinforcing circuitry that mediates cell-cycle transitions can translate small fluctuations in p53 signaling into large phenotypic changes.
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Affiliation(s)
- José Reyes
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Systems Biology PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Jia-Yun Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Kyle W Karhohs
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Systems Biology PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline S Mock
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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159
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Motea EA, Fattah FJ, Xiao L, Girard L, Rommel A, Morales JC, Patidar P, Zhou Y, Porter A, Xie Y, Minna JD, Boothman DA. Kub5-Hera RPRD1B Deficiency Promotes "BRCAness" and Vulnerability to PARP Inhibition in BRCA-proficient Breast Cancers. Clin Cancer Res 2018; 24:6459-6470. [PMID: 30108102 DOI: 10.1158/1078-0432.ccr-17-1118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 11/05/2017] [Accepted: 08/09/2018] [Indexed: 12/13/2022]
Abstract
PURPOSE Identification of novel strategies to expand the use of PARP inhibitors beyond BRCA deficiency is of great interest in personalized medicine. Here, we investigated the unannotated role of Kub5-HeraRPRD1B (K-H) in homologous recombination (HR) repair and its potential clinical significance in targeted cancer therapy. EXPERIMENTAL DESIGN Functional characterization of K-H alterations on HR repair of double-strand breaks (DSB) were assessed by targeted gene silencing, plasmid reporter assays, immunofluorescence, and Western blots. Cell survival with PARP inhibitors was evaluated through colony-forming assays and statistically analyzed for correlation with K-H expression in various BRCA1/2 nonmutated breast cancers. Gene expression microarray/qPCR analyses, chromatin immunoprecipitation, and rescue experiments were used to investigate molecular mechanisms of action. RESULTS K-H expression loss correlates with rucaparib LD50 values in a panel of BRCA1/2 nonmutated breast cancers. Mechanistically, K-H depletion promotes BRCAness, where extensive upregulation of PARP1 activity was required for the survival of breast cancer cells. PARP inhibition in these cells led to synthetic lethality that was rescued by wild-type K-H reexpression, but not by a mutant K-H (p.R106A) that weakly binds RNAPII. K-H mediates HR by facilitating recruitment of RNAPII to the promoter region of a critical DNA damage response and repair effector, cyclin-dependent kinase 1 (CDK1). CONCLUSIONS Cancer cells with low K-H expression may have exploitable BRCAness properties that greatly expand the use of PARP inhibitors beyond BRCA mutations. Our results suggest that aberrant K-H alterations may have vital translational implications in cellular responses/survival to DNA damage, carcinogenesis, and personalized medicine.
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Affiliation(s)
- Edward A Motea
- Departments of Pharmacology and Radiation Oncology, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.
| | - Farjana J Fattah
- Departments of Pharmacology and Radiation Oncology, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ling Xiao
- Departments of Pharmacology and Radiation Oncology, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Amy Rommel
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
| | - Julio C Morales
- Department of Neurosurgery, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma
| | - Praveen Patidar
- Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, New Mexico
| | - Yunyun Zhou
- Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Andrew Porter
- Center for Hematology, Imperial College, London, United Kingdom
| | - Yang Xie
- Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, Texas
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - David A Boothman
- Departments of Pharmacology and Radiation Oncology, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.
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160
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Jiang Y, Chu WK. Potential Roles of the Retinoblastoma Protein in Regulating Genome Editing. Front Cell Dev Biol 2018; 6:81. [PMID: 30109230 PMCID: PMC6079259 DOI: 10.3389/fcell.2018.00081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/13/2018] [Indexed: 01/15/2023] Open
Abstract
Genome editing is an important tool for modifying genomic DNA through introducing DNA insertion or deletion at specific locations of a genome. Recently CRISPR/Cas9 has been widely employed to improve the efficiency of genome editing. The Cas9 nuclease creates site-specific double strand breaks (DSBs) at targeted loci in the genome. Subsequently, the DSBs are repaired by two pathways: Homologous Recombination (HR) and Non-Homologous End-Joining (NHEJ). HR has been considered as "error-free" because it repairs DSBs by copying DNA sequences from a homologous DNA template, while NHEJ is "error-prone" as there are base deletions or insertions at the breakage site. Recently, RB1, a gene that is commonly mutated in retinoblastoma, has been reported to affect the repair efficiencies of HR and NHEJ. This review focuses on the roles of RB1 in repairing DNA DSBs, which have impacts on the precision and consequences of the genome editing, both at the targeted loci and the overall genome.
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Affiliation(s)
- Yuning Jiang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Wai Kit Chu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
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161
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Vallabhaneni H, Lynch PJ, Chen G, Park K, Liu Y, Goehe R, Mallon BS, Boehm M, Hursh DA. High Basal Levels of γH2AX in Human Induced Pluripotent Stem Cells Are Linked to Replication-Associated DNA Damage and Repair. Stem Cells 2018; 36:1501-1513. [PMID: 29873142 DOI: 10.1002/stem.2861] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 05/02/2018] [Accepted: 05/19/2018] [Indexed: 01/07/2023]
Abstract
Human induced pluripotent stem cells (iPSCs) have great potential as source cells for therapeutic uses. However, reports indicate that iPSCs carry genetic abnormalities, which may impede their medical use. Little is known about mechanisms contributing to intrinsic DNA damage in iPSCs that could lead to genomic instability. In this report, we investigated the level of DNA damage in human iPSC lines compared with their founder fibroblast line and derived mesenchymal stromal cell (MSC) lines using the phosphorylated histone variant, γH2AX, as a marker of DNA damage. We show that human iPSCs have elevated basal levels of γH2AX, which correlate with markers of DNA replication: 5-ethynyl-2'-deoxyuridine and the single-stranded binding protein, replication protein A. γH2AX foci in iPSCs also colocalize to BRCA1 and RAD51, proteins in the homologous repair pathway, implying γH2AX in iPSCs marks sites of double strand breaks. Our study demonstrates an association between increased basal levels of γH2AX and the rapid replication of iPSCs. Stem Cells 2018;36:1501-1513.
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Affiliation(s)
- Haritha Vallabhaneni
- Division of Cellular and Gene Therapy, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Patrick J Lynch
- Division of Biotechnology Review and Research II, Office of Pharmaceutical Quality, Center for Drugs Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Guibin Chen
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Kyeyoon Park
- Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Yangtengyu Liu
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Rachel Goehe
- Division of Cellular and Gene Therapy, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Barbara S Mallon
- Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Manfred Boehm
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Deborah A Hursh
- Division of Cellular and Gene Therapy, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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162
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Dhuppar S, Mazumder A. Measuring cell cycle-dependent DNA damage responses and p53 regulation on a cell-by-cell basis from image analysis. Cell Cycle 2018; 17:1358-1371. [PMID: 29963960 DOI: 10.1080/15384101.2018.1482136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
DNA damage in cells occurs from both endogenous and exogenous sources, and failure to repair such damage is associated with the emergence of different cancers, neurological disorders and aging. DNA damage responses (DDR) in cells are closely associated with the cell cycle. While most of our knowledge of DDR comes from bulk biochemistry, such methods require cells to be arrested at specific stages for cell cycle studies, potentially altering measured responses; nor is cell to cell variability in DDR or direct cell-level correlation of two response metrics measured in such methods. To overcome these limitations we developed a microscopy-based assay for determining cell cycle stages over large cell numbers. This method can be used to study cell-cycle-dependent DDR in cultured cells without the need for cell synchronization. Upon DNA damage γH2A.X induction was correlated to nuclear enrichment of p53 on a cell-by-cell basis and in a cell cycle dependent manner. Imaging-based cell cycle staging was combined with single molecule P53 mRNA detection and immunofluorescence for p53 protein in the very same cells to reveal an intriguing repression of P53 transcript numbers due to reduced transcription across different stages of the cell cycle during DNA damage. Our study hints at an unexplored mechanism for p53 regulation and underscores the importance of measuring single cell level responses to DNA damage.
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Affiliation(s)
- Shivnarayan Dhuppar
- a TIFR Centre for Interdisciplinary Sciences , TIFR Hyderabad , Hyderabad , India
| | - Aprotim Mazumder
- a TIFR Centre for Interdisciplinary Sciences , TIFR Hyderabad , Hyderabad , India
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163
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Michelena J, Lezaja A, Teloni F, Schmid T, Imhof R, Altmeyer M. Analysis of PARP inhibitor toxicity by multidimensional fluorescence microscopy reveals mechanisms of sensitivity and resistance. Nat Commun 2018; 9:2678. [PMID: 29992957 PMCID: PMC6041334 DOI: 10.1038/s41467-018-05031-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/12/2018] [Indexed: 02/06/2023] Open
Abstract
Exploiting the full potential of anti-cancer drugs necessitates a detailed understanding of their cytotoxic effects. While standard omics approaches are limited to cell population averages, emerging single cell techniques currently lack throughput and are not applicable for compound screens. Here, we employed a versatile and sensitive high-content microscopy-based approach to overcome these limitations and quantify multiple parameters of cytotoxicity at the single cell level and in a cell cycle resolved manner. Applied to PARP inhibitors (PARPi) this approach revealed an S-phase-specific DNA damage response after only 15 min, quantitatively differentiated responses to several clinically important PARPi, allowed for cell cycle resolved analyses of PARP trapping, and predicted conditions of PARPi hypersensitivity and resistance. The approach illuminates cellular mechanisms of drug synergism and, through a targeted multivariate screen, could identify a functional interaction between PARPi olaparib and NEDD8/SCF inhibition, which we show is dependent on PARP1 and linked to PARP1 trapping. Methods to study anti-cancer drugs cytotoxicity are often low throughput and rely on population average. Here the authors present an automated image-based cytometry method to quantify multiple cytotoxicity parameters in single cells, and use it to study the effect of PARP inhibitors in cancer cells.
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Affiliation(s)
- Jone Michelena
- Department of Molecular Mechanisms of Disease, University of Zurich, CH-8057, Zurich, Switzerland
| | - Aleksandra Lezaja
- Department of Molecular Mechanisms of Disease, University of Zurich, CH-8057, Zurich, Switzerland
| | - Federico Teloni
- Department of Molecular Mechanisms of Disease, University of Zurich, CH-8057, Zurich, Switzerland
| | - Thomas Schmid
- Department of Molecular Mechanisms of Disease, University of Zurich, CH-8057, Zurich, Switzerland
| | - Ralph Imhof
- Department of Molecular Mechanisms of Disease, University of Zurich, CH-8057, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, CH-8057, Zurich, Switzerland.
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164
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Schrank BR, Aparicio T, Li Y, Chang W, Chait BT, Gundersen GG, Gottesman ME, Gautier J. Nuclear ARP2/3 drives DNA break clustering for homology-directed repair. Nature 2018; 559:61-66. [PMID: 29925947 PMCID: PMC6145447 DOI: 10.1038/s41586-018-0237-5] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 04/17/2018] [Indexed: 11/18/2022]
Abstract
DNA double-strand breaks repaired by non-homologous end joining display limited DNA end-processing and chromosomal mobility. By contrast, double-strand breaks undergoing homology-directed repair exhibit extensive processing and enhanced motion. The molecular basis of this movement is unknown. Here, using Xenopus laevis cell-free extracts and mammalian cells, we establish that nuclear actin, WASP, and the actin-nucleating ARP2/3 complex are recruited to damaged chromatin undergoing homology-directed repair. We demonstrate that nuclear actin polymerization is required for the migration of a subset of double-strand breaks into discrete sub-nuclear clusters. Actin-driven movements specifically affect double-strand breaks repaired by homology-directed repair in G2 cell cycle phase; inhibition of actin nucleation impairs DNA end-processing and homology-directed repair. By contrast, ARP2/3 is not enriched at double-strand breaks repaired by non-homologous end joining and does not regulate non-homologous end joining. Our findings establish that nuclear actin-based mobility shapes chromatin organization by generating repair domains that are essential for homology-directed repair in eukaryotic cells.
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Affiliation(s)
- Benjamin R Schrank
- Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Tomas Aparicio
- Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Yinyin Li
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Wakam Chang
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Gregg G Gundersen
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Max E Gottesman
- Department of Biochemistry and Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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165
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Tyrosine kinase inhibitor-induced defects in DNA repair sensitize FLT3(ITD)-positive leukemia cells to PARP1 inhibitors. Blood 2018; 132:67-77. [PMID: 29784639 DOI: 10.1182/blood-2018-02-834895] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/15/2018] [Indexed: 01/03/2023] Open
Abstract
Mutations in FMS-like tyrosine kinase 3 (FLT3), such as internal tandem duplications (ITDs), can be found in up to 23% of patients with acute myeloid leukemia (AML) and confer a poor prognosis. Current treatment options for FLT3(ITD)-positive AMLs include genotoxic therapy and FLT3 inhibitors (FLT3i's), which are rarely curative. PARP1 inhibitors (PARP1i's) have been successfully applied to induce synthetic lethality in tumors harboring BRCA1/2 mutations and displaying homologous recombination (HR) deficiency. We show here that inhibition of FLT3(ITD) activity by the FLT3i AC220 caused downregulation of DNA repair proteins BRCA1, BRCA2, PALB2, RAD51, and LIG4, resulting in inhibition of 2 major DNA double-strand break (DSB) repair pathways, HR, and nonhomologous end-joining. PARP1i, olaparib, and BMN673 caused accumulation of lethal DSBs and cell death in AC220-treated FLT3(ITD)-positive leukemia cells, thus mimicking synthetic lethality. Moreover, the combination of FLT3i and PARP1i eliminated FLT3(ITD)-positive quiescent and proliferating leukemia stem cells, as well as leukemic progenitors, from human and mouse leukemia samples. Notably, the combination of AC220 and BMN673 significantly delayed disease onset and effectively reduced leukemia-initiating cells in an FLT3(ITD)-positive primary AML xenograft mouse model. In conclusion, we postulate that FLT3i-induced deficiencies in DSB repair pathways sensitize FLT3(ITD)-positive AML cells to synthetic lethality triggered by PARP1i's. Therefore, FLT3(ITD) could be used as a precision medicine marker for identifying AML patients that may benefit from a therapeutic regimen combining FLT3 and PARP1i's.
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166
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Juergens H, Varela JA, Gorter de Vries AR, Perli T, Gast VJM, Gyurchev NY, Rajkumar AS, Mans R, Pronk JT, Morrissey JP, Daran JMG. Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid. FEMS Yeast Res 2018; 18:4847887. [PMID: 29438517 PMCID: PMC6018904 DOI: 10.1093/femsyr/foy012] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/08/2018] [Indexed: 12/17/2022] Open
Abstract
While CRISPR-Cas9-mediated genome editing has transformed yeast research, current plasmids and cassettes for Cas9 and guide-RNA expression are species specific. CRISPR tools that function in multiple yeast species could contribute to the intensifying research on non-conventional yeasts. A plasmid carrying a pangenomic origin of replication and two constitutive expression cassettes for Cas9 and ribozyme-flanked gRNAs was constructed. Its functionality was tested by analyzing inactivation of the ADE2 gene in four yeast species. In two Kluyveromyces species, near-perfect targeting (≥96%) and homologous repair (HR) were observed in at least 24% of transformants. In two Ogataea species, Ade- mutants were not observed directly after transformation, but prolonged incubation of transformed cells resulted in targeting efficiencies of 9% to 63% mediated by non-homologous end joining (NHEJ). In an Ogataea parapolymorpha ku80 mutant, deletion of OpADE2 mediated by HR was achieved, albeit at low efficiencies (<1%). Furthermore the expression of a dual polycistronic gRNA array enabled simultaneous interruption of OpADE2 and OpYNR1 demonstrating flexibility of ribozyme-flanked gRNA design for multiplexing. While prevalence of NHEJ prevented HR-mediated editing in Ogataea, such targeted editing was possible in Kluyveromyces. This broad-host-range CRISPR/gRNA system may contribute to exploration of Cas9-mediated genome editing in other Saccharomycotina yeasts.
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Affiliation(s)
- Hannes Juergens
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Javier A Varela
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Arthur R Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Veronica J M Gast
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Nikola Y Gyurchev
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Arun S Rajkumar
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - John P Morrissey
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
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167
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Wilson MD, Durocher D. Reading chromatin signatures after DNA double-strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0280. [PMID: 28847817 DOI: 10.1098/rstb.2016.0280] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are DNA lesions that must be accurately repaired in order to preserve genomic integrity and cellular viability. The response to DSBs reshapes the local chromatin environment and is largely orchestrated by the deposition, removal and detection of a complex set of chromatin-associated post-translational modifications. In particular, the nucleosome acts as a central signalling hub and landing platform in this process by organizing the recruitment of repair and signalling factors, while at the same time coordinating repair with other DNA-based cellular processes. While current research has provided a descriptive overview of which histone marks affect DSB repair, we are only beginning to understand how these marks are interpreted to foster an efficient DSB response. Here we review how the modified chromatin surrounding DSBs is read, with a focus on the insights gleaned from structural and biochemical studies.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Marcus D Wilson
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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168
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Rother MB, van Attikum H. DNA repair goes hip-hop: SMARCA and CHD chromatin remodellers join the break dance. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0285. [PMID: 28847822 PMCID: PMC5577463 DOI: 10.1098/rstb.2016.0285] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2017] [Indexed: 12/20/2022] Open
Abstract
Proper signalling and repair of DNA double-strand breaks (DSB) is critical to prevent genome instability and diseases such as cancer. The packaging of DNA into chromatin, however, has evolved as a mere obstacle to these DSB responses. Posttranslational modifications and ATP-dependent chromatin remodelling help to overcome this barrier by modulating nucleosome structures and allow signalling and repair machineries access to DSBs in chromatin. Here we recap our current knowledge on how ATP-dependent SMARCA- and CHD-type chromatin remodellers alter chromatin structure during the signalling and repair of DSBs and discuss how their dysfunction impacts genome stability and human disease. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.
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Affiliation(s)
- Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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169
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Imseng S, Aylett CHS, Maier T. Architecture and activation of phosphatidylinositol 3-kinase related kinases. Curr Opin Struct Biol 2018; 49:177-189. [DOI: 10.1016/j.sbi.2018.03.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 12/23/2022]
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170
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Abstract
Most members of the poly(ADP-ribose)polymerase family, PARP family, have a catalytic activity that involves the transfer of ADP-ribose from a beta-NAD+-molecule to protein acceptors. It was recently discovered by Talhaoui et al. that DNA-dependent PARP1 and PARP2 can also modify DNA. Here, we demonstrate that DNA-dependent PARP3 can modify DNA and form a specific primed structure for further use by the repair proteins. We demonstrated that gapped DNA that was ADP-ribosylated by PARP3 could be ligated to double-stranded DNA by DNA ligases. Moreover, this ADP-ribosylated DNA could serve as a primed DNA substrate for PAR chain elongation by the purified proteins PARP1 and PARP2 as well as by cell-free extracts. We suggest that this ADP-ribose modification can be involved in cellular pathways that are important for cell survival in the process of double-strand break formation.
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Affiliation(s)
- E A Belousova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), SB RAS, Lavrentiev Av. 8, Novosibirsk, 630090, Russia
| | - А A Ishchenko
- Groupe Réparation de l'ADN, Equipe Labellisée par la Ligue Nationale Contre le Cancer, CNRS UMR8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805, Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805, Villejuif, France
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), SB RAS, Lavrentiev Av. 8, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russia.
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171
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Sunada S, Nakanishi A, Miki Y. Crosstalk of DNA double-strand break repair pathways in poly(ADP-ribose) polymerase inhibitor treatment of breast cancer susceptibility gene 1/2-mutated cancer. Cancer Sci 2018; 109:893-899. [PMID: 29427345 PMCID: PMC5891174 DOI: 10.1111/cas.13530] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 12/30/2022] Open
Abstract
Germline mutations in breast cancer susceptibility gene 1 or 2 (BRCA1 or BRCA2) significantly increase cancer risk in hereditary breast and ovarian cancer syndrome (HBOC). Both genes function in the homologous recombination (HR) pathway of the DNA double‐strand break (DSB) repair process. Therefore, the DNA‐repair defect characteristic of cancer cells brings about a therapeutic advantage for poly(ADP‐ribose) polymerase (PARP) inhibitor‐induced synthetic lethality. PARP inhibitor‐based therapeutics initially cause cancer lethality but acquired resistance mechanisms have been found and need to be elucidated. In particular, it is essential to understand in detail the mechanism of DNA damage and repair to PARP inhibitor treatment. Further investigations have shown the roles of BRCA1/2 and its associations to other molecules in the DSB repair system. Notably, the repair pathway chosen in BRCA1‐deficient cells could be entirely different from that in BRCA2‐deficient cells after PARP inhibitor treatment. The present review describes synthetic lethality and acquired resistance mechanisms to PARP inhibitor through the DSB repair pathway and subsequent repair process. In addition, recent knowledge of resistance mechanisms is discussed. Our model should contribute to the development of novel therapeutic strategies.
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Affiliation(s)
- Shigeaki Sunada
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akira Nakanishi
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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172
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Abstract
The recent implementation of next generation sequencing and multigene platforms has expanded the spectrum of hereditary breast and ovarian cancer syndrome, beyond the traditional genes BRCA1 and BRCA2. A large number of other moderate penetrance genes have now been uncovered, which also play critical roles in repairing double stranded DNA breaks through the homologous recombination pathway. This review discusses the landmark discoveries of BRCA1 and BRCA2, the homologous repair pathway and new genes discovered in hereditary breast and ovarian cancer syndrome, as well as their clinicopathologic significance and implications for genetic testing. It also highlights the new role of PARP inhibitors in the context of synthetic lethality and prophylactic surgical options.
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173
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Czyż M, Toma M, Gajos-Michniewicz A, Majchrzak K, Hoser G, Szemraj J, Nieborowska-Skorska M, Cheng P, Gritsyuk D, Levesque M, Dummer R, Sliwinski T, Skorski T. PARP1 inhibitor olaparib (Lynparza) exerts synthetic lethal effect against ligase 4-deficient melanomas. Oncotarget 2018; 7:75551-75560. [PMID: 27705909 PMCID: PMC5342760 DOI: 10.18632/oncotarget.12270] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/16/2016] [Indexed: 12/12/2022] Open
Abstract
Cancer including melanoma may be ''addicted" to double strand break (DSB) repair and targeting this process could sensitize them to the lethal effect of DNA damage. PARP1 exerts an important impact on DSB repair as it binds to both single- and double- strand breaks. PARP1 inhibitors might be highly effective drugs triggering synthetic lethality in patients whose tumors have germline or somatic defects in DNA repair genes. We hypothesized that PARP1-dependent synthetic lethality could be induced in melanoma cells displaying downregulation of DSB repair genes. We observed that PARP1 inhibitor olaparib sensitized melanomas with reduced expression of DNA ligase 4 (LIG4) to an alkylatimg agent dacarbazine (DTIC) treatment in vitro, while normal melanocytes remained intact. PARP1 inhibition caused accumulation of DSBs, which was associated with apoptosis in LIG4 deficient melanoma cells. Our hypothesis that olaparib is synthetic lethal with LIG4 deficiency in melanoma cells was supported by selective anti-tumor effects of olaparib used either alone or in combination with dacarbazine (DTIC) in LIG4 deficient, but not LIG4 proficient cells. In addition, olaparib combined with DTIC inhibited the growth of LIG4 deficient human melanoma xenografts. This work for the first time demonstrates the effectiveness of a combination of PARP1 inhibitor olaparib and alkylating agent DTIC for treating LIG4 deficient melanomas. In addition, analysis of the TCGA and transcriptome microarray databases revealed numerous individual melanoma samples potentially displaying specific defects in DSB repair pathways, which may predispose them to synthetic lethality triggered by PARP1 inhibitor combined with a cytotoxic drug.
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Affiliation(s)
- Małgorzata Czyż
- Department of Molecular Biology of Cancer, Medical University of Lodz, 92-215 Lodz, Poland
| | - Monika Toma
- Department of Molecular Genetics, University of Lodz, 90-236 Lodz, Poland
| | - Anna Gajos-Michniewicz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 92-215 Lodz, Poland
| | - Kinga Majchrzak
- Department of Molecular Biology of Cancer, Medical University of Lodz, 92-215 Lodz, Poland
| | - Grazyna Hoser
- Department of Flow Cytometry, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland
| | - Margaret Nieborowska-Skorska
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Phil Cheng
- Department of Dermatology, Faculty of Medicine, University Hospital Zürich, and University of Zürich, CH-8952, Zürich, Switzerland
| | - Daniel Gritsyuk
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Mitchell Levesque
- Department of Dermatology, Faculty of Medicine, University Hospital Zürich, and University of Zürich, CH-8952, Zürich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, Faculty of Medicine, University Hospital Zürich, and University of Zürich, CH-8952, Zürich, Switzerland
| | - Tomasz Sliwinski
- Department of Molecular Genetics, University of Lodz, 90-236 Lodz, Poland
| | - Tomasz Skorski
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
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174
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Wang Y, Xu H, Liu T, Huang M, Butter PP, Li C, Zhang L, Kao GD, Gong Y, Maity A, Koumenis C, Fan Y. Temporal DNA-PK activation drives genomic instability and therapy resistance in glioma stem cells. JCI Insight 2018; 3:98096. [PMID: 29415883 PMCID: PMC5821187 DOI: 10.1172/jci.insight.98096] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/28/2017] [Indexed: 01/06/2023] Open
Abstract
Cancer stem cells (CSCs) - known to be resistant to genotoxic radiation and chemotherapy - are fundamental to therapy failure and cancer relapse. Here, we reveal that glioma CSCs are hypersensitive to radiation, but a temporal DNA repair mechanism converts the intrinsic sensitivity to genomic instability and treatment resistance. Transcriptome analysis identifies DNA-dependent protein kinase (DNA-PK) as a predominant DNA repair enzyme in CSCs. Notably, DNA-PK activity is suppressed after irradiation when ROS induce the dissociation of DNA-PKcs with Ku70/80, resulting in delayed DNA repair and radiosensitivity; subsequently, after ROS clearance, the accumulated DNA damage and robust activation of DNA-PK induce genomic instability, facilitated by Rad50-mediated cell-cycle arrest, leading to enhanced malignancy, CSC overgrowth, and radioresistance. Finally, we show a requisite in vivo role for DNA-PK in CSC-mediated radioresistance and glioma progression. These findings identify a time-sensitive mechanism controlling CSC resistance to DNA-damaging treatments and suggest DNA-PK/Rad50 as promising targets for CSC eradication.
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Affiliation(s)
| | | | | | | | | | | | - Lin Zhang
- Department of Obstetrics & Gynecology
| | | | - Yanqing Gong
- Division of Human Genetics and Translational Medicine, Department of Medicine, and
| | | | | | - Yi Fan
- Department of Radiation Oncology
- Department of Neurosurgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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175
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Her J, Bunting SF. How cells ensure correct repair of DNA double-strand breaks. J Biol Chem 2018; 293:10502-10511. [PMID: 29414795 DOI: 10.1074/jbc.tm118.000371] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA double-strand breaks (DSBs) arise regularly in cells and when left unrepaired cause senescence or cell death. Homologous recombination (HR) and nonhomologous end-joining (NHEJ) are the two major DNA-repair pathways. Whereas HR allows faithful DSB repair and healthy cell growth, NHEJ has higher potential to contribute to mutations and malignancy. Many regulatory mechanisms influence which of these two pathways is used in DSB repair. These mechanisms depend on the cell cycle, post-translational modifications, and chromatin effects. Here, we summarize current research into these mechanisms, with a focus on mammalian cells, and also discuss repair by "alternative end-joining" and single-strand annealing.
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Affiliation(s)
- Joonyoung Her
- From the Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, New Jersey 08540
| | - Samuel F Bunting
- From the Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, New Jersey 08540
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176
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Simonetta M, de Krijger I, Serrat J, Moatti N, Fortunato D, Hoekman L, Bleijerveld OB, Altelaar AFM, Jacobs JJL. H4K20me2 distinguishes pre-replicative from post-replicative chromatin to appropriately direct DNA repair pathway choice by 53BP1-RIF1-MAD2L2. Cell Cycle 2018; 17:124-136. [PMID: 29160738 DOI: 10.1080/15384101.2017.1404210] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The main pathways for the repair of DNA double strand breaks (DSBs) are non-homologous end-joining (NHEJ) and homologous recombination directed repair (HDR). These operate mutually exclusive and are activated by 53BP1 and BRCA1, respectively. As HDR can only succeed in the presence of an intact copy of replicated DNA, cells employ several mechanisms to inactivate HDR in the G1 phase of cell cycle. As cells enter S-phase, these inhibitory mechanisms are released and HDR becomes active. However, during DNA replication, NHEJ and HDR pathways are both functional and non-replicated and replicated DNA regions co-exist, with the risk of aberrant HDR activity at DSBs in non-replicated DNA. It has become clear that DNA repair pathway choice depends on inhibition of DNA end-resection by 53BP1 and its downstream factors RIF1 and MAD2L2. However, it is unknown how MAD2L2 accumulates at DSBs to participate in DNA repair pathway control and how the NHEJ and HDR repair pathways are appropriately activated at DSBs with respect to the replication status of the DNA, such that NHEJ acts at DSBs in pre-replicative DNA and HDR acts on DSBs in post-replicative DNA. Here we show that MAD2L2 is recruited to DSBs in H4K20 dimethylated chromatin by forming a protein complex with 53BP1 and RIF1 and that MAD2L2, similar to 53BP1 and RIF1, suppresses DSB accumulation of BRCA1. Furthermore, we show that the replication status of the DNA locally ensures the engagement of the correct DNA repair pathway, through epigenetics. In non-replicated DNA, saturating levels of the 53BP1 binding site, di-methylated lysine 20 of histone 4 (H4K20me2), lead to robust 53BP1-RIF1-MAD2L2 recruitment at DSBs, with consequent exclusion of BRCA1. Conversely, replication-associated 2-fold dilution of H4K20me2 promotes the release of the 53BP1-RIF1-MAD2L2 complex and favours the access of BRCA1. Thus, the differential H4K20 methylation status between pre-replicative and post-replicative DNA represents an intrinsic mechanism that locally ensures appropriate recruitment of the 53BP1-RIF1-MAD2L2 complex at DNA DSBs, to engage the correct DNA repair pathway.
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Affiliation(s)
- Marco Simonetta
- a Division of Oncogenomics , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
| | - Inge de Krijger
- a Division of Oncogenomics , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
| | - Judit Serrat
- a Division of Oncogenomics , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
| | - Nathalie Moatti
- a Division of Oncogenomics , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
| | - Diogo Fortunato
- a Division of Oncogenomics , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
| | - Liesbeth Hoekman
- b Proteomics Facility , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
| | - Onno B Bleijerveld
- b Proteomics Facility , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
| | - A F Maarten Altelaar
- b Proteomics Facility , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands.,c Biomolecular Mass Spectrometry and Proteomics , Utrecht Institute for Pharmaceutical Sciences, University of Utrecht , Padualaan 8, 3584 CH Utrecht , The Netherlands
| | - Jacqueline J L Jacobs
- a Division of Oncogenomics , The Netherlands Cancer Institute , Plesmanlaan 121, 1066 CX Amsterdam , The Netherlands
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177
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Ma A, Dai X. The relationship between DNA single-stranded damage response and double-stranded damage response. Cell Cycle 2018; 17:73-79. [PMID: 29157089 PMCID: PMC5815444 DOI: 10.1080/15384101.2017.1403681] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/29/2017] [Indexed: 10/18/2022] Open
Abstract
The damage response of DNA single-stranded breaks(SSBs) and double-stranded breaks(DSBs) are two relatively independent processes involving different signaling pathways and protein factors, but there are still many overlapping parts. All of them can activate p53 protein, then the activated p53 regulates the damage response of single-stranded breaks or double-stranded breaks in transcriptional regulation and non-transcriptional regulation. Especially, the two types of damage would compete for RPA and ATR resources in damage repair process. The research has been focused on damage response of DNA single-stranded breaks or DNA double-stranded breaks. However, when single-stranded breaks and double-stranded breaks exist simultaneously, the DNA damage response remains to be elucidated. Here, we present a hybrid numerical model of p53 response and a hybrid numerical model of DNA damage repair exploring DNA damage repair and apoptosis mechanisms when DNA single-stranded breaks and DNA double-stranded breaks exist simultaneously. Firstly, when two kinds of damage are present at the same time, the response of p53 is graded, it means that p53 responds to single-stranded breaks preferentially; Secondly, DNA single-stranded breaks are repaired preferentially, and single-stranded breaks and double-stranded breaks can be repaired simultaneously after most of single-stranded breaks having been repaired; Moreover, single-stranded breaks are more likely to cause apoptosis, because the accumulation of p53 in DNA single-stranded breaks is faster than it in DNA double-stranded breaks and single-stranded breaks has lower threshold of apoptosis.
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Affiliation(s)
- Aiqing Ma
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xianhua Dai
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
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178
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Abstract
The ribosome is a complex molecular machine composed of numerous distinct proteins and nucleic acids and is responsible for protein synthesis in every living cell. Ribosome biogenesis is one of the most multifaceted and energy- demanding processes in biology, involving a large number of assembly and maturation factors, the functions of which are orchestrated by multiple cellular inputs, including mitogenic signals and nutrient availability. Although causal associations between inherited mutations affecting ribosome biogenesis and elevated cancer risk have been established over the past decade, mechanistic data have emerged suggesting a broader role for dysregulated ribosome biogenesis in the development and progression of most spontaneous cancers. In this Opinion article, we highlight the most recent findings that provide new insights into the molecular basis of ribosome biogenesis in cancer and offer our perspective on how these observations present opportunities for the design of new targeted cancer treatments.
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Affiliation(s)
- Joffrey Pelletier
- Laboratory of Cancer Metabolism, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - George Thomas
- Laboratory of Cancer Metabolism, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; at the Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA; and at the Unit of Biochemistry, Department of Physiological Sciences II, Faculty of Medicine, Campus Universitari de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), University of Barcelona, 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Siniša Volarević
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia; and at the Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia
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179
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Li J, Yang Q, Zhang Y, Huang K, Sun R, Zhao Q. Compound F779-0434 causes synthetic lethality in BRCA2-deficient cancer cells by disrupting RAD52–ssDNA association. RSC Adv 2018; 8:18859-18869. [PMID: 35539677 PMCID: PMC9080615 DOI: 10.1039/c8ra01919c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/04/2018] [Indexed: 11/21/2022] Open
Abstract
A novel compound named F779-0434 caused synthetic lethality in BRCA2-deficient cancer cells by disrupting RAD52–ssDNA associations.
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Affiliation(s)
- Jian Li
- School of Medicine
- Chengdu University
- Chengdu 610106
- China
- Sichuan Industrial Institute of Antibiotics
| | - Qianye Yang
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
| | - Yang Zhang
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
| | - Kejia Huang
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
| | - Rong Sun
- College of Life Sciences and Key Laboratory for Bio-Resources of Ministry of Education
- Sichuan University
- Chengdu 610064
- China
| | - Qi Zhao
- Sichuan Industrial Institute of Antibiotics
- Chengdu University
- Chengdu 610052
- China
- College of Pharmacy and Biological Engineering
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180
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Nieborowska-Skorska M, Maifrede S, Dasgupta Y, Sullivan K, Flis S, Le BV, Solecka M, Belyaeva EA, Kubovcakova L, Nawrocki M, Kirschner M, Zhao H, Prchal JT, Piwocka K, Moliterno AR, Wasik M, Koschmieder S, Green TR, Skoda RC, Skorski T. Ruxolitinib-induced defects in DNA repair cause sensitivity to PARP inhibitors in myeloproliferative neoplasms. Blood 2017; 130:2848-2859. [PMID: 29042365 PMCID: PMC5746670 DOI: 10.1182/blood-2017-05-784942] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023] Open
Abstract
Myeloproliferative neoplasms (MPNs) often carry JAK2(V617F), MPL(W515L), or CALR(del52) mutations. Current treatment options for MPNs include cytoreduction by hydroxyurea and JAK1/2 inhibition by ruxolitinib, both of which are not curative. We show here that cell lines expressing JAK2(V617F), MPL(W515L), or CALR(del52) accumulated reactive oxygen species-induced DNA double-strand breaks (DSBs) and were modestly sensitive to poly-ADP-ribose polymerase (PARP) inhibitors olaparib and BMN673. At the same time, primary MPN cell samples from individual patients displayed a high degree of variability in sensitivity to these drugs. Ruxolitinib inhibited 2 major DSB repair mechanisms, BRCA-mediated homologous recombination and DNA-dependent protein kinase-mediated nonhomologous end-joining, and, when combined with olaparib, caused abundant accumulation of toxic DSBs resulting in enhanced elimination of MPN primary cells, including the disease-initiating cells from the majority of patients. Moreover, the combination of BMN673, ruxolitinib, and hydroxyurea was highly effective in vivo against JAK2(V617F)+ murine MPN-like disease and also against JAK2(V617F)+, CALR(del52)+, and MPL(W515L)+ primary MPN xenografts. In conclusion, we postulate that ruxolitinib-induced deficiencies in DSB repair pathways sensitized MPN cells to synthetic lethality triggered by PARP inhibitors.
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Affiliation(s)
| | - Silvia Maifrede
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Yashodhara Dasgupta
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Katherine Sullivan
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Sylwia Flis
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Department of Pharmacology, National Medicines Institute, Warsaw, Poland
| | - Bac Viet Le
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Martyna Solecka
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Elizaveta A Belyaeva
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lucia Kubovcakova
- Department of Biomedicine, University Hospital Basel/University of Basel, Basel, Switzerland
| | - Morgan Nawrocki
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Huaqing Zhao
- Department of Clinical Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Josef T Prchal
- School of Medicine, University of Utah, Salt Lake City, UT
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Alison R Moliterno
- Division of Hematology, Department of Medicine, School of Medicine, The Johns Hopkins University, Baltimore, MD; and
| | - Mariusz Wasik
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Tony R Green
- Cambridge Institute for Medical Research
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, and
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; and
| | - Radek C Skoda
- Department of Biomedicine, University Hospital Basel/University of Basel, Basel, Switzerland
| | - Tomasz Skorski
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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181
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Zhang L, Peng Y, Uray IP, Shen J, Wang L, Peng X, Brown PH, Tu W, Peng G. Natural product β-thujaplicin inhibits homologous recombination repair and sensitizes cancer cells to radiation therapy. DNA Repair (Amst) 2017; 60:89-101. [PMID: 29112893 DOI: 10.1016/j.dnarep.2017.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/23/2017] [Indexed: 12/27/2022]
Abstract
Investigation of natural products is an attractive strategy to identify novel compounds for cancer prevention and treatment. Numerous studies have shown the efficacy and safety of natural products, and they have been widely used as alternative treatments for a wide range of illnesses, including cancers. However, it remains unknown whether natural products affect homologous recombination (HR)-mediated DNA repair and whether these compounds can be used as sensitizers with minimal toxicity to improve patients' responses to radiation therapy, a mainstay of treatment for many human cancers. In this study, in order to systematically identify natural products with an inhibitory effect on HR repair, we developed a high-throughput image-based HR repair screening assay and screened a chemical library containing natural products. Among the most interesting of the candidate compounds identified from the screen was β-thujaplicin, a bioactive compound isolated from the heart wood of plants in the Cupressaceae family, can significantly inhibit HR repair. We further demonstrated that β-thujaplicin inhibits HR repair by reducing the recruitment of a key HR repair protein, Rad51, to DNA double-strand breaks. More importantly, our results showed that β-thujaplicin can radiosensitize cancer cells. Additionally, β-thujaplicin sensitizes cancer cells to PARP inhibitor in different cancer cell lines. Collectively, our findings for the first time identify natural compound β-thujaplicin, which has a good biosafety profile, as a novel HR repair inhibitor with great potential to be translated into clinical applications as a sensitizer to DNA-damage-inducing treatment such as radiation and PARP inhibitor. In addition, our study provides proof of the principle that our robust high-throughput functional HR repair assay can be used for a large-scale screening system to identify novel natural products that regulate DNA repair and cellular responses to DNA damage-inducing treatments such as radiation therapy.
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Affiliation(s)
- Lihong Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ivan P Uray
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Clinical Oncology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Jianfeng Shen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Lulu Wang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Xiangdong Peng
- Department of Pharmacy, Third Xiangya Hospital, Central South University, Changsha, China.
| | - Powel H Brown
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Wei Tu
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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182
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Wu M, Ye H, Tang Z, Shao C, Lu G, Chen B, Yang Y, Wang G, Hao H. p53 dynamics orchestrates with binding affinity to target genes for cell fate decision. Cell Death Dis 2017; 8:e3130. [PMID: 29048401 PMCID: PMC5682658 DOI: 10.1038/cddis.2017.492] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/27/2017] [Accepted: 08/29/2017] [Indexed: 01/15/2023]
Abstract
Emerging evidence support that temporal dynamics is pivotal for signaling molecules in orchestrating smart responses to diverse stimuli. p53 is such a signaling molecule that employs temporal dynamics for the selective activation of downstream target genes and ultimately for cell fate decision. Yet how this fine-tuned p53 machinery is quantitatively decoded remains largely unclear. Here we report a quantitative mechanism defining how p53 dynamics orchestrates with binding affinity to target genes for cell fate decision. Treating cells with a genotoxic drug doxorubicin at various doses and durations, we found that a mild and prolonged challenge triggered sequential p53 pulses and ultimately resulted in a terminal pulse enacting apoptosis in a comparable rate with that induced by an acute and high-dose treatment. To transactivate proapoptotic genes and thereafter executing apoptosis, p53 must exceed a certain threshold and accumulate for sufficient time at levels above it. Effective cumulative levels above the threshold, defined as E∫p53, but not the total accumulation levels of p53, precisely discriminate survival and apoptotic cells. p53 accumulation below this threshold, even with prolonging time to reach a total level comparable to that from the accumulation over the threshold, could not transactivate proapoptotic genes to which the binding affinity of p53 is lower than that of proarrest genes, and this property is independent of dynamic features. Our findings indicate that the dynamic feature per se does not directly control cell fate, but rather it orchestrates with the binding affinity to target genes to confer an appropriate time window for cell fate choice. Our study provides a quantitative mechanism unifying p53 dynamics and binding affinity to target genes, providing novel insights to understand how p53 can respond quantitatively to chemotherapeutic drugs, and guiding the design of metronomic regimens for chemotherapeutic drugs.
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Affiliation(s)
- Mengqiu Wu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China.,Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, China
| | - Hui Ye
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Zhiyuan Tang
- Department of Respiratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Chang Shao
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Gaoyuan Lu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Baoqiang Chen
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Yuyu Yang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Guangji Wang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Haiping Hao
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
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183
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Venkatachalam G, Surana U, Clément MV. Replication stress-induced endogenous DNA damage drives cellular senescence induced by a sub-lethal oxidative stress. Nucleic Acids Res 2017; 45:10564-10582. [PMID: 28985345 PMCID: PMC5737622 DOI: 10.1093/nar/gkx684] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 07/16/2017] [Accepted: 07/27/2017] [Indexed: 11/19/2022] Open
Abstract
Although oxidative stress has been shown to induce senescence and replication stress independently, no study has implicated unresolved replication stress as the driver for cellular senescence in response to oxidative stress. Using cells exposed to increasing concentrations of hydrogen peroxide, we show that sub-lethal amount of exogenous hydrogen peroxide induces two waves of DNA damage. The first wave is rapid and transient while the second wave coincides with the cells transition from the S to the G2/M phases of cell cycle. Subsequently, cells enter growth arrest accompanied by the acquisition of senescence-associated characteristics. Furthermore, a p53-dependent decrease in Rad51, which is associated with the formation of DNA segments with chromatin alterations reinforcing senescence, and Lamin B1 that is involved in chromatin remodeling, is observed during the establishment of the senescent phenotype. On the other hand, increase in senescence associated-β-Gal activity, a classical marker of senescence and HMGA2, a marker of the senescence-associated heterochromatin foci, is shown to be independent of p53. Together, our findings implicate replication stress-induced endogenous DNA damage as the driver for the establishment of cellular senescence upon sub-lethal oxidative stress, and implicate the role of p53 in some but not all hallmarks of the senescent phenotype.
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Affiliation(s)
- Gireedhar Venkatachalam
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Proteos, Singapore 138673, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Proteos, Singapore 138673, Singapore
- Bioprocessing Technology Institute, Agency for Science Technology and Research, Centros, Singapore 138668, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117543, Singapore
| | - Marie-Véronique Clément
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
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184
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Ectopic expression of RAD52 and dn53BP1 improves homology-directed repair during CRISPR-Cas9 genome editing. Nat Biomed Eng 2017; 1:878-888. [PMID: 31015609 DOI: 10.1038/s41551-017-0145-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
Gene disruption by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is highly efficient and relies on the error-prone non-homologous end-joining pathway. Conversely, precise gene editing requires homology-directed repair (HDR), which occurs at a lower frequency than non-homologous end-joining in mammalian cells. Here, by testing whether manipulation of DNA repair factors improves HDR efficacy, we show that transient ectopic co-expression of RAD52 and a dominant-negative form of tumour protein p53-binding protein 1 (dn53BP1) synergize to enable efficient HDR using a single-stranded oligonucleotide DNA donor template at multiple loci in human cells, including patient-derived induced pluripotent stem cells. Co-expression of RAD52 and dn53BP1 improves multiplexed HDR-mediated editing, whereas expression of RAD52 alone enhances HDR with Cas9 nickase. Our data show that the frequency of non-homologous end-joining-mediated double-strand break repair in the presence of these two factors is not suppressed and suggest that dn53BP1 competitively antagonizes 53BP1 to augment HDR in combination with RAD52. Importantly, co-expression of RAD52 and dn53BP1 does not alter Cas9 off-target activity. These findings support the use of RAD52 and dn53BP1 co-expression to overcome bottlenecks that limit HDR in precision genome editing.
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185
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Abramenkovs A, Stenerlöw B. Measurement of DNA-Dependent Protein Kinase Phosphorylation Using Flow Cytometry Provides a Reliable Estimate of DNA Repair Capacity. Radiat Res 2017; 188:597-604. [PMID: 28952912 DOI: 10.1667/rr14693.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Uncontrolled generation of DNA double-strand breaks (DSBs) in cells is regarded as a highly toxic event that threatens cell survival. Radiation-induced DNA DSBs are commonly measured by pulsed-field gel electrophoresis, microscopic evaluation of accumulating DNA damage response proteins (e.g., 53BP1 or γ-H2AX) or flow cytometric analysis of γ-H2AX. The advantage of flow cytometric analysis is that DSB formation and repair can be studied in relationship to cell cycle phase or expression of other proteins. However, γ-H2AX is not able to monitor repair kinetics within the first 60 min postirradiation, a period when most DSBs undergo repair. A key protein in non-homologous end joining repair is the catalytic subunit of DNA-dependent protein kinase. Among several phosphorylation sites of DNA-dependent protein kinase, the threonine at position 2609 (T2609), which is phosphorylated by ataxia telangiectasia mutated (ATM) or DNA-dependent protein kinase catalytic subunit itself, activates the end processing of DSB. Using flow cytometry, we show here that phosphorylation at T2609 is faster in response to DSBs than γ-H2AX. Furthermore, flow cytometric analysis of T2609 resulted in a better representation of fast repair kinetics than analysis of γ-H2AX. In cells with reduced ligase IV activity, and wild-type cells where DNA-dependent protein kinase activity was inhibited, the reduced DSB repair capacity was observed by T2609 evaluation using flow cytometry. In conclusion, flow cytometric evaluation of DNA-dependent protein kinase T2609 can be used as a marker for early DSB repair and gives a better representation of early repair events than analysis of γ-H2AX.
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Affiliation(s)
- Andris Abramenkovs
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Bo Stenerlöw
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
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186
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Tsunekawa Y, Terhune RK, Fujita I, Shitamukai A, Suetsugu T, Matsuzaki F. Developing a de novo targeted knock-in method based on in utero electroporation into the mammalian brain. Development 2017; 143:3216-22. [PMID: 27578183 PMCID: PMC5047673 DOI: 10.1242/dev.136325] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/13/2016] [Indexed: 12/31/2022]
Abstract
Genome-editing technology has revolutionized the field of biology. Here, we report a novel de novo gene-targeting method mediated by in utero electroporation into the developing mammalian brain. Electroporation of donor DNA with the CRISPR/Cas9 system vectors successfully leads to knock-in of the donor sequence, such as EGFP, to the target site via the homology-directed repair mechanism. We developed a targeting vector system optimized to prevent anomalous leaky expression of the donor gene from the plasmid, which otherwise often occurs depending on the donor sequence. The knock-in efficiency of the electroporated progenitors reached up to 40% in the early stage and 20% in the late stage of the developing mouse brain. Furthermore, we inserted different fluorescent markers into the target gene in each homologous chromosome, successfully distinguishing homozygous knock-in cells by color. We also applied this de novo gene targeting to the ferret model for the study of complex mammalian brains. Our results demonstrate that this technique is widely applicable for monitoring gene expression, visualizing protein localization, lineage analysis and gene knockout, all at the single-cell level, in developmental tissues.
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Affiliation(s)
- Yuji Tsunekawa
- Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Raymond Kunikane Terhune
- Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Ikumi Fujita
- Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Atsunori Shitamukai
- Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Taeko Suetsugu
- Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Fumio Matsuzaki
- Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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187
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Du J, Shang J, Chen F, Zhang Y, Yin N, Xie T, Zhang H, Yu J, Liu F. A CRISPR/Cas9–Based Screening for Non-Homologous End Joining Inhibitors Reveals Ouabain and Penfluridol as Radiosensitizers. Mol Cancer Ther 2017; 17:419-431. [DOI: 10.1158/1535-7163.mct-17-0090] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/20/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
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188
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Ryl T, Kuchen EE, Bell E, Shao C, Flórez AF, Mönke G, Gogolin S, Friedrich M, Lamprecht F, Westermann F, Höfer T. Cell-Cycle Position of Single MYC-Driven Cancer Cells Dictates Their Susceptibility to a Chemotherapeutic Drug. Cell Syst 2017; 5:237-250.e8. [PMID: 28843484 DOI: 10.1016/j.cels.2017.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/25/2017] [Accepted: 07/24/2017] [Indexed: 12/26/2022]
Abstract
While many tumors initially respond to chemotherapy, regrowth of surviving cells compromises treatment efficacy in the long term. The cell-biological basis of this regrowth is not understood. Here, we characterize the response of individual, patient-derived neuroblastoma cells driven by the prominent oncogene MYC to the first-line chemotherapy, doxorubicin. Combining live-cell imaging, cell-cycle-resolved transcriptomics, and mathematical modeling, we demonstrate that a cell's treatment response is dictated by its expression level of MYC and its cell-cycle position prior to treatment. All low-MYC cells enter therapy-induced senescence. High-MYC cells, by contrast, disable their cell-cycle checkpoints, forcing renewed proliferation despite treatment-induced DNA damage. After treatment, the viability of high-MYC cells depends on their cell-cycle position during treatment: newborn cells promptly halt in G1 phase, repair DNA damage, and form re-growing clones; all other cells show protracted DNA repair and ultimately die. These findings demonstrate that fast-proliferating tumor cells may resist cytotoxic treatment non-genetically, by arresting within a favorable window of the cell cycle.
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Affiliation(s)
- Tatsiana Ryl
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Erika E Kuchen
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Emma Bell
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Chunxuan Shao
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Andrés F Flórez
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gregor Mönke
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sina Gogolin
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mona Friedrich
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Florian Lamprecht
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany.
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189
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Shibata A. Regulation of repair pathway choice at two-ended DNA double-strand breaks. Mutat Res 2017; 803-805:51-55. [PMID: 28781144 DOI: 10.1016/j.mrfmmm.2017.07.011] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/08/2017] [Accepted: 07/03/2017] [Indexed: 12/29/2022]
Abstract
A DNA double-strand break (DSB) is considered to be a critical DNA lesion because its misrepair can cause severe mutations, such as deletions or chromosomal translocations. For the precise repair of DSBs, the repair pathway that is optimal for the particular circumstance needs to be selected. Non-homologous end joining (NHEJ) functions in G1/S/G2 phase, while homologous recombination (HR) becomes active only in S/G2 phase after DNA replication. DSB end structure is another factor affecting the repair pathway. For example, one-ended DSBs in S phase are mainly repaired by HR due to the lack of a partner DSB end for NHEJ. In contrast, two-ended DSBs, which are mainly induced by ionizing radiation, are repaired by either NHEJ or HR in G2 cells. Under the current model in terms of DSB repair pathway usage in G2 phase, NHEJ repairs ∼70% of two-ended DSBs, whereas HR repairs only ∼30%. Recent studies propose that NHEJ factors can bind all the DSB ends and are then either used to progress that pathway of DSB repair, or the repair proceeds by HR. In addition, molecular regulation by BRCA1 and 53BP1 has also been proposed. At DSB sites, BRCA1 functions to alleviate the 53BP1 barrier to resection by promoting 53BP1 dephosphorylation, followed by RIF1 release and 53BP1 repositioning. This timely 53BP1 repositioning may be important for the establishment of a chromatin environment that promotes the recruitment of EXO1 for resection in HR. This review summarizes current knowledge on factors regulating DSB repair pathway choice in terms of spatiotemporal regulation by focusing on the repair events at two-ended DSBs in G2 cells.
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Affiliation(s)
- Atsushi Shibata
- Education and Research Support Center, Gunma University and Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
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190
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Lieberman R, You M. Corrupting the DNA damage response: a critical role for Rad52 in tumor cell survival. Aging (Albany NY) 2017; 9:1647-1659. [PMID: 28722656 PMCID: PMC5559167 DOI: 10.18632/aging.101263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 07/12/2017] [Indexed: 12/31/2022]
Abstract
The DNA damage response enables cells to survive, maintain genome integrity, and to safeguard the transmission of high-fidelity genetic information. Upon sensing DNA damage, cells respond by activating this multi-faceted DNA damage response leading to restoration of the cell, senescence, programmed cell death, or genomic instability if the cell survives without proper repair. However, unlike normal cells, cancer cells maintain a marked level of genomic instability. Because of this enhanced propensity to accumulate DNA damage, tumor cells rely on homologous recombination repair as a means of protection from the lethal effect of both spontaneous and therapy-induced double-strand breaks (DSBs) in DNA. Thus, modulation of DNA repair pathways have important consequences for genomic instability within tumor cell biology and viability maintenance under high genotoxic stress. Efforts are underway to manipulate specific components of the DNA damage response in order to selectively induce tumor cell death by augmenting genomic instability past a viable threshold. New evidence suggests that RAD52, a component of the homologous recombination pathway, is important for the maintenance of tumor genome integrity. This review highlights recent reports indicating that reducing homologous recombination through inhibition of RAD52 may represent an important focus for cancer therapy and the specific efforts that are already demonstrating potential.
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Affiliation(s)
- Rachel Lieberman
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ming You
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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191
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Maifrede S, Martin K, Podszywalow-Bartnicka P, Sullivan-Reed K, Langer SK, Nejati R, Dasgupta Y, Hulse M, Gritsyuk D, Nieborowska-Skorska M, Lupey-Green LN, Zhao H, Piwocka K, Wasik MA, Tempera I, Skorski T. IGH/MYC Translocation Associates with BRCA2 Deficiency and Synthetic Lethality to PARP1 Inhibitors. Mol Cancer Res 2017. [PMID: 28634224 DOI: 10.1158/1541-7786.mcr-16-0468] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Burkitt lymphoma/leukemia cells carry t(8;14)(q24;q32) chromosomal translocation encoding IGH/MYC, which results in the constitutive expression of the MYC oncogene. Here, it is demonstrated that untreated and cytarabine (AraC)-treated IGH/MYC-positive Burkitt lymphoma cells accumulate a high number of potentially lethal DNA double-strand breaks (DSB) and display low levels of the BRCA2 tumor suppressor protein, which is a key element of homologous recombination (HR)-mediated DSB repair. BRCA2 deficiency in IGH/MYC-positive cells was associated with diminished HR activity and hypersensitivity to PARP1 inhibitors (olaparib, talazoparib) used alone or in combination with cytarabine in vitro Moreover, talazoparib exerted a therapeutic effect in NGS mice bearing primary Burkitt lymphoma xenografts. In conclusion, IGH/MYC-positive Burkitt lymphoma/leukemia cells have decreased BRCA2 and are sensitive to PARP1 inhibition alone or in combination with other chemotherapies.Implications: This study postulates that IGH/MYC-induced BRCA2 deficiency may predispose Burkitt lymphoma cells to synthetic lethality triggered by PARP1 inhibitors.Visual Overview: http://mcr.aacrjournals.org/content/molcanres/15/8/967/F1.large.jpgMol Cancer Res; 15(8); 967-72. ©2017 AACR.
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Affiliation(s)
- Silvia Maifrede
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Kayla Martin
- Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Paulina Podszywalow-Bartnicka
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.,Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Katherine Sullivan-Reed
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Samantha K Langer
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Reza Nejati
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yashodhara Dasgupta
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Michael Hulse
- Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Daniel Gritsyuk
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Margaret Nieborowska-Skorska
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Lena N Lupey-Green
- Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Huaqing Zhao
- Temple University Lewis Katz School of Medicine, Department of Clinical Sciences, Philadelphia, Pennsylvania
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Mariusz A Wasik
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Italo Tempera
- Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.
| | - Tomasz Skorski
- Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania. .,Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
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192
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Chen YJ, Tsai CH, Wang PY, Teng SC. SMYD3 Promotes Homologous Recombination via Regulation of H3K4-mediated Gene Expression. Sci Rep 2017. [PMID: 28630472 PMCID: PMC5476597 DOI: 10.1038/s41598-017-03385-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SMYD3 is a methyltransferase highly expressed in many types of cancer. It usually functions as an oncogenic protein to promote cell cycle, cell proliferation, and metastasis. Here, we show that SMYD3 modulates another hallmark of cancer, DNA repair, by stimulating transcription of genes involved in multiple steps of homologous recombination. Deficiency of SMYD3 induces DNA-damage hypersensitivity, decreases levels of repair foci, and leads to impairment of homologous recombination. Moreover, the regulation of homologous recombination-related genes is via the methylation of H3K4 at the target gene promoters. These data imply that, besides its reported oncogenic abilities, SMYD3 may maintain genome integrity by ensuring expression levels of HR proteins to cope with the high demand of restart of stalled replication forks in cancers.
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Affiliation(s)
- Yun-Ju Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Cheng-Hui Tsai
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Pin-Yu Wang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan. .,Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, 10051, Taiwan.
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193
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Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Mol Cell 2017; 66:801-817. [PMID: 28622525 DOI: 10.1016/j.molcel.2017.05.015] [Citation(s) in RCA: 1152] [Impact Index Per Article: 164.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/09/2023]
Abstract
In vertebrate cells, the DNA damage response is controlled by three related kinases: ATM, ATR, and DNA-PK. It has been 20 years since the cloning of ATR, the last of the three to be identified. During this time, our understanding of how these kinases regulate DNA repair and associated events has grown profoundly, although major questions remain unanswered. Here, we provide a historical perspective of their discovery and discuss their established functions in sensing and responding to genotoxic stress. We also highlight what is known regarding their structural similarities and common mechanisms of regulation, as well as emerging non-canonical roles and how our knowledge of ATM, ATR, and DNA-PK is being translated to benefit human health.
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Affiliation(s)
- Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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194
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Abstract
The correct duplication and transmission of genetic material to daughter cells is the primary objective of the cell division cycle. DNA replication and chromosome segregation present both challenges and opportunities for DNA repair pathways that safeguard genetic information. As a consequence, there is a profound, two-way connection between DNA repair and cell cycle control. Here, we review how DNA repair processes, and DNA double-strand break repair in particular, are regulated during the cell cycle to optimize genomic integrity.
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195
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Sanders MA, Haynes B, Nangia-Makker P, Polin LA, Shekhar MP. Pharmacological targeting of RAD6 enzyme-mediated translesion synthesis overcomes resistance to platinum-based drugs. J Biol Chem 2017; 292:10347-10363. [PMID: 28490629 DOI: 10.1074/jbc.m117.792192] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/08/2017] [Indexed: 12/13/2022] Open
Abstract
Platinum drug-induced cross-link repair requires the concerted activities of translesion synthesis (TLS), Fanconi anemia (FA), and homologous recombination repair pathways. The E2 ubiquitin-conjugating enzyme RAD6 is essential for TLS. Here, we show that RAD6 plays a universal role in platinum-based drug tolerance. Using a novel RAD6-selective small-molecule inhibitor (SMI#9) targeting the RAD6 catalytic site, we demonstrate that SMI#9 potentiates the sensitivities of cancer cells with innate or acquired cisplatin or oxaliplatin resistance. 5-Iododeoxyuridine/5-chlorodeoxyuridine pulse-labeling experiments showed that RAD6 is necessary for overcoming cisplatin-induced replication fork stalling, as replication-restart was impaired in both SMI#9-pretreated and RAD6B-silenced cells. Consistent with the role of RAD6/TLS in late-S phase, SMI#9-induced DNA replication inhibition occurred preferentially in mid/late-S phase. The compromised DNA repair and chemosensitization induced by SMI#9 or RAD6B depletion were associated with decreased platinum drug-induced proliferating cell nuclear antigen (PCNA) and FANCD2 monoubiquitinations (surrogate markers of TLS and FA pathway activation, respectively) and with attenuated FANCD2, RAD6, γH2AX, and POL η foci formation and cisplatin-adduct removal. SMI#9 pretreatment synergistically increased cisplatin inhibition of MDA-MB-231 triple-negative breast cancer cell proliferation and tumor growth. Using an isogenic HCT116 colon cancer model of oxaliplatin resistance, we further show that γH2AX and monoubiquitinated PCNA and FANCD2 are constitutively up-regulated in oxaliplatin-resistant HCT116 (HCT116-OxR) cells and that γH2AX, PCNA, and FANCD2 monoubiquitinations are induced by oxaliplatin in parental HCT116 cells. SMI#9 pretreatment sensitized HCT116-OxR cells to oxaliplatin. These data deepen insights into the vital role of RAD6/TLS in platinum drug tolerance and reveal clinical benefits of targeting RAD6 with SMI#9 for managing chemoresistant cancers.
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Affiliation(s)
- Matthew A Sanders
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Brittany Haynes
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Pratima Nangia-Makker
- From the Karmanos Cancer Institute and.,Pathology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Lisa A Polin
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Malathy P Shekhar
- From the Karmanos Cancer Institute and .,the Departments of Oncology and.,Pathology, Wayne State University School of Medicine, Detroit, Michigan 48201
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196
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Nieborowska-Skorska M, Sullivan K, Dasgupta Y, Podszywalow-Bartnicka P, Hoser G, Maifrede S, Martinez E, Di Marcantonio D, Bolton-Gillespie E, Cramer-Morales K, Lee J, Li M, Slupianek A, Gritsyuk D, Cerny-Reiterer S, Seferynska I, Stoklosa T, Bullinger L, Zhao H, Gorbunova V, Piwocka K, Valent P, Civin CI, Muschen M, Dick JE, Wang JC, Bhatia S, Bhatia R, Eppert K, Minden MD, Sykes SM, Skorski T. Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells. J Clin Invest 2017; 127:2392-2406. [PMID: 28481221 DOI: 10.1172/jci90825] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/07/2017] [Indexed: 02/02/2023] Open
Abstract
Quiescent and proliferating leukemia cells accumulate highly lethal DNA double-strand breaks that are repaired by 2 major mechanisms: BRCA-dependent homologous recombination and DNA-dependent protein kinase-mediated (DNA-PK-mediated) nonhomologous end-joining, whereas DNA repair pathways mediated by poly(ADP)ribose polymerase 1 (PARP1) serve as backups. Here we have designed a personalized medicine approach called gene expression and mutation analysis (GEMA) to identify BRCA- and DNA-PK-deficient leukemias either directly, using reverse transcription-quantitative PCR, microarrays, and flow cytometry, or indirectly, by the presence of oncogenes such as BCR-ABL1. DNA-PK-deficient quiescent leukemia cells and BRCA/DNA-PK-deficient proliferating leukemia cells were sensitive to PARP1 inhibitors that were administered alone or in combination with current antileukemic drugs. In conclusion, GEMA-guided targeting of PARP1 resulted in dual cellular synthetic lethality in quiescent and proliferating immature leukemia cells, and is thus a potential approach to eradicate leukemia stem and progenitor cells that are responsible for initiation and manifestation of the disease. Further, an analysis of The Cancer Genome Atlas database indicated that this personalized medicine approach could also be applied to treat numerous solid tumors from individual patients.
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Affiliation(s)
- Margaret Nieborowska-Skorska
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Katherine Sullivan
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Yashodhara Dasgupta
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | | | - Grazyna Hoser
- The Center of Postgraduate Medical Education, Laboratory of Flow Cytometry, Warsaw, Poland
| | - Silvia Maifrede
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Esteban Martinez
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania, USA
| | - Daniela Di Marcantonio
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania, USA
| | - Elisabeth Bolton-Gillespie
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Kimberly Cramer-Morales
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Jaewong Lee
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - Min Li
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Artur Slupianek
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Daniel Gritsyuk
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
| | - Sabine Cerny-Reiterer
- Medical University of Vienna and Ludwig Boltzmann-Cluster Oncology, and Department of Internal Medicine I, Division of Hematology and Hemostaseology, Vienna, Austria
| | - Ilona Seferynska
- Department of Hematology, Institute of Hematology and Blood Transfusion, Warsaw, Poland
| | - Tomasz Stoklosa
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Lars Bullinger
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Huaqing Zhao
- Temple University Lewis Katz School of Medicine, Department of Clinical Sciences, Philadelphia, Pennsylvania, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, New York, USA
| | | | - Peter Valent
- Medical University of Vienna and Ludwig Boltzmann-Cluster Oncology, and Department of Internal Medicine I, Division of Hematology and Hemostaseology, Vienna, Austria
| | - Curt I Civin
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Markus Muschen
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jean Cy Wang
- Princess Margaret Cancer Centre, UHN, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Division of Medical Oncology and Hematology, UHN, Toronto, Ontario, Canada
| | | | - Ravi Bhatia
- Division of Hematology-Oncology, Department of Medicine, University of Alabama Birmingham, Birmingham, Alabama, USA
| | - Kolja Eppert
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Mark D Minden
- Princess Margaret Cancer Center, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Stephen M Sykes
- Research Institute of Fox Chase Cancer Center, Immune Cell Development and Host Defense, Philadelphia, Pennsylvania, USA
| | - Tomasz Skorski
- Temple University Lewis Katz School of Medicine, Department of Microbiology and Immunology and Fels Institute for Cancer Research & Molecular Biology, Philadelphia, Pennsylvania, USA
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197
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Spampinato CP. Protecting DNA from errors and damage: an overview of DNA repair mechanisms in plants compared to mammals. Cell Mol Life Sci 2017; 74:1693-1709. [PMID: 27999897 PMCID: PMC11107726 DOI: 10.1007/s00018-016-2436-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/10/2023]
Abstract
The genome integrity of all organisms is constantly threatened by replication errors and DNA damage arising from endogenous and exogenous sources. Such base pair anomalies must be accurately repaired to prevent mutagenesis and/or lethality. Thus, it is not surprising that cells have evolved multiple and partially overlapping DNA repair pathways to correct specific types of DNA errors and lesions. Great progress in unraveling these repair mechanisms at the molecular level has been made by several talented researchers, among them Tomas Lindahl, Aziz Sancar, and Paul Modrich, all three Nobel laureates in Chemistry for 2015. Much of this knowledge comes from studies performed in bacteria, yeast, and mammals and has impacted research in plant systems. Two plant features should be mentioned. Plants differ from higher eukaryotes in that they lack a reserve germline and cannot avoid environmental stresses. Therefore, plants have evolved different strategies to sustain genome fidelity through generations and continuous exposure to genotoxic stresses. These strategies include the presence of unique or multiple paralogous genes with partially overlapping DNA repair activities. Yet, in spite (or because) of these differences, plants, especially Arabidopsis thaliana, can be used as a model organism for functional studies. Some advantages of this model system are worth mentioning: short life cycle, availability of both homozygous and heterozygous lines for many genes, plant transformation techniques, tissue culture methods and reporter systems for gene expression and function studies. Here, I provide a current understanding of DNA repair genes in plants, with a special focus on A. thaliana. It is expected that this review will be a valuable resource for future functional studies in the DNA repair field, both in plants and animals.
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Affiliation(s)
- Claudia P Spampinato
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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198
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Mönke G, Cristiano E, Finzel A, Friedrich D, Herzel H, Falcke M, Loewer A. Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells. Sci Rep 2017; 7:46571. [PMID: 28417973 PMCID: PMC5394551 DOI: 10.1038/srep46571] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 01/07/2023] Open
Abstract
Cellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity. The resulting data-driven model reproduced all features of measured signaling responses and is sufficient to explain their heterogeneity in individual cells. We present evidence that heterogeneity in the levels of the feedback regulator Wip1 sets cell-specific thresholds for p53 activation, providing means to modulate its response through interacting signaling pathways. Our results demonstrate how excitable signaling networks can provide high specificity, sensitivity and robustness while retaining unique possibilities to adjust their function to the physiology of individual cells.
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Affiliation(s)
- Gregor Mönke
- Mathematical Cell Physiology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Elena Cristiano
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Ana Finzel
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Dhana Friedrich
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité and Humboldt University, Berlin, Germany
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
| | - Alexander Loewer
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany
- Department of Biology, Technische Universitaet Darmstadt, Germany
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199
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Abstract
DNA double-strand breaks (DSBs) are deleterious DNA lesions that must be properly repaired to maintain genome stability. Agents, generated both exogenously (environmental radiation, dental X-rays, etc.) and endogenously (reactive oxygen species, DNA replication, V(D)J recombination, etc.), induce numerous DSBs every day. To counter these DSBs, there are two major repair pathways in mammalian cells, nonhomologous end joining (NHEJ) and homologous recombination (HR). NHEJ directly mediates the religation of the broken DNA molecule and is active in all phases of the cell cycle. HR directs repair via the use of a homologous DNA sequence as a template and is primarily active in only S/G2 phases owing to the availability of a DNA template via a sister chromatid. As NHEJ and HR are active in multiple cell cycle phases, there is significant interest in how a cell chooses between the two DSB repair pathways. Therefore, it is essential to utilize assays to study DSB repair that can distinguish between the two DSB repair pathways and the different phases of the cell cycle. In this chapter, we describe methods to measure the contribution of DNA repair pathways in different phases of the cell cycle. These methods are simple, can be applied to most mammalian cell lines, and can be used as a broad utility to monitor cell cycle-dependent DSB repair.
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200
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Soniat MM, Myler LR, Schaub JM, Kim Y, Gallardo IF, Finkelstein IJ. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination. Methods Enzymol 2017; 592:259-281. [PMID: 28668123 PMCID: PMC5564670 DOI: 10.1016/bs.mie.2017.03.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Homologous recombination (HR) is a universally conserved DNA double-strand break repair pathway. Single-molecule fluorescence imaging approaches have revealed new mechanistic insights into nearly all aspects of HR. These methods are especially suited for studying protein complexes because multicolor fluorescent imaging can parse out subassemblies and transient intermediates that associate with the DNA substrates on the millisecond to hour timescales. However, acquiring single-molecule datasets remains challenging because most of these approaches are designed to measure one molecular reaction at a time. The DNA curtains platform facilitates high-throughput single-molecule imaging by organizing arrays of DNA molecules on the surface of a microfluidic flowcell. Here, we describe a second-generation UV lithography-based protocol for fabricating flowcells for DNA curtains. This protocol greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large datasets from individual single-molecule experiments. Drawing on our recent studies of human HR, we also provide an overview of how DNA curtains can be used for observing facilitated protein diffusion, processive enzyme translocation, and nucleoprotein filament dynamics on single-stranded DNA. Together, these protocols and case studies form a comprehensive introduction for other researchers that may want to adapt DNA curtains for high-throughput single-molecule studies of DNA replication, transcription, and repair.
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Affiliation(s)
- Michael M Soniat
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Logan R Myler
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Jeffrey M Schaub
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Yoori Kim
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Ignacio F Gallardo
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Ilya J Finkelstein
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, United States.
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